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Biswas S, Shahriar S, Bachay G, Arvanitis P, Jamoul D, Brunken WJ, Agalliu D. Glutamatergic neuronal activity regulates angiogenesis and blood-retinal barrier maturation via Norrin/β-catenin signaling. Neuron 2024; 112:1978-1996.e6. [PMID: 38599212 PMCID: PMC11189759 DOI: 10.1016/j.neuron.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/15/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Interactions among neuronal, glial, and vascular components are crucial for retinal angiogenesis and blood-retinal barrier (BRB) maturation. Although synaptic dysfunction precedes vascular abnormalities in many retinal pathologies, how neuronal activity, specifically glutamatergic activity, regulates retinal angiogenesis and BRB maturation remains unclear. Using in vivo genetic studies in mice, single-cell RNA sequencing (scRNA-seq), and functional validation, we show that deep plexus angiogenesis and paracellular BRB maturation are delayed in Vglut1-/- retinas where neurons fail to release glutamate. By contrast, deep plexus angiogenesis and paracellular BRB maturation are accelerated in Gnat1-/- retinas, where constitutively depolarized rods release excessive glutamate. Norrin expression and endothelial Norrin/β-catenin signaling are downregulated in Vglut1-/- retinas and upregulated in Gnat1-/- retinas. Pharmacological activation of endothelial Norrin/β-catenin signaling in Vglut1-/- retinas rescues defects in deep plexus angiogenesis and paracellular BRB maturation. Our findings demonstrate that glutamatergic neuronal activity regulates retinal angiogenesis and BRB maturation by modulating endothelial Norrin/β-catenin signaling.
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Affiliation(s)
- Saptarshi Biswas
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Sanjid Shahriar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Galina Bachay
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Panos Arvanitis
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Danny Jamoul
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; John Jay College of Criminal Justice, City University of New York, New York, NY 10019, USA
| | - William J Brunken
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Dritan Agalliu
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Zarco N, Dovas A, de Araujo Farias V, Nagaiah NK, Haddock A, Sims PA, Hambardzumyan D, Meyer CT, Canoll P, Rosenfeld SS, Kenchappa RS. Resistance to Spindle Inhibitors in Glioblastoma Depends on STAT3 and Therapy Induced Senescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598115. [PMID: 38895402 PMCID: PMC11185785 DOI: 10.1101/2024.06.09.598115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
While mitotic spindle inhibitors specifically kill proliferating tumor cells without the toxicities of microtubule poisons, resistance has limited their clinical utility. Treating glioblastomas with the spindle inhibitors ispinesib, alisertib, or volasertib creates a subpopulation of therapy induced senescent cells that resist these drugs by relying upon the anti-apoptotic and metabolic effects of activated STAT3. Furthermore, these senescent cells expand the repertoire of cells resistant to these drugs by secreting an array of factors, including TGFβ, which induce proliferating cells to exit mitosis and become quiescent-a state that also resists spindle inhibitors. Targeting STAT3 restores sensitivity to each of these drugs by depleting the senescent subpopulation and inducing quiescent cells to enter the mitotic cycle. These results support a therapeutic strategy of targeting STAT3-dependent therapy-induced senescence to enhance the efficacy of spindle inhibitors for the treatment of glioblastoma. Highlights • Resistance to non-microtubule spindle inhibitors limits their efficacy in glioblastoma and depends on STAT3.• Resistance goes hand in hand with development of therapy induced senescence (TIS).• Spindle inhibitor resistant glioblastomas consist of three cell subpopulations-proliferative, quiescent, and TIS-with proliferative cells sensitive and quiescent and TIS cells resistant.• TIS cells secrete TGFβ, which induces proliferative cells to become quiescent, thereby expanding the population of resistant cells in a spindle inhibitor resistant glioblastoma• Treatment with a STAT3 inhibitor kills TIS cells and restores sensitivity to spindle inhibitors.
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3
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Arrieta VA, Gould A, Kim KS, Habashy KJ, Dmello C, Vázquez-Cervantes GI, Palacín-Aliana I, McManus G, Amidei C, Gomez C, Dhiantravan S, Chen L, Zhang DY, Saganty R, Cholak ME, Pandey S, McCord M, McCortney K, Castro B, Ward R, Muzzio M, Bouchoux G, Desseaux C, Canney M, Carpentier A, Zhang B, Miska JM, Lesniak MS, Horbinski CM, Lukas RV, Stupp R, Lee-Chang C, Sonabend AM. Ultrasound-mediated delivery of doxorubicin to the brain results in immune modulation and improved responses to PD-1 blockade in gliomas. Nat Commun 2024; 15:4698. [PMID: 38844770 PMCID: PMC11156895 DOI: 10.1038/s41467-024-48326-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Given the marginal penetration of most drugs across the blood-brain barrier, the efficacy of various agents remains limited for glioblastoma (GBM). Here we employ low-intensity pulsed ultrasound (LIPU) and intravenously administered microbubbles (MB) to open the blood-brain barrier and increase the concentration of liposomal doxorubicin and PD-1 blocking antibodies (aPD-1). We report results on a cohort of 4 GBM patients and preclinical models treated with this approach. LIPU/MB increases the concentration of doxorubicin by 2-fold and 3.9-fold in the human and murine brains two days after sonication, respectively. Similarly, LIPU/MB-mediated blood-brain barrier disruption leads to a 6-fold and a 2-fold increase in aPD-1 concentrations in murine brains and peritumoral brain regions from GBM patients treated with pembrolizumab, respectively. Doxorubicin and aPD-1 delivered with LIPU/MB upregulate major histocompatibility complex (MHC) class I and II in tumor cells. Increased brain concentrations of doxorubicin achieved by LIPU/MB elicit IFN-γ and MHC class I expression in microglia and macrophages. Doxorubicin and aPD-1 delivered with LIPU/MB results in the long-term survival of most glioma-bearing mice, which rely on myeloid cells and lymphocytes for their efficacy. Overall, this translational study supports the utility of LIPU/MB to potentiate the antitumoral activities of doxorubicin and aPD-1 for GBM.
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Affiliation(s)
- Víctor A Arrieta
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- PECEM, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Andrew Gould
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kwang-Soo Kim
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karl J Habashy
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Crismita Dmello
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gustavo I Vázquez-Cervantes
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Irina Palacín-Aliana
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Deparment of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Graysen McManus
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christina Amidei
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cristal Gomez
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Silpol Dhiantravan
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Li Chen
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel Y Zhang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ruth Saganty
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Meghan E Cholak
- Department of Medicine, Division of Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Surya Pandey
- Department of Medicine, Division of Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Matthew McCord
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Deparment of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Brandyn Castro
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel Ward
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miguel Muzzio
- Life Sciences Group, IIT Research Institute, Chicago, IL, USA
| | | | | | | | - Alexandre Carpentier
- Sorbonne Université, Inserm, CNRS, UMR S 1127, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Service de Neurochirurgie, Paris, France
| | - Bin Zhang
- Department of Medicine, Division of Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jason M Miska
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Maciej S Lesniak
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rimas V Lukas
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Roger Stupp
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Division of Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Catalina Lee-Chang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Adam M Sonabend
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Cheng YL, Banu MA, Zhao W, Rosenfeld SS, Canoll P, Sims PA. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. Cell Rep 2024; 43:114139. [PMID: 38652658 PMCID: PMC11199018 DOI: 10.1016/j.celrep.2024.114139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target with roles in proliferation and invasion. Resistance to KIF11 inhibitors, which has mainly been studied in animal models, presents significant challenges. We use lineage-tracing barcodes and single-cell RNA sequencing to analyze resistance in patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lose their neural lineage identity and become mesenchymal, which is associated with poor prognosis. Conversely, cells subjected to long-term ispinesib treatment exhibit a proneural phenotype. We generate patient-derived xenografts and show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Moreover, treatment of human ex vivo GBM slices with ispinesib demonstrates phenotypic alignment with in vitro responses, underscoring the clinical relevance of our findings. Finally, using retrospective lineage tracing, we identify drugs that are synergistic with ispinesib.
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Affiliation(s)
- Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Peter Canoll
- Department of Pathology and 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; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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5
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Huang D, Mela A, Bhanu NV, Garcia BA, Canoll P, Casaccia P. PDGF-BB overexpression in p53 null oligodendrocyte progenitors increases H3K27me3 and induces transcriptional changes which favor proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594214. [PMID: 38798631 PMCID: PMC11118351 DOI: 10.1101/2024.05.14.594214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Proneural gliomas are brain tumors characterized by enrichment of oligodendrocyte progenitor cell (OPC) transcripts and genetic alterations. In this study we sought to identify transcriptional and epigenetic differences between OPCs with Trp53 deletion and PDGF-BB overexpression (BB-p53n), which form tumors when transplanted in mouse brains, and those carrying only p53 deletion (p53n), which do not. We used unbiased histone proteomics and RNA-seq analysis on these two genetically modified OPC populations and detected higher levels of H3K27me3 in BB-p53n compared to p53n OPCs. The BB-p53n OPC were characterized by higher levels of transcripts related to proliferation and lower levels of those related to differentiation. Pharmacological inhibition of histone H3K27 trimethylation in BB-p53n OPC reduced cell cycle transcripts and increased the expression of differentiation markers. These data suggest that PDGF-BB overexpression in p53 null OPC results in histone post-translational modifications and consequent transcriptional changes favoring proliferation while halting differentiation, thereby promoting the early stages of transformation.
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Wei C, Gao Y, Li P. THOC6 is a novel biomarker of glioma and a target of anti-glioma drugs: An analysis based on bioinformatics and molecular docking. Medicine (Baltimore) 2024; 103:e37999. [PMID: 38728502 PMCID: PMC11081617 DOI: 10.1097/md.0000000000037999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 05/12/2024] Open
Abstract
Glioma is a typical malignant tumor of the nervous system. It is of great significance to identify new biomarkers for accurate diagnosis of glioma. In this context, THOC6 has been studied as a highly diagnostic prognostic biomarker, which contributes to improve the dilemma in diagnosing gliomas. We used online databases and a variety of statistical methods, such as Wilcoxon rank sum test, Dunn test and t test. We analyzed the mutation, location and expression profile of THOC6, revealing the network of THOC6 interaction with disease. Wilcoxon rank sum test showed that THOC6 is highly expressed in gliomas (P < 0.001). Dunn test, Wilcoxon rank sum test and t test showed that THOC6 expression was correlated with multiple clinical features. Logistic regression analysis further confirmed that THOC6 gene expression was a categorical dependent variable related to clinical features of poor prognosis. Kaplan-Meier survival analysis showed that the overall survival (OS) of glioma patients with high expression of THOC6 was poor (P < 0.001). Both univariate (P < 0.001) and multivariate (P = 0.04) Cox analysis confirmed that THOC6 gene expression was an independent risk factor for OS in patients with glioma. ROC curve analysis showed that THOC6 had a high diagnostic value in glioma (AUC = 0.915). Based on this, we constructed a nomogram to predict patient survival. Enrichment analysis showed that THOC6 expression was associated with multiple signal pathways. Immuno-infiltration analysis showed that the expression of THOC6 in glioma was closely related to the infiltration level of multiple immune cells. Molecular docking results showed that THOC6 might be the target of anti-glioma drugs. THOC6 is a novel diagnostic factor and prognostic biomarker of glioma.
