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Samarelli AV, Tonelli R, Raineri G, Bruzzi G, Andrisani D, Gozzi F, Marchioni A, Costantini M, Fabbiani L, Genovese F, Pinetti D, Manicardi L, Castaniere I, Masciale V, Aramini B, Tabbì L, Rizzato S, Bettelli S, Manfredini S, Dominici M, Clini E, Cerri S. Proteomic profiling of formalin-fixed paraffine-embedded tissue reveals key proteins related to lung dysfunction in idiopathic pulmonary fibrosis. Front Oncol 2024; 13:1275346. [PMID: 38322285 PMCID: PMC10844556 DOI: 10.3389/fonc.2023.1275346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/29/2023] [Indexed: 02/08/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) severely affects the lung leading to aberrant deposition of extracellular matrix and parenchymal stiffness with progressive functional derangement. The limited availability of fresh tissues represents one of the major limitations to study the molecular profiling of IPF lung tissue. The primary aim of this study was to explore the proteomic profiling yield of archived formalin-fixed paraffin-embedded (FFPE) specimens of IPF lung tissues. Methods We further determined the protein expression according to respiratory functional decline at the time of biopsy. The total proteins isolated from 11 FFPE samples of IPF patients compared to 3 FFPE samples from a non-fibrotic lung defined as controls, were subjected to label-free quantitative proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) and resulted in the detection of about 400 proteins. Results After the pairwise comparison between controls and IPF, functional enrichment analysis identified differentially expressed proteins that were involved in extracellular matrix signaling pathways, focal adhesion and transforming growth factor β (TGF-β) signaling pathways strongly associated with IPF onset and progression. Five proteins were significantly over- expressed in the lung of IPF patients with either advanced disease stage (Stage II) or impaired pulmonary function (FVC<75, DLCO<55) compared to controls; these were lymphocyte cytosolic protein 1 (LCP1), peroxiredoxin-2 (PRDX2), transgelin 2 (TAGLN2), lumican (LUM) and mimecan (OGN) that might play a key role in the fibrogenic processes. Discussion Our work showed that the analysis of FFPE samples was able to identify key proteins that might be crucial for the IPF pathogenesis. These proteins are correlated with lung carcinogenesis or involved in the immune landscape of lung cancer, thus making possible common mechanisms between lung carcinogenesis and fibrosis progression, two pathological conditions at risk for each other in the real life.
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Affiliation(s)
- Anna Valeria Samarelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Roberto Tonelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Giulia Raineri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Giulia Bruzzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Dario Andrisani
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Filippo Gozzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Alessandro Marchioni
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Matteo Costantini
- Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Luca Fabbiani
- Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
- Immunohistochemistry Lab, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Filippo Genovese
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy
| | - Diego Pinetti
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy
| | - Linda Manicardi
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Ivana Castaniere
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Valentina Masciale
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
- Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Beatrice Aramini
- Division of Thoracic Surgery, Department of Medical and Surgical Sciences-Diagnostic and Specialty Medicine (DIMEC) of the Alma Mater Studiorum, University of Bologna G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy
| | - Luca Tabbì
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Simone Rizzato
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Stefania Bettelli
- Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy
| | - Samantha Manfredini
- Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
- Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Enrico Clini
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Stefania Cerri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
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Xiao B, Liu Y, Chandrasiri I, Overby C, Benoit DSW. Impact of Nanoparticle Physicochemical Properties on Protein Corona and Macrophage Polarization. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 36916683 DOI: 10.1021/acsami.2c22471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Macrophages, the major component of the mononuclear phagocyte system, uptake and clear systemically administered nanoparticles (NPs). Therefore, leveraging macrophages as a druggable target may be advantageous to enhance NP-mediated drug delivery. Despite many studies focused on NP-cell interactions, NP-mediated macrophage polarization mechanisms are still poorly understood. This work aimed to explore the effect of NP physicochemical parameters (size and charge) on macrophage polarization. Upon exposure to biological fluids, proteins rapidly adsorb to NPs and form protein coronas. To this end, we hypothesized that NP protein coronas govern NP-macrophage interactions, uptake, and subsequent macrophage polarization. To test this hypothesis, model polystyrene NPs with various charges and sizes, as well as NPs relevant to drug delivery, were utilized. Data suggest that cationic NPs potentiate both M1 and M2 macrophage markers, while anionic NPs promote M1-to-M2 polarization. Additionally, anionic polystyrene nanoparticles (APNs) of 50 nm exhibit the greatest influence on M2 polarization. Proteomics was pursued to further understand the effect of NPs physicochemical parameters on protein corona, which revealed unique protein patterns based on NP charge and size. Several proteins impacting M1 and M2 macrophage polarization were identified within cationic polystyrene nanoparticles (CPNs) corona, while APNs corona included fewer M1 but more M2-promoting proteins. Nevertheless, size impacts protein corona abundance but not identities. Altogether, protein corona identities varied based on NP surface charge and correlated to dramatic differences in macrophage polarization. In contrast, NP size differentially impacts macrophage polarization, which is dominated by NP uptake level rather than protein corona. In this work, specific corona proteins were identified as a function of NP physicochemical properties. These proteins are correlated to specific macrophage polarization programs and may provide design principles for developing macrophage-mediated NP drug delivery systems.
