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Guo J, Zhang W, Chen X, Yen A, Chen L, Shively CA, Li D, Wang T, Dougherty JD, Mitra RD. Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data. Bioinformatics 2024; 40:btae070. [PMID: 38323623 PMCID: PMC10881108 DOI: 10.1093/bioinformatics/btae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/25/2023] [Accepted: 02/05/2024] [Indexed: 02/08/2024] Open
Abstract
MOTIVATION Unraveling the transcriptional programs that control how cells divide, differentiate, and respond to their environments requires a precise understanding of transcription factors' (TFs) DNA-binding activities. Calling cards (CC) technology uses transposons to capture transient TF binding events at one instant in time and then read them out at a later time. This methodology can also be used to simultaneously measure TF binding and mRNA expression from single-cell CC and to record and integrate TF binding events across time in any cell type of interest without the need for purification. Despite these advantages, there has been a lack of dedicated bioinformatics tools for the detailed analysis of CC data. RESULTS We introduce Pycallingcards, a comprehensive Python module specifically designed for the analysis of single-cell and bulk CC data across multiple species. Pycallingcards introduces two innovative peak callers, CCcaller and MACCs, enhancing the accuracy and speed of pinpointing TF binding sites from CC data. Pycallingcards offers a fully integrated environment for data visualization, motif finding, and comparative analysis with RNA-seq and ChIP-seq datasets. To illustrate its practical application, we have reanalyzed previously published mouse cortex and glioblastoma datasets. This analysis revealed novel cell-type-specific binding sites and potential sex-linked TF regulators, furthering our understanding of TF binding and gene expression relationships. Thus, Pycallingcards, with its user-friendly design and seamless interface with the Python data science ecosystem, stands as a critical tool for advancing the analysis of TF functions via CC data. AVAILABILITY AND IMPLEMENTATION Pycallingcards can be accessed on the GitHub repository: https://github.com/The-Mitra-Lab/pycallingcards.
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Affiliation(s)
- Juanru Guo
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Wenjin Zhang
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Xuhua Chen
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Allen Yen
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Department of Psychiatry, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Lucy Chen
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Christian A Shively
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Daofeng Li
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- McDonnell Genome Institute, , Washington University in St. Louis School of Medicine, Saint Louis, MO, 63110, United States
| | - Joseph D Dougherty
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Department of Psychiatry, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO 63108, United States
| | - Robi D Mitra
- Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, United States
- McDonnell Genome Institute, , Washington University in St. Louis School of Medicine, Saint Louis, MO, 63110, United States
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO 63108, United States
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Mangoli A, Wu S, Liu HQ, Aksu M, Jain V, Foreman BE, Regal JA, Weidenhammer LB, Stewart CE, Guerra Garcia ME, Hocke E, Abramson K, Williams NT, Luo L, Deland K, Attardi L, Abe K, Hashizume R, Ashley DM, Becher OJ, Kirsch DG, Gregory SG, Reitman ZJ. Ataxia-telangiectasia mutated ( Atm ) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562892. [PMID: 37904990 PMCID: PMC10614905 DOI: 10.1101/2023.10.18.562892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by p53-inactivating mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress, which presents therapeutic opportunities. We used RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce K27M in the native H3f3a allele in a lineage- and spatially-directed manner, yielding primary mouse DMGs. Genetic or pharmacologic disruption of the DNA damage response kinase Ataxia-telangiectasia mutated (ATM) enhanced the efficacy of focal brain irradiation, extending mouse survival. This finding suggests that targeting ATM will enhance the efficacy of radiation therapy for p53-mutant DMG but not p53-wildtype DMG. We used spatial in situ transcriptomics and an allelic series of primary murine DMG models with different p53 mutations to identify transactivation-independent p53 activity as a key mediator of such radiosensitivity. These studies deeply profile a genetically faithful and versatile model of a lethal brain tumor to identify resistance mechanisms for a therapeutic strategy currently in clinical trials.
