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Melrose J. Hyaluronan hydrates and compartmentalises the CNS/PNS extracellular matrix and provides niche environments conducive to the optimisation of neuronal activity. J Neurochem 2023; 166:637-653. [PMID: 37492973 DOI: 10.1111/jnc.15915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/27/2023]
Abstract
The central nervous system/peripheral nervous system (CNS/PNS) extracellular matrix is a dynamic and highly interactive space-filling, cell-supportive, matrix-stabilising, hydrating entity that creates and maintains tissue compartments to facilitate regional ionic micro-environments and micro-gradients that promote optimal neural cellular activity. The CNS/PNS does not contain large supportive collagenous and elastic fibrillar networks but is dominated by a high glycosaminoglycan content, predominantly hyaluronan (HA) and collagen is restricted to the brain microvasculature, blood-brain barrier, neuromuscular junction and meninges dura, arachnoid and pia mater. Chondroitin sulphate-rich proteoglycans (lecticans) interactive with HA have stabilising roles in perineuronal nets and contribute to neural plasticity, memory and cognitive processes. Hyaluronan also interacts with sialoproteoglycan associated with cones and rods (SPACRCAN) to stabilise the interphotoreceptor matrix and has protective properties that ensure photoreceptor viability and function is maintained. HA also regulates myelination/re-myelination in neural networks. HA fragmentation has been observed in white matter injury, multiple sclerosis, and traumatic brain injury. HA fragments (2 × 105 Da) regulate oligodendrocyte precursor cell maturation, myelination/remyelination, and interact with TLR4 to initiate signalling cascades that mediate myelin basic protein transcription. HA and its fragments have regulatory roles over myelination which ensure high axonal neurotransduction rates are maintained in neural networks. Glioma is a particularly invasive brain tumour with extremely high mortality rates. HA, CD44 and RHAMM (receptor for HA-mediated motility) HA receptors are highly expressed in this tumour. Conventional anti-glioma drug treatments have been largely ineffective and surgical removal is normally not an option. CD44 and RHAMM glioma HA receptors can potentially be used to target gliomas with PEP-1, a cell-penetrating HA-binding peptide. PEP-1 can be conjugated to a therapeutic drug; such drug conjugates have successfully treated dense non-operative tumours in other tissues, therefore similar applications warrant exploration as potential anti-glioma treatments.
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Affiliation(s)
- James Melrose
- Raymond Purves Bone and Joint Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, New South Wales, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Sydney Medical School, Northern, The University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Royal North Shore Hospital, St. Leonards, New South Wales, Australia
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Yu H, Wang M, Wang X, Jiang X. Immune-related matrisomes are potential biomarkers to predict the prognosis and immune microenvironment of glioma patients. FEBS Open Bio 2022; 13:307-322. [PMID: 36560848 PMCID: PMC9900094 DOI: 10.1002/2211-5463.13541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 11/11/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The extracellular matrix (ECM) plays a vital role in the progression and metastasis of glioma and is an important part of the tumor microenvironment. The matrisome is composed of ECM components and related proteins. There have been several studies on the effects of matrisomes on the glioma immune microenvironment, but most of these studies were performed on individual glioma immune-related matrisomes rather than integral analysis. Hence, an overall analysis of all potential immune-related matrisomes in gliomas is needed. Here, we divided 667 glioma patients in The Cancer Genome Atlas (TCGA) database into low, moderate, and high immune infiltration groups. Immune-related matrisomes differentially expressed among the three groups were analyzed, and a risk signature was established. Eight immune-related matrisomes were screened, namely, LIF, LOX, MMP9, S100A4, SRPX2, SLIT1, SMOC1, and TIMP1. Kaplan-Meier analysis, operating characteristic curve analysis, and nomogram were constructed to analyze the relationships between risk signatures and the prognosis of glioma patients. The risk signature was significantly correlated with the overall survival of glioma patients. Both high- and low-risk signatures were also associated with some immune checkpoints. In addition, analysis of somatic mutations and anti-PD1/L1 immunotherapy responses in the high- and low-risk groups showed that the high-risk group had worse prognosis and a higher response to anti-PD1/L1 immunotherapy. Our analysis of immune-related matrisomes may improve understanding of the characteristics of the glioma immune microenvironment and provide direction for glioma immunotherapy development in the future.
