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Niu X, Sun J, Meng L, Fang T, Zhang T, Jiang J, Li H. A Five-lncRNAs Signature-Derived Risk Score Based on TCGA and CGGA for Glioblastoma: Potential Prospects for Treatment Evaluation and Prognostic Prediction. Front Oncol 2020; 10:590352. [PMID: 33392085 PMCID: PMC7773845 DOI: 10.3389/fonc.2020.590352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Accumulating studies have confirmed the crucial role of long non-coding RNAs (ncRNAs) as favorable biomarkers for cancer diagnosis, therapy, and prognosis prediction. In our recent study, we established a robust model which is based on multi-gene signature to predict the therapeutic efficacy and prognosis in glioblastoma (GBM), based on Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases. lncRNA-seq data of GBM from TCGA and CGGA datasets were used to identify differentially expressed genes (DEGs) compared to normal brain tissues. The DEGs were then used for survival analysis by univariate and multivariate COX regression. Then we established a risk score model, depending on the gene signature of multiple survival-associated DEGs. Subsequently, Kaplan-Meier analysis was used for estimating the prognostic and predictive role of the model. Gene set enrichment analysis (GSEA) was applied to investigate the potential pathways associated to high-risk score by the R package “cluster profile” and Wiki-pathway. And five survival associated lncRNAs of GBM were identified: LNC01545, WDR11-AS1, NDUFA6-DT, FRY-AS1, TBX5-AS1. Then the risk score model was established and shows a desirable function for predicting overall survival (OS) in the GBM patients, which means the high-risk score significantly correlated with lower OS both in TCGA and CGGA cohort. GSEA showed that the high-risk score was enriched with PI3K-Akt, VEGFA-VEGFR2, TGF-beta, Notch, T-Cell pathways. Collectively, the five-lncRNAs signature-derived risk score presented satisfactory efficacies in predicting the therapeutic efficacy and prognosis in GBM and will be significant for guiding therapeutic strategies and research direction for GBM.
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Affiliation(s)
- Xuegang Niu
- Department of Neurosurgery, Tianjin 4th Central Hospital, Tianjin, China
| | - Jiangnan Sun
- Department of Psychiatry, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, China
| | - Lingyin Meng
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Tao Fang
- Central Laboratory, Tianjin 4th Central Hospital, Tianjin, China
| | - Tongshuo Zhang
- Department of Laboratory, Jiangsu Provincial Corps Hospital of Chinese People's Armed Police Force, Yangzhou, China
| | - Jipeng Jiang
- Postgraduate School, Medical School of Chinese PLA, Beijing, China.,Department of Thoracic Surgery, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Huanming Li
- Central Laboratory, Tianjin 4th Central Hospital, Tianjin, China
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Sheybani ND, Batts AJ, Mathew AS, Thim EA, Price RJ. Focused Ultrasound Hyperthermia Augments Release of Glioma-derived Extracellular Vesicles with Differential Immunomodulatory Capacity. Theranostics 2020; 10:7436-7447. [PMID: 32642004 PMCID: PMC7330848 DOI: 10.7150/thno.46534] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Increasing evidence points to the critical role of extracellular vesicles (EVs) as molecular parcels that carry a diverse array of bioactive payloads for coordination of complex intracellular signaling. Focused ultrasound (FUS) hyperthermia is a technique for non-invasive, non-ionizing sublethal heating of cells in a near-instantaneous manner; while it has been shown to improve drug delivery and immunological recognition of tumors, its impact on EVs has not been explored to date. The goal of this study was to determine whether FUS impacts the release, proteomic profile, and immune-activating properties of tumor-derived EVs. Methods: Monolayered murine glioma cells were seeded within acoustically transparent cell culture chambers, and FUS hyperthermia was applied to achieve complete coverage of the chamber. Glioma-derived EVs (GEVs) were isolated for characterization by Nanoparticle Tracking Analysis, cryo-electron microscopy and mass spectrometry. An in vitro experimental setup was designed to further dissect the impact of GEVs on innate inflammation; immortalized murine dendritic cells (DCs) were pulsed with GEVs (either naïve or FUS hyperthermia-exposed) and assayed for production of IL-12p70, an important regulator of DC maturation and T helper cell polarization toward the interferon-γ-producing type 1 phenotype. Results: We confirmed that FUS hyperthermia significantly augments GEV release (by ~46%) as well as shifts the proteomic profile of these GEVs. Such shifts included enrichment of common EV-associated markers, downregulation of markers associated with cancer progression and resistance and modulation of inflammation-associated markers. When DCs were pulsed with GEVs, we noted that naïve GEVs suppressed IL-12p70 production by DCs in a GEV dose-dependent manner. In contrast, GEVs from cells exposed to FUS hyperthermia promoted a significant upregulation in IL-12p70 production by DCs, consistent with a pro-inflammatory stimulus. Conclusion: FUS hyperthermia triggers release of proteomically distinct GEVs that are capable of facilitating an important component of innate immune activation, lending both to a potential mechanism by which FUS interfaces with the tumor-immune landscape and to a role for GEV-associated biomarkers in monitoring response to FUS.