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Affiliation(s)
- Baixue Xiao
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
| | - Yuxuan Liu
- Materials Science Program, University of Rochester, Rochester, New York 14623, United States
| | - Indika Chandrasiri
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
| | - Clyde Overby
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
| | - Danielle S W Benoit
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14623, United States
- Materials Science Program, University of Rochester, Rochester, New York 14623, United States
- Phil and Penny Knight Campus for Accelerating Scientific Impact, Department of Bioengineering, University of Oregon, Eugene, Oregon 97403, United States
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Abolbaghaei A, Turner M, Thibodeau JF, Holterman CE, Kennedy CRJ, Burger D. The Proteome of Circulating Large Extracellular Vesicles in Diabetes and Hypertension. Int J Mol Sci 2023; 24:ijms24054930. [PMID: 36902363 PMCID: PMC10003702 DOI: 10.3390/ijms24054930] [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: 11/23/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Hypertension and diabetes induce vascular injury through processes that are not fully understood. Changes in extracellular vesicle (EV) composition could provide novel insights. Here, we examined the protein composition of circulating EVs from hypertensive, diabetic and healthy mice. EVs were isolated from transgenic mice overexpressing human renin in the liver (TtRhRen, hypertensive), OVE26 type 1 diabetic mice and wild-type (WT) mice. Protein content was analyzed using liquid chromatography-mass spectrometry. We identified 544 independent proteins, of which 408 were found in all groups, 34 were exclusive to WT, 16 were exclusive to OVE26 and 5 were exclusive to TTRhRen mice. Amongst the differentially expressed proteins, haptoglobin (HPT) was upregulated and ankyrin-1 (ANK1) was downregulated in OVE26 and TtRhRen mice compared with WT controls. Conversely, TSP4 and Co3A1 were upregulated and SAA4 was downregulated exclusively in diabetic mice; and PPN was upregulated and SPTB1 and SPTA1 were downregulated in hypertensive mice, compared to WT mice. Ingenuity pathway analysis identified enrichment in proteins associated with SNARE signaling, the complement system and NAD homeostasis in EVs from diabetic mice. Conversely, in EVs from hypertensive mice, there was enrichment in semaphroin and Rho signaling. Further analysis of these changes may improve understanding of vascular injury in hypertension and diabetes.
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Affiliation(s)
- Akram Abolbaghaei
- Chronic Disease Program, Kidney Research Centre, Ottawa Hospital Research Institute, Ottawa, ON K1H 8M5, Canada
| | - Maddison Turner
- Chronic Disease Program, Kidney Research Centre, Ottawa Hospital Research Institute, Ottawa, ON K1H 8M5, Canada
| | - Jean-François Thibodeau
- Chronic Disease Program, Kidney Research Centre, Ottawa Hospital Research Institute, Ottawa, ON K1H 8M5, Canada
| | - Chet E. Holterman
- Chronic Disease Program, Kidney Research Centre, Ottawa Hospital Research Institute, Ottawa, ON K1H 8M5, Canada
| | - Christopher R. J. Kennedy
- Chronic Disease Program, Kidney Research Centre, Ottawa Hospital Research Institute, Ottawa, ON K1H 8M5, Canada
- Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Dylan Burger
- Chronic Disease Program, Kidney Research Centre, Ottawa Hospital Research Institute, Ottawa, ON K1H 8M5, Canada
- Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Correspondence: ; Tel.: +1-613-562-5800 (ext. 8241)
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Li Y, Chen M, Chen Q, Yuan M, Zeng X, Zeng Y, He M, Wang B, Han B. Bioinformatics Identification of Therapeutic Gene Targets for Gastric Cancer. Adv Ther 2023; 40:1456-1473. [PMID: 36694099 DOI: 10.1007/s12325-023-02428-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023]
Abstract
INTRODUCTION The global prevalence of gastric cancer (GC) is increasing, and novel chemotherapeutic targets are needed. METHODS We searched for potential biomarkers for GC in three microarray data sets within the Gene Expression Omnibus (GEO) database. FunRich (v3.1.3) was used to perform Gene Ontology (GO) analyses and STRUN and Cytoscape (v3.6.0) were employed to construct a protein-protein interaction (PPI) network. To explore hub gene expression and survival, we used Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan-Meier (KM) plotter. Drugs that were closely related to key genes were screened by the Gene Set Cancer Analysis (GSCA), and relevant correlations were verified experimentally. We validated that the sensitivity of a GC cell line to these drugs was correlated with fibrillin 1 (FBN1) mRNA expression levels. RESULTS We identified 83 upregulated and 133 downregulated differentially expressed genes (DEGs) and these were enriched with regards to their cellular component (extracellular and exosomes), molecular function (extracellular matrix structural constituent and catalytic activity), and biological process (cell growth and/or maintenance and metabolism). The biological pathways most prominently involved were epithelial-to-mesenchymal transition (EMT) and β3 integrin cell surface interactions. For the PPI network, we selected 10 hub genes, and 70% of these were significantly connected to poor overall survival (OS) in patients with GC. We found a significant link between the expression of FBN1 and two small molecule drugs (PAC-1 and PHA-793887). CONCLUSIONS Overall, we suggest that these hub genes can be used as biomarkers and novel targets for GC. FBN1 may be associated with drug resistance in gastric cancer.
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Affiliation(s)
- Yuanting Li
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Minghao Chen
- Department of Nuclear Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Qing Chen
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Min Yuan
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Xi Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Yan Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Meibo He
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Baiqiang Wang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
| | - Bin Han
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
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Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
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Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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Ahmed MM, Tazyeen S, Ali R, Alam A, Imam N, Malik MZ, Ali S, Ishrat R. Network centrality approaches used to uncover and classify most influential nodes with their related miRNAs in cardiovascular diseases. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Study on the Mechanism of Üstikuddus Sherbiti in Ischemic Cerebrovascular Diseases: Based on Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5581864. [PMID: 35432563 PMCID: PMC9012636 DOI: 10.1155/2022/5581864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
This paper aims to study the potential biological mechanism of Üstikuddus Sherbiti (ÜS) in the treatment of ischemic cerebrovascular diseases (ICVD) by the network pharmacology method. Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was used to obtain effective constituents of ÜS by screening eligible oral utilization, drug similarity, and blood-brain barrier permeability threshold. By drug target prediction and stroke treatment target mining, 2 target data sets were analyzed to find intersection targets and the corresponding constituents were used as active constituents. An active constituent target network and an effective constituent target network were constructed by using Cytoscape 3.7.2 software. Degree parameters of the effective constituent target network were analyzed to find important effective constituents and targets. Through protein-protein interaction (PPI) analysis/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, potential signaling pathways of ÜS in ischemic stroke were found out. AutoDock was used for molecular docking verification. A total of 90 active constituents of ÜS were screened out. There were 10 active constituents against ICVD, including quercetin, luteolin, kaempferol, and naringenin, and 10 important targets for anticerebral ischemia, namely, PIK3CA, APP, PIK3R1, MAPK1, MAPK3, AKT1, PRKCD, Fyn, RAC1, and NF-κB1. Based on the protein interaction network, the important targets of ÜS were significantly enriched in PI3K-Akt signaling pathway, neuroactive ligand-receptor interaction pathway, Ras signaling pathway, etc. ÜS in ICVD has characteristics like multiple targets, multiple approaches, and multiple pathways. Results of molecular docking showed that the active components in ICVD had a good binding ability with the key targets. Its main biological mechanism may be related to the PI3K-Akt and Ras-MAPK centered signaling pathway. Our study demonstrated that ÜS exerted the effect of treating ICVD by regulating multiple targets and multiple channels with multiple components through the method of network pharmacology and molecular docking.