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Affiliation(s)
- Chuang Wei
- Institute for Translational Medicine, Qingdao University, Qingdao, China
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yijun Gao
- School of Medicine, Shanghai University, Shanghai, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, China
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Johnson AL, Lopez-Bertoni H. Cellular diversity through space and time: adding new dimensions to GBM therapeutic development. Front Genet 2024; 15:1356611. [PMID: 38774283 PMCID: PMC11106394 DOI: 10.3389/fgene.2024.1356611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/15/2024] [Indexed: 05/24/2024] Open
Abstract
The current median survival for glioblastoma (GBM) patients is only about 16 months, with many patients succumbing to the disease in just a matter of months, making it the most common and aggressive primary brain cancer in adults. This poor outcome is, in part, due to the lack of new treatment options with only one FDA-approved treatment in the last decade. Advances in sequencing techniques and transcriptomic analyses have revealed a vast degree of heterogeneity in GBM, from inter-patient diversity to intra-tumoral cellular variability. These cutting-edge approaches are providing new molecular insights highlighting a critical role for the tumor microenvironment (TME) as a driver of cellular plasticity and phenotypic heterogeneity. With this expanded molecular toolbox, the influence of TME factors, including endogenous (e.g., oxygen and nutrient availability and interactions with non-malignant cells) and iatrogenically induced (e.g., post-therapeutic intervention) stimuli, on tumor cell states can be explored to a greater depth. There exists a critical need for interrogating the temporal and spatial aspects of patient tumors at a high, cell-level resolution to identify therapeutically targetable states, interactions and mechanisms. In this review, we discuss advancements in our understanding of spatiotemporal diversity in GBM with an emphasis on the influence of hypoxia and immune cell interactions on tumor cell heterogeneity. Additionally, we describe specific high-resolution spatially resolved methodologies and their potential to expand the impact of pre-clinical GBM studies. Finally, we highlight clinical attempts at targeting hypoxia- and immune-related mechanisms of malignancy and the potential therapeutic opportunities afforded by single-cell and spatial exploration of GBM patient specimens.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Baltimore, MD, United States
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Baltimore, MD, United States
- Oncology, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, MD, United States
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8
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Liu Z, Mela A, Argenziano MG, Banu MA, Furnari J, Kotidis C, Sperring CP, Humala N, Mahajan A, Bruce JN, Canoll P, Sims PA. Single-cell analysis of 5-aminolevulinic acid intraoperative labeling specificity for glioblastoma. J Neurosurg 2024; 140:968-978. [PMID: 37773782 PMCID: PMC10535619 DOI: 10.3171/2023.7.jns23122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/11/2023] [Indexed: 10/01/2023]
Abstract
OBJECTIVE Glioblastoma (GBM) is the most common and aggressive malignant primary brain tumor, and resection is a key part of the standard of care. In fluorescence-guided surgery (FGS), fluorophores differentiate tumor tissue from surrounding normal brain. The heme synthesis pathway converts 5-aminolevulinic acid (5-ALA), a fluorogenic substrate used for FGS, to fluorescent protoporphyrin IX (PpIX). The resulting fluorescence is believed to be specific to neoplastic glioma cells, but this specificity has not been examined at a single-cell level. The objective of this study was to determine the specificity with which 5-ALA labels the diversity of cell types in GBM. METHODS The authors performed single-cell optical phenotyping and expression sequencing-version 2 (SCOPE-seq2), a paired single-cell imaging and RNA sequencing method, of individual cells on human GBM surgical specimens with macroscopically visible PpIX fluorescence from patients who received 5-ALA prior to surgery. SCOPE-seq2 allowed the authors to simultaneously image PpIX fluorescence and unambiguously identify neoplastic cells from single-cell RNA sequencing. Experiments were also conducted in cell culture and co-culture models of glioma and in acute slice cultures from a mouse glioma model to investigate cell- and tissue-specific uptake and secretion of 5-ALA and PpIX. RESULTS SCOPE-seq2 analysis of human GBM surgical specimens revealed that 5-ALA treatment resulted in labeling that was not specific to neoplastic glioma cells. The cell culture further demonstrated that nonneoplastic cells could be labeled by 5-ALA directly or by PpIX secreted from surrounding neoplastic cells. Acute slice cultures from mouse glioma models showed that 5-ALA preferentially labeled GBM tumor tissue over nonneoplastic brain tissue with significant labeling in the tumor margins, and that this contrast was not due to blood-brain barrier disruption. CONCLUSIONS Together, these findings support the use of 5-ALA as an indicator of GBM tissue but question the main advantage of 5-ALA for specific intracellular labeling of neoplastic glioma cells in FGS. Further studies are needed to systematically compare the performance of 5-ALA to that of potential alternatives for FGS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Peter A. Sims
- Departments of Systems Biology
- Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center
- Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, New York
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9
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Pytlarz M, Wojnicki K, Pilanc P, Kaminska B, Crimi A. Deep Learning Glioma Grading with the Tumor Microenvironment Analysis Protocol for Comprehensive Learning, Discovering, and Quantifying Microenvironmental Features. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2024:10.1007/s10278-024-01008-x. [PMID: 38413460 DOI: 10.1007/s10278-024-01008-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 02/29/2024]
Abstract
Gliomas are primary brain tumors that arise from neural stem cells, or glial precursors. Diagnosis of glioma is based on histological evaluation of pathological cell features and molecular markers. Gliomas are infiltrated by myeloid cells that accumulate preferentially in malignant tumors, and their abundance inversely correlates with survival, which is of interest for cancer immunotherapies. To avoid time-consuming and laborious manual examination of images, a deep learning approach for automatic multiclass classification of tumor grades was proposed. As an alternative way of investigating characteristics of brain tumor grades, we implemented a protocol for learning, discovering, and quantifying tumor microenvironment elements on our glioma dataset. Using only single-stained biopsies we derived characteristic differentiating tumor microenvironment phenotypic neighborhoods. The study was complicated by the small size of the available human leukocyte antigen stained on glioma tissue microarray dataset - 206 images of 5 classes - as well as imbalanced data distribution. This challenge was addressed by image augmentation for underrepresented classes. In practice, we considered two scenarios, a whole slide supervised learning classification, and an unsupervised cell-to-cell analysis looking for patterns of the microenvironment. In the supervised learning investigation, we evaluated 6 distinct model architectures. Experiments revealed that a DenseNet121 architecture surpasses the baseline's accuracy by a significant margin of 9% for the test set, achieving a score of 69%, increasing accuracy in discerning challenging WHO grade 2 and 3 cases. All experiments have been carried out in a cross-validation manner. The tumor microenvironment analysis suggested an important role for myeloid cells and their accumulation in the context of characterizing glioma grades. Those promising approaches can be used as an additional diagnostic tool to improve assessment during intraoperative examination or subtyping tissues for treatment selection, potentially easing the workflow of pathologists and oncologists.
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Affiliation(s)
- M Pytlarz
- Sano - Centre for Computational Personalised Medicine, Czarnowiejska 36, Kraków, 30-054, Poland.
| | - K Wojnicki
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, Warszawa, 02-093, Poland
| | - P Pilanc
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, Warszawa, 02-093, Poland
| | - B Kaminska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, Warszawa, 02-093, Poland
| | - A Crimi
- Sano - Centre for Computational Personalised Medicine, Czarnowiejska 36, Kraków, 30-054, Poland
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10
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Guo X, Huang Z, Ju F, Zhao C, Yu L. Highly Accurate Estimation of Cell Type Abundance in Bulk Tissues Based on Single-Cell Reference and Domain Adaptive Matching. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306329. [PMID: 38072669 PMCID: PMC10870031 DOI: 10.1002/advs.202306329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Indexed: 02/17/2024]
Abstract
Accurately identifies the cellular composition of complex tissues, which is critical for understanding disease pathogenesis, early diagnosis, and prevention. However, current methods for deconvoluting bulk RNA sequencing (RNA-seq) typically rely on matched single-cell RNA sequencing (scRNA-seq) as a reference, which can be limiting due to differences in sequencing distribution and the potential for invalid information from single-cell references. Hence, a novel computational method named SCROAM is introduced to address these challenges. SCROAM transforms scRNA-seq and bulk RNA-seq into a shared feature space, effectively eliminating distributional differences in the latent space. Subsequently, cell-type-specific expression matrices are generated from the scRNA-seq data, facilitating the precise identification of cell types within bulk tissues. The performance of SCROAM is assessed through benchmarking against simulated and real datasets, demonstrating its accuracy and robustness. To further validate SCROAM's performance, single-cell and bulk RNA-seq experiments are conducted on mouse spinal cord tissue, with SCROAM applied to identify cell types in bulk tissue. Results indicate that SCROAM is a highly effective tool for identifying similar cell types. An integrated analysis of liver cancer and primary glioblastoma is then performed. Overall, this research offers a novel perspective for delivering precise insights into disease pathogenesis and potential therapeutic strategies.
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Affiliation(s)
- Xinyang Guo
- School of Computer Science and TechnologyXidian UniversityXi'an710071China
| | - Zhaoyang Huang
- School of Computer Science and TechnologyXidian UniversityXi'an710071China
| | - Fen Ju
- Department of Rehabilitation MedicineXijing HospitalFourth Military Medical UniversityXi'an710032China
| | - Chenguang Zhao
- Department of Rehabilitation MedicineXijing HospitalFourth Military Medical UniversityXi'an710032China
| | - Liang Yu
- School of Computer Science and TechnologyXidian UniversityXi'an710071China
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11
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Biswas S, Shahriar S, Bachay G, Arvanitis P, Jamoul D, Brunken WJ, Agalliu D. Glutamatergic neuronal activity regulates angiogenesis and blood-retinal barrier maturation via Norrin/β-catenin signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.10.548410. [PMID: 37503079 PMCID: PMC10369888 DOI: 10.1101/2023.07.10.548410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Interactions among neuronal, glial and vascular components are crucial for retinal angiogenesis and blood-retinal barrier (BRB) maturation. Although synaptic dysfunction precedes vascular abnormalities in many retinal pathologies, how neuronal activity, specifically glutamatergic activity, regulates retinal angiogenesis and BRB maturation remains unclear. Using in vivo genetic studies in mice, single-cell RNA-sequencing and functional validation, we show that deep plexus angiogenesis and paracellular BRB maturation are delayed in Vglut1 -/- retinas where neurons fail to release glutamate. In contrast, deep plexus angiogenesis and paracellular BRB maturation are accelerated in Gnat1 -/- retinas where constitutively depolarized rods release excessive glutamate. Norrin expression and endothelial Norrin/β-catenin signaling are downregulated in Vglut1 -/- retinas, and upregulated in Gnat1 -/- retinas. Pharmacological activation of endothelial Norrin/β-catenin signaling in Vglut1 -/- retinas rescued defects in deep plexus angiogenesis and paracellular BRB maturation. Our findings demonstrate that glutamatergic neuronal activity regulates retinal angiogenesis and BRB maturation by modulating endothelial Norrin/β-catenin signaling.
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Picca A, Di Stefano AL, Savatovsky J, Ducray F, Chinot O, Moyal ECJ, Augereau P, Le Rhun E, Schmitt Y, Rousseaux N, Yepnang AMM, Estellat C, Charbonneau F, Letourneur Q, Branger DF, Meyronet D, Fardeau C, Mokhtari K, Bielle F, Iavarone A, Sanson M. TARGET: A phase I/II open-label multicenter study to assess safety and efficacy of fexagratinib in patients with relapsed/refractory FGFR fusion-positive glioma. Neurooncol Adv 2024; 6:vdae068. [PMID: 38813112 PMCID: PMC11135358 DOI: 10.1093/noajnl/vdae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
Background Oncogenic FGFR-TACC fusions are present in 3-5% of high-grade gliomas (HGGs). Fexagratinib (AZD4547) is an oral FGFR1-3 inhibitor with preclinical activity in FGFR-TACC+ gliomas. We tested its safety and efficacy in patients with recurrent FGFR-TACC + HGGs. Patients and Methods TARGET (NCT02824133) is a phase I/II open-label multicenter study that included adult patients with FGFR-TACC + HGGs relapsing after ≥1 line of standard chemoradiation. Patients received fexagratinib 80 mg bd on a continuous schedule until disease progression or unacceptable toxicity. The primary endpoint was the 6-month progression-free survival rate (PFS6). Results Twelve patients with recurrent IDH wildtype FGFR-TACC + HGGs (all FGFR3-TACC3+) were included in the efficacy cohort (male/female ratio = 1.4, median age = 61.5 years). Most patients (67%) were included at the first relapse. The PFS6 was 25% (95% confidence interval 5-57%), with a median PFS of 1.4 months. All patients without progression at 6 months (n = 3) were treated at first recurrence (versus 56% of those in progression) and remained progression-free for 14-23 months. The best response was RANO partial response in 1 patient (8%), stable disease in 5 (42%), and progressive disease in 6 (50%). Median survival was 17.5 months from inclusion. Grade 3 toxicities included lymphopenia, hyperglycaemia, stomatitis, nail changes, and alanine aminotransferase increase (n = 1 each). No grade 4-5 toxicities were seen. A 32-gene signature was associated with the benefit of FGFR inhibition in FGFR3-TACC3 + HGGs. Conclusions Fexagratinib exhibited acceptable toxicity but limited efficacy in recurrent FGFR3-TACC3 + HGGs. Patients treated at first recurrence appeared more likely to benefit, yet additional evidence is required.