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Wälchli T, Bisschop J, Carmeliet P, Zadeh G, Monnier PP, De Bock K, Radovanovic I. Shaping the brain vasculature in development and disease in the single-cell era. Nat Rev Neurosci 2023; 24:271-298. [PMID: 36941369 PMCID: PMC10026800 DOI: 10.1038/s41583-023-00684-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
The CNS critically relies on the formation and proper function of its vasculature during development, adult homeostasis and disease. Angiogenesis - the formation of new blood vessels - is highly active during brain development, enters almost complete quiescence in the healthy adult brain and is reactivated in vascular-dependent brain pathologies such as brain vascular malformations and brain tumours. Despite major advances in the understanding of the cellular and molecular mechanisms driving angiogenesis in peripheral tissues, developmental signalling pathways orchestrating angiogenic processes in the healthy and the diseased CNS remain incompletely understood. Molecular signalling pathways of the 'neurovascular link' defining common mechanisms of nerve and vessel wiring have emerged as crucial regulators of peripheral vascular growth, but their relevance for angiogenesis in brain development and disease remains largely unexplored. Here we review the current knowledge of general and CNS-specific mechanisms of angiogenesis during brain development and in brain vascular malformations and brain tumours, including how key molecular signalling pathways are reactivated in vascular-dependent diseases. We also discuss how these topics can be studied in the single-cell multi-omics era.
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Affiliation(s)
- Thomas Wälchli
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, and Division of Neurosurgery, University and University Hospital Zurich, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland.
- Group of Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada.
| | - Jeroen Bisschop
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, and Division of Neurosurgery, University and University Hospital Zurich, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Group of Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB & Department of Oncology, KU Leuven, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, People's Republic of China
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Philippe P Monnier
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Donald K. Johnson Research Institute, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Katrien De Bock
- Laboratory of Exercise and Health, Department of Health Science and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Ivan Radovanovic
- Group of Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada
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Antibody Profiling and In Silico Functional Analysis of Differentially Reactive Antibody Signatures of Glioblastomas and Meningiomas. Int J Mol Sci 2023; 24:ijms24021411. [PMID: 36674927 PMCID: PMC9866115 DOI: 10.3390/ijms24021411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/08/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Studies on tumor-associated antigens in brain tumors are sparse. There is scope for enhancing our understanding of molecular pathology, in order to improve on existing forms, and discover new forms, of treatment, which could be particularly relevant to immuno-oncological strategies. To elucidate immunological differences, and to provide another level of biological information, we performed antibody profiling, based on a high-density protein array (containing 8173 human transcripts), using IgG isolated from the sera of n = 12 preoperative and n = 16 postoperative glioblastomas, n = 26 preoperative and n = 29 postoperative meningiomas, and n = 27 healthy, cancer-free controls. Differentially reactive antigens were compared to gene expression data from an alternate public GBM data set from OncoDB, and were analyzed using the Reactome pathway browser. Protein array analysis identified approximately 350-800 differentially reactive antigens, and revealed different antigen profiles in the glioblastomas and meningiomas, with approximately 20-30%-similar and 10-15%-similar antigens in preoperative and postoperative sera, respectively. Seroreactivity did not correlate with OncoDB-derived gene expression. Antigens in the preoperative glioblastoma sera were enriched for signaling pathways, such as signaling by Rho-GTPases, COPI-mediated anterograde transport and vesicle-mediated transport, while the infectious disease, SRP-dependent membrane targeting cotranslational proteins were enriched in the meningiomas. The pre-vs. postoperative seroreactivity in the glioblastomas was enriched for antigens, e.g., platelet degranulation and metabolism of lipid pathways; in the meningiomas, the antigens were enriched in infectious diseases, metabolism of amino acids and derivatives, and cell cycle. Antibody profiling in both tumor entities elucidated several hundred antigens and characteristic signaling pathways that may provide new insights into molecular pathology and may be of interest for the development of new treatment strategies.
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Wu F, Yin YY, Fan WH, Zhai Y, Yu MC, Wang D, Pan CQ, Zhao Z, Li GZ, Zhang W. Immunological profiles of human oligodendrogliomas define two distinct molecular subtypes. EBioMedicine 2022; 87:104410. [PMID: 36525723 PMCID: PMC9772571 DOI: 10.1016/j.ebiom.2022.104410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human oligodendroglioma presents as a heterogeneous disease, primarily characterized by the isocitrate dehydrogenase (IDH) mutation and 1p/19q co-deletion. Therapy development for this tumor is hindered by incomplete knowledge of somatic driving alterations and suboptimal disease classification. We herein aim to identify intrinsic molecular subtypes through integrated analysis of transcriptome, genome and methylome. METHODS 137 oligodendroglioma patients from the Cancer Genome Atlas (TCGA) dataset were collected for unsupervised clustering analysis of immune gene expression profiles and comparative analysis of genome and methylome. Two independent datasets containing 218 patients were used for validation. FINDINGS We identified and independently validated two reproducible subtypes associated with distinct molecular characteristics and clinical outcomes. The proliferative subtype, named Oligo1, was characterized by more tumors of CNS WHO grade 3, as well as worse prognosis compared to the Oligo2 subtype. Besides the clinicopathologic features, Oligo1 exhibited enrichment of cell proliferation, regulation of cell cycle and Wnt signaling pathways, and significantly altered genes, such as EGFR, NOTCH1 and MET. In contrast, Oligo2, with favorable outcome, presented increased activation of immune response and metabolic process. Higher T cell/APC co-inhibition and inhibitory checkpoint levels were observed in Oligo2 tumors. Finally, multivariable analysis revealed our classification was an independent prognostic factor in oligodendrogliomas, and the robustness of these molecular subgroups was verified in the validation cohorts. INTERPRETATION This study provides further insights into patient stratification as well as presents opportunities for therapeutic development in human oligodendrogliomas. FUNDING The funders are listed in the Acknowledgement.