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Liu X, Yan J, Liu F, Zhou P, Lv X, Cheng N, Liu L. Overexpression of REST Causes Neuronal Injury and Decreases Cofilin Phosphorylation in Mice. J Alzheimers Dis 2022; 87:873-886. [DOI: 10.3233/jad-210285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: RE1-silencing transcription factor (REST) is known to silence target genes involved in synaptic plasticity and neuronal differentiation. Although previous studies implicate REST in neurodegenerative diseases, its function in the progression of Alzheimer’s disease (AD) is uncertain. Objective: The aim of the present work was to explore the mechanisms of AD and determine whether and how REST was involved in the pathogenesis of AD. Methods: We investigated the differentially expressed genes and key transcription factors in AD using bioinformatics analysis. In addition, we assessed the expression of REST under the influence of AD-related factors. Mice overexpressing REST were generated and analyzed by proteomics analysis. We used transmission electron microscopy, Golgi-cox staining, immunohistochemistry, and western blotting to examine the impact of REST on neurons. Results: The results of bioinformatics analysis revealed REST as a hub transcriptional regulator in AD. We demonstrate that the mRNA expression of REST was significantly upregulated compared with that in the control groups, not only in AD patients but also in APP/PS1 transgenic mice, lipopolysaccharide-induced neuroinflammatory mice, and oxidative and glutamate stressed neurons. Using proteomics analysis, we showed that the upregulation of REST increased the expression of genes involved in apoptotic and mitochondrial pathways. Long-term overexpression of REST significantly reduced the number of dendritic spines and increased the mitochondrial defect and apoptosis. Reduction of the cofilin phosphorylation may be one of its mechanisms, and cofilin activity could be affected through the P38 MAPK/CREB signaling pathway. Conclusion: These results demonstrated the possible mechanism underlying AD and indicated REST as a potential therapeutic target for AD.
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Affiliation(s)
- Xiang Liu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, PR China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Jie Yan
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Fangbo Liu
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Peipei Zhou
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Xinyue Lv
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Nengneng Cheng
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, PR China
| | - Li Liu
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
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Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics 2022; 220:6516514. [PMID: 35380657 PMCID: PMC8982048 DOI: 10.1093/genetics/iyac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html.
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Affiliation(s)
- Mahima Vedi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L Hill
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ketaki Thorat
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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10
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Wang JY, Li Y, Lv YY, Jiang L. Screening and identification of novel candidate biomarkers of focal cortical dysplasia type II via bioinformatics analysis. Childs Nerv Syst 2022; 38:953-960. [PMID: 35112146 PMCID: PMC8809227 DOI: 10.1007/s00381-022-05454-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Focal cortical dysplasia (FCD) is the most common developmental malformation that causes refractory epilepsy. FCD II is a common neuropathological finding in tissues resected therapeutically from patients with drug-resistant epilepsy. However, its molecular genetic etiology remains unclear. This study aimed to identify potential molecular markers of FCD II using bioinformatics analysis. METHODS We downloaded two datasets for FCD II from the Gene Expression Omnibus data repository. Differentially expressed genes (DEGs) between FCD II and normal brain tissues were identified, and functional enrichment analysis was performed. A protein-protein interaction network was constructed, and hub genes were identified from the DEGs. The hub gene expression was validated using WB in vitro. IHC staining was performed to verify the feasibility of the target molecular markers identified in the bioinformatics analysis. RESULTS One hundred sixty-seven common DEGs were identified between the datasets. The GO and KEGG analyses showed that variations were prominently enriched in some functions associated with gene expression. Five hub genes (i.e., FANCI, FANCA, BRCA2, RAD18, and KEAP1) were identified. Western blotting confirmed that all hub gene expressions were higher in the FCD II tissue than in the normal brain tissue. IHC staining showed that the FANCI expression significantly increased in the FCD II tissue. CONCLUSION There are DEGs between FCD II and normal brain tissues, which may be considered biomarkers for FCD II, along with FANCI. The DEGs and hub genes identified in the bioinformatics analysis could serve as candidate targets for diagnosing and treating FCD II.
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Affiliation(s)
- Jiang-ya Wang
- Department of Pediatrics, Hebei Medical University, Shijiazhuang, China ,Department of Pediatrics, Hebei General Hospital, Shijiazhuang, China
| | - Yang Li
- Department of Pediatrics, The Fourth Hospital of Hebei Medical University, Chang’an district, Shijiazhuang, 050000 China
| | - Yuan-yuan Lv
- Department of Pediatrics, Baoding First Central Hospital, Baoding, China
| | - Lian Jiang
- Department of Pediatrics, The Fourth Hospital of Hebei Medical University, Chang'an district, Shijiazhuang, 050000, China.
