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Wu H, Yang Z, Chang C, Wang Z, Zhang D, Guo Q, Zhao B. A novel disulfide death-related genes prognostic signature identifies the role of IPO4 in glioma progression. Cancer Cell Int 2024; 24:168. [PMID: 38734657 PMCID: PMC11088110 DOI: 10.1186/s12935-024-03358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND "Disulfide death," a form of cellular demise, is triggered by the abnormal accumulation of intracellular disulfides under conditions of glucose deprivation. However, its role in the prognosis of glioma remains undetermined. Therefore, the main objective of this study is to establish prognostic signature based on disulfide death-related genes (DDRGs) and to provide new solutions in choosing the effective treatment of glioma. METHODS The RNA transcriptome, clinical information, and mutation data of glioma samples were sourced from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), while normal samples were obtained from the Genotype-Tissue Expression (GTEx). DDRGs were compiled from previous studies and selected through differential analysis and univariate Cox regression analysis. The molecular subtypes were determined through consensus clustering analysis. Further, LASSO analysis was employed to select characteristic genes, and subsequently, a risk model comprising seven DDRGs was constructed based on multivariable Cox analysis. Kaplan-Meier survival curves were employed to assess survival differences between high and low-risk groups. Additionally, functional analyses (GO, KEGG, GSEA) were conducted to explore the potential biological functions and signaling pathways of genes associated with the model. The study also explored immune checkpoint (ICP) genes, immune cell infiltration levels, and immune stromal scores. Finally, the effect of Importin-4(IPO4) on glioma has been further confirmed through RT-qPCR, Western blot, and cell functional experiments. RESULTS 7 genes associated with disulfide death were obtained and two subgroups of patients with different prognosis and clinical characteristics were identified. Risk signature was subsequently developed and proved to serve as an prognostic predictor. Notably, the high-risk group exhibited an immunosuppressive microenvironment characterized by a high concentration of M2 macrophages and regulatory T cells (Tregs). In contrast, the low-risk group showed lower half-maximal inhibitory concentration (IC50) values. Therefore, patients in the high-risk group may benefit more from immunotherapy, while patients in the low-risk group may benefit more from chemotherapy. In addition, in vitro experiments have shown that inhibition of the expression of IPO4 leads to a significant reduction in the proliferation, migration, and invasion of glioma cells. CONCLUSION This study identified two glioma subtypes and constructed a prognostic signature based on DDRGs. The signature has the potential to optimize the selection of patients for immune- and chemotherapy and provided a potential therapeutic target for glioma.
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Affiliation(s)
- HaoYuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiHao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ChenXi Chang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiWei Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - DeRan Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - QingGuo Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China.
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Vibhavari RJA, Rao V, Cheruku SP, Kumar BH, Maity S, Nandakumar K, Kumar L, Mehta CH, Nayak U, Chamallamudi MR, Kumar N. Enhancing temozolomide antiglioma response by inhibiting O6-methylguanine-DNA methyltransferase with selected phytochemicals: in silico and in vitro approach. 3 Biotech 2023; 13:385. [PMID: 37928438 PMCID: PMC10622385 DOI: 10.1007/s13205-023-03821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/09/2023] [Indexed: 11/07/2023] Open
Abstract
The aim of our study was to investigate the potential of rutin, catechin, dehydrozingerone, naringenin, and quercetin, both alone and in combination with temozolomide, to inhibit the expression of O6-methylguanine-DNA methyltransferase (MGMT) in glioma cells. MGMT has been shown to be a major cause of temozolomide resistance in glioma. Our study used both in silico and in vitro methods to assess the inhibitory activity of these phytochemicals on MGMT, with the goal of identifying the most effective combination of compounds for reducing temozolomide resistance. After conducting an initial in silico screening of natural compounds against MGMT protein, five phytochemicals were chosen based on their high docking scores and favorable binding energies. From the molecular docking and simulation studies, we found that quercetin showed a good inhibitory effect of MGMT with its high binding affinity. C6 glioma cells showed increased cytotoxicity when treated with the temozolomide and quercetin combination. It was understood from the isobologram and combination index plot that the drug combination showed a synergistic effect at the lowest dose. Quercetin when combined with temozolomide significantly decreased the MGMT levels in C6 cells in comparison with the other drugs as estimated by ELISA. The percentage of apoptotic cells increased significantly in the temozolomide-quercetin group indicating the potency of quercetin in decreasing the resistance of temozolomide as confirmed by acridine orange/ethidium bromide staining. Our experiment hence suggests that temozolomide resistance can be reduced by combining the drug with quercetin which will serve as an effective therapeutic target for glioblastoma treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03821-7.
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Affiliation(s)
- R. J. A. Vibhavari
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Vanishree Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Sri Pragnya Cheruku
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - B. Harish Kumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Krishnadas Nandakumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Lalit Kumar
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chetan Hasmukh Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Usha Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Mallikarjuna Rao Chamallamudi
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Industrial Area, Vaishali, Hajipur, 844102 Bihar India
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3
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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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da Silva FF, Lupinacci FCS, Elias BDS, Beserra AO, Sanematsu P, Roffe M, Kulikowski LD, Costa FD, Santos TG, Hajj GNM. Establishment and Comprehensive Molecular Characterization of an Immortalized Glioblastoma Cell Line from a Brazilian Patient. Int J Mol Sci 2023; 24:15861. [PMID: 37958846 PMCID: PMC10649167 DOI: 10.3390/ijms242115861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults, with few effective treatment strategies. The research on the development of new treatments is often constrained by the limitations of preclinical models, which fail to accurately replicate the disease's essential characteristics. Herein, we describe the obtention, molecular, and functional characterization of the GBM33 cell line. This cell line belongs to the GBM class according to the World Health Organization 2021 Classification of Central Nervous System Tumors, identified by methylation profiling. GBM33 expresses the astrocytic marker GFAP, as well as markers of neuronal origin commonly expressed in GBM cells, such as βIII-tubulin and neurofilament. Functional assays demonstrated an increased growth rate when compared to the U87 commercial cell line and a similar sensitivity to temozolamide. GBM33 cells retained response to serum starvation, with reduced growth and diminished activation of the Akt signaling pathway. Unlike LN-18 and LN-229 commercial cell lines, GBM33 is able to produce primary cilia upon serum starvation. In summary, the successful establishment and comprehensive characterization of this GBM cell line provide researchers with invaluable tools for studying GBM biology, identifying novel therapeutic targets, and evaluating the efficacy of potential treatments.
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Affiliation(s)
- Fernanda F. da Silva
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.F.d.S.); (B.D.S.E.); (T.G.S.)
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo 01509-900, Brazil
| | - Fernanda C. S. Lupinacci
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.F.d.S.); (B.D.S.E.); (T.G.S.)
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo 01509-900, Brazil
| | - Bruno D. S. Elias
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.F.d.S.); (B.D.S.E.); (T.G.S.)
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo 01509-900, Brazil
| | - Adriano O. Beserra
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.F.d.S.); (B.D.S.E.); (T.G.S.)
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo 01509-900, Brazil
| | - Paulo Sanematsu
- Neurosurgery Department, A.C. Camargo Cancer Center, São Paulo 01509-010, Brazil
| | - Martin Roffe
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Leslie D. Kulikowski
- Cytogenomics Laboratory, Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-010, Brazil;
| | - Felipe D’almeida Costa
- Department of Anatomic Pathology, A.C. Camargo Cancer Center, São Paulo 01509-010, Brazil;
| | - Tiago G. Santos
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.F.d.S.); (B.D.S.E.); (T.G.S.)
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo 01509-900, Brazil
| | - Glaucia N. M. Hajj
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.F.d.S.); (B.D.S.E.); (T.G.S.)
