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Jose A, Kulkarni P, Thilakan J, Munisamy M, Malhotra AG, Singh J, Kumar A, Rangnekar VM, Arya N, Rao M. Integration of pan-omics technologies and three-dimensional in vitro tumor models: an approach toward drug discovery and precision medicine. Mol Cancer 2024; 23:50. [PMID: 38461268 PMCID: PMC10924370 DOI: 10.1186/s12943-023-01916-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/15/2023] [Indexed: 03/11/2024] Open
Abstract
Despite advancements in treatment protocols, cancer is one of the leading cause of deaths worldwide. Therefore, there is a need to identify newer and personalized therapeutic targets along with screening technologies to combat cancer. With the advent of pan-omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, and lipidomics, the scientific community has witnessed an improved molecular and metabolomic understanding of various diseases, including cancer. In addition, three-dimensional (3-D) disease models have been efficiently utilized for understanding disease pathophysiology and as screening tools in drug discovery. An integrated approach utilizing pan-omics technologies and 3-D in vitro tumor models has led to improved understanding of the intricate network encompassing various signalling pathways and molecular cross-talk in solid tumors. In the present review, we underscore the current trends in omics technologies and highlight their role in understanding genotypic-phenotypic co-relation in cancer with respect to 3-D in vitro tumor models. We further discuss the challenges associated with omics technologies and provide our outlook on the future applications of these technologies in drug discovery and precision medicine for improved management of cancer.
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Affiliation(s)
- Anmi Jose
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Pallavi Kulkarni
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jaya Thilakan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Murali Munisamy
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Anvita Gupta Malhotra
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Ashok Kumar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Vivek M Rangnekar
- Markey Cancer Center and Department of Radiation Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Neha Arya
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India.
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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2
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Li L, Yang Y, Wang Z, Xu C, Huang J, Li G. Prognostic role of METTL1 in glioma. Cancer Cell Int 2021; 21:633. [PMID: 34838021 PMCID: PMC8627054 DOI: 10.1186/s12935-021-02346-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/16/2021] [Indexed: 01/02/2023] Open
Abstract
Background Current treatment options for glioma are limited, and the prognosis of patients with glioma is poor as the available drugs show low therapeutic efficacy. Furthermore, the molecular mechanisms associated with glioma remain poorly understood. METTL1 mainly catalyzes the formation of N(7)-methylguanine at position 46 of the transfer RNA sequence, thereby regulating the translation process. However, the role of METTL1 in glioma has not been studied to date. The purpose of this study was to analyze the expression and prognosis of METTL1 in glioma, and to explore the potential analysis mechanism. Methods Data from five publicly available databases were used to analyze METTL1 expression across different tumor types and its differential expression between carcinoma and adjacent normal tissues. The expression of METTL1 in glioma was further validated using real-time polymerase chain reaction and immunohistochemistry. Meanwhile, siRNA was used to knockdown METTL1 in U87 glioma cells, and the resultant effect on glioma proliferation was verified using the Cell Counting Kit 8 (CCK8) assay. Furthermore, a nomogram was constructed to predict the association between METTL1 expression and the survival rate of patients with glioma. Results METTL1 expression increased with increasing glioma grades and was significantly higher in glioma than in adjacent noncancerous tissues. In addition, high expression of METTL1 promoted cell proliferation. Moreover, METTL1 expression was associated with common clinical risk factors and was significantly associated with the prognosis and survival of patients with glioma. Univariate and multivariate Cox regression analyses revealed that METTL1 expression may be used as an independent prognostic risk factor for glioma. Furthermore, results of functional enrichment and pathway analyses indicate that the mechanism of METTL1 in glioma is potentially related to the MAPK signaling pathway. Conclusions High METTL1 expression is significantly associated with poor prognosis of patients with glioma and may represent a valuable independent risk factor. In addition, high expression of METTL1 promotes glioma proliferation and may regulate mitogen-activated protein kinase (MAPK) signaling pathway. Thus, METTL1 may be a potential biomarker for glioma. Further investigations are warranted to explore its clinical use. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02346-4.
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Affiliation(s)
- Lun Li
- Department of Neurosurgery, Anshan Hospital of the First Hospital of China Medical University, Anshan, China
| | - Yi Yang
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Zhenshuang Wang
- Department of Orthopedics, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Chengran Xu
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jinhai Huang
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Guangyu Li
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, China.