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Affiliation(s)
- Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China,Corresponding author. Nan Si Huan Xi Lu 119, Fengtai District, Beijing 100070, China.
| | - Yi-Yun Yin
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Wen-Hua Fan
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - You Zhai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Ming-Chen Yu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Di Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Chang-Qing Pan
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China
| | - Wei Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, 100070, China,Corresponding author. Nan Si Huan Xi Lu 119, Fengtai District, Beijing 100070, China.
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Hsia T, Yekula A, Batool SM, Rosenfeld YB, You DG, Weissleder R, Lee H, Carter BS, Balaj L. Glioblastoma-derived extracellular vesicle subpopulations following 5-aminolevulinic acid treatment bear diagnostic implications. J Extracell Vesicles 2022; 11:e12278. [PMID: 36404434 PMCID: PMC9676504 DOI: 10.1002/jev2.12278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
Liquid biopsy is a minimally invasive alternative to surgical biopsy, encompassing different analytes including extracellular vesicles (EVs), circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), proteins, and metabolites. EVs are released by virtually all cells, but at a higher rate by faster cycling, malignant cells. They encapsulate cargo native to the originating cell and can thus provide a window into the tumour landscape. EVs are often analysed in bulk which hinders the analysis of rare, tumour-specific EV subpopulations from the large host EV background. Here, we fractionated EV subpopulations in vitro and in vivo and characterized their phenotype and generic cargo. We used 5-aminolevulinic acid (5-ALA) to induce release of endogenously fluorescent tumour-specific EVs (EVPpIX ). Analysis of five different subpopulations (EVPpIX , EVCD63 , EVCD9 , EVEGFR , EVCFDA ) from glioblastoma (GBM) cell lines revealed unique transcriptome profiles, with the EVPpIX transcriptome demonstrating closer alignment to tumorigenic processes over the other subpopulations. Similarly, isolation of tumour-specific EVs from GBM patient plasma showed enrichment in GBM-associated genes, when compared to bulk EVs from plasma. We propose that fractionation of EV populations facilitates detection and isolation of tumour-specific EVs for disease monitoring.
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Affiliation(s)
- Tiffaney Hsia
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Anudeep Yekula
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - S. Maheen Batool
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Yulia B. Rosenfeld
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Dong Gil You
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Ralph Weissleder
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusettsUSA
- Department of RadiologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Hakho Lee
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusettsUSA
- Department of RadiologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Bob S. Carter
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Leonora Balaj
- Department of NeurosurgeryMassachusetts General Hospital, Harvard Medical SchoolBostonMassachusettsUSA
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Testa E, Palazzo C, Mastrantonio R, Viscomi MT. Dynamic Interactions between Tumor Cells and Brain Microvascular Endothelial Cells in Glioblastoma. Cancers (Basel) 2022; 14:3128. [PMID: 35804908 PMCID: PMC9265028 DOI: 10.3390/cancers14133128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
GBM is the most aggressive brain tumor among adults. It is characterized by extensive vascularization, and its further growth and recurrence depend on the formation of new blood vessels. In GBM, tumor angiogenesis is a multi-step process involving the proliferation, migration and differentiation of BMECs under the stimulation of specific signals derived from the cancer cells through a wide variety of communication routes. In this review, we discuss the dynamic interaction between BMECs and tumor cells by providing evidence of how tumor cells hijack the BMECs for the formation of new vessels. Tumor cell-BMECs interplay involves multiple routes of communication, including soluble factors, such as chemokines and cytokines, direct cell-cell contact and extracellular vesicles that participate in and fuel this cooperation. We also describe how this interaction is able to modify the BMECs structure, metabolism and physiology in a way that favors tumor growth and invasiveness. Finally, we briefly reviewed the recent advances and the potential future implications of some high-throughput 3D models to better understanding the complexity of BMECs-tumor cell interaction.