- National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo 01509-900, Brazil
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5
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Ntafoulis I, Kleijn A, Ju J, Jimenez-Cowell K, Fabro F, Klein M, Chi Yen RT, Balvers RK, Li Y, Stubbs AP, Kers TV, Kros JM, Lawler SE, Beerepoot LV, Kremer A, Idbaih A, Verreault M, Byrne AT, O'Farrell AC, Connor K, Biswas A, Salvucci M, Prehn JHM, Lambrechts D, Dilcan G, Lodi F, Arijs I, van den Bent MJ, Dirven CMF, Leenstra S, Lamfers MLM. Ex vivo drug sensitivity screening predicts response to temozolomide in glioblastoma patients and identifies candidate biomarkers. Br J Cancer 2023; 129:1327-1338. [PMID: 37620410 PMCID: PMC10575865 DOI: 10.1038/s41416-023-02402-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: 12/08/2022] [Revised: 07/13/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Patient-derived glioma stem-like cells (GSCs) have become the gold-standard in neuro-oncological research; however, it remains to be established whether loss of in situ microenvironment affects the clinically-predictive value of this model. We implemented a GSC monolayer system to investigate in situ-in vitro molecular correspondence and the relationship between in vitro and patient response to temozolomide (TMZ). METHODS DNA/RNA-sequencing was performed on 56 glioblastoma tissues and 19 derived GSC cultures. Sensitivity to TMZ was screened across 66 GSC cultures. Viability readouts were related to clinical parameters of corresponding patients and whole-transcriptome data. RESULTS Tumour DNA and RNA sequences revealed strong similarity to corresponding GSCs despite loss of neuronal and immune interactions. In vitro TMZ screening yielded three response categories which significantly correlated with patient survival, therewith providing more specific prediction than the binary MGMT marker. Transcriptome analysis identified 121 genes related to TMZ sensitivity of which 21were validated in external datasets. CONCLUSION GSCs retain patient-unique hallmark gene expressions despite loss of their natural environment. Drug screening using GSCs predicted patient response to TMZ more specifically than MGMT status, while transcriptome analysis identified potential biomarkers for this response. GSC drug screening therefore provides a tool to improve drug development and precision medicine for glioblastoma.
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Affiliation(s)
- Ioannis Ntafoulis
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Anne Kleijn
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Jie Ju
- Department of Pathology & Clinical Bioinformatics, Erasmus MC, Rotterdam, Netherlands
| | - Kevin Jimenez-Cowell
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Federica Fabro
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Michelle Klein
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Romain Tching Chi Yen
- Information Technologies for Translational Medicine, Esch-Sur-Alzette, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Rutger K Balvers
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Yunlei Li
- Department of Pathology & Clinical Bioinformatics, Erasmus MC, Rotterdam, Netherlands
| | - Andrew P Stubbs
- Department of Pathology & Clinical Bioinformatics, Erasmus MC, Rotterdam, Netherlands
| | - Trisha V Kers
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Johan M Kros
- Department of Pathology & Clinical Bioinformatics, Erasmus MC, Rotterdam, Netherlands
| | - Sean E Lawler
- Dept of Pathology and Laboratory Medicine, Legorreta Cancer Center, Brown University, Providence, RI, USA
| | - Laurens V Beerepoot
- Department of Internal Medicine, Elisabeth-Tweesteden Hospital, Tilburg, Netherlands
| | - Andreas Kremer
- Information Technologies for Translational Medicine, Esch-Sur-Alzette, Luxembourg
| | - Ahmed Idbaih
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, Institut du Cerveau - Paris Brain Institute, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Maite Verreault
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alice C O'Farrell
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kate Connor
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Archita Biswas
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Diether Lambrechts
- Department of Human Genetics, Laboratory for Translational Genetics, KU Leuven, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Gonca Dilcan
- Department of Human Genetics, Laboratory for Translational Genetics, KU Leuven, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Francesca Lodi
- Department of Human Genetics, Laboratory for Translational Genetics, KU Leuven, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Ingrid Arijs
- Department of Human Genetics, Laboratory for Translational Genetics, KU Leuven, and VIB Center for Cancer Biology, Leuven, Belgium
| | - Martin J van den Bent
- Department of Neurology, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Clemens M F Dirven
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Sieger Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands
| | - Martine L M Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, Netherlands.
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Kardani K, Sanchez Gil J, Rabkin SD. Oncolytic herpes simplex viruses for the treatment of glioma and targeting glioblastoma stem-like cells. Front Cell Infect Microbiol 2023; 13:1206111. [PMID: 37325516 PMCID: PMC10264819 DOI: 10.3389/fcimb.2023.1206111] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Glioblastoma (GBM) is one of the most lethal cancers, having a poor prognosis and a median survival of only about 15 months with standard treatment (surgery, radiation, and chemotherapy), which has not been significantly extended in decades. GBM demonstrates remarkable cellular heterogeneity, with glioblastoma stem-like cells (GSCs) at the apex. GSCs are a subpopulation of GBM cells that possess the ability to self-renew, differentiate, initiate tumor formation, and manipulate the tumor microenvironment (TME). GSCs are no longer considered a static population of cells with specific markers but are quite flexible phenotypically and in driving tumor heterogeneity and therapeutic resistance. In light of these features, they are a critical target for successful GBM therapy. Oncolytic viruses, in particular oncolytic herpes simplex viruses (oHSVs), have many attributes for therapy and are promising agents to target GSCs. oHSVs are genetically-engineered to selectively replicate in and kill cancer cells, including GSCs, but not normal cells. Moreover, oHSV can induce anti-tumor immune responses and synergize with other therapies, such as chemotherapy, DNA repair inhibitors, and immune checkpoint inhibitors, to potentiate treatment effects and reduce GSC populations that are partly responsible for chemo- and radio-resistance. Herein, we present an overview of GSCs, activity of different oHSVs, clinical trial results, and combination strategies to enhance efficacy, including therapeutic arming of oHSV. Throughout, the therapeutic focus will be on GSCs and studies specifically targeting these cells. Recent clinical trials and approval of oHSV G47Δ in Japan for patients with recurrent glioma demonstrate the efficacy and promise of oHSV therapy.
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Affiliation(s)
| | | | - Samuel D. Rabkin
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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CD95 gene deletion may reduce clonogenic growth and invasiveness of human glioblastoma cells in a CD95 ligand-independent manner. Cell Death Dis 2022; 8:341. [PMID: 35906203 PMCID: PMC9338300 DOI: 10.1038/s41420-022-01133-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
CD95 (Fas/APO-1) is a multifunctional cell surface receptor with antithetic roles. First described to mediate cell death, interactions of CD95 with its natural ligand, CD95L, have also been described to induce tumor-promoting signaling leading to proliferation, invasion and stem cell maintenance, mainly in cancer cells that are resistant to CD95-mediated apoptosis. While activation of CD95-mediated apoptosis in cancer cells may not be clinically practicable due to toxicity, inhibition of tumor-promoting CD95 signaling holds therapeutic potential. In the present study, we characterized CD95 and CD95L expression in human glioma-initiating cells (GIC), a glioblastoma cell population with stem cell features, and investigated the consequences of CRISPR-Cas9-mediated CD95 or CD95L gene deletion. In vitro, GIC expressed CD95 but not CD95L and were sensitive to CD95-mediated apoptosis. Upon genetic deletion of CD95, GIC acquired resistance to CD95L-induced apoptosis but exhibited inferior clonogenic growth, sphere-forming capacity, and invasiveness compared with control cells, suggesting the existence of CD95L-independent constitutive CD95 signaling with tumor-promoting properties in GIC. In vivo, GIC expressed CD95 and a non-canonical form of CD95L lacking the CD95-binding region. CD95 genetic deletion did not prolong survival in immunocompromised GIC-bearing mice. Altogether, these data indicate that canonical CD95L may not be expressed in human GIC and suggest the existence of a CD95L-independent CD95-signaling pathway that maintains some malignancy traits of GIC. The lack of altered survival of tumor-bearing mice after genetic deletion of CD95 suggests that CD95 signaling is not essential to maintain the growth of human GIC xenografted into the brains of nude mice. The ligand-independent tumor-promoting role of constitutive CD95 in our GIC models in vitro highlights the complexity and challenges associated with targeting CD95 with therapeutic intent.