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3
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Mule SN, Gomes VDM, Wailemann RAM, Macedo-da-Silva J, Rosa-Fernandes L, Larsen MR, Labriola L, Palmisano G. HSPB1 influences mitochondrial respiration in ER-stressed beta cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140680. [PMID: 34051341 DOI: 10.1016/j.bbapap.2021.140680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 01/02/2023]
Abstract
Beta-cell death and dysfunction are involved in the development of type 1 and 2 diabetes. ER-stress impairs beta-cells function resulting in pro-apoptotic stimuli that promote cell death. Hence, the identification of protective mechanisms in response to ER-stress could lead to novel therapeutic targets and insight in the pathology of these diseases. Here, we report the identification of proteins involved in dysregulated pathways upon thapsigargin treatment of MIN6 cells. Utilizing quantitative proteomics we identified upregulation of proteins involved in protein folding, unfolded protein response, redox homeostasis, proteasome processes associated with endoplasmic reticulum and downregulation of TCA cycle, cellular respiration, lipid metabolism and ribosome assembly processes associated to mitochondria and eukaryotic initiation translation factor components. Subsequently, pro-inflammatory cytokine treatment was performed to mimic pathological changes observed in beta-cells during diabetes. Cytokines induced ER stress and impaired mitochondrial function in beta-cells corroborating the results obtained with the proteomic approach. HSPB1 levels are increased by prolactin on pancreatic beta-cells and this protein is a key factor for cytoprotection although its role has not been fully elucidated. Here we show that while up-regulation of HSPB1 was able to restore the mitochondrial dysfunction induced by beta-cells' exposure to inflammatory cytokines, silencing of this chaperone abrogated the beneficial effects promoted by PRL. Taken together, our results outline the importance of HSPB1 to mitigate beta-cell dysfunction. Further studies are needed to elucidate its role in diabetes.
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Affiliation(s)
- Simon Ngao Mule
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Vinícius De Morais Gomes
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Rosangela A M Wailemann
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Janaina Macedo-da-Silva
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | - Letícia Labriola
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil.
| | - Giuseppe Palmisano
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil.
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Sun S, Zhao Q, Xue C, Zheng C. Comparative Phosphoproteomics Reveals a Role for AMPK in Hypoxia Signaling in Testes of Oriental River Prawn ( Macrobrachium nipponense). J Proteome Res 2021; 20:2923-2934. [PMID: 33851848 DOI: 10.1021/acs.jproteome.1c00144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hypoxia is one of the major stresses in aquaculture animals. Recently, we reported that hypoxia disrupts the endocrine system and inhibits testicular function of oriental river prawns (Macrobrachium nipponense), but the molecular mechanism of testes responded to hypoxia remains largely unknown. In the present study, we aimed to integrate whole phosphoproteomic profiles of hypoxia-treated testes of the oriental river prawn (Macrobrachium nipponense). We successfully isolated sperm cells and evaluated the mitochondrial morphology and function using laser confocal microscopy, flow cytometry, and biochemical analyses. Quantitative proteomics identified 117 differentially abundant phosphorylated proteins, and these proteins are mainly involved in the pathways related to cellular processes, including autophagy, apoptosis, and the FoxO signaling pathway. Protein-protein interaction analysis clustered these phosphoproteins into three groups, many of which have been suggested to impact carbohydrate metabolism, autophagy, and signal regulation in testes. Western blotting confirmed that phosphorylated proteins including AMPK, ULK1, and TP53 (of the AMPK pathway) may contribute to testicular dysfunction caused by hypoxia. Further, we investigated the potential roles of AMP-activated protein kinase (AMPK)'s in testes mitochondrial autophagy and apoptosis in M. nipponense as induced by hypoxia. Simultaneous knockdown of AMPKα in sperm cells led to a decrease in FOXO3a phosphorylation at Ser413, upregulation of caspase-3 and caspase-9 activities, and an increased apoptosis rate. These results improve our understanding of hypoxia-induced energy metabolism disorders in the testes of M. nipponense.
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Affiliation(s)
- Shengming Sun
- Key Laboratory of Freshwater Aquatic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Qianqian Zhao
- Key Laboratory of Freshwater Aquatic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Cheng Xue
- Key Laboratory of Freshwater Aquatic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Cheng Zheng
- Key Laboratory of Freshwater Aquatic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
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5
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The Role of Biomimetic Hypoxia on Cancer Cell Behaviour in 3D Models: A Systematic Review. Cancers (Basel) 2021; 13:cancers13061334. [PMID: 33809554 PMCID: PMC7999912 DOI: 10.3390/cancers13061334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/05/2021] [Accepted: 03/13/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Cancer remains one of the leading causes of death worldwide. The advancements in 3D tumour models provide in vitro test-beds to study cancer growth, metastasis and response to therapy. We conducted this systematic review on existing experimental studies in order to identify and summarize key biomimetic tumour microenvironmental features which affect aspects of cancer biology. The review noted the significance of in vitro hypoxia and 3D tumour models on epithelial to mesenchymal transition, drug resistance, invasion and migration of cancer cells. We highlight the importance of various experimental parameters used in these studies and their subsequent effects on cancer cell behaviour. Abstract The development of biomimetic, human tissue models is recognized as being an important step for transitioning in vitro research findings to the native in vivo response. Oftentimes, 2D models lack the necessary complexity to truly recapitulate cellular responses. The introduction of physiological features into 3D models informs us of how each component feature alters specific cellular response. We conducted a systematic review of research papers where the focus was the introduction of key biomimetic features into in vitro models of cancer, including 3D culture and hypoxia. We analysed outcomes from these and compiled our findings into distinct groupings to ascertain which biomimetic parameters correlated with specific responses. We found a number of biomimetic features which primed cancer cells to respond in a manner which matched in vivo response.