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Affiliation(s)
- Erika Testa
- Sezione di Istologia ed Embriologia, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Roma, Italy; (C.P.); (R.M.)
| | - Claudia Palazzo
- Sezione di Istologia ed Embriologia, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Roma, Italy; (C.P.); (R.M.)
| | - Roberta Mastrantonio
- Sezione di Istologia ed Embriologia, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Roma, Italy; (C.P.); (R.M.)
| | - Maria Teresa Viscomi
- Sezione di Istologia ed Embriologia, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Roma, Italy; (C.P.); (R.M.)
- IRCCS, Fondazione Policlinico Universitario “Agostino Gemelli”, L.go A. Gemelli 8, 00168 Roma, Italy
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Demirci Y, Heger G, Katkat E, Papatheodorou I, Brazma A, Ozhan G. Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages. Front Cell Dev Biol 2022; 10:813314. [PMID: 35223842 PMCID: PMC8868567 DOI: 10.3389/fcell.2022.813314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most frequent type of brain cancers and characterized by continuous proliferation, inflammation, angiogenesis, invasion and dedifferentiation, which are also among the initiator and sustaining factors of brain regeneration during restoration of tissue integrity and function. Thus, brain regeneration and brain cancer should share more molecular mechanisms at early stages of regeneration where cell proliferation dominates. However, the mechanisms could diverge later when the regenerative response terminates, while cancer cells sustain proliferation. To test this hypothesis, we exploited the adult zebrafish that, in contrast to the mammals, can efficiently regenerate the brain in response to injury. By comparing transcriptome profiles of the regenerating zebrafish telencephalon at its three different stages, i.e., 1 day post-lesion (dpl)-early wound healing stage, 3 dpl-early proliferative stage and 14 dpl-differentiation stage, to those of two brain cancers, i.e., low-grade glioma (LGG) and glioblastoma (GBM), we reveal the common and distinct molecular mechanisms of brain regeneration and brain cancer. While the transcriptomes of 1 dpl and 3 dpl harbor unique gene modules and gene expression profiles that are more divergent from the control, the transcriptome of 14 dpl converges to that of the control. Next, by functional analysis of the transcriptomes of brain regeneration stages to LGG and GBM, we reveal the common and distinct molecular pathways in regeneration and cancer. 1 dpl and LGG and GBM resemble with regard to signaling pathways related to metabolism and neurogenesis, while 3 dpl and LGG and GBM share pathways that control cell proliferation and differentiation. On the other hand, 14 dpl and LGG and GBM converge with respect to developmental and morphogenetic processes. Finally, our global comparison of gene expression profiles of three brain regeneration stages, LGG and GBM exhibit that 1 dpl is the most similar stage to LGG and GBM while 14 dpl is the most distant stage to both brain cancers. Therefore, early convergence and later divergence of brain regeneration and brain cancer constitutes a key starting point in comparative understanding of cellular and molecular events between the two phenomena and development of relevant targeted therapies for brain cancers.