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8
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Mander S, Naffouje SA, Gao J, Li W, Christov K, Green A, Bongarzone ER, Das Gupta TK, Yamada T. Tumor-targeting cell-penetrating peptide, p28, for glioblastoma imaging and therapy. Front Oncol 2022; 12:940001. [PMID: 35936749 PMCID: PMC9353713 DOI: 10.3389/fonc.2022.940001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Despite recent advances in cancer research, glioblastoma multiforme (GBM) remains a highly aggressive brain tumor as its treatment options are limited. The current standard treatment includes surgery followed by radiotherapy and adjuvant chemotherapy. However, surgery without image guidance is often challenging to achieve maximal safe resection as it is difficult to precisely discern the lesion to be removed from surrounding brain tissue. In addition, the efficacy of adjuvant chemotherapy is limited by poor penetration of therapeutics through the blood-brain barrier (BBB) into brain tissues, and the lack of tumor targeting. In this regard, we utilized a tumor-targeting cell-penetration peptide, p28, as a therapeutic agent to improve the efficacy of a current chemotherapeutic agent for GBM, and as a carrier for a fluorescence imaging agent for a clear identification of GBM. Here, we show that a near-infrared (NIR) imaging agent, ICG-p28 (a chemical conjugate of an FDA-approved NIR dye, indocyanine green ICG, and tumor-targeting p28 peptide) can preferentially localize tumors in multiple GBM animal models. Moreover, xenograft studies show that p28, as a therapeutic agent, can enhance the cytotoxic activity of temozolomide (TMZ), one of the few effective drugs for brain tumors. Collectively, our findings highlight the important role of the tumor-targeting peptide, which has great potential for intraoperative image-guided surgery and the development of new therapeutic strategies for GBM.
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Affiliation(s)
- Sunam Mander
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Samer A. Naffouje
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Jin Gao
- Department of Electrical and Computer Engineering, University of Illinois College of Engineering, Chicago, IL, United States
| | - Weiguo Li
- Richard & Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering, Chicago, IL, United States
| | - Konstantin Christov
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Albert Green
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Ernesto R. Bongarzone
- Department of Anatomy and Cell Biology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Tapas K. Das Gupta
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, United States
- Richard & Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering, Chicago, IL, United States
- *Correspondence: Tohru Yamada,
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9
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Zheng Y, Yue X, Fang C, Jia Z, Chen Y, Xie H, Zhao J, Yang Z, Li L, Chen Z, Bian E, Zhao B. A Novel Defined Endoplasmic Reticulum Stress-Related lncRNA Signature for Prognosis Prediction and Immune Therapy in Glioma. Front Oncol 2022; 12:930923. [PMID: 35847925 PMCID: PMC9282894 DOI: 10.3389/fonc.2022.930923] [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: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Gliomas are a group of the most aggressive primary central nervous system tumors with limited treatment options. The abnormal expression of long non-coding RNA (lncRNA) is related to the prognosis of glioma. However, the role of endoplasmic reticulum (ER) stress-associated lncRNAs in glioma prognosis has not been reported. In this paper, we obtained ER stress-related lncRNAs by co-expression analysis, and then a risk signature composed of 6 ER stress-related lncRNAs was constructed using Cox regression analysis. Glioma samples in The Cancer Genome Atlas (TCGA) were separated into high- and low-risk groups based on the median risk score. Compared with the low-risk group, patients in the high-risk group had shorter survival times. Additionally, we verified the predictive ability of these candidate lncRNAs in the testing set. Three glioma patient subgroups (cluster 1/2/3) were identified by consensus clustering. We further analysed the abundance of immune-infiltrating cells and the expression levels of immune checkpoint molecules in both three subgroups and two risk groups, respectively. Immunotherapy and anticancer drug response prediction showed that ER stress-related lncRNA risk signature positively correlates with responding to immune checkpoints and chemosensitivity. Functional analysis showed that these gene sets are enriched in the malignant process of tumors. Finally, LINC00519 was chosen for functional experiments. The silence of LINC00519 restrained the migration and invasion of glioma cells. Hence, those results indicated that ER stress-related lncRNA risk signature could be a potential treatment target and a prognosis biomarker for glioma patients.
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Affiliation(s)
- Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Cheng Fang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhuang Jia
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yuxiang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Jiajia Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
- *Correspondence: Erbao Bian, ; Bing Zhao,
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
- *Correspondence: Erbao Bian, ; Bing Zhao,
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10
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Boccellato C, Rehm M. Glioblastoma, from disease understanding towards optimal cell-based in vitro models. Cell Oncol (Dordr) 2022; 45:527-541. [PMID: 35763242 PMCID: PMC9424171 DOI: 10.1007/s13402-022-00684-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Abstract
Background
Glioblastoma (GBM) patients are notoriously difficult to treat and ultimately all succumb to disease. This unfortunate scenario motivates research into better characterizing and understanding this disease, and into developing novel research tools by which potential novel therapeutics and treatment options initially can be evaluated pre-clinically. Here, we provide a concise overview of glioblastoma epidemiology, disease classification, the challenges faced in the treatment of glioblastoma and current novel treatment strategies. From this, we lead into a description and assessment of advanced cell-based models that aim to narrow the gap between pre-clinical and clinical studies. Such invitro models are required to deliver reliable and meaningful data for the development and pre-validation of novel therapeutics and treatments.
Conclusions
The toolbox for GBM cell-based models has expanded substantially, with the possibility of 3D printing tumour tissues and thereby replicating invivo tissue architectures now looming on the horizon. A comparison of experimental cell-based model systems and techniques highlights advantages and drawbacks of the various tools available, based on which cell-based models and experimental approaches best suited to address a diversity of research questions in the glioblastoma research field can be selected.
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Affiliation(s)
- Chiara Boccellato
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
- Stuttgart Research Center Systems Biology, University of Stuttgart, 70569, Stuttgart, Germany.
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11
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Anti-glioblastoma effects of phenolic variants of benzoylphenoxyacetamide (BPA) with high potential for blood brain barrier penetration. Sci Rep 2022; 12:3384. [PMID: 35232976 PMCID: PMC8888627 DOI: 10.1038/s41598-022-07247-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
Glioblastomas are the most aggressive brain tumors for which therapeutic options are limited. Current therapies against glioblastoma include surgical resection, followed by radiotherapy plus concomitant treatment and maintenance with temozolomide (TMZ), however, these standard therapies are often ineffective, and average survival time for glioblastoma patients is between 12 and 18 months. We have previously reported a strong anti-glioblastoma activity of several metabolic compounds, which were synthetized based compounds, which were synthetized based on the chemical structure of a common lipid-lowering drug, fenofibrate, and share a general molecular skeleton of benzoylphenoxyacetamide (BPA). Extensive computational analyses of phenol and naphthol moieties added to the BPA skeleton were performed in this study with the objective of selecting new BPA variants for subsequent compound preparation and anti-glioblastoma testing. Initially, 81 structural variations were considered and their physical properties such as solubility (logS), blood–brain partitioning (logBB), and probability of entering the CNS calculated by the Central Nervous System—Multiparameter Optimization (MPO-CNS) algorithm were evaluated. From this initial list, 18 compounds were further evaluated for anti-glioblastoma activity in vitro. Nine compounds demonstrated desirable glioblastoma cell toxicity in cell culture, and two of them, HR51, and HR59 demonstrated significantly improved capability of crossing the model blood–brain-barrier (BBB) composed of endothelial cells, astrocytes and pericytes.
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12
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Gravina GL, Colapietro A, Mancini A, Rossetti A, Martellucci S, Ventura L, Di Franco M, Marampon F, Mattei V, Biordi LA, Otterlei M, Festuccia C. ATX-101, a Peptide Targeting PCNA, Has Antitumor Efficacy Alone or in Combination with Radiotherapy in Murine Models of Human Glioblastoma. Cancers (Basel) 2022; 14:289. [PMID: 35053455 PMCID: PMC8773508 DOI: 10.3390/cancers14020289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 02/01/2023] Open
Abstract
Cell proliferation requires the orchestrated actions of a myriad of proteins regulating DNA replication, DNA repair and damage tolerance, and cell cycle. Proliferating cell nuclear antigen (PCNA) is a master regulator which interacts with multiple proteins functioning in these processes, and this makes PCNA an attractive target in anticancer therapies. Here, we show that a cell-penetrating peptide containing the AlkB homolog 2 PCNA-interacting motif (APIM), ATX-101, has antitumor activity in a panel of human glioblastoma multiforme (GBM) cell lines and patient-derived glioma-initiating cells (GICs). Their sensitivity to ATX-101 was not related to cellular levels of PCNA, or p53, PTEN, or MGMT status. However, ATX-101 reduced Akt/mTOR and DNA-PKcs signaling, and a correlation between high Akt activation and sensitivity for ATX-101 was found. ATX-101 increased the levels of γH2AX, DNA fragmentation, and apoptosis when combined with radiotherapy (RT). In line with the in vitro results, ATX-101 strongly reduced tumor growth in two subcutaneous xenografts and two orthotopic GBM models, both as a single agent and in combination with RT. The ability of ATX-101 to sensitize cells to RT is promising for further development of this compound for use in GBM.