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Stanković T, Ranđelović T, Dragoj M, Stojković Burić S, Fernández L, Ochoa I, Pérez-García VM, Pešić M. In vitro biomimetic models for glioblastoma-a promising tool for drug response studies. Drug Resist Updat 2021; 55:100753. [PMID: 33667959 DOI: 10.1016/j.drup.2021.100753] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
The poor response of glioblastoma to current treatment protocols is a consequence of its intrinsic drug resistance. Resistance to chemotherapy is primarily associated with considerable cellular heterogeneity, and plasticity of glioblastoma cells, alterations in gene expression, presence of specific tumor microenvironment conditions and blood-brain barrier. In an attempt to successfully overcome chemoresistance and better understand the biological behavior of glioblastoma, numerous tri-dimensional (3D) biomimetic models were developed in the past decade. These novel advanced models are able to better recapitulate the spatial organization of glioblastoma in a real time, therefore providing more realistic and reliable evidence to the response of glioblastoma to therapy. Moreover, these models enable the fine-tuning of different tumor microenvironment conditions and facilitate studies on the effects of the tumor microenvironment on glioblastoma chemoresistance. This review outlines current knowledge on the essence of glioblastoma chemoresistance and describes the progress achieved by 3D biomimetic models. Moreover, comprehensive literature assessment regarding the influence of 3D culturing and microenvironment mimicking on glioblastoma gene expression and biological behavior is also provided. The contribution of the blood-brain barrier as well as the blood-tumor barrier to glioblastoma chemoresistance is also reviewed from the perspective of 3D biomimetic models. Finally, the role of mathematical models in predicting 3D glioblastoma behavior and drug response is elaborated. In the future, technological innovations along with mathematical simulations should create reliable 3D biomimetic systems for glioblastoma research that should facilitate the identification and possibly application in preclinical drug testing and precision medicine.
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Affiliation(s)
- Tijana Stanković
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060, Belgrade, Serbia
| | - Teodora Ranđelović
- Tissue Microenvironment Lab (TME), Aragón Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Aragon 50018, Spain; Institute for Health Research Aragon (IIS Aragón), Instituto de Salud Carlos III, Zaragoza, Spain
| | - Miodrag Dragoj
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060, Belgrade, Serbia
| | - Sonja Stojković Burić
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060, Belgrade, Serbia
| | - Luis Fernández
- Tissue Microenvironment Lab (TME), Aragón Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Aragon 50018, Spain; Centro Investigación Biomédica en Red. Bioingenieria, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Aragon 50018, Spain; Institute for Health Research Aragon (IIS Aragón), Instituto de Salud Carlos III, Zaragoza, Spain
| | - Ignacio Ochoa
- Tissue Microenvironment Lab (TME), Aragón Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Aragon 50018, Spain; Centro Investigación Biomédica en Red. Bioingenieria, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Aragon 50018, Spain; Institute for Health Research Aragon (IIS Aragón), Instituto de Salud Carlos III, Zaragoza, Spain
| | - Victor M Pérez-García
- Departamento de Matemáticas, E.T.S.I. Industriales and Instituto de Matemática Aplicada a la Ciencia y la Ingeniería (IMACI), Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
| | - Milica Pešić
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060, Belgrade, Serbia.
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7
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Pieters VM, Co IL, Wu NC, McGuigan AP. Applications of Omics Technologies for Three-Dimensional In Vitro Disease Models. Tissue Eng Part C Methods 2021; 27:183-199. [PMID: 33406987 DOI: 10.1089/ten.tec.2020.0300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, multiomics, and integrated modalities, have greatly contributed to our understanding of various diseases by enabling researchers to probe the molecular wiring of cellular systems in a high-throughput and precise manner. With the development of tissue-engineered three-dimensional (3D) in vitro disease models, such as organoids and spheroids, there is potential of integrating omics technologies with 3D disease models to elucidate the complex links between genotype and phenotype. These 3D disease models have been used to model cancer, infectious disease, toxicity, neurological disorders, and others. In this review, we provide an overview of omics technologies, highlight current and emerging studies, discuss the associated experimental design considerations, barriers and challenges of omics technologies, and provide an outlook on the future applications of omics technologies with 3D models. Overall, this review aims to provide a valuable resource for tissue engineers seeking to leverage omics technologies for diving deeper into biological discovery. Impact statement With the emergence of three-dimensional (3D) in vitro disease models, tissue engineers are increasingly interested to investigate these systems to address biological questions related to disease mechanism, drug target discovery, therapy resistance, and more. Omics technologies are a powerful and high-throughput approach, but their application for 3D disease models is not maximally utilized. This review illustrates the achievements and potential of using omics technologies to leverage the full potential of 3D in vitro disease models. This will improve the quality of such models, advance our understanding of disease, and contribute to therapy development.