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Affiliation(s)
- Natasha D. Sheybani
- Department of Biomedical Engineering; University of Virginia, Charlottesville, VA 22908
| | - Alec J. Batts
- Department of Biomedical Engineering; University of Virginia, Charlottesville, VA 22908
| | - Alexander S. Mathew
- Department of Biomedical Engineering; University of Virginia, Charlottesville, VA 22908
| | - E. Andrew Thim
- Department of Biomedical Engineering; University of Virginia, Charlottesville, VA 22908
| | - Richard J. Price
- Department of Biomedical Engineering; University of Virginia, Charlottesville, VA 22908
- Department of Radiology & Medical Imaging, University of Virginia, Charlottesville, VA 22908
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Park JE, Kim HS, Park SY, Jung SC, Kim JH, Heo HY. Identification of Early Response to Anti-Angiogenic Therapy in Recurrent Glioblastoma: Amide Proton Transfer–weighted and Perfusion-weighted MRI compared with Diffusion-weighted MRI. Radiology 2020; 295:397-406. [DOI: 10.1148/radiol.2020191376] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ji Eun Park
- From the Department of Radiology and Research Institute of Radiology (J.E.P., H.S.K., S.C.J.), Department of Clinical Epidemiology and Biostatistics (S.Y.P.), and Department of Neurosurgery (J.H.K.), University of Ulsan College of Medicine, Asan Medical Center, 43 Olympic-ro 88, Songpa-Gu, Seoul 05505, Korea; and Department of Radiology, Johns Hopkins University, Baltimore, Md (H.Y.H.)
| | - Ho Sung Kim
- From the Department of Radiology and Research Institute of Radiology (J.E.P., H.S.K., S.C.J.), Department of Clinical Epidemiology and Biostatistics (S.Y.P.), and Department of Neurosurgery (J.H.K.), University of Ulsan College of Medicine, Asan Medical Center, 43 Olympic-ro 88, Songpa-Gu, Seoul 05505, Korea; and Department of Radiology, Johns Hopkins University, Baltimore, Md (H.Y.H.)
| | - Seo Young Park
- From the Department of Radiology and Research Institute of Radiology (J.E.P., H.S.K., S.C.J.), Department of Clinical Epidemiology and Biostatistics (S.Y.P.), and Department of Neurosurgery (J.H.K.), University of Ulsan College of Medicine, Asan Medical Center, 43 Olympic-ro 88, Songpa-Gu, Seoul 05505, Korea; and Department of Radiology, Johns Hopkins University, Baltimore, Md (H.Y.H.)
| | - Seung Chai Jung
- From the Department of Radiology and Research Institute of Radiology (J.E.P., H.S.K., S.C.J.), Department of Clinical Epidemiology and Biostatistics (S.Y.P.), and Department of Neurosurgery (J.H.K.), University of Ulsan College of Medicine, Asan Medical Center, 43 Olympic-ro 88, Songpa-Gu, Seoul 05505, Korea; and Department of Radiology, Johns Hopkins University, Baltimore, Md (H.Y.H.)