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11
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Zhu R, Jiang H, Wang J, Bao C, Liu H, Li F, Lei L. Dynamic immune response characteristics of piglets infected with Actinobacillus pleuropneumoniae through omic. AMB Express 2021; 11:175. [PMID: 34952961 PMCID: PMC8709809 DOI: 10.1186/s13568-021-01336-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Porcine infectious pleuropneumonia is characterized by a high-rate of carriage and mixed infection with other pathogens. The host immune response induced by Actinobacillus pleuropneumoniae (APP) is the basis for elucidating pathogenesis and controlling disease. However, there is currently no comprehensive and dynamic data characterising the host immune response. In this study, piglets were infected with APP and differentially expressed proteins of bronchoalveolar lavage fluid (BALF) and peripheral serum were identified by iTRAQ-LC-MS/MS, and differentially expressed genes of peripheral blood mononuclear cells (PBMC) by RNA-seq. The results of the integrated analysis of serum, BALF and PBMC showed significant metabolism and local immune responses in BALF, the general immune response in PBMC mainly involves cytokines, while that in serum mainly involves biosynthesis, phagosome, and complement and coagulation cascades. Furthermore, immune responses in PBMCs and serum were rapid and maintained compared to the lung where metabolism and cell adhesion activities were enriched. Some innate immunity pathways of the cellular response to ROS, neutrophil mediated immunity, granulocyte activation and leukocyte cell-cell adhesion were identified as central points, connecting multiple signaling pathways to form an integrated large network. At 24 h post-infection, 14 molecules were up regulated in BALF, 10 of which were shared with PBMC, but at 120 h, 20 down-regulated molecules were identified in BALF, 11 of them still up- regulated in PBMC. We conclude that, the immune response in the lung is different from that in blood, but there is a similarity in response in PBMC and serum.
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12
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Ye JB, Wen JJ, Wu DL, Hu BX, Luo MQ, Lin YQ, Ning YS, Li Y. Elevated DLL3 in stomach cancer by tumor-associated macrophages enhances cancer-cell proliferation and cytokine secretion of macrophages. Gastroenterol Rep (Oxf) 2021; 10:goab052. [PMID: 35382168 PMCID: PMC8973010 DOI: 10.1093/gastro/goab052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/13/2021] [Accepted: 10/26/2021] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
The notch signal pathway is important in the development of both tumor-associated macrophages (TAMs) and stomach cancer, but how Notch signaling affects TAMs in stomach cancer is barely understood.
Methods
The expressions of Notch1, Notch2, Notch3, Notch4, hes family bHLH transcription factor 1 (Hes1), and delta-like canonical Notch ligand 3 (DLL3) were detected by Western blot and the expressions of interleukin (IL)-10, IL-12, and IL1-β were detected using enzyme-linked immunosorbent assay after the co-culture of macrophages and stomach-cancer cells. The proliferation and migration of cancer cells were detected using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and scratch assay, respectively, and the cell cycle was detected using Annexin V/propidium iodide assay. The protein interactions with DLL3 were detected using co-immunoprecipitation and mass spectrometry.
Results
The co-culture of macrophages and stomach-cancer cells MKN45 and BGC823 could enhance cell proliferation accompanied by the activation of Notch1/Notch2 signaling and upregulation of DLL3. Notch signaling gamma-secretase inhibitor (DAPT) blocked this process. The overexpression of DLL3 in stomach-cancer cells could promote the proliferation of cancer cells, enhance the activation of Notch1/Notch2 signaling, induce the expression of IL-33, lead to the degradation of galectin-3–binding protein (LG3BP) and heat shock cognate 71 kDa protein (HSPA8), and result in elevated IL-1β, IL-12, and IL-10 secretion by macrophages. Higher expression of DLL3 or IL-33 could lead to a lower survival rate based on University of California, Santa Cruz Xena Functional Genomics Explorer and The Cancer Genome Atlas data set.
Conclusions
This is evidence that DLL3 regulates macrophages in stomach cancer, suggesting that DLL3 may be a novel and potential target for stomach-cancer therapy.
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Affiliation(s)
- Jian-Bin Ye
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jun-Jie Wen
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Dan-Lin Wu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Bing-Xin Hu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Mei-Qun Luo
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yan-Qing Lin
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yun-Shan Ning
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
- Service Union Medicine, Southern Medical University, Zhuhai, Guangdong, P.R. China
| | - Yan Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P.R. China
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13
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Nakao Y, Fukushima M, Mauer AS, Liao CY, Ferris A, Dasgupta D, Heppelmann CJ, Vanderboom PM, Saraswat M, Pandey A, Nair KS, Allen AM, Nakao K, Malhi H. A Comparative Proteomic Analysis of Extracellular Vesicles Associated With Lipotoxicity. Front Cell Dev Biol 2021; 9:735001. [PMID: 34805145 PMCID: PMC8600144 DOI: 10.3389/fcell.2021.735001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are emerging mediators of intercellular communication in nonalcoholic steatohepatitis (NASH). Palmitate, a lipotoxic saturated fatty acid, activates hepatocellular endoplasmic reticulum stress, which has been demonstrated to be important in NASH pathogenesis, including in the release of EVs. We have previously demonstrated that the release of palmitate-stimulated EVs is dependent on the de novo synthesis of ceramide, which is trafficked by the ceramide transport protein, STARD11. The trafficking of ceramide is a critical step in the release of lipotoxic EVs, as cells deficient in STARD11 do not release palmitate-stimulated EVs. Here, we examined the hypothesis that protein cargoes are trafficked to lipotoxic EVs in a ceramide-dependent manner. We performed quantitative proteomic analysis of palmitate-stimulated EVs in control and STARD11 knockout hepatocyte cell lines. Proteomics was performed on EVs isolated by size exclusion chromatography, ultracentrifugation, and density gradient separation, and EV proteins were measured by mass spectrometry. We also performed human EV proteomics from a control and a NASH plasma sample, for comparative analyses with hepatocyte-derived lipotoxic EVs. Size exclusion chromatography yielded most unique EV proteins. Ceramide-dependent lipotoxic EVs contain damage-associated molecular patterns and adhesion molecules. Haptoglobin, vascular non-inflammatory molecule-1, and insulin-like growth factor-binding protein complex acid labile subunit were commonly detected in NASH and hepatocyte-derived ceramide-dependent EVs. Lipotoxic EV proteomics provides novel candidate proteins to investigate in NASH pathogenesis and as diagnostic biomarkers for hepatocyte-derived EVs in NASH patients.