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Affiliation(s)
- Vera M Pieters
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Ileana L Co
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Nila C Wu
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Alison P McGuigan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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8
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Multifunctional neuron-specific enolase: its role in lung diseases. Biosci Rep 2020; 39:220911. [PMID: 31642468 PMCID: PMC6859115 DOI: 10.1042/bsr20192732] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 12/13/2022] Open
Abstract
Neuron-specific enolase (NSE), also known as gamma (γ) enolase or enolase-2 (Eno2), is a form of glycolytic enolase isozyme and is considered a multifunctional protein. NSE is mainly expressed in the cytoplasm of neurons and neuroendocrine cells, especially in those of the amine precursor uptake and decarboxylation (APUD) lineage such as pituitary, thyroid, pancreas, intestine and lung. In addition to its well-established glycolysis function in the cytoplasm, changes in cell localization and differential expression of NSE are also associated with several pathologies such as infection, inflammation, autoimmune diseases and cancer. This article mainly discusses the role and diagnostic potential of NSE in some lung diseases.
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Analysis of gene expression profiles of lung cancer subtypes with machine learning algorithms. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165822. [PMID: 32360590 DOI: 10.1016/j.bbadis.2020.165822] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022]
Abstract
Lung cancer is one of the most common cancer types worldwide and causes more than one million deaths annually. Lung adenocarcinoma (AC) and lung squamous cell cancer (SCC) are two major lung cancer subtypes and have different characteristics in several aspects. Identifying their differentially expressed genes and different gene expression patterns can deepen our understanding of these two subtypes at the transcriptomic level. In this work, we used several machine learning algorithms to investigate the gene expression profiles of lung AC and lung SCC samples retrieved from Gene Expression Omnibus. First, the profiles were analyzed by using a powerful feature selection method, namely, Monte Carlo feature selection. A feature list, ranking all features according to their importance, and some informative features were obtained. Then, the feature list was used in the incremental feature selection method to extract optimal features, which can allow the support vector machine (SVM) to yield the best performance for classifying lung AC and lung SCC samples. Some top genes (CSTA, TP63, SERPINB13, CLCA2, BICD2, PERP, FAT2, BNC1, ATP11B, FAM83B, KRT5, PARD6G, PKP1) were extensively analyzed to prove that they can be differentially expressed genes between lung AC and lung SCC. Meanwhile, a rule learning procedure was applied on informative features to construct the classification rules. These rules provide a clear procedure of classification and show some different gene expression patterns between lung AC and lung SCC.
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10
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Yastreb TO, Kolupaev YE, Havva EN, Horielova EI, Dmitriev AP. Involvement of the JIN1/MYC2 Transcription Factor in Inducing Salt Resistance in Arabidopsis Plants by Exogenous Hydrogen Sulfide. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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de Gooijer MC, Guillén Navarro M, Bernards R, Wurdinger T, van Tellingen O. An Experimenter's Guide to Glioblastoma Invasion Pathways. Trends Mol Med 2018; 24:763-780. [PMID: 30072121 DOI: 10.1016/j.molmed.2018.07.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022]
Abstract
Glioblastoma is a highly aggressive brain tumor that is characterized by its unparalleled invasiveness. Invasive glioblastoma cells not only escape surgery and focal therapies but also are more resistant to current radio- and chemo-therapeutic approaches. Thus, any curative therapy for this deadly disease likely should include treatment strategies that interfere with glioblastoma invasiveness. Understanding glioblastoma invasion mechanisms is therefore critical. We discuss the strengths and weaknesses of various glioblastoma invasion models and conclude that robust experimental evidence has been obtained for a pro-invasive role of Ephrin receptors, Rho GTPases, and casein kinase 2 (CK2). Extensive interplay occurs between these proteins, suggesting the existence of a glioblastoma invasion signaling network that comprises several targets for therapy.
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Affiliation(s)
- Mark C de Gooijer
- Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; These authors contributed equally to this work
| | - Miriam Guillén Navarro
- Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; These authors contributed equally to this work
| | - Rene Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, VU University Medical Center, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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Gebhard C, Miller I, Hummel K, Neschi née Ondrovics M, Schlosser S, Walter I. Comparative proteome analysis of monolayer and spheroid culture of canine osteosarcoma cells. J Proteomics 2018; 177:124-136. [DOI: 10.1016/j.jprot.2018.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/20/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
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13
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Narayan RS, Gasol A, Slangen PLG, Cornelissen FMG, Lagerweij T, Veldman HYYE, Dik R, van den Berg J, Slotman BJ, Würdinger T, Haas-Kogan DA, Stalpers LJA, Baumert BG, Westerman BA, Theys J, Sminia P. Identification of MEK162 as a Radiosensitizer for the Treatment of Glioblastoma. Mol Cancer Ther 2017; 17:347-354. [PMID: 28958992 DOI: 10.1158/1535-7163.mct-17-0480] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/11/2017] [Accepted: 09/08/2017] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is a highly aggressive and lethal brain cancer type. PI3K and MAPK inhibitors have been studied preclinically in GBM as monotherapy, but not in combination with radiotherapy, which is a key component of the current standard treatment of GBM. In our study, GBM cell lines and patient representative primary cultures were grown as multicellular spheroids. Spheroids were treated with a panel of small-molecule drugs including MK2206, RAD001, BEZ235, MLN0128, and MEK162, alone and in combination with irradiation. Following treatment, spheroid growth parameters (growth rate, volume reduction, and time to regrow), cell-cycle distribution and expression of key target proteins were evaluated. In vivo, the effect of irradiation (3 × 2 Gy) without or with MEK162 (50 mg/kg) was studied in orthotopic GBM8 brain tumor xenografts with endpoints tumor growth and animal survival. The MAPK-targeting agent MEK162 was found to enhance the effect of irradiation as demonstrated by growth inhibition of spheroids. MEK162 downregulated and dephosphorylated the cell-cycle checkpoint proteins CDK1/CDK2/WEE1 and DNA damage response proteins p-ATM/p-CHK2. When combined with radiation, this led to a prolonged DNA damage signal. In vivo data on tumor-bearing animals demonstrated a significantly reduced growth rate, increased growth delay, and prolonged survival time. In addition, RNA expression of responsive cell cultures correlated to mesenchymal stratification of patient expression data. In conclusion, the MAPK inhibitor MEK162 was identified as a radiosensitizer in GBM spheroids in vitro and in orthotopic GBM xenografts in vivo The data are supportive for implementation of this targeted agent in an early-phase clinical study in GBM patients. Mol Cancer Ther; 17(2); 347-54. ©2017 AACRSee all articles in this MCT Focus section, "Developmental Therapeutics in Radiation Oncology."