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Affiliation(s)
- Alberto Picca
- Service de Neuro-Oncologie, Institut de Neurologie, DMU Neurosciences, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Paris, France
| | - Anna Luisa Di Stefano
- Department of Neurology, Foch Hospital, Suresnes, France
- Division of Neurosurgery, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, Livorno, Italy
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Paris, France
| | - Julien Savatovsky
- Department of Radiology, Hôpital Fondation A. de Rothschild, Paris, France
| | - François Ducray
- Department of Neuro-Oncology, East Group Hospital, Hospices Civils de Lyon, Lyon, France
| | - Olivier Chinot
- Department of Neuro-Oncology, AP-HM, University Hospital Timone, Marseille, France
| | - Elisabeth Cohen-Jonathan Moyal
- Department of Radiotherapy, Claudius Regaud Institute, Cancer University Institute of Toulouse, Oncopole 1, Paul Sabatier University, Toulouse III, Toulouse, France
| | - Paule Augereau
- Department of Medical Oncology, Institut de Cancérologie de L’ouest- Paul Papin, Angers, France
| | - Emilie Le Rhun
- Department of Neurosurgery, Lille University Hospital, Lille, France
| | - Yohann Schmitt
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Paris, France
| | - Nabila Rousseaux
- Service de Neuro-Oncologie, Institut de Neurologie, DMU Neurosciences, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | | | - Candice Estellat
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique—IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, Paris, France
| | | | - Quentin Letourneur
- Sorbonne Université, INSERM, UMR S 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | | | - David Meyronet
- Department of Neuropathology, Hospices Civils de Lyon, Lyon, France
| | - Christine Fardeau
- Department of Ophthalmology, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Karima Mokhtari
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Paris, France
- Department of Neuropathology, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Franck Bielle
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Paris, France
- Department of Neuropathology, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA
- Department of Neurological Surgery, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Marc Sanson
- Service de Neuro-Oncologie, Institut de Neurologie, DMU Neurosciences, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Paris, France
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Shah S. Novel Therapies in Glioblastoma Treatment: Review of Glioblastoma; Current Treatment Options; and Novel Oncolytic Viral Therapies. Med Sci (Basel) 2023; 12:1. [PMID: 38249077 PMCID: PMC10801585 DOI: 10.3390/medsci12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
One of the most prevalent primary malignant brain tumors is glioblastoma (GB). About 6 incidents per 100,000 people are reported annually. Most frequently, these tumors are linked to a poor prognosis and poor quality of life. There has been little advancement in the treatment of GB. In recent years, some innovative medicines have been tested for the treatment of newly diagnosed cases of GB and recurrent cases of GB. Surgery, radiotherapy, and alkylating chemotherapy are all common treatments for GB. A few of the potential alternatives include immunotherapy, tumor-treating fields (TTFs), and medications that target specific cellular receptors. To provide new multimodal therapies that focus on the molecular pathways implicated in tumor initiation and progression in GB, novel medications, delivery technologies, and immunotherapy approaches are being researched. Of these, oncolytic viruses (OVs) are among the most recent. Coupling OVs with certain modern treatment approaches may have significant benefits for GB patients. Here, we discuss several OVs and how they work in conjunction with other therapies, as well as virotherapy for GB. The study was based on the PRISMA guidelines. Systematic retrieval of information was performed on PubMed. A total of 307 articles were found in a search on oncolytic viral therapies for glioblastoma. Out of these 83 articles were meta-analyses, randomized controlled trials, reviews, and systematic reviews. A total of 42 articles were from the years 2018 to 2023. Appropriate studies were isolated, and important information from each of them was understood and entered into a database from which the information was used in this article. One of the most prevalent malignant brain tumors is still GB. Significant promise and opportunity exist for oncolytic viruses in the treatment of GB and in boosting immune response. Making the most of OVs in the treatment of GB requires careful consideration and evaluation of a number of its application factors.
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Affiliation(s)
- Siddharth Shah
- Department of Neurosurgery, University of Florida, Gainesville, FL 32608, USA
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Wang M, Wang W, You S, Hou Z, Ji M, Xue N, Du T, Chen X, Jin J. ACAT1 deficiency in myeloid cells promotes glioblastoma progression by enhancing the accumulation of myeloid-derived suppressor cells. Acta Pharm Sin B 2023; 13:4733-4747. [PMID: 38045043 PMCID: PMC10692383 DOI: 10.1016/j.apsb.2023.09.005] [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: 05/30/2023] [Revised: 07/09/2023] [Accepted: 08/09/2023] [Indexed: 12/05/2023] Open
Abstract
Glioblastoma (GBM) is a highly aggressive and lethal brain tumor with an immunosuppressive tumor microenvironment (TME). In this environment, myeloid cells, such as myeloid-derived suppressor cells (MDSCs), play a pivotal role in suppressing antitumor immunity. Lipometabolism is closely related to the function of myeloid cells. Here, our study reports that acetyl-CoA acetyltransferase 1 (ACAT1), the key enzyme of fatty acid oxidation (FAO) and ketogenesis, is significantly downregulated in the MDSCs infiltrated in GBM patients. To investigate the effects of ACAT1 on myeloid cells, we generated mice with myeloid-specific (LyzM-cre) depletion of ACAT1. The results show that these mice exhibited a remarkable accumulation of MDSCs and increased tumor progression both ectopically and orthotopically. The mechanism behind this effect is elevated secretion of C-X-C motif ligand 1 (CXCL1) of macrophages (Mφ). Overall, our findings demonstrate that ACAT1 could serve as a promising drug target for GBM by regulating the function of MDSCs in the TME.
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Affiliation(s)
- Mingjin Wang
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Weida Wang
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shen You
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhenyan Hou
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ming Ji
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Nina Xue
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Tingting Du
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiaoguang Chen
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jing Jin
- Department of Pharmacology, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Nale V, Chiodi A, Di Nanni N, Cifola I, Moscatelli M, Cocola C, Gnocchi M, Piscitelli E, Sula A, Zucchi I, Reinbold R, Milanesi L, Mezzelani A, Pelucchi P, Mosca E. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC Bioinformatics 2023; 24:445. [PMID: 38012590 PMCID: PMC10680269 DOI: 10.1186/s12859-023-05563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
INTRODUCTION Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data. RESULTS scMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics. CONCLUSIONS The analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.
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Affiliation(s)
- Valentina Nale
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alice Chiodi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ingrid Cifola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Marco Moscatelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Cinzia Cocola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Matteo Gnocchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Eleonora Piscitelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ada Sula
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ileana Zucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Rolland Reinbold
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alessandra Mezzelani
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Paride Pelucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
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Xiao Z, Li J, Liang C, Liu Y, Zhang Y, Zhang Y, Liu Q, Yan X. Identification of M5c regulator-medicated methylation modification patterns for prognosis and immune microenvironment in glioma. Aging (Albany NY) 2023; 15:12275-12295. [PMID: 37934565 PMCID: PMC10683591 DOI: 10.18632/aging.205179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023]
Abstract
Glioma is a common intracranial tumor and is generally associated with poor prognosis. Recently, numerous studies illustrated the importance of 5-methylcytosine (m5C) RNA modification to tumorigenesis. However, the prognostic value and immune correlation of m5C in glioma remain unclear. We obtained RNA expression and clinical information from The Cancer Genome Atlas (TCGA) and The Chinese Glioma Genome Atlas (CGGA) datasets to analyze. Nonnegative matrix factorization (NMF) was used to classify patients into two subgroups and compare these patients in survival and clinicopathological characteristics. CIBERSORT and single-sample gene-set algorithm (ssGSEA) methods were used to investigate the relationship between m5C and the immune environment. The Weighted correlation network analysis (WGCNA) and univariate Cox proportional hazard model (CoxPH) were used to construct a m5C-related signature. Most of m5C RNA methylation regulators presented differential expression and prognostic values. There were obvious relationships between immune infiltration cells and m5C regulators, especially NSUN7. In the m5C-related module from WGCNA, we found SEPT3, CHI3L1, PLBD1, PHYHIPL, SAMD8, RAP1B, B3GNT5, RER1, PTPN7, SLC39A1, and MXI1 were prognostic factors for glioma, and they were used to construct the signature. The great significance of m5C-related signature in predicting the survival of patients with glioma was confirmed in the validation sets and CGGA cohort.
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Affiliation(s)
- Zhenyong Xiao
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
| | - Jinwei Li
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Cong Liang
- Department of Pharmacy, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
| | - Yamei Liu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
| | - Yuxiu Zhang
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
| | - Yuxia Zhang
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
| | - Quan Liu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
| | - Xianlei Yan
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou 545000, Guangxi, China
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu 610000, Sichuan, China
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Liu Y, Jin H, Liu H. Identification of T-cell exhaustion-related gene signature for predicting prognosis in glioblastoma multiforme. J Cell Mol Med 2023; 27:3503-3513. [PMID: 37635346 PMCID: PMC10660619 DOI: 10.1111/jcmm.17927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 08/29/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a highly malignant primary brain tumour with a poor prognosis in adults. Identifying biomarkers that can aid in the molecular classification and risk stratification of GBM is critical. Here, we conducted a transcriptional profiling analysis of T-cell immunity in the tumour microenvironment of GBM patients and identified two novel T cell exhaustion (TEX)-related GBM subtypes (termed TEX-C1 and TEX-C2) using the consensus clustering. Our multi-omics analysis revealed distinct immunological, molecular and clinical characteristics for these two subtypes. Specifically, the TEX-C1 subtype had higher infiltration levels of immune cells and expressed higher levels of immune checkpoint molecules than the TEX-C2 subtype. Functional analysis revealed that upregulated genes in the TEX-C1 subtype were significantly enriched in immune response and signal transduction pathways, and upregulated genes in the TEX-C2 subtype were predominantly associated with cell fate and nervous system development pathways. Notably, patients with activated T-cell activity status in the TEX-C1 subgroup demonstrated a significantly worse prognosis than those with severe T cell exhaustion status in the TEX-C2 subgroup. Finally, we proposed a machine-learning-derived novel gene signature comprising 12 TEX-related genes (12TexSig) to indicate tumour subtyping. In the TCGA cohort, the 12TexSig demonstrated the ability to accurately predict the prognosis of GBM patients, and this prognostic value was further confirmed in two independent external cohorts. Taken together, our results suggest that the TEX-derived subtyping and gene signature has the potential to serve as a clinically helpful biomarker for guiding the management of GBM patients, pending further prospective validation.
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Affiliation(s)
- Yue‐hui Liu
- Department of NeurologyAffiliated Hospital of Inner Mongolia Minzu UniversityTongliaoChina
| | - Hong‐quan Jin
- Department of NeurologyAffiliated Hospital of Inner Mongolia Minzu UniversityTongliaoChina
| | - Hai‐ping Liu
- College of Life Science and Food EngineeringInner Mongolia Minzu UniversityTongliaoChina
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18
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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19
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Cheng YL, Banu MA, Zhao W, Rosenfeld SS, Canoll P, Sims PA. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557001. [PMID: 37745469 PMCID: PMC10515771 DOI: 10.1101/2023.09.09.557001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target because of its dual roles in proliferation and invasion. The clinical utility of KIF11 inhibitors has been limited by drug resistance, which has mainly been studied in animal models. We used multiplexed lineage tracing barcodes and scRNA-seq to analyze drug resistance time courses for patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lost their neural lineage identity and transitioned to a mesenchymal phenotype, which is associated with poor prognosis. In contrast, cells subjected to long-term ispinesib treatment exhibited a proneural phenotype. We generated patient-derived xenografts to show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Finally, we used lineage barcodes to nominate drug combination targets by retrospective analysis of ispinesib-resistant clones in the drug-naïve setting and identified drugs that are synergistic with ispinesib.
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Affiliation(s)
- Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Wenting Zhao
- Department of Systems Biology, 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
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
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20
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Sutter PA, Ménoret A, Jellison ER, Nicaise AM, Bradbury AM, Vella AT, Bongarzone ER, Crocker SJ. CD8+ T cell depletion prevents neuropathology in a mouse model of globoid cell leukodystrophy. J Exp Med 2023; 220:e20221862. [PMID: 37310382 PMCID: PMC10266545 DOI: 10.1084/jem.20221862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/10/2023] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
Globoid cell leukodystrophy (GLD) or Krabbe's disease is a fatal genetic demyelinating disease of the central nervous system caused by loss-of-function mutations in the galactosylceramidase (galc) gene. While the metabolic basis for disease is known, the understanding of how this results in neuropathology is not well understood. Herein, we report that the rapid and protracted elevation of CD8+ cytotoxic T lymphocytes occurs coincident with clinical disease in a mouse model of GLD. Administration of a function-blocking antibody against CD8α effectively prevented disease onset, reduced morbidity and mortality, and prevented CNS demyelination in mice. These data indicate that subsequent to the genetic cause of disease, neuropathology is driven by pathogenic CD8+ T cells, thus offering novel therapeutic potential for treatment of GLD.