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Affiliation(s)
- Yeliz Demirci
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Esra Katkat
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
| | - Irene Papatheodorou
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
- *Correspondence: Gunes Ozhan,
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9
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Steele JL, Morrow MM, Sarnat HB, Alkhunaizi E, Brandt T, Chitayat DA, DeFilippo CP, Douglas GV, Dubbs HA, Elloumi HZ, Glassford MR, Hannibal MC, Héron B, Kim LE, Marco EJ, Mignot C, Monaghan KG, Myers KA, Parikh S, Quinonez SC, Rajabi F, Shankar SP, Shinawi MS, van de Kamp JJP, Veerapandiyan A, Waldman AT, Graf WD. Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome. Pediatr Neurol 2022; 126:65-73. [PMID: 34740135 DOI: 10.1016/j.pediatrneurol.2021.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Semaphorins and plexins are ligands and cell surface receptors that regulate multiple neurodevelopmental processes such as axonal growth and guidance. PLXNA3 is a plexin gene located on the X chromosome that encodes the most widely expressed plexin receptor in fetal brain, plexin-A3. Plexin-A3 knockout mice demonstrate its role in semaphorin signaling in vivo. The clinical manifestations of semaphorin/plexin neurodevelopmental disorders have been less widely explored. This study describes the neurological and neurodevelopmental phenotypes of boys with maternally inherited hemizygous PLXNA3 variants. METHODS Data-sharing through GeneDx and GeneMatcher allowed identification of individuals with autism or intellectual disabilities (autism/ID) and hemizygous PLXNA3 variants in collaboration with their physicians and genetic counselors, who completed questionnaires about their patients. In silico analyses predicted pathogenicity for each PLXNA3 variant. RESULTS We assessed 14 boys (mean age, 10.7 [range 2 to 25] years) with maternally inherited hemizygous PLXNA3 variants and autism/ID ranging from mild to severe. Other findings included fine motor dyspraxia (92%), attention-deficit/hyperactivity traits, and aggressive behaviors (63%). Six patients (43%) had seizures. Thirteen boys (93%) with PLXNA3 variants showed novel or very low allele frequencies and probable damaging/disease-causing pathogenicity in one or more predictors. We found a genotype-phenotype correlation between PLXNA3 cytoplasmic domain variants (exons 22 to 32) and more severe neurodevelopmental disorder phenotypes (P < 0.05). CONCLUSIONS We report 14 boys with maternally inherited, hemizygous PLXNA3 variants and a range of neurodevelopmental disorders suggesting a novel X-linked intellectual disability syndrome. Greater understanding of PLXNA3 variant pathogenicity in humans will require additional clinical, computational, and experimental validation.
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Affiliation(s)
| | | | - Harvey B Sarnat
- Departments of Paediatrics, Pathology (Neuropathology), and Clinical Neurosciences, University of Calgary Cumming School of Medicine and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Ebba Alkhunaizi
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - David A Chitayat
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Colette P DeFilippo
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, University of California-Davis, Sacramento, California
| | | | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Megan R Glassford
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Mark C Hannibal
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Bénédicte Héron
- Hôpital Armand Trousseau, Service de Neurologie Pédiatrique, Paris, France
| | - Linda E Kim
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Elysa J Marco
- Department of Neurodevelopmental Medicine, CorticaCare, San Diego, California
| | - Cyril Mignot
- Clinical Genetic Department, Pitié Salpétrière University Hospital, Paris, France
| | | | - Kenneth A Myers
- Division of Neurology, Department of Pediatrics, McGill University Health Centre, Montreal, Canada
| | - Sumit Parikh
- Department of Mitochondrial Medicine & Genetics, Cleveland Clinic, Cleveland, Ohio
| | - Shane C Quinonez
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Suma P Shankar
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, University of California-Davis, Sacramento, California
| | - Marwan S Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | | | - Aravindhan Veerapandiyan
- Division of Neurology, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Arkansas
| | - Amy T Waldman
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - William D Graf
- Division of Neurology, Department of Pediatrics, Connecticut Children's, University of Connecticut, Farmington, Connecticut.
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Neufeld L, Yeini E, Reisman N, Shtilerman Y, Ben-Shushan D, Pozzi S, Madi A, Tiram G, Eldar-Boock A, Ferber S, Grossman R, Ram Z, Satchi-Fainaro R. Microengineered perfusable 3D-bioprinted glioblastoma model for in vivo mimicry of tumor microenvironment. SCIENCE ADVANCES 2021; 7:eabi9119. [PMID: 34407932 PMCID: PMC8373143 DOI: 10.1126/sciadv.abi9119] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/28/2021] [Indexed: 05/04/2023]
Abstract
Many drugs show promising results in laboratory research but eventually fail clinical trials. We hypothesize that one main reason for this translational gap is that current cancer models are inadequate. Most models lack the tumor-stroma interactions, which are essential for proper representation of cancer complexed biology. Therefore, we recapitulated the tumor heterogenic microenvironment by creating fibrin glioblastoma bioink consisting of patient-derived glioblastoma cells, astrocytes, and microglia. In addition, perfusable blood vessels were created using a sacrificial bioink coated with brain pericytes and endothelial cells. We observed similar growth curves, drug response, and genetic signature of glioblastoma cells grown in our 3D-bioink platform and in orthotopic cancer mouse models as opposed to 2D culture on rigid plastic plates. Our 3D-bioprinted model could be the basis for potentially replacing cell cultures and animal models as a powerful platform for rapid, reproducible, and robust target discovery; personalized therapy screening; and drug development.