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Affiliation(s)
- Yasuhiko Nakao
- Division of Gastroenterology and Hepatology, Rochester, MN, United States.,Department of Gastroenterology and Hepatology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masanori Fukushima
- Division of Gastroenterology and Hepatology, Rochester, MN, United States.,Department of Gastroenterology and Hepatology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Amy S Mauer
- Division of Gastroenterology and Hepatology, Rochester, MN, United States
| | - Chieh-Yu Liao
- Division of Gastroenterology and Hepatology, Rochester, MN, United States
| | - Anya Ferris
- Division of Gastroenterology and Hepatology, Rochester, MN, United States.,California Polytechnic State University, San Luis Obispo, CA, United States
| | - Debanjali Dasgupta
- Division of Gastroenterology and Hepatology, Rochester, MN, United States.,Department of Physiology and Biomedical Engineering, Manipal, India
| | | | - Patrick M Vanderboom
- Mayo Clinic Medical Genome Facility-Proteomics Core, Manipal, India.,Mayo Endocrine Research Unit, Manipal, India
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Rochester, MN, United States.,Institute of Bioinformatics, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Rochester, MN, United States.,Institute of Bioinformatics, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Center for Individualized Medicine, Rochester, MN, United States
| | | | - Alina M Allen
- Division of Gastroenterology and Hepatology, Rochester, MN, United States
| | - Kazuhiko Nakao
- Department of Gastroenterology and Hepatology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Rochester, MN, United States
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Guo Y, Huang B, Li R, Li J, Tian S, Peng C, Dong W. Low APOA-1 Expression in Hepatocellular Carcinoma Patients Is Associated With DNA Methylation and Poor Overall Survival. Front Genet 2021; 12:760744. [PMID: 34790226 PMCID: PMC8591198 DOI: 10.3389/fgene.2021.760744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/04/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is the most frequent fatal malignancy, and it has a poor prognosis. Apolipoprotein 1 (APOA-1), the main protein component of high-density lipoproteins, is involved in numerous biological processes. Thus, this study was performed to detect the clinical significance of APOA-1 mRNA, APOA-1 expression, and APOA-1DNA methylation in patients with HCC. Methods: Data mining was performed using clinical and survival data from the Cancer Genome Atlas (TCGA) and Oncomine databases. The serum concentration of APOA-1 was measured in 316 patients with HCC and 100 healthy individuals at Renmin Hospital of Wuhan University, and the intact clinical information was reviewed and determined using univariate and multivariate Cox hazard models. Results: Bioinformatic analysis revealed that APOA-1 mRNA was present at lower levels in the serum of patients with HCC than in that of healthy individuals, and there was a strong negative correlation between levels of APOA-1 mRNA and APOA-1 DNA methylation. High expression of APOA-1 transcription correlated with better overall survival (p = 0.003), and APOA-1 hypermethylation correlated with progress-free survival (p = 0.045) in HCC sufferers. Next, the clinical data analysis demonstrated that APOA-1 protein levels in the serum were significantly lower in patients with HCC than in healthy controls. Furthermore, the expression of APOA-1 was significantly associated with some significant clinical indexes, and elevated APOA-1 expression was significantly associated with favorable (OS; HR:1.693, 95% CI: 1.194–2.401, p = 0.003) and better progression-free survival (PFS; HR = 1.33, 95% CI = 1.194–2.401, p = 0.045). Finally, enrichment analysis suggested that co-expressed genes of APOA-1 were involved in lipoprotein metabolism and FOXA2/3 transcription factor networks. Conclusion: APOA-1 mRNA expression is negatively regulated by DNA methylation in HCC. Low expression of APOA-1 might be a potential risk biomarker to predict survival in patients with HCC.
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Affiliation(s)
- Yingyun Guo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Binglu Huang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ruixue Li
- Department of Gastroenterology, Macheng Renmin Hospital, Macheng, Huanggang, China
| | - Jiao Li
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shan Tian
- Department of Infectious, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Peng
- Department of Infectious, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
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15
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Bioinformatics Analysis: The Regulatory Network of hsa_circ_0007843 and hsa_circ_0007331 in Colon Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6662897. [PMID: 34337040 PMCID: PMC8324362 DOI: 10.1155/2021/6662897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 12/19/2022]
Abstract
Objective To analyze the molecular regulation network of circular RNA (circRNA) in colon cancer (CC) by bioinformatics method. Methods hsa_circ_0007843 and hsa_circ_0007331 proved to be associated with CC in previous studies were chosen as the research object. ConSite database was used to predict the transcription factors associated with circRNA, and the CC-associated transcription factors were screened out after intersection. The CircInteractome database was used to predict the RNA-binding proteins (RBPs) interacting with circRNAs and screen out the CC-associated RBPs after an intersection. Furthermore, the CircInteractome database was used to predict the miRNAs interrelated with circRNAs, and the HMDD v3.2 database was used to search for miRNAs associated with CC. The target mRNAs of miRNA were predicted by the miRWalk v3.0 database. CC-associated target genes were screened out from the GeneCards database, and the upregulated genes were enriched and analyzed by the FunRich 3.1.3 software. Finally, the molecular regulatory network diagram of circRNA in CC was plotted. Results The ConSite database predicted a total of 14 common transcription factors of hsa_circ_0007843 and hsa_circ_0007331, among which Snail, SOX17, HNF3, C-FOS, and RORα-1 were related to CC. The CircInteractome database predicted that the RBPs interacting with these two circRNAs were AGO2 and EIF4A3, and both of them were related to CC. A total of 17 miRNAs interacting with hsa_circ_0007843 and hsa_circ_0007331 were predicted by CircInteractome database. miR-145-5p, miR-21, miR-330-5p, miR-326, and miR-766 were associated with CC according to the HMDDv3.2 database. miR-145-5p and miR-330-5p, lowly expressed in CC, were analyzed in the follow-up study. A total of 676 common target genes of these two miRNAs were predicted by the miRWalk3.0 database. And 57 target genes were involved in the occurrence and development of CC from the GeneCards database, with 23 genes downregulated and 34 genes upregulated. Additionally, GO analysis showed that the 34 upregulated genes were mainly enriched in biological processes such as signal transduction and cell communication. KEGG pathway analysis showed that the upregulated genes were closely related to integrin, ErbB receptor, and ALK1 signal pathways. Finally, a complete regulatory network of hsa_circ_0007843 and hsa_circ_0007331 in CC was proposed, whereby each one of the participants was either directly or indirectly associated and whose deregulation may result in CC progression. Conclusion Predicting the molecular regulatory network of circRNAs by bioinformatics provides a new theoretical basis for further occurrence and development pathogenesis of CC and good guidance for future experimental research.