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Affiliation(s)
- Pearl A. Sutter
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Antoine Ménoret
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Evan R. Jellison
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Alexandra M. Nicaise
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
- Department of Clinical Neuroscience and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Allison M. Bradbury
- Department of Pediatrics, Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Anthony T. Vella
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ernesto R. Bongarzone
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephen J. Crocker
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, USA
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21
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Zhang L, Bordey A. Advances in glioma models using in vivo electroporation to highjack neurodevelopmental processes. Biochim Biophys Acta Rev Cancer 2023; 1878:188951. [PMID: 37433417 DOI: 10.1016/j.bbcan.2023.188951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Glioma is the most prevalent type of neurological malignancies. Despite decades of efforts in neurosurgery, chemotherapy and radiation therapy, glioma remains one of the most treatment-resistant brain tumors with unfavorable outcomes. Recent progresses in genomic and epigenetic profiling have revealed new concepts of genetic events involved in the etiology of gliomas in humans, meanwhile, revolutionary technologies in gene editing and delivery allows to code these genetic "events" in animals to genetically engineer glioma models. This approach models the initiation and progression of gliomas in a natural microenvironment with an intact immune system and facilitates probing therapeutic strategies. In this review, we focus on recent advances in in vivo electroporation-based glioma modeling and outline the established genetically engineered glioma models (GEGMs).
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Affiliation(s)
- Longbo Zhang
- Departments of Neurosurgery, Changde hospital, Xiangya School of Medicine, Central South University, 818 Renmin Street, Wuling District, Changde, Hunan 415003, China; Departments of Neurosurgery, and National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China; Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8082, USA.
| | - Angelique Bordey
- Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8082, USA
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22
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Zhou H, Chen B, Zhang L, Li C. Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response. Comput Struct Biotechnol J 2023; 21:3827-3840. [PMID: 37560125 PMCID: PMC10407594 DOI: 10.1016/j.csbj.2023.07.029] [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: 03/06/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
Glioma stem cells (GSCs) remodel their tumor microenvironment to sustain a supportive niche. Identification and stratification of stemness related characteristics in patients with glioma might aid in the diagnosis and treatment of the disease. In this study, we calculated the mRNA stemness index in bulk and single-cell RNA-sequencing datasets using machine learning methods and investigated the correlation between stemness and clinicopathological characteristics. A glioma stemness-associated score (GSScore) was constructed using multivariate Cox regression analysis. We also generated a GSC cell line derived from a patient diagnosed with glioma and used glioma cell lines to validate the performance of the GSScore in predicting chemotherapeutic responses. Differentially expressed genes (DEGs) between GSCs with high and low GSScores were used to cluster lower-grade glioma (LGG) samples into three stemness subtypes. Differences in clinicopathological characteristics, including survival, copy number variations, mutations, tumor microenvironment, and immune and chemotherapeutic responses, among the three LGG stemness-associated subtypes were identified. Using machine learning methods, we further identified genes as subtype predictors and validated their performance using the CGGA datasets. In the current study, we identified a GSScore that correlated with LGG chemotherapeutic response. Through the score, we also identified a novel classification of the LGG subtype and associated subtype predictors, which might facilitate the development of precision therapy.
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Affiliation(s)
- Hongshu Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Bo Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Clinical Diagnosis and Therapy Center for Glioma, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Chuntao Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Clinical Diagnosis and Therapy Center for Glioma, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
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23
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Hobson BD, Stanley AT, De Los Santos MB, Culbertson B, Mosharov EV, Sims PA, Sulzer D. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain Behav Immun 2023; 111:277-291. [PMID: 37100211 PMCID: PMC10460506 DOI: 10.1016/j.bbi.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023] Open
Abstract
Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it has been unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We found that IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were similar in neurons and glia, but with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, which were the only cells to undergo cellular proliferation and express MHC classII (MHC-II) and associated genes. To determine if neurons respond directly via cell-autonomous IFN-γ receptor (IFNGR) signaling, we produced mutant mice with a deletion of the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, which resulted in a complete loss of dopaminergic neuronal responses to IFN-γ. Our results demonstrate that IFN-γ induces neuronal IFNGR signaling and upregulation of MHC-I and related genes in vivo, although the expression level is low compared to oligodendrocytes, astrocytes, and microglia.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Adrien T Stanley
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Mark B De Los Santos
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Bruce Culbertson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Eugene V Mosharov
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, United States; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
| | - David Sulzer
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
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24
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Eisenbarth D, Wang YA. Glioblastoma heterogeneity at single cell resolution. Oncogene 2023; 42:2155-2165. [PMID: 37277603 PMCID: PMC10913075 DOI: 10.1038/s41388-023-02738-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Glioblastoma (GBM) is one of the deadliest types of cancer and highly refractory to chemoradiation and immunotherapy. One of the main reasons for this resistance to therapy lies within the heterogeneity of the tumor and its associated microenvironment. The vast diversity of cell states, composition of cells, and phenotypical characteristics makes it difficult to accurately classify GBM into distinct subtypes and find effective therapies. The advancement of sequencing technologies in recent years has further corroborated the heterogeneity of GBM at the single cell level. Recent studies have only begun to elucidate the different cell states present in GBM and how they correlate with sensitivity to therapy. Furthermore, it has become clear that GBM heterogeneity not only depends on intrinsic factors but also strongly differs between new and recurrent GBM, and treatment naïve and experienced patients. Understanding and connecting the complex cellular network that underlies GBM heterogeneity will be indispensable in finding new ways to tackle this deadly disease. Here, we present an overview of the multiple layers of GBM heterogeneity and discuss novel findings in the age of single cell technologies.
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Affiliation(s)
- David Eisenbarth
- The Brown Center for Immunotherapy, Department of Medicine, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Y Alan Wang
- The Brown Center for Immunotherapy, Department of Medicine, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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25
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Al-Dalahmah O, Argenziano MG, Kannan A, Mahajan A, Furnari J, Paryani F, Boyett D, Save A, Humala N, Khan F, Li J, Lu H, Sun Y, Tuddenham JF, Goldberg AR, Dovas A, Banu MA, Sudhakar T, Bush E, Lassman AB, McKhann GM, Gill BJA, Youngerman B, Sisti MB, Bruce JN, Sims PA, Menon V, Canoll P. Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states. Nat Commun 2023; 14:2586. [PMID: 37142563 PMCID: PMC10160047 DOI: 10.1038/s41467-023-38186-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
Glioblastoma (GBM) diffusely infiltrates the brain and intermingles with non-neoplastic brain cells, including astrocytes, neurons and microglia/myeloid cells. This complex mixture of cell types forms the biological context for therapeutic response and tumor recurrence. We used single-nucleus RNA sequencing and spatial transcriptomics to determine the cellular composition and transcriptional states in primary and recurrent glioma and identified three compositional 'tissue-states' defined by cohabitation patterns between specific subpopulations of neoplastic and non-neoplastic brain cells. These tissue-states correlated with radiographic, histopathologic, and prognostic features and were enriched in distinct metabolic pathways. Fatty acid biosynthesis was enriched in the tissue-state defined by the cohabitation of astrocyte-like/mesenchymal glioma cells, reactive astrocytes, and macrophages, and was associated with recurrent GBM and shorter survival. Treating acute slices of GBM with a fatty acid synthesis inhibitor depleted the transcriptional signature of this pernicious tissue-state. These findings point to therapies that target interdependencies in the GBM microenvironment.
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Affiliation(s)
- Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Michael G Argenziano
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Adithya Kannan
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Julia Furnari
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Fahad Paryani
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Deborah Boyett
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Akshay Save
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Nelson Humala
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Fatima Khan
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Juncheng Li
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Hong Lu
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Yu Sun
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - John F Tuddenham
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Alexander R Goldberg
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Tejaswi Sudhakar
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Erin Bush
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Andrew B Lassman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Guy M McKhann
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Brian J A Gill
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Brett Youngerman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Michael B Sisti
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Jeffrey N Bruce
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Peter A Sims
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA.
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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26
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Murdaugh RL, Anastas JN. Applying single cell multi-omic analyses to understand treatment resistance in pediatric high grade glioma. Front Pharmacol 2023; 14:1002296. [PMID: 37205910 PMCID: PMC10191214 DOI: 10.3389/fphar.2023.1002296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
Despite improvements in cancer patient outcomes seen in the past decade, tumor resistance to therapy remains a major impediment to achieving durable clinical responses. Intratumoral heterogeneity related to genetic, epigenetic, transcriptomic, proteomic, and metabolic differences between individual cancer cells has emerged as a driver of therapeutic resistance. This cell to cell heterogeneity can be assessed using single cell profiling technologies that enable the identification of tumor cell clones that exhibit similar defining features like specific mutations or patterns of DNA methylation. Single cell profiling of tumors before and after treatment can generate new insights into the cancer cell characteristics that confer therapeutic resistance by identifying intrinsically resistant sub-populations that survive treatment and by describing new cellular features that emerge post-treatment due to tumor cell evolution. Integrative, single cell analytical approaches have already proven advantageous in studies characterizing treatment-resistant clones in cancers where pre- and post-treatment patient samples are readily available, such as leukemia. In contrast, little is known about other cancer subtypes like pediatric high grade glioma, a class of heterogeneous, malignant brain tumors in children that rapidly develop resistance to multiple therapeutic modalities, including chemotherapy, immunotherapy, and radiation. Leveraging single cell multi-omic technologies to analyze naïve and therapy-resistant glioma may lead to the discovery of novel strategies to overcome treatment resistance in brain tumors with dismal clinical outcomes. In this review, we explore the potential for single cell multi-omic analyses to reveal mechanisms of glioma resistance to therapy and discuss opportunities to apply these approaches to improve long-term therapeutic response in pediatric high grade glioma and other brain tumors with limited treatment options.
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Affiliation(s)
- Rebecca L. Murdaugh
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, United States
- Program in Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Jamie N. Anastas
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, United States
- Program in Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
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27
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Wei Y, Li G, Feng J, Wu F, Zhao Z, Bao Z, Zhang W, Su X, Li J, Qi X, Duan Z, Zhang Y, Vega SF, Jakola AS, Sun Y, Carén H, Jiang T, Fan X. Stalled oligodendrocyte differentiation in IDH-mutant gliomas. Genome Med 2023; 15:24. [PMID: 37055795 PMCID: PMC10103394 DOI: 10.1186/s13073-023-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized. METHODS Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers. RESULTS Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas. CONCLUSIONS Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.
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Affiliation(s)
- Yanfei Wei
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jing Feng
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zhaoshi Bao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Wei Zhang
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Xiaodong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jiuyi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Xueling Qi
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Zejun Duan
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Yunqiu Zhang
- Center of Growth Metabolism & Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, 41390, Sweden
| | - Yingyu Sun
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden.
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
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28
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Zhang D, Li AM, Hu G, Huang M, Yang F, Zhang L, Wellen KE, Xu X, Conn CS, Zou W, Kahn M, Rhoades SD, Weljie AM, Fuchs SY, Amankulor N, Yoshor D, Ye J, Koumenis C, Gong Y, Fan Y. PHGDH-mediated endothelial metabolism drives glioblastoma resistance to chimeric antigen receptor T cell immunotherapy. Cell Metab 2023; 35:517-534.e8. [PMID: 36804058 PMCID: PMC10088869 DOI: 10.1016/j.cmet.2023.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 10/24/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023]
Abstract
The efficacy of immunotherapy is limited by the paucity of T cells delivered and infiltrated into the tumors through aberrant tumor vasculature. Here, we report that phosphoglycerate dehydrogenase (PHGDH)-mediated endothelial cell (EC) metabolism fuels the formation of a hypoxic and immune-hostile vascular microenvironment, driving glioblastoma (GBM) resistance to chimeric antigen receptor (CAR)-T cell immunotherapy. Our metabolome and transcriptome analyses of human and mouse GBM tumors identify that PHGDH expression and serine metabolism are preferentially altered in tumor ECs. Tumor microenvironmental cues induce ATF4-mediated PHGDH expression in ECs, triggering a redox-dependent mechanism that regulates endothelial glycolysis and leads to EC overgrowth. Genetic PHGDH ablation in ECs prunes over-sprouting vasculature, abrogates intratumoral hypoxia, and improves T cell infiltration into the tumors. PHGDH inhibition activates anti-tumor T cell immunity and sensitizes GBM to CAR T therapy. Thus, reprogramming endothelial metabolism by targeting PHGDH may offer a unique opportunity to improve T cell-based immunotherapy.