| | - Jeong Hoon Kim
- From the Department of Radiology and Research Institute of Radiology (J.E.P., H.S.K., S.C.J.), Department of Clinical Epidemiology and Biostatistics (S.Y.P.), and Department of Neurosurgery (J.H.K.), University of Ulsan College of Medicine, Asan Medical Center, 43 Olympic-ro 88, Songpa-Gu, Seoul 05505, Korea; and Department of Radiology, Johns Hopkins University, Baltimore, Md (H.Y.H.)
| | - Hye-Young Heo
- From the Department of Radiology and Research Institute of Radiology (J.E.P., H.S.K., S.C.J.), Department of Clinical Epidemiology and Biostatistics (S.Y.P.), and Department of Neurosurgery (J.H.K.), University of Ulsan College of Medicine, Asan Medical Center, 43 Olympic-ro 88, Songpa-Gu, Seoul 05505, Korea; and Department of Radiology, Johns Hopkins University, Baltimore, Md (H.Y.H.)
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Okuchi S, Hammam A, Golay X, Kim M, Thust S. Endogenous Chemical Exchange Saturation Transfer MRI for the Diagnosis and Therapy Response Assessment of Brain Tumors: A Systematic Review. Radiol Imaging Cancer 2020; 2:e190036. [PMID: 33778693 PMCID: PMC7983695 DOI: 10.1148/rycan.2020190036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/13/2019] [Accepted: 10/21/2019] [Indexed: 01/09/2023]
Abstract
Purpose To generate a narrative synthesis of published data on the use of endogenous chemical exchange saturation transfer (CEST) MRI in brain tumors. Materials and Methods A systematic database search (PubMed, Ovid Embase, Cochrane Library) was used to collate eligible studies. Two researchers independently screened publications according to predefined exclusion and inclusion criteria, followed by comprehensive data extraction. All included studies were subjected to a bias risk assessment using the Quality Assessment of Diagnostic Accuracy Studies tool. Results The electronic database search identified 430 studies, of which 36 fulfilled the inclusion criteria. The final selection of included studies was categorized into five groups as follows: grading gliomas, 19 studies (area under the receiver operating characteristic curve [AUC], 0.500-1.000); predicting molecular subtypes of gliomas, five studies (AUC, 0.610-0.920); distinction of different brain tumor types, seven studies (AUC, 0.707-0.905); therapy response assessment, three studies (AUC not given); and differentiating recurrence from treatment-related changes, five studies (AUC, 0.880-0.980). A high bias risk was observed in a substantial proportion of studies. Conclusion Endogenous CEST MRI offers valuable, potentially unique information in brain tumors, but its diagnostic accuracy remains incompletely known. Further research is required to assess the method's role in support of molecular genetic diagnosis, to investigate its use in the posttreatment phase, and to compare techniques with a view to standardization.Keywords: Brain/Brain Stem, MR-Imaging, Neuro-OncologySupplemental material is available for this article.© RSNA, 2020.
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Affiliation(s)
- Sachi Okuchi
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Ahmed Hammam
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Xavier Golay
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Mina Kim
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Stefanie Thust
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
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Ma Y, Wang Q, Dong Q, Zhan L, Zhang J. How to differentiate pseudoprogression from true progression in cancer patients treated with immunotherapy. Am J Cancer Res 2019; 9:1546-1553. [PMID: 31497342 PMCID: PMC6726978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023] Open
Abstract
Immunotherapy has achieved unprecedented clinical efficacy in patients with various types of advanced tumors; however, some patients experience delayed tumor shrinkage following an increase in tumor burden after such a therapeutic method. This phenomenon is called pseudoprogression and can lead to premature cessation of efficacious immunotherapeutic agents. Consequently, we summarized the available data on methods to differentiate pseudoprogression from true progression in patients who have been treated with immunotherapy including biomarkers, medical imaging techniques and biopsy. We also introduce hyperprogression and special pseudoprogression for improved evaluation of immunotherapy.