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Affiliation(s)
- Giovanni Luca Gravina
- Department of Biotechnological and Applied Clinical Sciences, Division of Radiation Oncology, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Alessandro Colapietro
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
| | - Andrea Mancini
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
| | - Alessandra Rossetti
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
| | - Stefano Martellucci
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Cellular Pathology, University of L’Aquila, 67100 L’Aquila, Italy;
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy;
| | - Luca Ventura
- Division of Pathology, San Salvatore Hospital, 67100 L’Aquila, Italy; (L.V.); (M.D.F.)
| | - Martina Di Franco
- Division of Pathology, San Salvatore Hospital, 67100 L’Aquila, Italy; (L.V.); (M.D.F.)
| | - Francesco Marampon
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00100 Rome, Italy;
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy;
| | - Leda Assunta Biordi
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Medical Oncology, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Marit Otterlei
- APIM Therapeutics A/S, N-7100 Rissa, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7006 Trondheim, Norway
| | - Claudio Festuccia
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
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13
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Lei H, Gertz EM, Schäffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Li G, Xu L, Hou Y, Wu K, Shi X, Dean M, Ried T, Schwartz R. Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinformatics 2021; 37:4704-4711. [PMID: 34289030 PMCID: PMC8665747 DOI: 10.1093/bioinformatics/btab504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation (SV) events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate. RESULTS In the present work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization (miFISH) to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. By integrating such information in an integer linear programming (ILP) framework, we demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence, and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data. AVAILABILITY Source code is available on Github at https://github.com/CMUSchwartzLab/FISH_deconvolution.
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Affiliation(s)
- Haoyun Lei
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - E Michael Gertz
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuecong Fu
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Yifeng Tao
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Irianna Torres
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guibo Li
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Liqin Xu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Yong Hou
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Kui Wu
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Xulian Shi
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, U.S. National Institutes of Health, Gaithersburg, MD, 20814, USA
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Russell Schwartz
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Dept. of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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14
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Sarkar S, Yang R, Mirzaei R, Rawji K, Poon C, Mishra MK, Zemp FJ, Bose P, Kelly J, Dunn JF, Yong VW. Control of brain tumor growth by reactivating myeloid cells with niacin. Sci Transl Med 2021; 12:12/537/eaay9924. [PMID: 32238578 DOI: 10.1126/scitranslmed.aay9924] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
Abstract
Glioblastomas are generally incurable partly because monocytes, macrophages, and microglia in afflicted patients do not function in an antitumor capacity. Medications that reactivate these macrophages/microglia, as well as circulating monocytes that become macrophages, could thus be useful to treat glioblastoma. We have discovered that niacin (vitamin B3) is a potential stimulator of these inefficient myeloid cells. Niacin-exposed monocytes attenuated the growth of brain tumor-initiating cells (BTICs) derived from glioblastoma patients by producing anti-proliferative interferon-α14. Niacin treatment of mice bearing intracranial BTICs increased macrophage/microglia representation within the tumor, reduced tumor size, and prolonged survival. These therapeutic outcomes were negated in mice depleted of circulating monocytes or harboring interferon-α receptor-deleted BTICs. Combination treatment with temozolomide enhanced niacin-promoted survival. Monocytes from glioblastoma patients had increased interferon-α14 upon niacin exposure and were reactivated to reduce BTIC growth in culture. We highlight niacin, a common vitamin that can be quickly translated into clinical application, as an immune stimulator against glioblastomas.
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Affiliation(s)
- Susobhan Sarkar
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Runze Yang
- Department of Radiology and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Reza Mirzaei
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Khalil Rawji
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Candice Poon
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Manoj K Mishra
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Franz J Zemp
- Department of Oncology and the Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Pinaki Bose
- Department of Oncology and the Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Surgery, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - John Kelly
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Oncology and the Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Jeff F Dunn
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Radiology and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences and the Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada. .,Department of Oncology and the Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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15
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Dugandžija T, Drljača J, Bulajić D, Isaković A, Stilinović N, Sekulić S, Čapo I. Hallmarks of tumor-associated microglia response to experimental U87 human glioblastoma xenograft. Tissue Cell 2021; 72:101557. [PMID: 34051646 DOI: 10.1016/j.tice.2021.101557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022]
Abstract
Glioblastoma (GBM) is one of the deadliest primary brain neoplasm, heavily infiltrated with tumor-associated microglia/macrophages (TAM), which has received a great deal of interest. Bearing in mind that the number of peripheral macrophages by the 14th day is negligible, in our study TAM were referred to as microglia. Here we evaluated histopathological characterization of TAM and kinetics of their infiltration in U87 orthotopic GBM, a commonly used model in preclinical research. To mimic different stages of GBM growth, we evaluated three-time points. Our data showed that the highest areal density of TAM was 7 days after GBM inoculation, with ability to proliferate early after initiation of GBM growth. The areal density of TAM within the tumor correlated with GBM growth and proliferation. Moreover, microglia underwent substantial morphological changes upon exposure to GBM cells. A transition from ramified morphology in peritumoral area to ameboid shape with larger soma and shortened, thick branches in the tumor core was observed. Higher areal fraction of blood vessels also correlated with the areal density of TAM. Given these pro-invasive features of microglia, this GBM model represents a good basis for further testing microglia as a target and new strategy to fight with.
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Affiliation(s)
- Tihomir Dugandžija
- Faculty of Medicine, Department of Epidemiology, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia; Oncology Institute of Vojvodina, Put doktora Goldmana 4, Sremska Kamenica, 21204, Serbia
| | - Jovana Drljača
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia; Center for Medical and Pharmaceutical Investigations and Quality Control, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia.
| | - Dragica Bulajić
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia; Center for Medical and Pharmaceutical Investigations and Quality Control, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia
| | - Aleksandra Isaković
- Institute of Medical and Clinical Biochemistry, School of Medicine, University of Belgrade, Pasterova 2, Belgrade, 11000, Serbia
| | - Nebojša Stilinović
- Faculty of Medicine, Department of Pharmacology, Toxicology and Clinical Pharmacology, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia
| | - Slobodan Sekulić
- Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia; Department of Neurology, University Hospital, Clinical Center of Vojvodina, Hajduk Veljkova 1-7, Novi Sad, 21000, Serbia
| | - Ivan Čapo
- Center for Medical and Pharmaceutical Investigations and Quality Control, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia; Faculty of Medicine, Department of Histology and Embryology, University of Novi Sad, Hajduk Veljkova 3, Novi Sad, 21000, Serbia
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16
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In silico identification of the prognostic biomarkers and therapeutic targets associated with cancer stem cell characteristics of glioma. Biosci Rep 2021; 40:225916. [PMID: 32725165 PMCID: PMC7418212 DOI: 10.1042/bsr20201037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Glioma is the common histological subtype of malignancy in central nervous system, with a high morbidity and mortality. Cancer stem cells (CSCs) play an important role in regulating the tumorigenesis and progression of glioma; however, the prognostic biomarkers and therapeutic targets associated with CSC characteristics have not been fully acknowledged in glioma. In order to identify the prognostic stemness-related genes (SRGs) of glioma in silico, the RNA sequencing data of patients with glioma were retrieved from The Cancer Genome Atlas (TCGA) databases. The mRNA expression-based stemness index (mRNAsi) was significantly associated with the glioma histologic grade, isocitrate dehydrogenase 1 (IDH1) mutation and overall survival of glioma patients by the nonparametric test and Kaplan–Meier survival analysis. A total of 340 SRGs were identified as the overlapped stemness-related differential expressed genes (DEGs) of different histologic grade screened by the univariate Cox analysis. Based on 11 prognostic SRGs, the predict nomogram was constructed with the AUC of 0.832. Moreover, the risk score of the nomogram was an independent prognostic factor, indicating its significant applicability. Besides other eight reported biomarkers of glioma, we found that F2RL2, CLCNKA and LOXL4 were first identified as prognostic biomarkers for glioma. In conclusion, this bioinformatics study demonstrates the mRNAsi as a reliable index for the IDH1 mutation, histologic grade and OS of glioma patients and provides a well-applied model for predicting the OS for patients with glioma based on prognostic SRGs. Additionally, this in silico study also identifies three novel prognostic biomarkers (F2RL2, CLCNKA and LOXL4) for glioma patients.