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Affiliation(s)
- Ravi S Narayan
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ana Gasol
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Paul L G Slangen
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Neuro-oncology Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | - Fleur M G Cornelissen
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Neuro-oncology Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | - Tonny Lagerweij
- Department of Neurosurgery, Neuro-oncology Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | - Hou Y Y E Veldman
- Department of Neurosurgery, Neuro-oncology Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | - Rogier Dik
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Jaap van den Berg
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ben J Slotman
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Tom Würdinger
- Department of Neurosurgery, Neuro-oncology Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | - Daphne A Haas-Kogan
- Department or Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lukas J A Stalpers
- Department of Radiation Oncology, Academic Medical Center, Amsterdam, the Netherlands
| | - Brigitta G Baumert
- Department of Radiation Oncology (MAASTRO), Maastricht University Medical Center (MUMC) and GROW (School for Oncology), Maastricht, the Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Neuro-oncology Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | - Jan Theys
- Department of Radiation Oncology (MAASTRO), Maastricht University Medical Center (MUMC) and GROW (School for Oncology), Maastricht, the Netherlands
| | - Peter Sminia
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands.
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14
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Yue X, Lukowski JK, Weaver EM, Skube SB, Hummon AB. Quantitative Proteomic and Phosphoproteomic Comparison of 2D and 3D Colon Cancer Cell Culture Models. J Proteome Res 2016; 15:4265-4276. [PMID: 27696853 DOI: 10.1021/acs.jproteome.6b00342] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined, and notable differences in both the proteome and the phosphoproteome were determined by nanoliquid chromatography tandem mass spectrometry (LC-MS/MS) to assess how growth configuration affects molecular expression. A total of 5867 protein groups, including 2523 phosphoprotein groups and 8733 phosphopeptides were identified in the samples. The Gene Ontology analysis revealed enriched GO terms in the 3D samples for RNA binding, nucleic acid binding, enzyme binding, cytoskeletal protein binding, and histone binding for their molecular functions (MF) and in the process of cell cycle, cytoskeleton organization, and DNA metabolic process for the biological process (BP). The KEGG pathway analysis indicated that 3D cultures are enriched for oxidative phosphorylation pathways, metabolic pathways, peroxisome pathways, and biosynthesis of amino acids. In contrast, analysis of the phosphoproteomes indicated that 3D cultures have decreased phosphorylation correlating with slower growth rates and lower cell-to-extracellular matrix interactions. In sum, these results provide quantitative assessments of the effects on the proteome and phosphoproteome of culturing cells in 2D versus 3D cell culture configurations.
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Affiliation(s)
- Xiaoshan Yue
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Jessica K Lukowski
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Eric M Weaver
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Susan B Skube
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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15
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Biau J, Chautard E, Court F, Pereira B, Verrelle P, Devun F, De Koning L, Dutreix M. Global Conservation of Protein Status between Cell Lines and Xenografts. Transl Oncol 2016; 9:313-21. [PMID: 27567954 PMCID: PMC5006813 DOI: 10.1016/j.tranon.2016.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 01/23/2023] Open
Abstract
Common preclinical models for testing anticancer treatment include cultured human tumor cell lines in monolayer, and xenografts derived from these cell lines in immunodeficient mice. Our goal was to determine how similar the xenografts are compared with their original cell line and to determine whether it is possible to predict the stability of a xenograft model beforehand. We studied a selection of 89 protein markers of interest in 14 human cell cultures and respective subcutaneous xenografts using the reverse-phase protein array technology. We specifically focused on proteins and posttranslational modifications involved in DNA repair, PI3K pathway, apoptosis, tyrosine kinase signaling, stress, cell cycle, MAPK/ERK signaling, SAPK/JNK signaling, NFκB signaling, and adhesion/cytoskeleton. Using hierarchical clustering, most cell culture-xenograft pairs cluster together, suggesting a global conservation of protein signature. Particularly, Akt, NFkB, EGFR, and Vimentin showed very stable protein expression and phosphorylation levels highlighting that 4 of 10 pathways were highly correlated whatever the model. Other proteins were heterogeneously conserved depending on the cell line. Finally, cell line models with low Akt pathway activation and low levels of Vimentin gave rise to more reliable xenograft models. These results may be useful for the extrapolation of cell culture experiments to in vivo models in novel targeted drug discovery.