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Affiliation(s)
- Duo Zhang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Albert M Li
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Guanghui Hu
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Menggui Huang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fan Yang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowei Xu
- Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Crystal S Conn
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Zou
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Kahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seth D Rhoades
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Serge Y Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Yoshor
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yanqing Gong
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA.
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29
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Hoogstrate Y, Draaisma K, Ghisai SA, van Hijfte L, Barin N, de Heer I, Coppieters W, van den Bosch TPP, Bolleboom A, Gao Z, Vincent AJPE, Karim L, Deckers M, Taphoorn MJB, Kerkhof M, Weyerbrock A, Sanson M, Hoeben A, Lukacova S, Lombardi G, Leenstra S, Hanse M, Fleischeuer REM, Watts C, Angelopoulos N, Gorlia T, Golfinopoulos V, Bours V, van den Bent MJ, Robe PA, French PJ. Transcriptome analysis reveals tumor microenvironment changes in glioblastoma. Cancer Cell 2023; 41:678-692.e7. [PMID: 36898379 DOI: 10.1016/j.ccell.2023.02.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/20/2022] [Accepted: 02/14/2023] [Indexed: 03/12/2023]
Abstract
A better understanding of transcriptional evolution of IDH-wild-type glioblastoma may be crucial for treatment optimization. Here, we perform RNA sequencing (RNA-seq) (n = 322 test, n = 245 validation) on paired primary-recurrent glioblastoma resections of patients treated with the current standard of care. Transcriptional subtypes form an interconnected continuum in a two-dimensional space. Recurrent tumors show preferential mesenchymal progression. Over time, hallmark glioblastoma genes are not significantly altered. Instead, tumor purity decreases over time and is accompanied by co-increases in neuron and oligodendrocyte marker genes and, independently, tumor-associated macrophages. A decrease is observed in endothelial marker genes. These composition changes are confirmed by single-cell RNA-seq and immunohistochemistry. An extracellular matrix-associated gene set increases at recurrence and bulk, single-cell RNA, and immunohistochemistry indicate it is expressed mainly by pericytes. This signature is associated with significantly worse survival at recurrence. Our data demonstrate that glioblastomas evolve mainly by microenvironment (re-)organization rather than molecular evolution of tumor cells.
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Affiliation(s)
- Youri Hoogstrate
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands.
| | - Kaspar Draaisma
- Department of Neurosurgery, UMC Utrecht, 3584CX Utrecht, the Netherlands
| | - Santoesha A Ghisai
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Levi van Hijfte
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands; Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Nastaran Barin
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands; Department of Precision and Microsystems Engineering, Delft University of Technology, 2628CD Delft, the Netherlands
| | - Iris de Heer
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Wouter Coppieters
- Genomics Platform, GIGA Institute, Université de Liège, 4000 Liège, Belgium
| | | | - Anne Bolleboom
- Deparment of Neuroscience, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands; Department of Neurosurgery, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Zhenyu Gao
- Deparment of Neuroscience, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Arnaud J P E Vincent
- Department of Neurosurgery, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Latifa Karim
- Genomics Platform, GIGA Institute, Université de Liège, 4000 Liège, Belgium
| | - Manon Deckers
- Genomics Platform, GIGA Institute, Université de Liège, 4000 Liège, Belgium
| | - Martin J B Taphoorn
- Department of Neurology, Haaglanden Medical Center, 2512VA The Hague, the Netherlands; Department of Neurology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Melissa Kerkhof
- Department of Neurology, Haaglanden Medical Center, 2512VA The Hague, the Netherlands
| | - Astrid Weyerbrock
- Department of Neurosurgery, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79085 Freiburg, Germany
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Ann Hoeben
- Department of Internal Medicine, Division of Medical Oncology, GROW, Maastricht University Medical Center, 6229ER Maastricht, the Netherlands
| | - Slávka Lukacova
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Sieger Leenstra
- Department of Neurosurgery, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Monique Hanse
- Department of Neurology, Catharina Hospital, 5623EJ Eindhoven, the Netherlands
| | - Ruth E M Fleischeuer
- Department of Pathology, Elisabeth-TweeSteden Hospital, 5042AD Tilburg, the Netherlands
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2SY Birmingham, UK
| | - Nicos Angelopoulos
- Systems Immunity Research Institute, Medical School, Cardiff University, CF14 4XN Cardiff, UK
| | | | | | - Vincent Bours
- Université de Liège, Department of Human Genetics, 4000 Liège, Belgium
| | | | - Pierre A Robe
- Department of Neurosurgery, UMC Utrecht, 3584CX Utrecht, the Netherlands; Université de Liège, Department of Human Genetics, 4000 Liège, Belgium
| | - Pim J French
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands.
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30
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De Falco A, Caruso F, Su XD, Iavarone A, Ceccarelli M. A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data. Nat Commun 2023; 14:1074. [PMID: 36841879 PMCID: PMC9968345 DOI: 10.1038/s41467-023-36790-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Single-cell RNA sequencing is the reference technology to characterize the composition of the tumor microenvironment and to study tumor heterogeneity at high resolution. Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of the clonal substructure of tumors from single-cell RNA-seq data. It uses a multichannel segmentation algorithm exploiting the assumption that all the cells in a given copy number clone share the same breakpoints. Thus, the smoothed expression profile of every individual cell constitutes part of the evidence of the copy number profile in each subclone. SCEVAN can automatically and accurately discriminate between malignant and non-malignant cells, resulting in a practical framework to analyze tumors and their microenvironment. We apply SCEVAN to datasets encompassing 106 samples and 93,322 cells from different tumor types and technologies. We demonstrate its application to characterize the intratumor heterogeneity and geographic evolution of malignant brain tumors.
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Affiliation(s)
- Antonio De Falco
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples 'Federico II', 80128, Naples, Italy.,BIOGEM Institute of Molecular Biology and Genetics, 83031, Ariano Irpino, Italy
| | - Francesca Caruso
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples 'Federico II', 80128, Naples, Italy.,BIOGEM Institute of Molecular Biology and Genetics, 83031, Ariano Irpino, Italy
| | - Xiao-Dong Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Road, Haidian District, 100871, Beijing, China
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA.,Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples 'Federico II', 80128, Naples, Italy. .,BIOGEM Institute of Molecular Biology and Genetics, 83031, Ariano Irpino, Italy.
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31
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Banu MA, Dovas A, Argenziano MG, Zhao W, Grajal HC, Higgins DM, Sperring CP, Pereira B, Ye LF, Mahajan A, Humala N, Furnari JL, Upadhyayula PS, Zandkarimi F, Nguyen TTT, Wu PB, Hai L, Karan C, Razavilar A, Siegelin MD, Kitajewski J, Bruce JN, Stockwell BR, Sims PA, Canoll PD. A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529581. [PMID: 36865302 PMCID: PMC9980114 DOI: 10.1101/2023.02.22.529581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Glioma cells hijack developmental transcriptional programs to control cell state. During neural development, lineage trajectories rely on specialized metabolic pathways. However, the link between tumor cell state and metabolic programs is poorly understood in glioma. Here we uncover a glioma cell state-specific metabolic liability that can be leveraged therapeutically. To model cell state diversity, we generated genetically engineered murine gliomas, induced by deletion of p53 alone (p53) or with constitutively active Notch signaling (N1IC), a pathway critical in controlling cellular fate. N1IC tumors harbored quiescent astrocyte-like transformed cell states while p53 tumors were predominantly comprised of proliferating progenitor-like cell states. N1IC cells exhibit distinct metabolic alterations, with mitochondrial uncoupling and increased ROS production rendering them more sensitive to inhibition of the lipid hydroperoxidase GPX4 and induction of ferroptosis. Importantly, treating patient-derived organotypic slices with a GPX4 inhibitor induced selective depletion of quiescent astrocyte-like glioma cell populations with similar metabolic profiles.
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Affiliation(s)
- Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael G. Argenziano
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Dominique M.O. Higgins
- Department of Neurological Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Colin P. Sperring
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brianna Pereira
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ling F. Ye
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nelson Humala
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia L. Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, 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
| | - Fereshteh Zandkarimi
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Trang T. T. Nguyen
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter B. Wu
- Department of Neurological Surgery, UCLA Geffen School of Medicine, Los Angeles, CA, USA
| | - Li Hai
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | - Charles Karan
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | - Aida Razavilar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Markus D. Siegelin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jan Kitajewski
- University of Illinois Cancer Center, Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, USA
| | - Jeffrey N. Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brent R. Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Peter A. Sims
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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32
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Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma. Front Med 2023; 17:240-262. [PMID: 36645634 DOI: 10.1007/s11684-022-0936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 01/17/2023]
Abstract
Detailed characterizations of genomic alterations have not identified subtype-specific vulnerabilities in adult gliomas. Mapping gliomas into developmental programs may uncover new vulnerabilities that are not strictly related to genomic alterations. After identifying conserved gene modules co-expressed with EGFR or PDGFRA (EM or PM), we recently proposed an EM/PM classification scheme for adult gliomas in a histological subtype- and grade-independent manner. By using cohorts of bulk samples, paired primary and recurrent samples, multi-region samples from the same glioma, single-cell RNA-seq samples, and clinical samples, we here demonstrate the temporal and spatial stability of the EM and PM subtypes. The EM and PM subtypes, which progress in a subtype-specific mode, are robustly maintained in paired longitudinal samples. Elevated activities of cell proliferation, genomic instability and microenvironment, rather than subtype switching, mark recurrent gliomas. Within individual gliomas, the EM/PM subtype was preserved across regions and single cells. Malignant cells in the EM and PM gliomas were correlated to neural stem cell and oligodendrocyte progenitor cell compartment, respectively. Thus, while genetic makeup may change during progression and/or within different tumor areas, adult gliomas evolve within a neurodevelopmental framework of the EM and PM molecular subtypes. The dysregulated developmental pathways embedded in these molecular subtypes may contain subtype-specific vulnerabilities.
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33
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Takacs GP, Kreiger CJ, Luo D, Tian G, Garcia JS, Deleyrolle LP, Mitchell DA, Harrison JK. Glioma-derived CCL2 and CCL7 mediate migration of immune suppressive CCR2 +/CX3CR1 + M-MDSCs into the tumor microenvironment in a redundant manner. Front Immunol 2023; 13:993444. [PMID: 36685592 PMCID: PMC9854274 DOI: 10.3389/fimmu.2022.993444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Glioblastoma (GBM) is the most common and malignant primary brain tumor, resulting in poor survival despite aggressive therapies. GBM is characterized in part by a highly heterogeneous and immunosuppressive tumor microenvironment (TME) made up predominantly of infiltrating peripheral immune cells. One significant immune cell type that contributes to glioma immune evasion is a population of immunosuppressive, hematopoietic cells, termed myeloid-derived suppressor cells (MDSCs). Previous studies suggest that a potent subset of myeloid cells, expressing monocytic (M)-MDSC markers, distinguished by dual expression of chemokine receptors CCR2 and CX3CR1, utilize CCR2 to infiltrate into the TME. This study evaluated the T cell suppressive function and migratory properties of CCR2+/CX3CR1+ MDSCs. Bone marrow-derived CCR2+/CX3CR1+ cells adopt an immune suppressive cell phenotype when cultured with glioma-derived factors. Recombinant and glioma-derived CCL2 and CCL7 induce the migration of CCR2+/CX3CR1+ MDSCs with similar efficacy. KR158B-CCL2 and -CCL7 knockdown murine gliomas contain equivalent percentages of CCR2+/CX3CR1+ MDSCs compared to KR158B gliomas. Combined neutralization of CCL2 and CCL7 completely blocks CCR2-expressing cell migration to KR158B cell conditioned media. CCR2+/CX3CR1+ cells are also reduced within KR158B gliomas upon combination targeting of CCL2 and CCL7. High levels of CCL2 and CCL7 are also associated with negative prognostic outcomes in GBM patients. These data provide a more comprehensive understanding of the function of CCR2+/CX3CR1+ MDSCs and the role of CCL2 and CCL7 in the recruitment of these immune suppressive cells and further support the significance of targeting this chemokine axis in GBM.