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17
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Hussein D, Dallol A, Quintas R, Schulten HJ, Alomari M, Baeesa S, Bangash M, Alghamdi F, Khan I, ElAssouli MZM, Saka M, Carracedo A, Chaudhary A, Abuzenadah A. Overlapping variants in the blood, tissues and cell lines for patients with intracranial meningiomas are predominant in stem cell-related genes. Heliyon 2020; 6:e05632. [PMID: 33305042 PMCID: PMC7710648 DOI: 10.1016/j.heliyon.2020.e05632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/19/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Bulk tissue genomic analysis of meningiomas identified common somatic mutations, however, it often excluded blood-related variants. In contrast, genomic characterisation of primary cell lines that can provide critical information regarding growth and proliferation, have been rare. In our work, we identified the variants that are present in the blood, tissues and corresponding cell lines that are likely to be predictive, tumorigenic and progressive. METHOD Whole-exome sequencing was used to identify variants and distinguish related pathways that exist in 42 blood, tissues and corresponding cell lines (BTCs) samples for patients with intracranial meningiomas. Conventional sequencing was used for the confirmation of variants. Integrative analysis of the gene expression for the corresponding samples was utilised for further interpretations. RESULTS In total, 926 BTC variants were detected, implicating 845 genes. A pathway analysis of all BTC genes with damaging variants indicated the 'cell morphogenesis involved in differentiation' stem cell-related pathway to be the most frequently affected pathway. Concordantly, five stem cell-related genes, GPRIN2, ALDH3B2, ASPN, THSD7A and SIGLEC6, showed BTC variants in at least five of the patients. Variants that were heterozygous in the blood and homozygous in the tissues or the corresponding cell lines were rare (average: 1.3 ± 0.3%), and included variants in the RUNX2 and CCDC114 genes. An analysis comparing the variants detected only in tumours with aggressive features indicated a total of 240 BTC genes, implicating the 'homophilic cell adhesion via plasma membrane adhesion molecules' pathway, and identifying the stem cell-related transcription coactivator NCOA3/AIB1/SRC3 as the most frequent BTC gene. Further analysis of the possible impact of the poly-Q mutation present in the NCOA3 gene indicated associated deregulation of 15 genes, including the up-regulation of the stem cell related SEMA3D gene and the angiogenesis related VEGFA gene. CONCLUSION Stem cell-related pathways and genes showed high prevalence in the BTC variants, and novel variants in stem cell-related genes were identified for meningioma. These variants can potentially be used as predictive, tumorigenic and progressive biomarkers for meningioma.
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Affiliation(s)
- Deema Hussein
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Ashraf Dallol
- Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rita Quintas
- Galician Foundation of Genomic Medicine-SERGAS, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona Alomari
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Saleh Baeesa
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed Bangash
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fahad Alghamdi
- Pathology Department, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishaq Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - M-Zaki Mustafa ElAssouli
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Mohamad Saka
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Angel Carracedo
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Galician Foundation of Genomic Medicine-SERGAS, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Adeel Chaudhary
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
- Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Adel Abuzenadah
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
- Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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18
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De Boeck A, Ahn BY, D'Mello C, Lun X, Menon SV, Alshehri MM, Szulzewsky F, Shen Y, Khan L, Dang NH, Reichardt E, Goring KA, King J, Grisdale CJ, Grinshtein N, Hambardzumyan D, Reilly KM, Blough MD, Cairncross JG, Yong VW, Marra MA, Jones SJM, Kaplan DR, McCoy KD, Holland EC, Bose P, Chan JA, Robbins SM, Senger DL. Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression. Nat Commun 2020; 11:4997. [PMID: 33020472 PMCID: PMC7536425 DOI: 10.1038/s41467-020-18569-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Despite a deeper molecular understanding, human glioblastoma remains one of the most treatment refractory and fatal cancers. It is known that the presence of macrophages and microglia impact glioblastoma tumorigenesis and prevent durable response. Herein we identify the dual function cytokine IL-33 as an orchestrator of the glioblastoma microenvironment that contributes to tumorigenesis. We find that IL-33 expression in a large subset of human glioma specimens and murine models correlates with increased tumor-associated macrophages/monocytes/microglia. In addition, nuclear and secreted functions of IL-33 regulate chemokines that collectively recruit and activate circulating and resident innate immune cells creating a pro-tumorigenic environment. Conversely, loss of nuclear IL-33 cripples recruitment, dramatically suppresses glioma growth, and increases survival. Our data supports the paradigm that recruitment and activation of immune cells, when instructed appropriately, offer a therapeutic strategy that switches the focus from the cancer cell alone to one that includes the normal host environment.
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Affiliation(s)
- Astrid De Boeck
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bo Young Ahn
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Charlotte D'Mello
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Xueqing Lun
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Shyam V Menon
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mana M Alshehri
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Frank Szulzewsky
- Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Lubaba Khan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elliott Reichardt
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kimberly-Ann Goring
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer King
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Natalie Grinshtein
- Department of Molecular Genetics, University of Toronto and Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute and the Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Karlyne M Reilly
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Michael D Blough
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - J Gregory Cairncross
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - David R Kaplan
- Department of Molecular Genetics, University of Toronto and Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Eric C Holland
- Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Pinaki Bose
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Chan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Stephen M Robbins
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Donna L Senger
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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19
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Lin S, Xu H, Zhang A, Ni Y, Xu Y, Meng T, Wang M, Lou M. Prognosis Analysis and Validation of m 6A Signature and Tumor Immune Microenvironment in Glioma. Front Oncol 2020; 10:541401. [PMID: 33123464 PMCID: PMC7571468 DOI: 10.3389/fonc.2020.541401] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/24/2020] [Indexed: 01/21/2023] Open
Abstract
Glioma is one of the most typical intracranial tumors, comprising about 80% of all brain malignancies. Several key molecular signatures have emerged as prognostic biomarkers, which indicate room for improvement in the current approach to glioma classification. In order to construct a more veracious prediction model and identify the potential prognosis-biomarker, we explore the differential expressed m6A RNA methylation regulators in 665 gliomas from TCGA-GBM and TCGA-LGG. Consensus clustering was applied to the m6A RNA methylation regulators, and two glioma subgroups were identified with a poorer prognosis and a higher grade of WHO classification in cluster 1. The further chi-squared test indicated that the immune infiltration was significantly enriched in cluster 1, indicating a close relation between m6A regulators and immune infiltration. In order to explore the potential biomarkers, the weighted gene co-expression network analysis (WGCNA), along with Least absolute shrinkage and selection operator (LASSO), between high/low immune infiltration and m6A cluster 1/2 groups were utilized for the hub genes, and four genes (TAGLN2, PDPN, TIMP1, EMP3) were identified as prognostic biomarkers. Besides, a prognostic model was constructed based on the four genes with a good prediction and applicability for the overall survival (OS) of glioma patients (the area under the curve of ROC achieved 0.80 (0.76-0.83) and 0.72 (0.68-0.76) in TCGA and Chinese Glioma Genome Atlas (CGGA), respectively). Moreover, we also found PDPN and TIMP1 were highly expressed in high-grade glioma from The Human Protein Atlas database and both of them were correlated with m6A and immune cell marker in glioma tissue samples. In conclusion, we construct a novel prognostic model which provides new insights into glioma prognosis. The PDPN and TIMP1 may serve as potential biomarkers for prognosis of glioma.
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Affiliation(s)
- Shaojian Lin
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Houshi Xu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Anke Zhang
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunjia Ni
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanzhi Xu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tong Meng
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingjie Wang
- Department of Digestive Diseases, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiqing Lou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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20
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Lei H, Lyu B, Gertz EM, Schäffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R. Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. J Comput Biol 2020; 27:565-598. [PMID: 32181683 DOI: 10.1089/cmb.2019.0302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Characterizing intratumor heterogeneity (ITH) is crucial to understanding cancer development, but it is hampered by limits of available data sources. Bulk DNA sequencing is the most common technology to assess ITH, but involves the analysis of a mixture of many genetically distinct cells in each sample, which must then be computationally deconvolved. Single-cell sequencing is a promising alternative, but its limitations-for example, high noise, difficulty scaling to large populations, technical artifacts, and large data sets-have so far made it impractical for studying cohorts of sufficient size to identify statistically robust features of tumor evolution. We have developed strategies for deconvolution and tumor phylogenetics combining limited amounts of bulk and single-cell data to gain some advantages of single-cell resolution with much lower cost, with specific focus on deconvolving genomic copy number data. We developed a mixed membership model for clonal deconvolution via non-negative matrix factorization balancing deconvolution quality with similarity to single-cell samples via an associated efficient coordinate descent algorithm. We then improve on that algorithm by integrating deconvolution with clonal phylogeny inference, using a mixed integer linear programming model to incorporate a minimum evolution phylogenetic tree cost in the problem objective. We demonstrate the effectiveness of these methods on semisimulated data of known ground truth, showing improved deconvolution accuracy relative to bulk data alone.