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Affiliation(s)
- Hao Yu
- Department of Neurosurgery, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Minjie Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical CollegeWuhanChina
| | - Xuan Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical CollegeWuhanChina
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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MZF1 Transcriptionally Activated MicroRNA-328-3p Suppresses the Malignancy of Stomach Adenocarcinoma via Inhibiting CD44. J Immunol Res 2022; 2022:5819295. [PMID: 35669102 PMCID: PMC9167131 DOI: 10.1155/2022/5819295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022] Open
Abstract
MicroRNA-328-3p (miR-328-3p) plays a critical role in mediating the progression of multiple types of cancers. To date, no study has concentrated on the molecular mechanism of miR-328-3p in mediating stomach adenocarcinoma (STAD). In this study, it was found that miR-328-3p was downregulated in STAD, and inhibition of miR-328-3p significantly promoted the growth, migration, invasion, and stemness of STAD cells, while miR-328-3p overexpression exerted reverse effects. Through bioinformatics analysis, it was uncovered that a cluster of differentiation 44 (CD44) was upregulated in STAD and closely associated with the prognosis of STAD patients. Mechanistically, we identified CD44 as the target gene of miR-328-3p. Notably, knockdown of CD44 abolished the promoting function of miR-328-3p inhibitor in the development of STAD. Moreover, myeloid zinc finger protein 1 (MZF1) was confirmed as an upstream transcription factor for miR-328-3p, which is involved in enhancing miR-328-3p expression. In addition, the role of MZF1 downregulation in the malignant traits of STAD cells was blocked by miR-328-3p overexpression. More importantly, upregulation of miR-328-3p efficiently suppressed STAD tumor growth in vivo. Collectively, our findings illustrated that MZF1-mediated miR-328-3p acted as a cancer suppressor in STAD progression via regulation of CD44, which suggested the possibility of the MZF1/miR-328-3p/CD44 axis as a novel promising therapeutic candidate for STAD.
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Xiao Y, Yang K, Wang Z, Zhao M, Deng Y, Ji W, Zou Y, Qian C, Liu Y, Xiao H, Liu H. CD44-Mediated Poor Prognosis in Glioma Is Associated With M2-Polarization of Tumor-Associated Macrophages and Immunosuppression. Front Surg 2022; 8:775194. [PMID: 35187044 PMCID: PMC8850306 DOI: 10.3389/fsurg.2021.775194] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022] Open
Abstract
Background Glioma is the most common primary brain tumor with a poor prognosis. Key genes that are negatively related to prognosis may provide the therapy targets to cure glioma. To clarify the role of CD44 in glioma, we explored its function at bulk-transcriptome, spatial and single-cell transcriptome levels. Methods In total, expression profiles with survival data of whole-grade glioma from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), RNA-seq data with anatomic information of glioblastoma (GBM) from the Ivy Glioblastoma Atlas Project, RNA-sequencing (RNA-seq) data from recurrent GBM receiving adjuvant anti-PD-1 immunotherapy accessed through GSE121810, and single-cell RNA-seq data of GBM under accession GSE103224 were enrolled in this study. CD44-specific findings were further analyzed by R language. Results CD44 is positively correlated with WHO grade of malignancy and is negatively related to prognosis in glioma. Meanwhile, CD44 predominantly expresses in GBM mesenchymal subtype, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses reveal that CD44 positively coexpressed genes are closely related to glioma immunity. Moreover, CD44+ cells mainly distribute in perinecrotic region with high expression of immune factors. At single-cell resolution, only malignant tumor cells, tumor-associated macrophages (TAMs), and T cells express CD44 in GBM. CD44+ malignant tumor cells are in mesenchymal-1-like (MES1-like) cellular state, and CD44+ TAMs are in M2 phenotype. CD44+ T cells have high expression of both PD-1 and PD-L1. CD44 and its directly interacted inhibitory immunomodulators are upregulated in patients with nonresponder recurrent GBM treated with PD-1 blockade therapy. Conclusion Our work demonstrates that CD44, a new M2 TAM biomarker, is involved in immune suppressor and promote glioma progression in glioma microenvironment. These results expand our understanding of CD44-specific clinical and immune features in glioma.