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Affiliation(s)
- Gregory P. Takacs
- Department of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL, United States
| | - Christian J. Kreiger
- Department of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL, United States
| | - Defang Luo
- Department of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL, United States
| | - Guimei Tian
- Department of Neurosurgery, University of Florida College of Medicine, Gainesville, FL, United States
| | - Julia S. Garcia
- Department of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL, United States
| | - Loic P. Deleyrolle
- Department of Neurosurgery, University of Florida College of Medicine, Gainesville, FL, United States
| | - Duane A. Mitchell
- Department of Neurosurgery, University of Florida College of Medicine, Gainesville, FL, United States
| | - Jeffrey K. Harrison
- Department of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL, United States
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34
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Fang C, Zhang Z, Han Y, Xu H, Zhu Z, Du Y, Hou P, Yuan L, Shao A, Zhang A, Lou M. URB2 as an important marker for glioma prognosis and immunotherapy. Front Pharmacol 2023; 14:1113182. [PMID: 37033651 PMCID: PMC10080038 DOI: 10.3389/fphar.2023.1113182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction: Glioma is the most common primary brain tumor and primary malignant tumor of the brain in clinical practice. Conventional treatment has not significantly altered the prognosis of patients with glioma. As research into immunotherapy continues, glioma immunotherapy has shown great potential. Methods: The clinical data were acquired from the Chinese Glioma Genome Atlas (CGGA) database and validated by the Gene Expression Omnibus (GEO) database, The Cancer Genome Atlas (TCGA) dataset, Clinical Proteomic Tumor Analysis Consortium (CPTAP) database, and Western blot (WB) analysis. By Cox regression analyses, we examined the association between different variables and overall survival (OS) and its potential as an independent prognostic factor. By constructing a nomogram that incorporates both clinicopathological variables and the expression of URB2, we provide a model for the prediction of prognosis. Moreover, we explored the relationship between immunity and URB2 and elucidated its underlying mechanism of action. Results: Our study shows that URB2 likely plays an oncogenic role in glioma and confirms that URB2 is a prognostic independent risk factor for glioma. Furthermore, we revealed a close relationship between immunity and URB2, which suggests a new approach for the immunotherapy of glioma. Conclusion: URB2 can be used for prognosis prediction and immunotherapy of glioma.
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Affiliation(s)
- Chaoyou Fang
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zeyu Zhang
- Department of Neurosurgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongquan Han
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Houshi Xu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengyang Zhu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yichao Du
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pinpin Hou
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ling Yuan
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Anwen Shao
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, China
- Clinical Research Center for Neurological Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Meiqing Lou, ; Anke Zhang, ; Anwen Shao,
| | - Anke Zhang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, China
- Clinical Research Center for Neurological Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Meiqing Lou, ; Anke Zhang, ; Anwen Shao,
| | - Meiqing Lou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Meiqing Lou, ; Anke Zhang, ; Anwen Shao,
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35
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Cell signaling activation and extracellular matrix remodeling underpin glioma tumor microenvironment heterogeneity and organization. Cell Oncol 2022; 46:589-602. [PMID: 36567397 DOI: 10.1007/s13402-022-00763-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Tumor cells thrive by adapting to the signals in their microenvironment. To adapt, cancer cells activate signaling and transcriptional programs and migrate to establish micro-niches, in response to signals from neighboring cells and non-cellular stromal factors. Understanding how the tumor microenvironment evolves during disease progression is crucial to deciphering the mechanisms underlying the functional behavior of cancer cells. METHODS Multiplex immunohistochemistry, spatial analysis and histological dyes were used to identify and measure immune cell infiltration, cell signal activation and extracellular matrix deposition in low-grade, high-grade astrocytoma and glioblastoma. RESULTS We show that lower grade astrocytoma tissue is largely devoid of infiltrating immune cells and extracellular matrix proteins, while high-grade astrocytoma exhibits abundant immune cell infiltration, activation, and extensive tissue remodeling. Spatial analysis shows that most T-cells are restricted to perivascular regions, but bone marrow-derived macrophages penetrate deep into neoplastic cell-rich regions. The tumor microenvironment is characterized by heterogeneous PI3K, MAPK and CREB signaling, with specific signaling profiles correlating with distinct pathological hallmarks, including angiogenesis, tumor cell density and regions where neoplastic cells border the extracellular matrix. Our results also show that tissue remodeling is important in regulating the architecture of the tumor microenvironment during tumor progression. CONCLUSION The tumor microenvironment in malignant astrocytoma, exhibits changes in cell composition, cell signaling activation and extracellular matrix deposition during disease development and that targeting the extracellular matrix, as well as cell signaling activation will be critical to designing personalized therapy.
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36
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Bayik D, Bartels CF, Lovrenert K, Watson DC, Zhang D, Kay K, Lee J, Lauko A, Johnson S, Lo A, Silver DJ, McGraw M, Grabowski M, Mohammadi AM, Veglia F, Fan Y, Vogelbaum MA, Scacheri P, Lathia JD. Distinct Cell Adhesion Signature Defines Glioblastoma Myeloid-Derived Suppressor Cell Subsets. Cancer Res 2022; 82:4274-4287. [PMID: 36126163 PMCID: PMC9664137 DOI: 10.1158/0008-5472.can-21-3840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023]
Abstract
In multiple types of cancer, an increased frequency in myeloid-derived suppressor cells (MDSC) is associated with worse outcomes and poor therapeutic response. In the glioblastoma (GBM) microenvironment, monocytic (m) MDSCs represent the predominant subset. However, the molecular basis of mMDSC enrichment in the tumor microenvironment compared with granulocytic (g) MDSCs has yet to be determined. Here we performed the first broad epigenetic profiling of MDSC subsets to define underlying cell-intrinsic differences in behavior and found that enhanced gene accessibility of cell adhesion programs in mMDSCs is linked to their tumor-accelerating ability in GBM models upon adoptive transfer. Mouse and human mMDSCs expressed higher levels of integrin β1 and dipeptidyl peptidase-4 (DPP-4) compared with gMDSCs as part of an enhanced cell adhesion signature. Integrin β1 blockade abrogated the tumor-promoting phenotype of mMDSCs and altered the immune profile in the tumor microenvironment, whereas treatment with a DPP-4 inhibitor extended survival in preclinical GBM models. Targeting DPP-4 in mMDSCs reduced pERK signaling and their migration towards tumor cells. These findings uncover a fundamental difference in the molecular basis of MDSC subsets and suggest that integrin β1 and DPP-4 represent putative immunotherapy targets to attenuate myeloid cell-driven immune suppression in GBM. SIGNIFICANCE Epigenetic profiling uncovers cell adhesion programming as a regulator of the tumor-promoting functions of monocytic myeloid-derived suppressor cells in glioblastoma, identifying therapeutic targets that modulate the immune response and suppress tumor growth.
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Affiliation(s)
- Defne Bayik
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Cynthia F. Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Katreya Lovrenert
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Dionysios C. Watson
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
- University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Duo Zhang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristen Kay
- Lerner Research Institute, Cleveland Clinic, Ohio
| | - Juyeun Lee
- Lerner Research Institute, Cleveland Clinic, Ohio
| | - Adam Lauko
- Lerner Research Institute, Cleveland Clinic, Ohio
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio
- Case Western Reserve University, Medical Science Training Program, Cleveland, Ohio
| | | | - Alice Lo
- Lerner Research Institute, Cleveland Clinic, Ohio
| | - Daniel J. Silver
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Mary McGraw
- Rose Ella Burkhardt Brain Tumor Center, Cleveland Clinic, Ohio
| | | | | | - Filippo Veglia
- Department of Immunology, Moffitt Cancer Center, Tampa, Florida
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Peter Scacheri
- Case Comprehensive Cancer Center, Cleveland, Ohio
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Justin D. Lathia
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
- Rose Ella Burkhardt Brain Tumor Center, Cleveland Clinic, Ohio
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Spinazzi EF, Argenziano MG, Upadhyayula PS, Banu MA, Neira JA, Higgins DMO, Wu PB, Pereira B, Mahajan A, Humala N, Al-Dalahmah O, Zhao W, Save AV, Gill BJA, Boyett DM, Marie T, Furnari JL, Sudhakar TD, Stopka SA, Regan MS, Catania V, Good L, Zacharoulis S, Behl M, Petridis P, Jambawalikar S, Mintz A, Lignelli A, Agar NYR, Sims PA, Welch MR, Lassman AB, Iwamoto FM, D'Amico RS, Grinband J, Canoll P, Bruce JN. Chronic convection-enhanced delivery of topotecan for patients with recurrent glioblastoma: a first-in-patient, single-centre, single-arm, phase 1b trial. Lancet Oncol 2022; 23:1409-1418. [PMID: 36243020 PMCID: PMC9641975 DOI: 10.1016/s1470-2045(22)00599-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Topotecan is cytotoxic to glioma cells but is clinically ineffective because of drug delivery limitations. Systemic delivery is limited by toxicity and insufficient brain penetrance, and, to date, convection-enhanced delivery (CED) has been restricted to a single treatment of restricted duration. To address this problem, we engineered a subcutaneously implanted catheter-pump system capable of repeated, chronic (prolonged, pulsatile) CED of topotecan into the brain and tested its safety and biological effects in patients with recurrent glioblastoma. METHODS We did a single-centre, open-label, single-arm, phase 1b clinical trial at Columbia University Irving Medical Center (New York, NY, USA). Eligible patients were at least 18 years of age with solitary, histologically confirmed recurrent glioblastoma showing radiographic progression after surgery, radiotherapy, and chemotherapy, and a Karnofsky Performance Status of at least 70. Five patients had catheters stereotactically implanted into the glioma-infiltrated peritumoural brain and connected to subcutaneously implanted pumps that infused 146 μM topotecan 200 μL/h for 48 h, followed by a 5-7-day washout period before the next infusion, with four total infusions. After the fourth infusion, the pump was removed and the tumour was resected. The primary endpoint of the study was safety of the treatment regimen as defined by presence of serious adverse events. Analyses were done in all treated patients. The trial is closed, and is registered with ClinicalTrials.gov, NCT03154996. FINDINGS Between Jan 22, 2018, and July 8, 2019, chronic CED of topotecan was successfully completed safely in all five patients, and was well tolerated without substantial complications. The only grade 3 adverse event related to treatment was intraoperative supplemental motor area syndrome (one [20%] of five patients in the treatment group), and there were no grade 4 adverse events. Other serious adverse events were related to surgical resection and not the study treatment. Median follow-up was 12 months (IQR 10-17) from pump explant. Post-treatment tissue analysis showed that topotecan significantly reduced proliferating tumour cells in all five patients. INTERPRETATION In this small patient cohort, we showed that chronic CED of topotecan is a potentially safe and active therapy for recurrent glioblastoma. Our analysis provided a unique tissue-based assessment of treatment response without the need for large patient numbers. This novel delivery of topotecan overcomes limitations in delivery and treatment response assessment for patients with glioblastoma and could be applicable for other anti-glioma drugs or other CNS diseases. Further studies are warranted to determine the effect of this drug delivery approach on clinical outcomes. FUNDING US National Institutes of Health, The William Rhodes and Louise Tilzer Rhodes Center for Glioblastoma, the Michael Weiner Glioblastoma Research Into Treatment Fund, the Gary and Yael Fegel Foundation, and The Khatib Foundation.
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Affiliation(s)
- Eleonora F Spinazzi
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael G Argenziano
- Department of Neurological Surgery, 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
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Justin A Neira
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Dominique M O Higgins
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter B Wu
- Department of Neurological Surgery, UCLA Geffen School of Medicine, Los Angeles, CA, USA
| | - Brianna Pereira
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Nelson Humala
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Akshay V Save
- Department of Neurological Surgery, NYU Grossman School of Medicine, New York, NY, USA
| | - Brian J A Gill
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Deborah M Boyett
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Tamara Marie
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia L Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Tejaswi D Sudhakar
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Sylwia A Stopka
- Department of Neurosurgery and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vanessa Catania
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Good
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Stergios Zacharoulis
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Meenu Behl
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Petros Petridis
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachin Jambawalikar
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Akiva Mintz
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Angela Lignelli
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute Boston, MA, USA
| | - Peter A Sims
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mary R Welch
- Division of Neuro-Oncology, Department of Neurology and the Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Hospital, New York, NY, USA
| | - Andrew B Lassman
- Division of Neuro-Oncology, Department of Neurology and the Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Hospital, New York, NY, USA
| | - Fabio M Iwamoto
- Division of Neuro-Oncology, Department of Neurology and the Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Hospital, New York, NY, USA
| | - Randy S D'Amico
- Department of Neurosurgery, Lenox Hill Hospital, New York, NY, USA
| | - Jack Grinband
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, USA; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Canoll
- Department of Pathology and 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.