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Affiliation(s)
- Yiming Ma
- Medical Oncology Department of Gastrointestinal Tumors, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute No. 44, Xiaohe Road, Dadong District, Shenyang 110042, Liaoning Province, China
| | - Qiwei Wang
- Medical Oncology Department of Gastrointestinal Tumors, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute No. 44, Xiaohe Road, Dadong District, Shenyang 110042, Liaoning Province, China
| | - Qian Dong
- Medical Oncology Department of Gastrointestinal Tumors, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute No. 44, Xiaohe Road, Dadong District, Shenyang 110042, Liaoning Province, China
| | - Lei Zhan
- Medical Oncology Department of Gastrointestinal Tumors, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute No. 44, Xiaohe Road, Dadong District, Shenyang 110042, Liaoning Province, China
| | - Jingdong Zhang
- Medical Oncology Department of Gastrointestinal Tumors, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute No. 44, Xiaohe Road, Dadong District, Shenyang 110042, Liaoning Province, China
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Cang J, Savier E, Barchini J, Liu X. Visual Function, Organization, and Development of the Mouse Superior Colliculus. Annu Rev Vis Sci 2018; 4:239-262. [PMID: 29852095 DOI: 10.1146/annurev-vision-091517-034142] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The superior colliculus (SC) is the most prominent visual center in mice. Studies over the past decade have greatly advanced our understanding of the function, organization, and development of the mouse SC, which has rapidly become a popular model in vision research. These studies have described the diverse and cell-type-specific visual response properties in the mouse SC, revealed their laminar and topographic organizations, and linked the mouse SC and downstream pathways with visually guided behaviors. Here, we summarize these findings, compare them with the rich literature of SC studies in other species, and highlight important gaps and exciting future directions. Given its clear importance in mouse vision and the available modern neuroscience tools, the mouse SC holds great promise for understanding the cellular, circuit, and developmental mechanisms that underlie visual processing, sensorimotor transformation, and, ultimately, behavior.
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Affiliation(s)
- Jianhua Cang
- Department of Biology and Department of Psychology, University of Virginia, Charlottesville, Virginia 22904, USA;
| | - Elise Savier
- Department of Biology and Department of Psychology, University of Virginia, Charlottesville, Virginia 22904, USA;
| | - Jad Barchini
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458, USA
| | - Xiaorong Liu
- Department of Biology and Department of Psychology, University of Virginia, Charlottesville, Virginia 22904, USA;
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Pseudomonas aeruginosa cells attached to a surface display a typical proteome early as 20 minutes of incubation. PLoS One 2017; 12:e0180341. [PMID: 28678862 PMCID: PMC5498041 DOI: 10.1371/journal.pone.0180341] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/14/2017] [Indexed: 12/21/2022] Open
Abstract
Biofilms are present in all environments and often result in negative effects due to properties of the biofilm lifestyle and especially antibiotics resistance. Biofilms are associated with chronic infections. Controlling bacterial attachment, the first step of biofilm formation, is crucial for fighting against biofilm and subsequently preventing the persistence of infection. Thus deciphering the underlying molecular mechanisms involved in attachment could allow discovering molecular targets from it would be possible to develop inhibitors against bacterial colonization and potentiate antibiotherapy. To identify the key components and pathways that aid the opportunistic pathogen Pseudomonas aeruginosa in attachment we performed for the first time a proteomic analysis as early as after 20 minutes of incubation using glass wool fibers as a surface. We compared the protein contents of the attached and unattached bacteria. Using mass spectrometry, 3043 proteins were identified. Our results showed that, as of 20 minutes of incubation, using stringent quantification criteria 616 proteins presented a modification of their abundance in the attached cells compared to their unattached counterparts. The attached cells presented an overall reduced gene expression and characteristics of slow-growing cells. The over-accumulation of outer membrane proteins, periplasmic folding proteins and O-antigen chain length regulators was also observed, indicating a profound modification of the cell envelope. Consistently the sigma factor AlgU required for cell envelope homeostasis was highly over-accumulated in attached cells. In addition our data suggested a role of alarmone (p)ppGpp and polyphosphate during the early attachment phase. Furthermore, almost 150 proteins of unknown function were differentially accumulated in the attached cells. Our proteomic analysis revealed the existence of distinctive biological features in attached cells as early as 20 minutes of incubation. Analysis of some mutants demonstrated the interest of this proteomic approach in identifying genes involved in the early phase of adhesion to a surface.