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16
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Aneesh Kumar A, Ajith Kumar GS, Satheesh G, Surendran A, Chandran M, Kartha CC, Jaleel A. Proteomics Analysis Reveals Diverse Molecular Characteristics between Endocardial and Aortic-Valvular Endothelium. Genes (Basel) 2021; 12:genes12071005. [PMID: 34208790 PMCID: PMC8304717 DOI: 10.3390/genes12071005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022] Open
Abstract
The variations in the protein profile of aortic-valvular (AVE) and endocardial endothelial (EE) cells are currently unknown. The current study's objective is to identify differentially expressed proteins and associated pathways in both the endothelial cells. We used endothelial cells isolated from the porcine (Sus scrofa) aortic valve and endocardium for the profiling of proteins. Label-free proteomics was performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our proteomics analysis revealed that 29 proteins were highly expressed, and 25 proteins were less expressed in the valve than the endocardial endothelium. The cell surface markers, such as CD63, ICAM1, PECAM1, PROCR, and TFRC, were highly expressed in EE. In contrast, CD44 was highly expressed in AVE. The pathway analysis showed that metabolic process-related proteins and extracellular matrix-related proteins were enriched in valves. Differential enrichment of signaling pathways was observed in the endocardium. The hemostasis function-related proteins were increased in both endothelial cells. The proteins and pathways enriched in aortic-valvular and endocardial endothelial cells revealed the distinct phenotype of these two closely related cells.
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Affiliation(s)
- A. Aneesh Kumar
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.A.K.); (G.S.A.K.); (G.S.); (C.C.K.)
| | - G. S. Ajith Kumar
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.A.K.); (G.S.A.K.); (G.S.); (C.C.K.)
| | - Gopika Satheesh
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.A.K.); (G.S.A.K.); (G.S.); (C.C.K.)
| | - Arun Surendran
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.S.); (M.C.)
| | - Mahesh Chandran
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.S.); (M.C.)
| | - Chandrasekharan C. Kartha
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.A.K.); (G.S.A.K.); (G.S.); (C.C.K.)
| | - Abdul Jaleel
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.A.K.); (G.S.A.K.); (G.S.); (C.C.K.)
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India; (A.S.); (M.C.)
- Correspondence: ; Tel.: +91-471-252-9540; Fax: +91-471-234-8096
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17
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Wu H, Jiang W, Ji G, Xu R, Zhou G, Yu H. Exploring microRNA target genes and identifying hub genes in bladder cancer based on bioinformatic analysis. BMC Urol 2021; 21:90. [PMID: 34112125 PMCID: PMC8194198 DOI: 10.1186/s12894-021-00857-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/04/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Bladder cancer (BC) is the second most frequent malignancy of the urinary system. The aim of this study was to identify key microRNAs (miRNAs) and hub genes associated with BC as well as analyse their targeted relationships. METHODS According to the microRNA dataset GSE112264 and gene microarray dataset GSE52519, differentially expressed microRNAs (DEMs) and differentially expressed genes (DEGs) were obtained using the R limma software package. The FunRich software database was used to predict the miRNA-targeted genes. The overlapping common genes (OCGs) between miRNA-targeted genes and DEGs were screened to construct the PPI network. Then, gene ontology (GO) analysis was performed through the "cluster Profiler" and "org.Hs.eg.db" R packages. The differential expression analysis and hierarchical clustering of these hub genes were analysed through the GEPIA and UCSC Cancer Genomics Browser databases, respectively. KEGG pathway enrichment analyses of hub genes were performed through gene set enrichment analysis (GSEA). RESULTS A total of 12 DEMs and 10 hub genes were identified. Differential expression analysis of the hub genes using the GEPIA database was consistent with the results for the UCSC Cancer Genomics Browser database. The results indicated that these hub genes were oncogenes, but VCL, TPM2, and TPM1 were tumour suppressor genes. The GSEA also showed that hub genes were most enriched in those pathways that were closely associated with tumour proliferation and apoptosis. CONCLUSIONS In this study, we built a miRNA-mRNA regulatory targeted network, which explores an understanding of the pathogenesis of cancer development and provides key evidence for novel targeted treatments for BC.
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Affiliation(s)
- Hongjian Wu
- Department of Urology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, 317000, Zhejiang, People's Republic of China
| | - Wubing Jiang
- Department of Urology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, 317000, Zhejiang, People's Republic of China
| | - Guanghua Ji
- Department of Urology, Taizhou Municipal Hospital, Taizhou, 317000, Zhejiang, People's Republic of China
| | - Rong Xu
- Department of Urology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, 317000, Zhejiang, People's Republic of China
| | - Gaobo Zhou
- Department of Urology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, 317000, Zhejiang, People's Republic of China
| | - Hongyuan Yu
- Department of Urology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, 317000, Zhejiang, People's Republic of China.