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Affiliation(s)
- Lena Neufeld
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Eilam Yeini
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noa Reisman
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Shtilerman
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dikla Ben-Shushan
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sabina Pozzi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Asaf Madi
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Galia Tiram
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anat Eldar-Boock
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shiran Ferber
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rachel Grossman
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Zvi Ram
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel
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11
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Vásquez X, Sánchez-Gómez P, Palma V. Netrin-1 in Glioblastoma Neovascularization: The New Partner in Crime? Int J Mol Sci 2021; 22:8248. [PMID: 34361013 PMCID: PMC8348949 DOI: 10.3390/ijms22158248] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive and common primary tumor of the central nervous system. It is characterized by having an infiltrating growth and by the presence of an excessive and aberrant vasculature. Some of the mechanisms that promote this neovascularization are angiogenesis and the transdifferentiation of tumor cells into endothelial cells or pericytes. In all these processes, the release of extracellular microvesicles by tumor cells plays an important role. Tumor cell-derived extracellular microvesicles contain pro-angiogenic molecules such as VEGF, which promote the formation of blood vessels and the recruitment of pericytes that reinforce these structures. The present study summarizes and discusses recent data from different investigations suggesting that Netrin-1, a highly versatile protein recently postulated as a non-canonical angiogenic ligand, could participate in the promotion of neovascularization processes in GBM. The relevance of determining the angiogenic signaling pathways associated with the interaction of Netrin-1 with its receptors is posed. Furthermore, we speculate that this molecule could form part of the microvesicles that favor abnormal tumor vasculature. Based on the studies presented, this review proposes Netrin-1 as a novel biomarker for GBM progression and vascularization.
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Affiliation(s)
- Ximena Vásquez
- Laboratory of Stem Cells and Developmental Biology, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile;
| | - Pilar Sánchez-Gómez
- Neurooncology Unit, Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Verónica Palma
- Laboratory of Stem Cells and Developmental Biology, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile;
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12
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Zhang YF, Zhang Y, Jia DD, Yang HY, Cheng MD, Zhu WX, Xin H, Li PF, Zhang YF. Insights into the regulatory role of Plexin D1 signalling in cardiovascular development and diseases. J Cell Mol Med 2021; 25:4183-4194. [PMID: 33837646 PMCID: PMC8093976 DOI: 10.1111/jcmm.16509] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/04/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
Plexin D1 (PLXND1), which was previously thought to mediate semaphorin signalling, belongs to the Plexin family of transmembrane proteins. PLXND1 cooperates mostly with the coreceptor neuropilin and participates in many aspects of axonal guidance. PLXND1 can also act as both a tumour promoter and a tumour suppressor. Emerging evidence suggests that mutations in PLXND1 or Semaphorin 3E, the canonical ligand of PLXND1, can lead to serious cardiovascular diseases, such as congenital heart defects, CHARGE syndrome and systemic sclerosis. Upon ligand binding, PLXND1 can act as a GTPase‐activating protein (GAP) and modulate integrin‐mediated cell adhesion, cytoskeletal dynamics and cell migration. These effects may play regulatory roles in the development of the cardiovascular system and disease. The cardiovascular effects of PLXND1 signalling have gradually been elucidated. PLXND1 was recently shown to detect physical forces and translate them into intracellular biochemical signals in the context of atherosclerosis. Therefore, the role of PLXND1 in cardiovascular development and diseases is gaining research interest because of its potential as a biomarker and therapeutic target. In this review, we describe the cardiac effects, vascular effects and possible molecular mechanisms of PLXND1 signalling.
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Affiliation(s)
- Yi-Fei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dong-Dong Jia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hong-Yu Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Meng-Die Cheng
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wen-Xiu Zhu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Xin
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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13
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Jiao B, Liu S, Tan X, Lu P, Wang D, Xu H. Class-3 semaphorins: Potent multifunctional modulators for angiogenesis-associated diseases. Biomed Pharmacother 2021; 137:111329. [PMID: 33545660 DOI: 10.1016/j.biopha.2021.111329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 11/29/2022] Open
Abstract
Semaphorins, the neuronal guidance cues, were shown to have broad influences on pathophysiological processes such as bone remodeling, immune responses, and angiogenesis. In particular, Class-3 Semaphorins (SEMA3) is considered a vital regulator involved in angiogenesis. Scientific evidence has pointed to the role of angiogenesis in many diseases, and numerous efforts have been made to explore the possibilities of curing those diseases by targeting angiogenesis. Nevertheless, the efficacies are limited owing to the complex mechanisms of angiogenesis. Hence, investigating the mechanisms of SEMA3 in angiogenesis may contribute to novel therapeutics for diseases. Previous reviews mainly focused on the various functions of semaphorins in one particular disease, and the specific angiogenesis mechanism of SEMA3 in diverse diseases has not been well elucidated. Additionally, the role of SEMA3 in angiogenesis remains elusive, as contradicting results have been found in different disease types. Some evidence from recent studies implies that, while most SEMA3 molecules inhibit pathological angiogenesis in different diseases, occasionally SEMA3 may also promote angiogenesis. This review summarizes the specific role of SEMA3 in a variety of angiogenesis-associated diseases, and documents SEMA3 may be a promising therapeutic target for treating angiogenesis-associated diseases.