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Affiliation(s)
- Yong Xiao
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Kun Yang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhen Wang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Mengjie Zhao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Wei Ji
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Yuanjie Zou
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Chunfa Qian
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yong Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hong Xiao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- *Correspondence: Hong Xiao
| | - Hongyi Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Hongyi Liu
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Du Z, Wang Y, Liang J, Gao S, Cai X, Yu Y, Qi Z, Li J, Xie Y, Wang Z. Association of glioma CD44 expression with glial dynamics in the tumour microenvironment and patient prognosis. Comput Struct Biotechnol J 2022; 20:5203-5217. [PMID: 36187921 PMCID: PMC9508470 DOI: 10.1016/j.csbj.2022.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022] Open
Abstract
Because of the heterogeneity of lower-grade gliomas (LGGs), patients show various survival outcomes that are not reliably predicted by histological classification. The tumour microenvironment (TME) contributes to the initiation and progression of brain LGGs. Identifying potential prognostic markers based on the immune and stromal components in the TME will provide new insights into the dynamic modulation of these two components of the TME in LGGs. We applied ESTIMATE to calculate the ratio of immune and stromal components from The Cancer Genome Atlas database. After combined differential gene expression analysis, protein–protein interaction network construction and survival analysis, CD44 was screened as an independent prognostic factor and subsequently validated utilizing data from the Chinese Glioma Genome Atlas database. To decipher the association of glioma cell CD44 expression with stromal cells in the TME and tumour progression, RT–qPCR, cell viability and wound healing assays were employed to determine whether astrocytes enhance glioma cell viability and migration by upregulating CD44 expression. Surprisingly, M1 macrophages were identified as positively correlated with CD44 expression by CIBERSORT analysis. CD44+ glioma cells were further suggested to interact with microglia-derived macrophages (M1 phenotype) via osteopontin signalling on the basis of single-cell sequencing data. Overall, we found that astrocytes could elevate the CD44 expression level of glioma cells, enhancing the recruitment of M1 macrophages that may promote glioma stemness via osteopontin-CD44 signalling. Thus, glioma CD44 expression might coordinate with glial activities in the TME and serve as a potential therapeutic target and prognostic marker for LGGs.
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Quintelier K, Couckuyt A, Emmaneel A, Aerts J, Saeys Y, Van Gassen S. Analyzing high-dimensional cytometry data using FlowSOM. Nat Protoc 2021; 16:3775-3801. [PMID: 34172973 DOI: 10.1038/s41596-021-00550-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023]
Abstract
The dimensionality of cytometry data has strongly increased in the last decade, and in many situations the traditional manual downstream analysis becomes insufficient. The field is therefore slowly moving toward more automated approaches, and in this paper we describe the protocol for analyzing high-dimensional cytometry data using FlowSOM, a clustering and visualization algorithm based on a self-organizing map. FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and can help to gain deeper insights in fields such as immunology and oncology. Since the original FlowSOM publication (2015), we have validated the tool on a wide variety of datasets, and to write this protocol, we made use of this experience to improve the user-friendliness of the package (e.g., comprehensive functions replacing commonly required scripts). Where the original paper focused mainly on the algorithm description, this protocol offers user guidelines on how to implement the procedure, detailed parameter descriptions and troubleshooting recommendations. The protocol provides clearly annotated R code, and is therefore relevant for all scientists interested in computational high-dimensional analyses without requiring a strong bioinformatics background. We demonstrate the complete workflow, starting from data preparation (such as compensation, transformation and quality control), including detailed discussion of the different FlowSOM parameters and visualization options, and concluding with how the results can be further used to answer biological questions, such as statistical comparison between groups of interest. An average FlowSOM analysis takes 1-3 h to complete, though quality issues can increase this time considerably.
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Affiliation(s)
- Katrien Quintelier
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Artuur Couckuyt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Annelies Emmaneel
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Joachim Aerts
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Sofie Van Gassen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium. .,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium.