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Affiliation(s)
- Julian Biau
- Institut Curie, Centre de Recherche, 91400 Orsay/75248 Paris, France; UMR3347, Centre National de la Recherche Scientifique, 91400 Orsay, France; U1021, Institut National de la Santé et de la Recherche Médicale, 91400 Orsay, France; Université Paris Sud, 91400 Orsay, France; Clermont Auvergne University, EA7283 CREaT, 63011 Clermont-Ferrand, France; Radiotherapy Department, Centre Jean Perrin, 63011 Clermont-Ferrand, France.
| | - Emmanuel Chautard
- Clermont Auvergne University, EA7283 CREaT, 63011 Clermont-Ferrand, France; Radiotherapy Department, Centre Jean Perrin, 63011 Clermont-Ferrand, France
| | - Frank Court
- U1103, Institut National de la Santé et de la Recherche Médicale, 63001 Clermont-Ferrand, France; UMR 6293, Centre National de la Recherche Scientifique, 63001 Clermont-Ferrand, France; Clermont Auvergne University, GReD Laboratory, Clermont-Ferrand, 63000, France
| | - Bruno Pereira
- Biostatistics Department, DRCI, Clermont-Ferrand Hospital, Clermont-Ferrand, 63003, France
| | - Pierre Verrelle
- Institut Curie, Centre de Recherche, 91400 Orsay/75248 Paris, France; UMR3347, Centre National de la Recherche Scientifique, 91400 Orsay, France; U1021, Institut National de la Santé et de la Recherche Médicale, 91400 Orsay, France; Clermont Auvergne University, EA7283 CREaT, 63011 Clermont-Ferrand, France; Radiotherapy Department, Institut Curie, 75005 Paris, France
| | - Flavien Devun
- Institut Curie, Centre de Recherche, 91400 Orsay/75248 Paris, France; DNA Therapeutics, Evry, Paris, France
| | - Leanne De Koning
- Institut Curie, Department of Translational Research, RPPA platform,75248 Paris cedex05, France
| | - Marie Dutreix
- Institut Curie, Centre de Recherche, 91400 Orsay/75248 Paris, France; UMR3347, Centre National de la Recherche Scientifique, 91400 Orsay, France; U1021, Institut National de la Santé et de la Recherche Médicale, 91400 Orsay, France; Université Paris Sud, 91400 Orsay, France
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16
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Falkenberg N, Höfig I, Rosemann M, Szumielewski J, Richter S, Schorpp K, Hadian K, Aubele M, Atkinson MJ, Anastasov N. Three-dimensional microtissues essentially contribute to preclinical validations of therapeutic targets in breast cancer. Cancer Med 2016; 5:703-10. [PMID: 26763588 PMCID: PMC4831289 DOI: 10.1002/cam4.630] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/23/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
A 3D microtissues using T47D and JIMT‐1 cells were generated to analyze tissue‐like response of breast cancer cells after combined human epidermal growth factor receptor 2 (HER2)‐targeted treatment and radiation. Following lentiviral knockdown of HER2, we compared growth rate alterations using 2D monolayers, 3D microtissues, and mouse xenografts. Additionally, to model combined therapeutic strategies, we treated HER2‐depleted T47D cells and 3D microtissues using trastuzumab (anti‐HER2 antibody) in combination with irradiation. Comparison of HER2 knockdown with corresponding controls revealed growth impairment due to HER2 knockdown in T47D 2D monolayers, 3D microtissues, and xenografts (after 2, 12, and ≥40 days, respectively). In contrast, HER2 knockdown was less effective in inhibiting growth of trastuzumab‐resistant JIMT‐1 cells in vitro and in vivo. Combined administration of trastuzumab and radiation treatment was also analyzed using T47D 3D microtissues. Administration of both, radiation (5 Gy) and trastuzumab, significantly enhanced the growth inhibiting effect in 3D microtissues. To improve the predictive power of potential drugs—as single agents or in combination—here, we show that regarding tumor growth analyses, 3D microtissues are highly comparable to outcomes derived from xenografts. Considering increased limitations for animal experiments on the one hand and strong need of novel drugs on the other hand, it is indispensable to include highly reproducible 3D microtissue platform in preclinical analyses to validate more accurately the capacity of future drug‐combined radiotherapy.