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Brooks LJ, Simpson Ragdale H, Hill CS, Clements M, Parrinello S. Injury programs shape glioblastoma. Trends Neurosci 2022; 45:865-876. [PMID: 36089406 DOI: 10.1016/j.tins.2022.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/30/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022]
Abstract
Glioblastoma is the most common and aggressive primary brain cancer in adults and is almost universally fatal due to its stark therapeutic resistance. During the past decade, although survival has not substantially improved, major advances have been made in our understanding of the underlying biology. It has become clear that these devastating tumors recapitulate features of neurodevelopmental hierarchies which are influenced by the microenvironment. Emerging evidence also highlights a prominent role for injury responses in steering cellular phenotypes and contributing to tumor heterogeneity. This review highlights how the interplay between injury and neurodevelopmental programs impacts on tumor growth, invasion, and treatment resistance, and discusses potential therapeutic considerations in view of these findings.
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Affiliation(s)
- Lucy J Brooks
- Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, University College London Cancer Institute, London, UK.
| | - Holly Simpson Ragdale
- Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Ciaran Scott Hill
- Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, University College London Cancer Institute, London, UK; Department of Neurosurgery, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust (UCLH), London, UK
| | - Melanie Clements
- Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, University College London Cancer Institute, London, UK.
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Hao L, Chen Q, Chen X, Zhou Q. Integrated analysis of bulk and single-cell RNA-seq reveals the role of MYC signaling in lung adenocarcinoma. Front Genet 2022; 13:1021978. [PMID: 36299592 PMCID: PMC9589149 DOI: 10.3389/fgene.2022.1021978] [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: 08/18/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
MYC is one of the well-known oncogenes, and its important role in cancer still remains largely unknown. We obtained lung adenocarcinoma (LUAD) multi-omics data including genome, transcriptome, and single-cell sequencing data from multiple cohorts. We calculated the GSVA score of the MYC target v1 using the ssGSEA method, and obtained the genes highly correlated with this score by Spearman correlation analysis. Subsequent hierarchical clustering divided these genes into two gene sets highly associated with MYC signaling (S1 and S2). Unsupervised clustering based on these genes divided the LUAD samples into two distinct subgroups, namely, the MYC signaling inhibition group (C1) and activation group (C2). The MCP counter package in R was used to assess tumor immune cell infiltration abundance and ssGSEA was used to calculate gene set scores. The scRNA-seq was used to verify the association of MYC signaling to cell differentiation. We observed significant differences in prognosis, clinical characteristics, immune microenvironment, and genomic alterations between MYC signaling inhibition and MYC signaling activation groups. MYC-signaling is associated with genomic instability and can mediate the immunosuppressive microenvironment and promote cell proliferation, tumor stemness. Moreover, MYC-signaling activation is also subject to complex post-transcriptional regulation and is highly associated with cell differentiation. In conclusion, MYC signaling is closely related to the genomic instability, genetic alteration and regulation, the immune microenvironment landscape, cell differentiation, and disease survival in LUAD. The findings of this study provide a valuable reference to revealing the mechanism of cancer-promoting action of MYC in LUAD.
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Affiliation(s)
- Lu Hao
- Science and Education Department, Shenzhen Baoan Shiyan People’s Hospital, Shenzhen, China
| | - Qiuyan Chen
- Science and Education Department, Shenzhen Baoan Shiyan People’s Hospital, Shenzhen, China
| | - Xi Chen
- Central Laboratory, The People’s Hospital of Baoan Shenzhen, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qing Zhou
- Central Laboratory, The People’s Hospital of Baoan Shenzhen, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Qing Zhou,
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Ge X, Xu M, Cheng T, Hu N, Sun P, Lu B, Wang Z, Li J. TP53I13 promotes metastasis in glioma via macrophages, neutrophils, and fibroblasts and is a potential prognostic biomarker. Front Immunol 2022; 13:974346. [PMID: 36275718 PMCID: PMC9585303 DOI: 10.3389/fimmu.2022.974346] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background TP53I13 is a protein coding tumor suppression gene encoded by the tumor protein p53. Overexpression of TP53I13 impedes tumor cell proliferation. Nevertheless, TP53I13 role and expression in the emergence and progression of glioma (low-grade glioma and glioblastoma) are yet to be identified. Thus, we aim to use comprehensive bioinformatics analyses to investigate TP53I13 and its prognostic value in gliomas. Methods Multiple databases were consulted to evaluate and assess the expression of TP53I13, such as the Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), GeneMANIA, and Gene Expression Profiling Interactive. TP53I13 expression was further explored using immunohistochemistry (IHC) and multiplex immunohistochemistry (mIHC). Through Gene Set Enrichment Analysis (GSEA), the biological functions of TP53I13 and metastatic processes associated with it were studied. Results The expression of TP53I13 was higher in tumor samples compared to normal samples. In samples retrieved from the TCGA and CGGA databases, high TP53I13 expression was associated with poor survival outcomes. The analysis of multivariate Cox showed that TP53I13 might be an independent prognostic marker of glioma. It was also found that increased expression of TP53I13 was significantly correlated with PRS type, status, 1p/19q codeletion status, IDH mutation status, chemotherapy, age, and tumor grade. According to CIBERSORT (Cell-type Identification by Estimating Relative Subsets of RNA Transcript), the expression of TP53I13 correlates with macrophages, neutrophils, and dendritic cells. GSEA shows a close correlation between TP53I13 and p53 signaling pathways, DNA replication, and the pentose phosphate pathway. Conclusion Our results reveal a close correlation between TP53I13 and gliomas. Further, TP53I13 expression could affect the survival outcomes in glioma patients. In addition, TP53I13 was an independent marker that was crucial in regulating the infiltration of immune cells into tumors. As a result of these findings, TP53I13 might represent a new biomarker of immune infiltration and prognosis in patients with gliomas.
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Affiliation(s)
- Xinqi Ge
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Manyu Xu
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Tong Cheng
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Nan Hu
- Medical School of Nantong University, Nantong, China
| | - Pingping Sun
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Bing Lu
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ziheng Wang
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
- *Correspondence: Jian Li, ; Ziheng Wang,
| | - Jian Li
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- *Correspondence: Jian Li, ; Ziheng Wang,
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Johnson AL, Laterra J, Lopez-Bertoni H. Exploring glioblastoma stem cell heterogeneity: Immune microenvironment modulation and therapeutic opportunities. Front Oncol 2022; 12:995498. [PMID: 36212415 PMCID: PMC9532940 DOI: 10.3389/fonc.2022.995498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Despite its growing use in cancer treatment, immunotherapy has been virtually ineffective in clinical trials for gliomas. The inherently cold tumor immune microenvironment (TIME) in gliomas, characterized by a high ratio of pro-tumor to anti-tumor immune cell infiltrates, acts as a seemingly insurmountable barrier to immunotherapy. Glioma stem cells (GSCs) within these tumors are key contributors to this cold TIME, often functioning indirectly through activation and recruitment of pro-tumor immune cell types. Furthermore, drivers of GSC plasticity and heterogeneity (e.g., reprogramming transcription factors, epigenetic modifications) are associated with induction of immunosuppressive cell states. Recent studies have identified GSC-intrinsic mechanisms, including functional mimicry of immune suppressive cell types, as key determinants of anti-tumor immune escape. In this review, we cover recent advancements in our understanding of GSC-intrinsic mechanisms that modulate GSC-TIME interactions and discuss cutting-edge techniques and bioinformatics platforms available to study immune modulation at high cellular resolution with exploration of both malignant (i.e., GSC) and non-malignant (i.e., immune) cell fractions. Finally, we provide insight into the therapeutic opportunities for targeting immunomodulatory GSC-intrinsic mechanisms to potentiate immunotherapy response in gliomas.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
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Chanoch-Myers R, Wider A, Suva ML, Tirosh I. Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis. Genome Med 2022; 14:106. [PMID: 36123598 PMCID: PMC9484143 DOI: 10.1186/s13073-022-01109-8] [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: 01/11/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022] Open
Abstract
Background Multiple glioblastoma studies have described a mesenchymal (MES) state, with each study defining the MES program by distinct sets of genes and highlighting distinct functional associations, including both immune activation and suppression. These variable descriptions complicate our understanding of the MES state and its implications. Here, we hypothesize that there is a range of glioma MES states, possibly reflecting distinct prior states in which a MES program can be induced, and/or distinct mechanisms that induce the MES states in those cells. Methods We integrated multiple published single-cell and bulk RNA sequencing datasets and MES signatures to define a core MES program that recurs across studies, as well as multiple function-specific MES signatures that vary across MES cells. We then examined the co-occurrence of these signatures and their associations with genetic and microenvironmental features. Results Based on co-occurrence of MES signatures, we found three main variants of MES states: hypoxia-related (MES-Hyp), astrocyte-related (MES-Ast), and an intermediate state. Notably, the MES states are differentially associated with genetic and microenvironmental features. MES-Hyp is preferentially associated with NF1 deletion, overall macrophage abundance, a high macrophage/microglia ratio, and M2-related macrophages, consistent with previous studies that associated MES with immune suppression. In contrast, MES-Ast is associated with T cell abundance and cytotoxicity, consistent with immune activation through expression of MHC-I/II. Conclusions Diverse MES states occur in glioblastoma. These states share a subset of core genes but differ primarily in their association with hypoxia vs. astrocytic expression programs, and with immune suppression vs. activation, respectively. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01109-8.
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Affiliation(s)
- Rony Chanoch-Myers
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Wider
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Roopa Sowjanya P, Shilpa P, Patil GP, Babu DK, Sharma J, Sangnure VR, Mundewadikar DM, Natarajan P, Marathe AR, Reddy UK, Singh VN. Reference quality genome sequence of Indian pomegranate cv. 'Bhagawa' ( Punica granatum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:947164. [PMID: 36186044 PMCID: PMC9521485 DOI: 10.3389/fpls.2022.947164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 06/16/2023]
Abstract
Pomegranate is an important fruit crop for ensuring livelihood and nutrition security in fragile semi-arid regions of the globe having limited irrigation resources. This is a high-value, nutritionally rich, and export-oriented agri-commodity that ensures high returns on investment to growers across the world. Although it is a valuable fruit crop, it has received only a limited genomics research outcome. To fast-track the pomegranate improvement program, de novo whole-genome sequencing of the main Indian cultivar 'Bhagawa' was initiated by the Indian Council of Agricultural Research-National Research Center on Pomegranate (ICAR-NRCP). We have demonstrated that a combination of commercially available technologies from Illumina, PacBio, 10X Genomics, and BioNano Genomics could be used efficiently for sequencing and reference-grade de novo assembly of the pomegranate genome. The research led to a final reference-quality genome assembly for 'Bhagawa' of 346.08 Mb in 342 scaffolds and an average N50 of 16.12 Mb and N90 of 1088.62 Kb. This assembly covered more than 98% of the estimated pomegranate genome size, 352.54 Mb. The LTR assembly index (LAI) value of 10 and 93.68% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score over the 1,440 ortholog genes of the completed pomegranate genome indicates the quality of the assembled pomegranate genome. Furthermore, 29,435 gene models were discovered with a mean transcript length of 2,954 bp and a mean coding sequence length 1,090 bp. Four transcript data samples of pomegranate tissues were mapped over the assembled 'Bhagawa' genome up to 95% significant matches, indicating the high quality of the assembled genome. We have compared the 'Bhagawa' genome with the genomes of the pomegranate cultivars 'Dabenzi' and 'Taishanhong.' We have also performed whole-genome phylogenetic analysis using Computational Analysis of Gene Family Evolution (CAFE) and found that Eucalyptus grandis and pomegranate diverged 64 (60-70) million years ago. About 1,573 protein-coding resistance genes identified in the 'Bhagawa' genome were classified into 32 domains. In all, 314 copies of miRNA belonging to 26 different families were identified in the 'Bhagawa' genome. The reference-quality genome assembly of 'Bhagawa' is certainly a significant genomic resource for accelerated pomegranate improvement.