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Deng S, Zheng Y, Mo Y, Xu X, Li Y, Zhang Y, Liu J, Chen J, Tian Y, Ke Y. Ferroptosis Suppressive Genes Correlate with Immunosuppression in Glioblastoma. World Neurosurg 2021; 152:e436-e448. [PMID: 34062295 DOI: 10.1016/j.wneu.2021.05.098] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Glioblastoma (GBM) is the most lethal primary tumor in the central nervous system. Ferroptosis is a type of programmed iron-dependent cell death. In the present study, we aimed to identify prognostic ferroptosis-related genes and their role in tumor immunity. METHODS We used differential and survival analysis and The Cancer Genome Atlas (TCGA) GBM RNA sequencing data. We also used systematic bioinformatic methods. RESULTS Using differential and survival analysis, we found that a ferroptosis suppressor was predominant within ferroptosis-related genes in TCGA GBM RNA sequencing data. By integrating TCGA and gene expression omnibus GBM cohorts, 12 dysregulated ferroptosis suppressors were detected. Among the suppressors, CD44, heat shock protein family B (small) member 1 (HSPB1), and solute carrier family 40 member 1 (SLC40A1) were relevant to overall survival. Using systematic bioinformatic methods, we observed that ferroptosis suppressor expression correlated with immunosuppression, which could be attributed to T-cell exhaustion and cytotoxic T-lymphocyte evasion. Finally, we observed that a potential ferroptosis-inducing drug, acetaminophen, interacted with CD44, HSPB1, and SLC40A1. CONCLUSIONS The ferroptosis suppressors CD44, HSPB1, and SLC40A1 were significantly associated with prognosis in GBM and correlated with immunosuppression (i.e., T-cell exhaustion and cytotoxic T-lymphocyte evasion). Acetaminophen might have an antitumor function in GBM by regulating CD44, HSPB1, and SLC40A1 to induce ferroptosis. Our results are expected to be of great significance in developing new immunotherapy strategies for GBM.
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Affiliation(s)
- Shaokang Deng
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yaofeng Zheng
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yunzhao Mo
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiangdong Xu
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yan Li
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuxuan Zhang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Liu
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianqiu Chen
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yixin Tian
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yiquan Ke
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Ruiz-Moreno AJ, Reyes-Romero A, Dömling A, Velasco-Velázquez MA. In Silico Design and Selection of New Tetrahydroisoquinoline-Based CD44 Antagonist Candidates. Molecules 2021; 26:molecules26071877. [PMID: 33810348 PMCID: PMC8037692 DOI: 10.3390/molecules26071877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 02/07/2023] Open
Abstract
CD44 promotes metastasis, chemoresistance, and stemness in different types of cancer and is a target for the development of new anti-cancer therapies. All CD44 isoforms share a common N-terminal domain that binds to hyaluronic acid (HA). Herein, we used a computational approach to design new potential CD44 antagonists and evaluate their target-binding ability. By analyzing 30 crystal structures of the HA-binding domain (CD44HAbd), we characterized a subdomain that binds to 1,2,3,4-tetrahydroisoquinoline (THQ)-containing compounds and is adjacent to residues essential for HA interaction. By computational combinatorial chemistry (CCC), we designed 168,190 molecules and compared their conformers to a pharmacophore containing the key features of the crystallographic THQ binding mode. Approximately 0.01% of the compounds matched the pharmacophore and were analyzed by computational docking and molecular dynamics (MD). We identified two compounds, Can125 and Can159, that bound to human CD44HAbd (hCD44HAbd) in explicit-solvent MD simulations and therefore may elicit CD44 blockage. These compounds can be easily synthesized by multicomponent reactions for activity testing and their binding mode, reported here, could be helpful in the design of more potent CD44 antagonists.
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Affiliation(s)
- Angel J. Ruiz-Moreno
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico 04510, Mexico;
- Unidad Periférica de Investigación en Biomedicina Translacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Félix Cuevas 540, Ciudad de Mexico 03229, Mexico
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico 04510, Mexico
- Drug Design Group, Department of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands;
| | - Atilio Reyes-Romero
- Drug Design Group, Department of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands;
| | - Alexander Dömling
- Drug Design Group, Department of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands;
- Correspondence: (A.D.); (M.A.V.-V.); Tel.: +31-50-363-330 (A.D.); +52-55-5623-2282 (M.A.V.-V.)
| | - Marco A. Velasco-Velázquez
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico 04510, Mexico;
- Unidad Periférica de Investigación en Biomedicina Translacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Félix Cuevas 540, Ciudad de Mexico 03229, Mexico
- Correspondence: (A.D.); (M.A.V.-V.); Tel.: +31-50-363-330 (A.D.); +52-55-5623-2282 (M.A.V.-V.)