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Affiliation(s)
- Natalie Falkenberg
- Institute of Pathology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Ines Höfig
- Institute of Radiation Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Michael Rosemann
- Institute of Radiation Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Justine Szumielewski
- Institute of Pathology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Sabine Richter
- Institute of Radiation Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Kenji Schorpp
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Michaela Aubele
- Institute of Pathology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Michael J Atkinson
- Institute of Radiation Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany.,Radiation Biology, Technical University of Munich, Ismaninger Strasse 22, 81675, Munich, Germany
| | - Nataša Anastasov
- Institute of Radiation Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
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17
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Eke I, Hehlgans S, Zong Y, Cordes N. Comprehensive analysis of signal transduction in three-dimensional ECM-based tumor cell cultures. J Biol Methods 2015; 2. [PMID: 26618185 DOI: 10.14440/jbm.2015.96] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Analysis of signal transduction and protein phosphorylation is fundamental to understanding physiological and pathological cell behavior and identifying novel therapeutic targets. Despite the fact that the use of physiological three-dimensional cell culture assays is increasing, 3D proteomics and phosphoproteomics remain challenging due to difficulties with easy, robust and reproducible sample preparation. Here, we present an easy-to-perform, reliable and time-efficient method for the production of 3D cell lysates that does not compromise cell adhesion before cell lysis. The samples can be used for western blotting as well as phosphoproteome array technology. This technique will be of interest for researchers working in all fields of biology and drug development.
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Affiliation(s)
- Iris Eke
- OncoRay - National Center for Radiation Research in Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany ; Radiation Oncology Branch, Center for Cancer Research, National Institutes of Health/National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephanie Hehlgans
- OncoRay - National Center for Radiation Research in Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany ; Department of Radiotherapy and Oncology, University of Frankfurt, 60590 Frankfurt am Main, Germany
| | - Yaping Zong
- Full Moon BioSystems Inc., Sunnyvale, CA 94085, USA
| | - Nils Cordes
- OncoRay - National Center for Radiation Research in Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany ; Department of Radiation Oncology, University Hospital and Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany ; Helmholtz Center Dresden-Rossendorf, Institute of Radiooncology, 01328 Dresden, Germany ; German Cancer Consortium (DKTK), 01307 Dresden, Germany ; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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18
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Vizin T, Kos J. Gamma-enolase: a well-known tumour marker, with a less-known role in cancer. Radiol Oncol 2015; 49:217-26. [PMID: 26401126 PMCID: PMC4577217 DOI: 10.1515/raon-2015-0035] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/13/2015] [Indexed: 12/16/2022] Open
Abstract
Background Gamma-enolase, known also as neuron-specific enolase (NSE), is an enzyme of the glycolytic pathway, which is expressed predominantly in neurons and cells of the neuroendocrine system. As a tumour marker it is used in diagnosis and prognosis of cancer; however, the mechanisms enrolling it in malignant progression remain elusive. As a cytoplasmic enzyme gamma-enolase is involved in increased aerobic glycolysis, the main source of energy in cancer cells, supporting cell proliferation. However, different cellular localisation at pathophysiological conditions, proposes other cellular engagements. Conclusions The C-terminal part of the molecule, which is not related to glycolytic pathway, was shown to promote survival of neuronal cells by regulating neuronal growth factor receptor dependent signalling pathways, resulting also in extensive actin cytoskeleton remodelling. This additional function could be important also in cancer cells either to protect cells from stressful conditions and therapeutic agents or to promote tumour cell migration and invasion. Gamma-enolase might therefore have a multifunctional role in cancer progression: it supports increased tumour cell metabolic demands, protects tumour cells from stressful conditions and promotes their invasion and migration.
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Affiliation(s)
- Tjasa Vizin
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Janko Kos
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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19
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DelNero P, Lane M, Verbridge SS, Kwee B, Kermani P, Hempstead B, Stroock A, Fischbach C. 3D culture broadly regulates tumor cell hypoxia response and angiogenesis via pro-inflammatory pathways. Biomaterials 2015; 55:110-8. [PMID: 25934456 DOI: 10.1016/j.biomaterials.2015.03.035] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 03/16/2015] [Accepted: 03/20/2015] [Indexed: 01/08/2023]
Abstract
Oxygen status and tissue dimensionality are critical determinants of tumor angiogenesis, a hallmark of cancer and an enduring target for therapeutic intervention. However, it is unclear how these microenvironmental conditions interact to promote neovascularization, due in part to a lack of comprehensive, unbiased data sets describing tumor cell gene expression as a function of oxygen levels within three-dimensional (3D) culture. Here, we utilized alginate-based, oxygen-controlled 3D tumor models to study the interdependence of culture context and the hypoxia response. Microarray gene expression analysis of tumor cells cultured in 2D versus 3D under ambient or hypoxic conditions revealed striking interdependence between culture dimensionality and hypoxia response, which was mediated in part by pro-inflammatory signaling pathways. In particular, interleukin-8 (IL-8) emerged as a major player in the microenvironmental regulation of the hypoxia program. Notably, this interaction between dimensionality and oxygen status via IL-8 increased angiogenic sprouting in a 3D endothelial invasion assay. Taken together, our data suggest that pro-inflammatory pathways are critical regulators of tumor hypoxia response within 3D environments that ultimately impact tumor angiogenesis, potentially providing important therapeutic targets. Furthermore, these results highlight the importance of pathologically relevant tissue culture models to study the complex physical and chemical processes by which the cancer microenvironment mediates new vessel formation.