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Affiliation(s)
- Haoyun Lei
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Bochuan Lyu
- Department of Mathematics, Rose-Hulman Institute of Technology, Terre Haute, Indiana
| | - E Michael Gertz
- National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, Maryland.,Cancer Data Science Laboratory, National Cancer Institute, U.S. National Institutes of Health, Bethesda, Maryland
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, Maryland.,Cancer Data Science Laboratory, National Cancer Institute, U.S. National Institutes of Health, Bethesda, Maryland
| | | | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, U.S. National Institutes of Health, Gaithersburg, Maryland
| | - Russell Schwartz
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
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21
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Vaubel RA, Tian S, Remonde D, Schroeder MA, Mladek AC, Kitange GJ, Caron A, Kollmeyer TM, Grove R, Peng S, Carlson BL, Ma DJ, Sarkar G, Evers L, Decker PA, Yan H, Dhruv HD, Berens ME, Wang Q, Marin BM, Klee EW, Califano A, LaChance DH, Eckel-Passow JE, Verhaak RG, Sulman EP, Burns TC, Meyer FB, O'Neill BP, Tran NL, Giannini C, Jenkins RB, Parney IF, Sarkaria JN. Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma. Clin Cancer Res 2020; 26:1094-1104. [PMID: 31852831 PMCID: PMC7056576 DOI: 10.1158/1078-0432.ccr-19-0909] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/25/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Glioblastoma is the most frequent and lethal primary brain tumor. Development of novel therapies relies on the availability of relevant preclinical models. We have established a panel of 96 glioblastoma patient-derived xenografts (PDX) and undertaken its genomic and phenotypic characterization. EXPERIMENTAL DESIGN PDXs were established from glioblastoma, IDH-wildtype (n = 93), glioblastoma, IDH-mutant (n = 2), diffuse midline glioma, H3 K27M-mutant (n = 1), and both primary (n = 60) and recurrent (n = 34) tumors. Tumor growth rates, histopathology, and treatment response were characterized. Integrated molecular profiling was performed by whole-exome sequencing (WES, n = 83), RNA-sequencing (n = 68), and genome-wide methylation profiling (n = 76). WES data from 24 patient tumors was compared with derivative models. RESULTS PDXs recapitulate many key phenotypic and molecular features of patient tumors. Orthotopic PDXs show characteristic tumor morphology and invasion patterns, but largely lack microvascular proliferation and necrosis. PDXs capture common and rare molecular drivers, including alterations of TERT, EGFR, PTEN, TP53, BRAF, and IDH1, most at frequencies comparable with human glioblastoma. However, PDGFRA amplification was absent. RNA-sequencing and genome-wide methylation profiling demonstrated broad representation of glioblastoma molecular subtypes. MGMT promoter methylation correlated with increased survival in response to temozolomide. WES of 24 matched patient tumors showed preservation of most genetic driver alterations, including EGFR amplification. However, in four patient-PDX pairs, driver alterations were gained or lost on engraftment, consistent with clonal selection. CONCLUSIONS Our PDX panel captures the molecular heterogeneity of glioblastoma and recapitulates many salient genetic and phenotypic features. All models and genomic data are openly available to investigators.
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Affiliation(s)
| | | | - Dioval Remonde
- Brody School of Medicine at East Carolina University, Greenville, North Carolina
| | | | | | | | | | | | | | - Sen Peng
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | | | - Lisa Evers
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | | | | | | | | | | | | | | | | | - Roel G Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Erik P Sulman
- New York University Langone Health, New York, New York
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22
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Jensen KV, Hao X, Aman A, Luchman HA, Weiss S. EGFR blockade in GBM brain tumor stem cells synergizes with JAK2/STAT3 pathway inhibition to abrogate compensatory mechanisms in vitro and in vivo. Neurooncol Adv 2020; 2:vdaa020. [PMID: 32226941 PMCID: PMC7086303 DOI: 10.1093/noajnl/vdaa020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background The EGFR pathway is frequently mutated in glioblastoma (GBM). However, to date, EGFR therapies have not demonstrated efficacy in clinical trials. Poor brain penetration of conventional inhibitors, lack of patient stratification for EGFR status, and mechanisms of resistance are likely responsible for the failure of EGFR-targeted therapy. We aimed to address these elements in a large panel of molecularly diverse patient-derived GBM brain tumor stem cells (BTSCs). Methods In vitro growth inhibition and on-target efficacy of afatinib, pacritinib, or a combination were assessed by cell viability, neurosphere formation, cytotoxicity, limiting dilution assays, and western blotting. In vivo efficacy was assessed with mass spectrometry, immunohistochemistry, magnetic resonance imaging, and intracranial xenograft models. Results We show that afatinib and pacritinib decreased BTSC growth and sphere-forming capacity in vitro. Combinations of the 2 drugs were synergistic and abrogated the activation of STAT3 signaling observed upon EGFR inhibition in vitro and in vivo. We further demonstrate that the brain-penetrant EGFR inhibitor, afatinib, improved survival in EGFRvIII mt orthotopic xenograft models. However, upregulation of the oncogenic STAT3 signaling pathway was observed following afatinib treatment. Combined inhibition with 2 clinically relevant drugs, afatinib and pacritinib, synergistically decreased BTSC viability and abrogated this compensatory mechanism of resistance to EGFR inhibition. A significant decrease in tumor burden in vivo was observed with the combinatorial treatment. Conclusions These data demonstrate that brain-penetrant combinatorial therapies targeting the EGFR and STAT3 signaling pathways hold therapeutic promise for GBM.
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Affiliation(s)
- Katharine V Jensen
- Hotchkiss Brain Institute and Arnie Charbonneau Cancer Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoguang Hao
- Hotchkiss Brain Institute and Arnie Charbonneau Cancer Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - H Artee Luchman
- Hotchkiss Brain Institute and Arnie Charbonneau Cancer Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute and Arnie Charbonneau Cancer Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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23
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Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments. Proc Natl Acad Sci U S A 2019; 116:19098-19108. [PMID: 31471491 DOI: 10.1073/pnas.1813495116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most deadly brain tumor, and currently lacks effective treatment options. Brain tumor-initiating cells (BTICs) and orthotopic xenografts are widely used in investigating GBM biology and new therapies for this aggressive disease. However, the genomic characteristics and molecular resemblance of these models to GBM tumors remain undetermined. We used massively parallel sequencing technology to decode the genomes and transcriptomes of BTICs and xenografts and their matched tumors in order to delineate the potential impacts of the distinct growth environments. Using data generated from whole-genome sequencing of 201 samples and RNA sequencing of 118 samples, we show that BTICs and xenografts resemble their parental tumor at the genomic level but differ at the mRNA expression and epigenomic levels, likely due to the different growth environment for each sample type. These findings suggest that a comprehensive genomic understanding of in vitro and in vivo GBM model systems is crucial for interpreting data from drug screens, and can help control for biases introduced by cell-culture conditions and the microenvironment in mouse models. We also found that lack of MGMT expression in pretreated GBM is linked to hypermutation, which in turn contributes to increased genomic heterogeneity and requires new strategies for GBM treatment.