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Liu X, Guo Z, Liu W, Sun W, Ma C. Differential proteome analysis of hippocampus and temporal cortex using label-free based 2D-LC-MS/MS. J Proteomics 2017. [PMID: 28627465 DOI: 10.1016/j.jprot.2017.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hippocampus and temporal cortex are important brain regions, which play distinct, but complimentary roles in mediating learning and memory. Herein, we utilized label-free differential proteome strategy to explore function of normal human hippocampus and temporal cortex in learning and memory. As a result, a total of 5529 and 5702 proteins were identified in hippocampus and temporal cortex, respectively, 516 of which were significantly differential expressed, with abundance span 5 orders of magnitudes. Pathways analysis showed that temporal cortex was involved in growth of axons growth and synapse density regulation, through which could regulate long-term potentiation and long-term retention of trace memory. Hippocampus was involved in regulation of cell survival and cell viability, and regulates neurons proliferation by actin dynamics changes, through which involved in both short-term memory and long-term memory. Four selected differential proteins were further validated by Western blot and immunohistochemistry. For the first time, we identified proteins and associated pathways of hippocampus and temporal cortex in human cognition process using proteomic strategy, which would provide references for generating corresponding insights in hippocampus and temporal cortex-related cognitive function. The original data files can be downloaded at http://211.102.209.254/page/PSV023.html;?url=1489542083729AFHp (password: kYxh). SIGNIFICANCE This study explored the potential molecular mechanism of hippocampus and temporal cortex in human cognition function using proteomics strategy, which will offer a baseline reference for further cognitive disorders study and reveal insights into physiology of temporal cortex and hippocampus.
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Affiliation(s)
- Xiaoyan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Sheta R, Woo CM, Roux-Dalvai F, Fournier F, Bourassa S, Droit A, Bertozzi CR, Bachvarov D. A metabolic labeling approach for glycoproteomic analysis reveals altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. J Proteomics 2016; 145:91-102. [PMID: 27095597 PMCID: PMC5436706 DOI: 10.1016/j.jprot.2016.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/31/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022]
Abstract
UNLABELLED Epithelial ovarian cancer (EOC) is a disease responsible for more deaths among women in the Western world than all other gynecologic malignancies. There is urgent need for new therapeutic targets and a better understanding of EOC initiation and progression. We have previously identified the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene, a member of the GalNAc-transferases (GalNAc-Ts) gene family, as hypomethylated and overexpressed in high-grade serous EOC tumors, compared to low malignant potential EOC tumors and normal ovarian tissues. This data also suggested for a role of GALNT3 in aberrant EOC glycosylation, possibly implicated in disease progression. To evaluate differential glycosylation in EOC caused by modulations in GALNT3 expression, we used a metabolic labeling strategy for enrichment and mass spectrometry-based characterization of glycoproteins following GALNT3 gene knockdown (KD) in A2780s EOC cells. A total of 589 differentially expressed glycoproteins were identified upon GALNT3 KD. Most identified proteins were involved in mechanisms of cellular metabolic functions, post-translational modifications, and some have been reported to be implicated in EOC etiology. The GALNT3-dependent glycoproteins identified by this metabolic labeling approach support the oncogenic role of GALNT3 in EOC dissemination and may be pursued as novel EOC biomarkers and/or therapeutic targets. BIOLOGICAL SIGNIFICANCE Knowledge of the O-glycoproteome has been relatively elusive, and the functions of the individual polypeptide GalNAc-Ts have been poorly characterized. Alterations in GalNAc-Ts expression were shown to provide huge variability in the O-glycoproteome in various pathologies, including cancer. The application of a chemical biology approach for the metabolic labeling and subsequent characterization of O-glycoproteins in EOC using the Ac4GalNAz metabolite has provided a strategy allowing for proteomic discovery of GalNAc-Ts specific functions. Our study supports an essential role of one of the GalNAc-Ts - GALNT3, in EOC dissemination, including its implication in modulating PTMs and EOC metabolism. Our approach validates the use of the applied metabolic strategy to identify important functions of GalNAc-Ts in normal and pathological conditions.