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Vartholomatos E, Vartholomatos G, Alexiou GA, Markopoulos GS. The Past, Present and Future of Flow Cytometry in Central Nervous System Malignancies. Methods Protoc 2021; 4:mps4010011. [PMID: 33530325 PMCID: PMC7839046 DOI: 10.3390/mps4010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Central nervous system malignancies (CNSMs) are categorized among the most aggressive and deadly types of cancer. The low median survival in patients with CNSMs is partly explained by the objective difficulties of brain surgeries as well as by the acquired chemoresistance of CNSM cells. Flow Cytometry is an analytical technique with the ability to quantify cell phenotype and to categorize cell populations on the basis of their characteristics. In the current review, we summarize the Flow Cytometry methodologies that have been used to study different phenotypic aspects of CNSMs. These include DNA content analysis for the determination of malignancy status and phenotypic characterization, as well as the methodologies used during the development of novel therapeutic agents. We conclude with the historical and current utility of Flow Cytometry in the field, and we propose how we can exploit current and possible future methodologies in the battle against this dreadful type of malignancy.
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Affiliation(s)
- Evrysthenis Vartholomatos
- Faculty of Medicine, Neurosurgical Institute, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.V.); (G.A.A.)
| | - George Vartholomatos
- Haematology Laboratory-Unit of Molecular Biology, University Hospital of Ioannina, 45110 Ioannina, Greece;
| | - George A. Alexiou
- Faculty of Medicine, Neurosurgical Institute, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.V.); (G.A.A.)
- Department of Neurosurgery, University of Ioannina, 45110 Ioannina, Greece
| | - Georgios S. Markopoulos
- Faculty of Medicine, Neurosurgical Institute, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.V.); (G.A.A.)
- Haematology Laboratory-Unit of Molecular Biology, University Hospital of Ioannina, 45110 Ioannina, Greece;
- Correspondence:
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He D, Zhang X, Tu J. Diagnostic significance and carcinogenic mechanism of pan-cancer gene POU5F1 in liver hepatocellular carcinoma. Cancer Med 2020; 9:8782-8800. [PMID: 32978904 PMCID: PMC7724499 DOI: 10.1002/cam4.3486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/30/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The prognostic and clinicopathological significance of POU Class 5 Homeobox 1 (POU5F1) among various cancers are disputable heretofore. The diagnostic value and functional mechanism of POU5F1 in liver hepatocellular carcinoma (LIHC) have not been studied thoroughly. METHODS An integrative strategy of meta-analysis, bioinformatics, and wet-lab approach was used to explore the diagnostic and prognostic significance of POU5F1 in various types of tumors, especially in LIHC. Meta-analysis was utilized to investigate the impact of POU5F1 on prognosis and clinicopathological parameters in various cancers. The expression level and diagnostic value of POU5F1 were assessed by qPCR in plasma collected from LIHC patients and controls. The correlation between POU5F1 and tumor infiltrating immune cells (TIICs) in LIHC was evaluated by CIBERSORT. Gene set enrichment analysis (GSEA) was performed based on TCGA. Hub genes and related pathways were identified on the basis of co-expression genes of POU5F1. RESULTS Elevated POU5F1 was associated with poor OS, DFS, RFS, and DSS in various cancers. POU5F1 was confirmed as an independent risk factor for LIHC and correlated with tumor occurrence, stage, and invasion depth. The combination of POU5F1 and AFP in plasma was with high diagnostic validity (AUC = 0.902, p < .001). Specifically, the level of POU5F1 was correlated with infiltrating levels of B cells, T cells, dendritic cells, and monocytes in LIHC. GSEA indicated that POU5F1 participated in multiple cancer-related pathways and cell proliferation pathways. Moreover, CBX3, CCHCR1, and NFYC were filtered as the central hub genes of POU5F1. CONCLUSION Our study identified POU5F1 as a pan-cancer gene that could not only be a prognostic and diagnostic biomarker in various cancers, especially in LIHC, but functionally carcinogenic in LIHC.
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Affiliation(s)
- Dingdong He
- Center for Gene Diagnosis, and Clinical LabZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Xiaokang Zhang
- Center for Gene Diagnosis, and Clinical LabZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Jiancheng Tu
- Center for Gene Diagnosis, and Clinical LabZhongnan Hospital of Wuhan UniversityWuhanChina
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