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Affiliation(s)
- Bo Jiao
- Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shiyang Liu
- Department of Thyroid and Breast Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xi Tan
- Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Pei Lu
- Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Danning Wang
- Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hui Xu
- Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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14
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Lysosomal Function and Axon Guidance: Is There a Meaningful Liaison? Biomolecules 2021; 11:biom11020191. [PMID: 33573025 PMCID: PMC7911486 DOI: 10.3390/biom11020191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/25/2023] Open
Abstract
Axonal trajectories and neural circuit activities strongly rely on a complex system of molecular cues that finely orchestrate the patterning of neural commissures. Several of these axon guidance molecules undergo continuous recycling during brain development, according to incompletely understood intracellular mechanisms, that in part rely on endocytic and autophagic cascades. Based on their pivotal role in both pathways, lysosomes are emerging as a key hub in the sophisticated regulation of axonal guidance cue delivery, localization, and function. In this review, we will attempt to collect some of the most relevant research on the tight connection between lysosomal function and axon guidance regulation, providing some proof of concepts that may be helpful to understanding the relation between lysosomal storage disorders and neurodegenerative diseases.
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15
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Xiao G, Lyu M, Li Z, Cao L, Liu X, Wang Y, He S, Chen Z, Du H, Feng Y, Wang J, Zhu Y. Restoration of early deficiency of axonal guidance signaling by guanxinning injection as a novel therapeutic option for acute ischemic stroke. Pharmacol Res 2021; 165:105460. [PMID: 33513357 DOI: 10.1016/j.phrs.2021.105460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/22/2020] [Accepted: 01/22/2021] [Indexed: 01/12/2023]
Abstract
Despite of its high morbidity and mortality, there is still a lack of effective treatment for ischemic stroke in part due to our incomplete understanding of molecular mechanisms of its pathogenesis. In this study, we demonstrate that SHH-PTCH1-GLI1-mediated axonal guidance signaling and its related neurogenesis, a central pathway for neuronal development, also plays a critical role in early stage of an acute stroke model. Specifically, in vivo, we evaluated the effect of GXNI on ischemic stroke mice via using the middle cerebral artery embolization model, and found that GXNI significantly alleviated cerebral ischemic reperfusion (I/R) injury by reducing the volume of cerebral infarction, neurological deficit score and cerebral edema, reversing the BBB permeability and histopathological changes. A combined approach of RNA-seq and network pharmacology analysis was used to reveal the underlying mechanisms of GXNI followed by RT-PCR, immunohistochemistry and western blotting validation. It was pointed out that axon guidance signaling pathway played the most prominent role in GXNI action with Shh, Ptch1, and Gli1 genes as the critical contributors in brain protection. In addition, GXNI markedly prevented primary cortical neuron cells from oxygen-glucose deprivation/reoxygenation damage in vitro, and promoted axon growth and synaptogenesis of damaged neurons, which further confirmed the results of in vivo experiments. Moreover, due to the inhibition of the SHH-PTCH1-GLI1 signaling pathway by cyclopropylamine, the effect of GXNI was significantly weakened. Hence, our study provides a novel option for the clinical treatment of acute ischemic stroke by GXNI via SHH-PTCH1-GLI1-mediated axonal guidance signaling, a neuronal development pathway previously considered for after-stroke recovery.
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Affiliation(s)
- Guangxu Xiao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Ming Lyu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhixiong Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Linghua Cao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Xinyan Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Yule Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Shuang He
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Zihao Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Hongxia Du
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Yuxin Feng
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China
| | - Jigang Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yan Zhu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Beihua South Road, JingHai District, Tianjin, 301617, China; Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology & Medicine, 220 Dongting Road, TEDA, Tianjin, 300457, China.