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Affiliation(s)
- Razan Sheta
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, PQ, Canada
| | - Christina M Woo
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - Sylvie Bourassa
- Centre de recherche du CHU de Québec, CHUL, Québec, PQ, Canada
| | - Arnaud Droit
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, CHUL, Québec, PQ, Canada
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Dimcho Bachvarov
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, PQ, Canada
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10
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Proteomic dataset for altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. Data Brief 2016; 8:342-9. [PMID: 27331112 PMCID: PMC4908283 DOI: 10.1016/j.dib.2016.05.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/12/2016] [Accepted: 05/24/2016] [Indexed: 01/20/2023] Open
Abstract
This article contains raw and processed data related to research published in "Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation" [1]. The data presented here was obtained with the application of a bioorthogonal chemical reporter strategy analyzing differential glycoprotein expression following the knock-down (KD) of the GALNT3 gene in the epithelial ovarian cancer (EOC) cell line A2780s. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. The obtained data also uncover numerous novel glycoproteins; some of which could represent new potential EOC biomarkers and/or therapeutic targets.
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11
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Ma B, Blakeley JO, Hong X, Zhang H, Jiang S, Blair L, Zhang Y, Heo HY, Zhang M, van Zijl PCM, Zhou J. Applying amide proton transfer-weighted MRI to distinguish pseudoprogression from true progression in malignant gliomas. J Magn Reson Imaging 2016; 44:456-62. [PMID: 26788865 DOI: 10.1002/jmri.25159] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/04/2016] [Indexed: 11/07/2022] Open
Abstract
PURPOSE To assess amide proton transfer-weighted (APTW) imaging features in patients with malignant gliomas after chemoradiation and the diagnostic performance of APT imaging for distinguishing true progression from pseudoprogression. MATERIALS AND METHODS After approval by the Institutional Review Board, 32 patients with clinically suspected tumor progression in the first 3 months after chemoradiation were enrolled and scanned at 3T. Longitudinal routine magnetic resonance imaging (MRI) changes and medical records were assessed to confirm true progression versus pseudoprogression. True progression was defined as lesions progressing on serial imaging over 6 months, and pseudoprogression was defined as lesions stabilizing or regressing without intervention. The APTWmean and APTWmax signals were obtained from three to five regions of interests for each patient and compared between the true progression and pseudoprogression groups. The diagnostic performance was assessed with receiver operating characteristic curve analysis. RESULTS The true progression was associated with APTW hyperintensity (APTWmean = 2.75% ± 0.42%), while pseudoprogression was associated with APTW isointensity to mild hyperintensity (APTWmean = 1.56% ± 0.42%). The APTW signal intensities were significantly higher in the true progression group (n = 20) than in the pseudoprogression group (P < 0.001; n = 12). The cutoff APTWmean and APTWmax intensity values to distinguish between true progression and pseudoprogression were 2.42% (with a sensitivity of 85.0% and a specificity of 100%) and 2.54% (with a sensitivity of 95.0% and a specificity of 91.7%), respectively. CONCLUSION The APTW-MRI signal is a valuable imaging biomarker for distinguishing pseudoprogression from true progression in glioma patients. J. Magn. Reson. Imaging 2016;44:456-462.
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Affiliation(s)
- Bo Ma
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, PR China.,Department of Radiology, Henan Provincial People's Hospital, Zhengzhou, Henan, PR China
| | - Jaishri O Blakeley
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Xiaohua Hong
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hongyan Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shanshan Jiang
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lindsay Blair
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Neurology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yi Zhang
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hye-Young Heo
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mingzhi Zhang
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, PR China
| | - Peter C M van Zijl
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Jinyuan Zhou
- Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
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