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24
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Skaga E, Kulesskiy E, Fayzullin A, Sandberg CJ, Potdar S, Kyttälä A, Langmoen IA, Laakso A, Gaál-Paavola E, Perola M, Wennerberg K, Vik-Mo EO. Intertumoral heterogeneity in patient-specific drug sensitivities in treatment-naïve glioblastoma. BMC Cancer 2019; 19:628. [PMID: 31238897 PMCID: PMC6593575 DOI: 10.1186/s12885-019-5861-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/20/2019] [Indexed: 02/15/2023] Open
Abstract
Background A major barrier to effective treatment of glioblastoma (GBM) is the large intertumoral heterogeneity at the genetic and cellular level. In early phase clinical trials, patient heterogeneity in response to therapy is commonly observed; however, how tumor heterogeneity is reflected in individual drug sensitivities in the treatment-naïve glioblastoma stem cells (GSC) is unclear. Methods We cultured 12 patient-derived primary GBMs as tumorspheres and validated tumor stem cell properties by functional assays. Using automated high-throughput screening (HTS), we evaluated sensitivity to 461 anticancer drugs in a collection covering most FDA-approved anticancer drugs and investigational compounds with a broad range of molecular targets. Statistical analyses were performed using one-way ANOVA and Spearman correlation. Results Although tumor stem cell properties were confirmed in GSC cultures, their in vitro and in vivo morphology and behavior displayed considerable tumor-to-tumor variability. Drug screening revealed significant differences in the sensitivity to anticancer drugs (p < 0.0001). The patient-specific vulnerabilities to anticancer drugs displayed a heterogeneous pattern. They represented a variety of mechanistic drug classes, including apoptotic modulators, conventional chemotherapies, and inhibitors of histone deacetylases, heat shock proteins, proteasomes and different kinases. However, the individual GSC cultures displayed high biological consistency in drug sensitivity patterns within a class of drugs. An independent laboratory confirmed individual drug responses. Conclusions This study demonstrates that patient-derived and treatment-naïve GSC cultures maintain patient-specific traits and display intertumoral heterogeneity in drug sensitivity to anticancer drugs. The heterogeneity in patient-specific drug responses highlights the difficulty in applying targeted treatment strategies at the population level to GBM patients. However, HTS can be applied to uncover patient-specific drug sensitivities for functional precision medicine. Electronic supplementary material The online version of this article (10.1186/s12885-019-5861-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erlend Skaga
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317, Oslo, Norway.
| | - Evgeny Kulesskiy
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Tukholmankatu 8, 00290, Helsinki, Finland
| | - Artem Fayzullin
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317, Oslo, Norway
| | - Cecilie J Sandberg
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424, Oslo, Norway
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Tukholmankatu 8, 00290, Helsinki, Finland
| | - Aija Kyttälä
- National Institute for Health and Welfare, Genomics and Biomarkers Unit, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Iver A Langmoen
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317, Oslo, Norway
| | - Aki Laakso
- Department of Neurosurgery, Helsinki University Hospital and Clinical Neurosciences, University of Helsinki, Topeliuksenkatu 5, 00260, Helsinki, Finland
| | - Emília Gaál-Paavola
- Department of Neurosurgery, Helsinki University Hospital and Clinical Neurosciences, University of Helsinki, Topeliuksenkatu 5, 00260, Helsinki, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Tukholmankatu 8, 00290, Helsinki, Finland.,National Institute for Health and Welfare, Genomics and Biomarkers Unit, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Tukholmankatu 8, 00290, Helsinki, Finland
| | - Einar O Vik-Mo
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317, Oslo, Norway
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25
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Skaga E, Skaga IØ, Grieg Z, Sandberg CJ, Langmoen IA, Vik-Mo EO. The efficacy of a coordinated pharmacological blockade in glioblastoma stem cells with nine repurposed drugs using the CUSP9 strategy. J Cancer Res Clin Oncol 2019; 145:1495-1507. [PMID: 31028540 PMCID: PMC6527541 DOI: 10.1007/s00432-019-02920-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/15/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Constructed from a theoretical framework, the coordinated undermining of survival paths in glioblastoma (GBM) is a combination of nine drugs approved for non-oncological indications (CUSP9; aprepitant, auranofin, captopril, celecoxib, disulfiram, itraconazole, minocycline, quetiapine, and sertraline) combined with temozolomide (TMZ). The availability of these drugs outside of specialized treatment centers has led patients to embark on combination treatments without systematic follow-up. However, no experimental data on efficacy using the CUSP9 strategy in GBM have been reported. METHODS Using patient-derived glioblastoma stem cell (GSC) cultures from 15 GBM patients, we described stem cell properties of individual cultures, determined the dose-response relationships of the drugs in the CUSP9, and assessed the efficacy the CUSP9 combination with TMZ in concentrations clinically achievable. The efficacy was evaluated by cell viability, cytotoxicity, and sphere-forming assays in both primary and recurrent GSC cultures. RESULTS We found that CUSP9 with TMZ induced a combination effect compared to the drugs individually (p < 0.0001). Evaluated by cell viability and cytotoxicity, 50% of the GSC cultures displayed a high sensitivity to the drug combination. In clinical plasma concentrations, the effect of the CUSP9 with TMZ was superior to TMZ monotherapy (p < 0.001). The Wnt-signaling pathway has been shown important in GSC, and CUSP9 significantly reduces Wnt-activity. CONCLUSIONS Adding experimental data to the theoretical rationale of CUSP9, our results demonstrate that the CUSP9 treatment strategy can induce a combination effect in both treatment-naïve and pretreated GSC cultures; however, predicting response in individual cultures will require further profiling of GSCs.
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Affiliation(s)
- Erlend Skaga
- Vilhelm Magnus Laboratory, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424, Oslo, Norway.
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, P.O. Box 1112, Blindern, 0317, Oslo, Norway.
| | - Ida Ø Skaga
- Vilhelm Magnus Laboratory, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, P.O. Box 1112, Blindern, 0317, Oslo, Norway
| | - Zanina Grieg
- Vilhelm Magnus Laboratory, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424, Oslo, Norway
| | - Cecilie J Sandberg
- Vilhelm Magnus Laboratory, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424, Oslo, Norway
| | - Iver A Langmoen
- Vilhelm Magnus Laboratory, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, P.O. Box 1112, Blindern, 0317, Oslo, Norway
| | - Einar O Vik-Mo
- Vilhelm Magnus Laboratory, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, P.O. Box 4950, Nydalen, 0424, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, P.O. Box 1112, Blindern, 0317, Oslo, Norway
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The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity. Stem Cells Int 2019; 2019:2617030. [PMID: 30984267 PMCID: PMC6431486 DOI: 10.1155/2019/2617030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/01/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant human brain tumour, characterized by rapid progression, invasion, intense angiogenesis, high genomic instability, and resistance to therapies. Despite countless experimental researches for new therapeutic strategies and promising clinical trials, the prognosis remains extremely poor, with a mean survival of less than 14 months. GBM aggressive behaviour is due to a subpopulation of tumourigenic stem-like cells, GBM stem cells (GSCs), which hierarchically drive onset, proliferation, and tumour recurrence. The morbidity and mortality of this disease strongly encourage exploring genetic characteristics of GSCs. Here, using array-CGH platform, we investigated genetic and genomic aberration profiles of GBM parent tumour (n = 10) and their primarily derived GSCs. Statistical analysis was performed by using R software and complex heatmap and corrplot packages. Pearson correlation and K-means algorithm were exploited to compare genetic alterations and to group similar genetic profiles in matched pairs of GBM and derived GSCs. We identified, in both GBM and matched GSCs, recurrent copy number alterations, as chromosome 7 polysomy, chromosome 10 monosomy, and chromosome 9p21deletions, which are typical features of primary GBM, essential for gliomagenesis. These observations suggest a condition of strong genomic instability both in GBM as GSCs. Our findings showed the robust similarity between GBM mass and GSCs (Pearson corr.≥0.65) but also highlighted a marked variability among different patients. Indeed, the heatmap reporting Gain/Loss State for 21022 coding/noncoding genes demonstrated high interpatient divergence. Furthermore, K-means algorithm identified an impairment of pathways related to the development and progression of cancer, such as angiogenesis, as well as pathways related to the immune system regulation, such as T cell activation. Our data confirmed the preservation of the genomic landscape from tumour tissue to GSCs, supporting the relevance of this cellular model to test in vitro new target therapies for GBM.