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Affiliation(s)
- Peter DelNero
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Maureen Lane
- Department of Medicine, Weill Cornell Medical School, New York, NY 10065, USA
| | - Scott S Verbridge
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA 24061, USA
| | - Brian Kwee
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Pouneh Kermani
- Department of Medicine, Weill Cornell Medical School, New York, NY 10065, USA
| | - Barbara Hempstead
- Department of Medicine, Weill Cornell Medical School, New York, NY 10065, USA
| | - Abraham Stroock
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - Claudia Fischbach
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA; Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA.
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20
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Friedman GK, Nan L, Haas MC, Kelly VM, Moore BP, Langford CP, Xu H, Han X, Beierle EA, Markert JM, Cassady KA, Gillespie GY. γ₁34.5-deleted HSV-1-expressing human cytomegalovirus IRS1 gene kills human glioblastoma cells as efficiently as wild-type HSV-1 in normoxia or hypoxia. Gene Ther 2015; 22:348-55. [PMID: 25427614 PMCID: PMC4383690 DOI: 10.1038/gt.2014.107] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/22/2014] [Accepted: 10/30/2014] [Indexed: 11/30/2022]
Abstract
Pathophysiological hypoxia, which fosters the glioma stem-like cell (GSC) phenotype, is present in high-grade gliomas and has been linked to tumor development, invasiveness and resistance to chemotherapy and radiation. Oncolytic virotherapy with engineered herpes simplex virus-1 (HSV-1) is a promising therapy for glioblastoma; however, the efficacy of γ(1)34.5-deleted HSVs, which have been used in clinical trials, was diminished in hypoxia. We investigated the ability of a chimeric human cytolomegalovirus (HCMV)/HSV-1 virus, which expresses the human CMV protein kinase R evasion gene IRS1 and is in preparation for clinical trials, to infect and kill adult and pediatric patient-derived glioblastoma xenografts in hypoxia and normoxia. Infectivity, cytotoxicity and viral recovery were significantly greater with the chimeric virus compared with the γ(1)34.5-deleted virus, regardless of oxygen tension. The chimeric virus infected and killed CD133+ GSCs similarly to wild-type HSV-1. Increased activation of mitogen-activated protein kinase p38 and its substrate heat-shock protein 27 (Hsp27) was seen after viral infection in normoxia compared with hypoxia. Hsp27 knockdown or p38 inhibition reduced virus recovery, indicating that the p38 pathway has a role in the reduced efficacy of the γ(1)34.5-deleted virus in hypoxia. Taken together, these findings demonstrate that chimeric HCMV/HSV-1 efficiently targets both CD133+ GSCs and glioma cells in hypoxia.
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Affiliation(s)
- Gregory K. Friedman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Li Nan
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Marilyn C. Haas
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Virginia M. Kelly
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Blake P. Moore
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Catherine P. Langford
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Hui Xu
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Xiaosi Han
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Elizabeth A. Beierle
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - James M. Markert
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Kevin A. Cassady
- Division of Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - G. Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA 35233
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21
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Tang Z, Araysi LM, Fathallah-Shaykh HM. c-Src and neural Wiskott-Aldrich syndrome protein (N-WASP) promote low oxygen-induced accelerated brain invasion by gliomas. PLoS One 2013; 8:e75436. [PMID: 24069415 PMCID: PMC3777891 DOI: 10.1371/journal.pone.0075436] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/16/2013] [Indexed: 11/22/2022] Open
Abstract
Malignant gliomas remain associated with poor prognosis and high morbidity because of their ability to invade the brain; furthermore, human gliomas exhibit a phenotype of accelerated brain invasion in response to anti-angiogenic drugs. Here, we study 8 human glioblastoma cell lines; U251, U87, D54 and LN229 show accelerated motility in low ambient oxygen. Src inhibition by Dasatinib abrogates this phenotype. Molecular discovery and validation studies evaluate 46 molecules related to motility or the src pathway in U251 cells. Demanding that the molecular changes induced by low ambient oxygen are reversed by Dasatinib in U251 cells, identifies neural Wiskott-Aldrich syndrome protein (NWASP), Focal adhesion Kinase (FAK), -Catenin, and Cofilin. However, only Src-mediated NWASP phosphorylation distinguishes the four cell lines that exhibit enhanced motility in low ambient oxygen. Downregulating c-Src or NWASP by RNA interference abrogates the low-oxygen-induced enhancement in motility by in vitro assays and in organotypic brain slice cultures. The findings support the idea that c-Src and NWASP play key roles in mediating the molecular pathogenesis of low oxygen-induced accelerated brain invasion by gliomas.
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Affiliation(s)
- Zhuo Tang
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Lita M. Araysi
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Hassan M Fathallah-Shaykh
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Mathematics, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Mechanical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The UAB Comprehensive Neuroscience Center, Birmingham, Alabama, United States of America
- The UAB Comprehensive Cancer Center, Birmingham, Alabama, United States of America
- * E-mail:
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