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Kääriäinen A, Pesola V, Dittmann A, Kontio J, Koivunen J, Pihlajaniemi T, Izzi V. Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer. Int J Mol Sci 2020; 21:E8837. [PMID: 33266472 PMCID: PMC7700160 DOI: 10.3390/ijms21228837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
The expression and regulation of matrisome genes-the ensemble of extracellular matrix, ECM, ECM-associated proteins and regulators as well as cytokines, chemokines and growth factors-is of paramount importance for many biological processes and signals within the tumor microenvironment. The availability of large and diverse multi-omics data enables mapping and understanding of the regulatory circuitry governing the tumor matrisome to an unprecedented level, though such a volume of information requires robust approaches to data analysis and integration. In this study, we show that combining Pan-Cancer expression data from The Cancer Genome Atlas (TCGA) with genomics, epigenomics and microenvironmental features from TCGA and other sources enables the identification of "landmark" matrisome genes and machine learning-based reconstruction of their regulatory networks in 74 clinical and molecular subtypes of human cancers and approx. 6700 patients. These results, enriched for prognostic genes and cross-validated markers at the protein level, unravel the role of genetic and epigenetic programs in governing the tumor matrisome and allow the prioritization of tumor-specific matrisome genes (and their regulators) for the development of novel therapeutic approaches.
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Affiliation(s)
- Anni Kääriäinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Vilma Pesola
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Annalena Dittmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Juho Kontio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Jarkko Koivunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Taina Pihlajaniemi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
- Faculty of Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland
- Finnish Cancer Institute, 00130 Helsinki, Finland
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A SEMA3 Signaling Pathway-Based Multi-Biomarker for Prediction of Glioma Patient Survival. Int J Mol Sci 2020; 21:ijms21197396. [PMID: 33036421 PMCID: PMC7582960 DOI: 10.3390/ijms21197396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 12/13/2022] Open
Abstract
Glioma is a lethal central nervous system tumor with poor patient survival prognosis. Because of the molecular heterogeneity, it is a challenge to precisely determine the type of the tumor and to choose the most effective treatment. Therefore, novel biomarkers are essential to improve the diagnosis and prognosis of glioma tumors. Class 3 semaphorin proteins (SEMA3) play an important role in tumor biology. SEMA3 transduce their signals by using neuropilin and plexin receptors, which functionally interact with the vascular endothelial growth factor-mediated signaling pathways. Therefore, the aim of this study was to explore the potential of SEMA3 signaling molecules for prognosis of glioma patient survival. The quantitative real-time PCR method was used to evaluate mRNA expression of SEMA3(A-G), neuropilins (NRP1 and NRP2), plexins (PLXNA2 and PLXND1), cadherins (CDH1 and CDH2), integrins (ITGB1, ITGB3, ITGA5, and ITGAV), VEGFA and KDR genes in 59 II-IV grade glioma tissues. Seven genes significantly associated with patient overall survival were used for multi-biomarker construction, which showed 64%, 75%, and 68% of accuracy of predicting the survival of 1-, 2-, and 3-year glioma patients, respectively. The results suggest that the seven-gene signature could serve as a novel multi-biomarker for more accurate prognosis of a glioma patient’s outcome.
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The role of semaphorins in small vessels of the eye and brain. Pharmacol Res 2020; 160:105044. [PMID: 32590102 DOI: 10.1016/j.phrs.2020.105044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022]
Abstract
Small vessel diseases, such as ischemic retinopathy and cerebral small vessel disease (CSVD), are increasingly recognized in patients with diabetes, dementia and cerebrovascular disease. The mechanisms of small vessel diseases are poorly understood, but the latest studies suggest a role for semaphorins. Initially identified as axon guidance cues, semaphorins are mainly studied in neuronal morphogenesis, neural circuit assembly, and synapse assembly and refinement. In recent years, semaphorins have been found to play important roles in regulating vascular growth and development and in many pathophysiological processes, including atherosclerosis, angiogenesis after stroke and retinopathy. Growing evidence indicates that semaphorins affect the occurrence, perfusion and regression of both the macrovasculature and microvasculature by regulating the proliferation, apoptosis, migration, barrier function and inflammatory response of endothelial cells, vascular smooth muscle cells (VSMCs) and pericytes. In this review, we concentrate on the regulatory effects of semaphorins on the cell components of the vessel wall and their potential roles in microvascular diseases, especially in the retina and cerebral small vessel. Finally, we discuss potential molecular approaches in targeting semaphorins as therapies for microvascular disorders in the eye and brain.
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