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27
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Genetically distinct glioma stem-like cell xenografts established from paired glioblastoma samples harvested before and after molecularly targeted therapy. Sci Rep 2019; 9:139. [PMID: 30644426 PMCID: PMC6333836 DOI: 10.1038/s41598-018-37437-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
Intratumoural heterogeneity underlies tumour escape from molecularly targeted therapy in glioblastoma. A cell-based model preserving the evolving molecular profiles of a tumour during treatment is key to understanding the recurrence mechanisms and development of strategies to overcome resistance. In this study, we established a matched pair of glioblastoma stem-like cell (GSC) cultures from patient glioblastoma samples before and after epidermal growth factor receptor (EGFR)-targeted therapy. A patient with recurrent glioblastoma (MGG70R) harboring focal, high-level EGFR amplification received the irreversible EGFR tyrosine kinase inhibitor dacomitinib. The tumour that subsequently recurred (MGG70RR) showed diploid EGFR, suggesting inhibitor-mediated elimination of EGFR-amplified tumour cells and propagation of EGFR non-amplified cell subpopulations. The MGG70R-GSC line established from MGG70R formed xenografts retaining EGFR amplification and EGFR overexpression, while MGG70RR-GSC established from MGG70RR generated tumours that lacked EGFR amplification and EGFR overexpression. MGG70R-GSC-derived intracranial xenografts were more proliferative than MGG70RR-GSC xenografts, which had upregulated mesenchymal markers, mirroring the pathological observation in the corresponding patient tumours. In vitro MGG70R-GSC was more sensitive to EGFR inhibitors than MGG70RR-GSC. Thus, these molecularly distinct GSC lines recapitulated the subpopulation alteration that occurred during glioblastoma evasion of targeted therapy, and offer a valuable model facilitating therapeutic development for recurrent glioblastoma.
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28
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Festuccia C, Mancini A, Colapietro A, Gravina GL, Vitale F, Marampon F, Delle Monache S, Pompili S, Cristiano L, Vetuschi A, Tombolini V, Chen Y, Mehrling T. The first-in-class alkylating deacetylase inhibitor molecule tinostamustine shows antitumor effects and is synergistic with radiotherapy in preclinical models of glioblastoma. J Hematol Oncol 2018; 11:32. [PMID: 29486795 PMCID: PMC5830080 DOI: 10.1186/s13045-018-0576-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Background The use of alkylating agents such as temozolomide in association with radiotherapy (RT) is the therapeutic standard of glioblastoma (GBM). This regimen modestly prolongs overall survival, also if, in light of the still dismal prognosis, further improvements are desperately needed, especially in the patients with O6-methylguanine-DNA-methyltransferase (MGMT) unmethylated tumors, in which the benefit of standard treatment is less. Tinostamustine (EDO-S101) is a first-in-class alkylating deacetylase inhibitor (AK-DACi) molecule that fuses the DNA damaging effect of bendamustine with the fully functional pan-histone deacetylase (HDAC) inhibitor, vorinostat, in a completely new chemical entity. Methods Tinostamustine has been tested in models of GBM by using 13 GBM cell lines and seven patient-derived GBM proliferating/stem cell lines in vitro. U87MG and U251MG (MGMT negative), as well as T98G (MGMT positive), were subcutaneously injected in nude mice, whereas luciferase positive U251MG cells and patient-derived GBM stem cell line (CSCs-5) were evaluated the orthotopic intra-brain in vivo experiments. Results We demonstrated that tinostamustine possesses stronger antiproliferative and pro-apoptotic effects than those observed for vorinostat and bendamustine alone and similar to their combination and irrespective of MGMT expression. In addition, we observed a stronger radio-sensitization of single treatment and temozolomide used as control due to reduced expression and increased time of disappearance of γH2AX indicative of reduced signal and DNA repair. This was associated with higher caspase-3 activation and reduction of RT-mediated autophagy. In vivo, tinostamustine increased time-to-progression (TTP) and this was additive/synergistic to RT. Tinostamustine had significant therapeutic activity with suppression of tumor growth and prolongation of DFS (disease-free survival) and OS (overall survival) in orthotopic intra-brain models that was superior to bendamustine, RT and temozolomide and showing stronger radio sensitivity. Conclusions Our data suggest that tinostamustine deserves further investigation in patients with glioblastoma. Electronic supplementary material The online version of this article (10.1186/s13045-018-0576-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudio Festuccia
- Laboratory of Radiobiology, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy.
| | - Andrea Mancini
- Laboratory of Radiobiology, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Alessandro Colapietro
- Laboratory of Radiobiology, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Giovanni Luca Gravina
- Laboratory of Radiobiology, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy.,Division of Radiotherapy, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Flora Vitale
- Division of Neurosciences, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Francesco Marampon
- Division of Radiotherapy, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Simona Delle Monache
- Division of Applied Biology, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Simona Pompili
- Division of Human Anatomy, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Loredana Cristiano
- Laboratory of Applied Biology, Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Antonella Vetuschi
- Division of Human Anatomy, Department of Applied Clinical Sciences and Biotechnologies, University of L'Aquila, L'Aquila, Italy
| | - Vincenzo Tombolini
- Division of Radiotherapy, Department of Experimental Medicine, University of Rome "La Sapienza", Rome, Italy
| | - Yi Chen
- Northlake International LLC, Pleasanton, CA, USA
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29
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Rosenberg S, Verreault M, Schmitt C, Guegan J, Guehennec J, Levasseur C, Marie Y, Bielle F, Mokhtari K, Hoang-Xuan K, Ligon K, Sanson M, Delattre JY, Idbaih A. Multi-omics analysis of primary glioblastoma cell lines shows recapitulation of pivotal molecular features of parental tumors. Neuro Oncol 2017; 19:219-228. [PMID: 27571888 DOI: 10.1093/neuonc/now160] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Glioblastoma (GBM) is the deadliest primary brain cancer in adults. Emerging innovative therapies hold promise for personalized cancer treatment. Improving therapeutic options depends on research relying on relevant preclinical models. In this line we have established in the setting of the GlioTex project (GBM and Experimental Therapeutics) a GBM patient-derived cell line (GBM-PDCL) library. A multi-omic approach was used to determine the molecular landscape of PDCL and the extent to which they represent GBM tumors. Methods Single nucleotide polymorphism array, expression arrays, exome sequencing, and RNA sequencing were used to measure and compare the molecular landscapes of 20 samples representing 10 human GBM tumors and paired GBM-PDCLs. Results Copy number variations were similar for a median of 85% of the genome and for 59% of the major focal events. Somatic point mutations were similar in a median of 41%. Mutations in GBM driver and "druggable" genes were maintained in 67% of events. Mutations that were not conserved in the PDCL were mainly low allelic fraction and/or non-driver mutations. Based on RNA expression profiling, PDCLs cluster closely to their parental tumor with overexpression of pathways associated with cancer progression in PDCL. Conclusions Overall, PDCLs recapitulate pivotal molecular alterations of paired-parental tumors supporting their use as a preclinical model of GBM. However, some driver aberrations are lost or gained in the passage from tumor to PDCL. Our results support using PDCL as a relevant preclinical model of GBM. Further investigations of changes between PDCLs and their parental tumor may provide insights into GBM biology.
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Affiliation(s)
- Shai Rosenberg
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Hadassah - Hebrew University Medical Center, Israel
| | - Maïté Verreault
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Charlotte Schmitt
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Justine Guegan
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Jeremy Guehennec
- Bioinformatics/Biostatistics Core Facility, IHU-A-ICM, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Camille Levasseur
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Yannick Marie
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Institut du Cerveau et de la Moelle épinière (ICM), Plateforme de Génotypage Séquençage, Paris, France
| | - Franck Bielle
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie-Escourolle, Paris, France
| | - Karima Mokhtari
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie-Escourolle, Paris, France
| | - Khê Hoang-Xuan
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Keith Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Marc Sanson
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Jean-Yves Delattre
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Ahmed Idbaih
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
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30
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Poon CC, Sarkar S, Yong VW, Kelly JJP. Glioblastoma-associated microglia and macrophages: targets for therapies to improve prognosis. Brain 2017; 140:1548-1560. [PMID: 28334886 DOI: 10.1093/brain/aww355] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/20/2016] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is the most common and most malignant primary adult human brain tumour. Diagnosis of glioblastoma carries a dismal prognosis. Treatment resistance and tumour recurrence are the result of both cancer cell proliferation and their interaction with the tumour microenvironment. A large proportion of the tumour microenvironment consists of an inflammatory infiltrate predominated by microglia and macrophages, which are thought to be subverted by glioblastoma cells for tumour growth. Thus, glioblastoma-associated microglia and macrophages are logical therapeutic targets. Their emerging roles in glioblastoma progression are reflected in the burgeoning research into therapeutics directed at their modification or elimination. Here, we review the biology of glioblastoma-associated microglia and macrophages, and model systems used to study these cells in vitro and in vivo. We discuss translation of results using these model systems and review recent advances in immunotherapies targeting microglia and macrophages in glioblastoma. Significant challenges remain but medications that affect glioblastoma-associated microglia and macrophages hold considerable promise to improve the prognosis for patients with this disease.
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Affiliation(s)
- Candice C Poon
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Susobhan Sarkar
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - John J P Kelly
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
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