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18
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Ashok G, Miryala SK, Anbarasu A, Ramaiah S. Integrated systems biology approach using gene network analysis to identify the important pathways and new potential drug targets for Neuroblastoma. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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The mantle exosome proteins of Hyriopsis cumingii participate in shell and nacre color formation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100844. [PMID: 33971400 DOI: 10.1016/j.cbd.2021.100844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/30/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
Pearl color is closely related to the nacre color of shell in Hyriopsis cumingii, and pearl color has a huge impact on its price. The nacre is an important part of the shell, and studies have suggested that mantle exosomes participated in shell formation. Exosomes contain many different proteins that are involved in different biological processes. In this study, exosomes were extracted from mantles of mussels with different nacre color. TMT quantitative proteome sequencing analysis was performed on purple and white mussel mantle exosomes, and 4861 proteins were obtained. Based on the standard of (|log2 (Fold change)| ≥ 1.2 or ≤ 0.83 and p-value ≤ 0.05), a total of 758 differentially expressed proteins were found. Some proteins involved in shell and nacre color formation were predicted with the proteins annotate, GO classification system. Moreover, 14 differentially expressed proteins (including eight up-regulated proteins and six down-regulated proteins) were validated using parallel reaction monitoring (PRM) assays. Overall, this information will be useful to improve our understanding of the molecular mechanisms of shell and nacre color formation in H. cumingii.
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Wang Q, Wang G, Xu X, Chen Z. miR-760 mediated the proliferation and metastasis of hepatocellular carcinoma cells by regulating HMGA2. Pathol Res Pract 2021; 222:153420. [PMID: 33887625 DOI: 10.1016/j.prp.2021.153420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The purpose of our study was to investigate the roles of miR-760 and its potential mechanisms in HCC. METHODS The functions of miR-760 were identified and measured by MTT, colony formation, transwell, and flow cytometry assays. Luciferase assay was applied to verify the direct binding of miR-760 on HMGA2 3'untranslated region (3'UTR). Then, in vitro experiment was used to investigate the biological effects of miR-760 and HMGA2. Luciferase and ChIP assays were used to detect the validity of SP1 binding sites on the miR-760 promoter. RESULTS We demonstrated that miR-760 overexpression suppressed cell proliferation, migration, and invasion in HCC. Besides, HMGA2 was demonstrated as a direct target gene of miR-760. Furthermore, we found that methylation may result in the downregulation of miR-760, and SP1 could inhibit the transcription of miR-760. CONCLUSIONS Our study demonstrated that SP1/miR-760/HMGA2 may serve as a molecular regulatory axis for HCC treatment.
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Affiliation(s)
- Quhui Wang
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, China
| | - Gang Wang
- Department of Anesthesiology, Union Hospital Affiliated With Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Xiaodong Xu
- Department of General Surgery, The 4th Affiliated Hospital of Nantong University, Yancheng, 224000, China
| | - Zhong Chen
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, China; Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China.
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21
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Tan S, Chen W, Xiang H, Kong G, Zou L, Wei L. Screening druggable targets and predicting therapeutic drugs for COVID-19 via integrated bioinformatics analysis. Genes Genomics 2021; 43:55-67. [PMID: 33428154 PMCID: PMC7797890 DOI: 10.1007/s13258-020-01021-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/25/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND Since the outbreak of coronavirus disease 2019 (COVID-19) in China, numerous research institutions have invested in the development of anti-COVID-19 vaccines and screening for efficacious drugs to manage the virus. OBJECTIVE To explore the potential targets and therapeutic drugs for the prevention and treatment of COVID-19 through data mining and bioinformatics. METHODS We integrated and profoundly analyzed 10 drugs previously assessed to have promising therapeutic potential in COVID-19 management, and have been recommended for clinical trials. To explore the mechanisms by which these drugs may be involved in the treatment of COVID-19, gene-drug interactions were identified using the DGIdb database after which functional enrichment analysis, protein-protein interaction (PPI) network, and miRNA-gene network construction were performed. We adopted the DGIdb database to explore the candidate drugs for COVID-19. RESULTS A total of 43 genes associated with the 10 potential COVID-19 drugs were identified. Function enrichment analysis revealed that these genes were mainly enriched in response to other invasions, toll-like receptor pathways, and they play positive roles in the production of cytokines such as IL-6, IL-8, and INF-β. TNF, TLR3, TLR7, TLR9, and CXCL10 were identified as crucial genes in COVID-19. Through the DGIdb database, we predicted 87 molecules as promising druggable molecules for managing COVID-19. CONCLUSIONS Findings from this work may provide new insights into COVID-19 mechanisms and treatments. Further, the already identified candidate drugs may improve the efficiency of pharmaceutical treatment in this rapidly evolving global situation.
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Affiliation(s)
- Siyou Tan
- grid.411427.50000 0001 0089 3695Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, No.61 Jiefang West Road, Furong District, Changsha, 410002 Hunan China
| | - Wenyan Chen
- grid.411427.50000 0001 0089 3695Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, No.61 Jiefang West Road, Furong District, Changsha, 410002 Hunan China
| | - Hongxian Xiang
- grid.411427.50000 0001 0089 3695Department of Cardiothoracic Surgery, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410002 Hunan China
| | - Gaoyin Kong
- grid.411427.50000 0001 0089 3695Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, No.61 Jiefang West Road, Furong District, Changsha, 410002 Hunan China ,Clinical Research Center for Anesthesiology of ERAS in Hunan Province, Changsha, 410002 Hunan China
| | - Lianhong Zou
- grid.411427.50000 0001 0089 3695Hunan Provincial Institute of Emergency Medicine, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410002 Hunan China ,Hunan Provincial Key Laboratory of Emergency and Critical Care Metabonomics, Changsha, 410002 Hunan China
| | - Lai Wei
- grid.411427.50000 0001 0089 3695Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, No.61 Jiefang West Road, Furong District, Changsha, 410002 Hunan China ,Clinical Research Center for Anesthesiology of ERAS in Hunan Province, Changsha, 410002 Hunan China
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22