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Affiliation(s)
| | | | | | | | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | | | | | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | | | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
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Xiong A, Zhang J, Chen Y, Zhang Y, Yang F. Integrated single-cell transcriptomic analyses reveal that GPNMB-high macrophages promote PN-MES transition and impede T cell activation in GBM. EBioMedicine 2022; 83:104239. [PMID: 36054938 PMCID: PMC9437813 DOI: 10.1016/j.ebiom.2022.104239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/27/2022] Open
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45
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Ma K, Chen S, Chen X, Yang C, Yang J. S100A10 Is a New Prognostic Biomarker Related to the Malignant Molecular Features and Immunosuppression Process of Adult Gliomas. World Neurosurg 2022; 165:e650-e663. [PMID: 35779750 DOI: 10.1016/j.wneu.2022.06.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Previous studies have demonstrated the role of S100A10 in the progression of several tumors; however, few studies have investigated its immunological characteristics in adult gliomas. In this study, we systematically explored its biological features and clinical significance in adult gliomas. METHODS Altogether, 325 glioma cases from the Chinese Glioma Genome Atlas and 699 glioma cases from The Cancer Genome Atlas were included as the training and validation cohorts. R software was used for data analysis and mapping using the RNA sequencing data from these cases. One-way analysis of variance and Student's t-test were used to assess the differences between the groups. Differences were considered statistically significant at P < 0.05. RESULTS We found that S100A10 was remarkably highly expressed in high-grade glioma, isocitrate dehydrogenase wild type, 1p19q noncodeletion type, O6-methylguanine-DNA methyltransferase promoter unmethylation type, and mesenchymal-like molecular subtype. S100A10 specifically and sensitively indicates the mesenchymal-like molecular subtype. Upregulated S100A10 levels were independently correlated with poor survival. S100A10-related biological processes in gliomas mainly concentrate on immunoreaction and inflammatory response. We then proved that S100A10 was positively related to most inflammatory metagenes, except IgG, including HCK, LCK, MHC II, STAT1, and interferon. More importantly, the levels of glioma-infiltrating immune cells were positively associated with the expression of S100A10, especially in tumor-related macrophages, regulatory T cells, and myeloid-derived suppressor cells. CONCLUSIONS S100A10 is closely related to malignant pathological subtypes, worse prognosis, and immunosuppressive immune cell infiltration in adult gliomas, making it a promising biomarker and potential target in the diagnosis, treatment, and prognostic assessment of gliomas.
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Affiliation(s)
- Kaiming Ma
- Department of Neurosurgery, Peking University Third Hospital, Beijing, China
| | - Suhua Chen
- Department of Neurosurgery, Peking University Third Hospital, Beijing, China
| | - Xin Chen
- Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, China
| | - Chenlong Yang
- Department of Neurosurgery, Peking University Third Hospital, Beijing, China
| | - Jun Yang
- Department of Neurosurgery, Peking University Third Hospital, Beijing, China; Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, China.
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Ma K, Chen S, Chen X, Zhao X, Yang J. CD93 is Associated with Glioma-related Malignant Processes and Immunosuppressive Cell Infiltration as an Inspiring Biomarker of Survivance. J Mol Neurosci 2022; 72:2106-2124. [PMID: 36006582 DOI: 10.1007/s12031-022-02060-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
Previous reports have confirmed the significance of CD93 in the progression of multiple tumors; however, there are few studies examining its immune properties for gliomas. Here, we methodically investigated the pathophysiological characteristics and clinical manifestations of gliomas. Six hundred ninety-nine glioma patients in TCGA along with 325 glioma patients in CGGA were correspondingly collected for training and validating. We analyzed and visualized total statistics using RStudio. One-way ANOVA and Student's t-test were used to assess groups' differences. All differences were considered statistically significant at the level of P < 0.05. CD93 markedly upregulated among HGG, MGMT promoter unmethylated subforms, IDH wild forms, 1p19q non-codeletion subforms, and mesenchyme type gliomas. ROC analysis illustrated the favorable applicability of CD93 in estimating mesenchyme subform. Kaplan-Meier curves together with multivariable Cox analyses upon survivance identified high-expression CD93 as a distinct prognostic variable for glioma patients. GO analysis of CD93 documented its predominant part in glioma-related immunobiological processes and inflammation responses. We examined the associations of CD93 with immune-related meta-genes, and CD93 positively correlated with HCK, LCK, MHC I, MHC II, STAT1 and IFN, while adverse with IgG. Association analyses between CD93 and gliomas-infiltrating immunocytes indicated that the infiltrating degrees of most immunocytes exhibited positive correlations with CD93, particularly these immunosuppressive subsets such as TAM, Treg, and MDSCs. CD93 is markedly associated with adverse pathology types, unfavorable survival, and immunosuppressive immunocytes infiltration among gliomas, thus identifying CD93 as a practicable marker and a promising target for glioma-based precise diagnosis and therapeutic strategies.
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Affiliation(s)
- Kaiming Ma
- Department of Neurosurgery, Peking University Third Hospital, Haidian District, 49 North Garden Rd, Beijing, 100191, China
| | - Suhua Chen
- Department of Neurosurgery, Peking University Third Hospital, Haidian District, 49 North Garden Rd, Beijing, 100191, China
| | - Xin Chen
- Department of Neurosurgery, Peking University Third Hospital, Haidian District, 49 North Garden Rd, Beijing, 100191, China.,Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, China
| | - Xiaofang Zhao
- Department of Neurosurgery, Peking University Third Hospital, Haidian District, 49 North Garden Rd, Beijing, 100191, China
| | - Jun Yang
- Department of Neurosurgery, Peking University Third Hospital, Haidian District, 49 North Garden Rd, Beijing, 100191, China. .,Center for Precision Neurosurgery and Oncology of Peking University Health Science Center, Beijing, China.
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Wu H, Fu R, Zhang YH, Liu Z, Chen ZH, Xu J, Tian Y, Jin W, Wong SZH, Wu QF. Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. Front Immunol 2022; 13:903246. [PMID: 35844565 PMCID: PMC9281506 DOI: 10.3389/fimmu.2022.903246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Ependymoma (EPN) is a malignant glial tumor occurring throughout central nervous system, which commonly presents in children. Although recent studies have characterized EPN samples at both the bulk and single-cell level, intratumoral heterogeneity across subclones remains a confounding factor that impedes understanding of EPN biology. In this study, we generated a high-resolution single-cell dataset of pediatric ependymoma with a particular focus on the comparison of subclone differences within tumors and showed upregulation of cilium-associated genes in more highly differentiated subclone populations. As a proxy to traditional pseudotime analysis, we applied a novel trajectory scoring method to reveal cellular compositions associated with poor survival outcomes across primary and relapsed patients. Furthermore, we identified putative cell–cell communication features between relapsed and primary samples and showed upregulation of pathways associated with immune cell crosstalk. Our results revealed both inter- and intratumoral heterogeneity in EPN and provided a framework for studying transcriptomic signatures of individual subclones at single-cell resolution.
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Affiliation(s)
- Haoda Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Ruiqing Fu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yu-Hong Zhang
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiming Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhen-Hua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingkai Xu
- Department of Dermatology, China–Japan Friendship Hospital, Beijing, China
| | - Yongji Tian
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Samuel Zheng Hao Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Beijing Children Hospital, Capital Medical University, Beijing, China
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48
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Yun D, Wang X, Wang W, Ren X, Li J, Wang X, Liang J, Liu J, Fan J, Ren X, Zhang H, Shang G, Sun J, Chen L, Li T, Zhang C, Yu S, Yang X. A Novel Prognostic Signature Based on Glioma Essential Ferroptosis-Related Genes Predicts Clinical Outcomes and Indicates Treatment in Glioma. Front Oncol 2022; 12:897702. [PMID: 35756689 PMCID: PMC9232254 DOI: 10.3389/fonc.2022.897702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/05/2022] [Indexed: 12/11/2022] Open
Abstract
Background Ferroptosis is a form of programmed cell death (PCD) that has been implicated in cancer progression, although the specific mechanism is not known. Here, we used the latest DepMap release CRISPR data to identify the essential ferroptosis-related genes (FRGs) in glioma and their role in patient outcomes. Methods RNA-seq and clinical information on glioma cases were obtained from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). FRGs were obtained from the FerrDb database. CRISPR-screened essential genes (CSEGs) in glioma cell lines were downloaded from the DepMap portal. A series of bioinformatic and machine learning approaches were combined to establish FRG signatures to predict overall survival (OS) in glioma patients. In addition, pathways analysis was used to identify the functional roles of FRGs. Somatic mutation, immune cell infiltration, and immune checkpoint gene expression were analyzed within the risk subgroups. Finally, compounds for reversing high-risk gene signatures were predicted using the GDSC and L1000 datasets. Results Seven FRGs (ISCU, NFS1, MTOR, EIF2S1, HSPA5, AURKA, RPL8) were included in the model and the model was found to have good prognostic value (p < 0.001) in both training and validation groups. The risk score was found to be an independent prognostic factor and the model had good efficacy. Subgroup analysis using clinical parameters demonstrated the general applicability of the model. The nomogram indicated that the model could effectively predict 12-, 36-, and 60-months OS and progression-free interval (PFI). The results showed the presence of more aggressive phenotypes (lower numbers of IDH mutations, higher numbers of EGFR and PTEN mutations, greater infiltration of immune suppressive cells, and higher expression of immune checkpoint inhibitors) in the high-risk group. The signaling pathways enriched closely related to the cell cycle and DNA damage repair. Drug predictions showed that patients with higher risk scores may benefit from treatment with RTK pathway inhibitors, including compounds that inhibit RTKs directly or indirectly by targeting downstream PI3K or MAPK pathways. Conclusion In summary, the proposed cancer essential FRG signature predicts survival and treatment response in glioma.
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Affiliation(s)
- Debo Yun
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China.,Department of Neurosurgery, Nanchong Central Hospital, Nanchong, China
| | - Xuya Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Wenbo Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xiao Ren
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jiabo Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xisen Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jianshen Liang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jie Liu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jikang Fan
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xiude Ren
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Hao Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Guanjie Shang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jingzhang Sun
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Lei Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Tao Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Chen Zhang
- Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Shengping Yu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xuejun Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China.,Department of Neurosurgery, Beijing Tsinghua Changgung Hospital, Beijing, China
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49
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Kenchappa RS, Dovas A, Argenziano MG, Meyer CT, Stopfer LE, Banu MA, Pereira B, Griffith J, Mohammad A, Talele S, Haddock A, Zarco N, Elmquist W, White F, Quaranta V, Sims P, Canoll P, Rosenfeld SS. Activation of STAT3 through combined SRC and EGFR signaling drives resistance to a mitotic kinesin inhibitor in glioblastoma. Cell Rep 2022; 39:110991. [PMID: 35732128 PMCID: PMC10018805 DOI: 10.1016/j.celrep.2022.110991] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/27/2022] [Accepted: 06/01/2022] [Indexed: 01/19/2023] Open
Abstract
Inhibitors of the mitotic kinesin Kif11 are anti-mitotics that, unlike vinca alkaloids or taxanes, do not disrupt microtubules and are not neurotoxic. However, development of resistance has limited their clinical utility. While resistance to Kif11 inhibitors in other cell types is due to mechanisms that prevent these drugs from disrupting mitosis, we find that in glioblastoma (GBM), resistance to the Kif11 inhibitor ispinesib works instead through suppression of apoptosis driven by activation of STAT3. This form of resistance requires dual phosphorylation of STAT3 residues Y705 and S727, mediated by SRC and epidermal growth factor receptor (EGFR), respectively. Simultaneously inhibiting SRC and EGFR reverses this resistance, and combined targeting of these two kinases in vivo with clinically available inhibitors is synergistic and significantly prolongs survival in ispinesib-treated GBM-bearing mice. We thus identify a translationally actionable approach to overcoming Kif11 inhibitor resistance that may work to block STAT3-driven resistance against other anti-cancer therapies as well.
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Affiliation(s)
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael G Argenziano
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Christian T Meyer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Lauren E Stopfer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matei A Banu
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brianna Pereira
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jessica Griffith
- Department of Pharmaceutics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Afroz Mohammad
- Department of Pharmaceutics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surabhi Talele
- Department of Pharmaceutics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashley Haddock
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Natanael Zarco
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - William Elmquist
- Department of Pharmaceutics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Forest White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Peter Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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50
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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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