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Chen X, Sun Y, Zhang T, Roepstorff P, Yang F. Comprehensive Analysis of the Proteome and PTMomes of C2C12 Myoblasts Reveals that Sialylation Plays a Role in the Differentiation of Skeletal Muscle Cells. J Proteome Res 2020; 20:222-235. [PMID: 33216553 DOI: 10.1021/acs.jproteome.0c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The C2C12 myoblast is a model that has been used extensively to study the process of skeletal muscle differentiation. Proteomics has advanced our understanding of skeletal muscle biology and also the differentiation process of skeletal muscle cells. However, there is still no comprehensive analysis of C2C12 myoblast proteomes, which is important for the understanding of key drivers for the differentiation of skeletal muscle cells. Here, we conducted multidimensional proteome profiling to get a comprehensive analysis of proteomes and PTMomes of C2C12 myoblasts with a TiSH strategy. A total of 8313 protein groups were identified, including 7827 protein groups from nonmodified peptides, 3803 phosphoproteins, and 977 formerly sialylated N-linked glycoproteins. Integrated analysis of proteomic and PTMomic data showed that almost all of the kinases and transcription factors in the muscle cell differentiation pathway were phosphorylated. Further analysis indicated that sialylation might play a role in the differentiation of C2C12 myoblasts. Further functional analysis demonstrated that C2C12 myoblasts showed a decreased level of sialylation during skeletal muscle cell differentiation. Inhibition of sialylation with the sialyltransferase inhibitor 3Fax-Neu5Ac resulted in the lower expression of MHC and suppression of myoblast fusion. In all, these results indicate that sialylation has an effect on the differentiation of skeletal muscle cells.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
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23
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Pustulka SM, Ling K, Pish SL, Champion JA. Protein Nanoparticle Charge and Hydrophobicity Govern Protein Corona and Macrophage Uptake. ACS APPLIED MATERIALS & INTERFACES 2020; 12:48284-48295. [PMID: 33054178 DOI: 10.1021/acsami.0c12341] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein nanoparticles are biomaterials composed entirely of proteins, with the protein sequence and structure determining the nanoparticle physicochemical properties. Upon exposure to physiological or environmental fluids, it is likely that protein nanoparticles, like synthetic nanoparticles, will adsorb proteins and this protein corona will be dependent on the surface properties of the protein nanoparticles. As there is little understanding of this phenomenon for engineered protein nanoparticles, the purpose of this work was to create protein nanoparticles with variable surface hydrophobicity and surface charge and establish the effect of these properties on the mass and composition of the adsorbed corona, using the fetal bovine serum as a model physiological solution. Albumin, cationic albumin, and ovalbumin cross-linked nanoparticles were developed for this investigation and their adsorbed protein coronas were isolated and characterized by gel electrophoresis and nanoliquid chromatography mass spectrometry. Distinct trends in corona mass and composition were identified for protein nanoparticles based on surface charge and surface hydrophobicity. Proteomic analyses revealed unique protein corona patterns and identified distinct proteins that are known to affect nanoparticle clearance in vivo. Further, the protein corona influenced nanoparticle internalization in vitro in a macrophage cell line. Altogether, these results demonstrate the strong effect protein identity and properties have on the corona formed on nanoparticles made from that protein. This work builds the foundation for future study of protein coronas on the wide array of protein nanoparticles used in nanomedicine and environmental applications.
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Affiliation(s)
- Samantha M Pustulka
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Kevin Ling
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Stephanie L Pish
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Julie A Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United States
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24
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Serpente M, Fenoglio C, D'Anca M, Arcaro M, Sorrentino F, Visconte C, Arighi A, Fumagalli GG, Porretti L, Cattaneo A, Ciani M, Zanardini R, Benussi L, Ghidoni R, Scarpini E, Galimberti D. MiRNA Profiling in Plasma Neural-Derived Small Extracellular Vesicles from Patients with Alzheimer's Disease. Cells 2020; 9:cells9061443. [PMID: 32531989 PMCID: PMC7349735 DOI: 10.3390/cells9061443] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Small extracellular vesicles (EVs) are able to pass from the central nervous system (CNS) into peripheral blood and contain molecule markers of their parental origin. The aim of our study was to isolate and characterize total and neural-derived small EVs (NDEVs) and their micro RNA (miRNA) cargo in Alzheimer's disease (AD) patients. Small NDEVs were isolated from plasma in a population consisting of 40 AD patients and 40 healthy subjects (CTRLs) using high throughput Advanced TaqMan miRNA OpenArrays®, which enables the simultaneous determination of 754 miRNAs. MiR-23a-3p, miR-223-3p, miR-100-3p and miR-190-5p showed a significant dysregulation in small NDEVs from AD patients as compared with controls (1.16 ± 0.49 versus 7.54 ± 2.5, p = 0.026; 9.32 ± 2.27 versus 0.66 ± 0.18, p <0.0001; 0.069 ± 0.01 versus 0.5 ± 0.1, p < 0.0001 and 2.9 ± 1.2 versus 1.93 ± 0.9, p < 0.05, respectively). A further validation analysis confirmed that miR-23a-3p, miR-223-3p and miR-190a-5p levels in small NDEVs from AD patients were significantly upregulated as compared with controls (p = 0.008; p = 0.016; p = 0.003, respectively) whereas miR-100-3p levels were significantly downregulated (p = 0.008). This is the first study that carries out the comparison between total plasma small EV population and NDEVs, demonstrating the presence of a specific AD NDEV miRNA signature.
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Affiliation(s)
- Maria Serpente
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Chiara Fenoglio
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Marianna D'Anca
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Marina Arcaro
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Federica Sorrentino
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, CRC Molecular Basis of Neuro-Psycho-Geriatrics Diseases, University of Milan, 20122 Milan, Italy
| | - Caterina Visconte
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Arighi
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giorgio G Fumagalli
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Laura Porretti
- Flow Cytometry Service, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Alessandra Cattaneo
- Department of Transfusion Medicine and Haematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Roberta Zanardini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Elio Scarpini
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, CRC Molecular Basis of Neuro-Psycho-Geriatrics Diseases, University of Milan, 20122 Milan, Italy
| | - Daniela Galimberti
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, CRC Molecular Basis of Neuro-Psycho-Geriatrics Diseases, University of Milan, 20122 Milan, Italy
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25
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Lin HJ, Sheu PCY, Tsai JJP, Wang CCN, Chou CY. Text mining in a literature review of urothelial cancer using topic model. BMC Cancer 2020; 20:462. [PMID: 32448176 PMCID: PMC7245902 DOI: 10.1186/s12885-020-06931-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 05/05/2020] [Indexed: 01/16/2023] Open
Abstract
Background Urothelial cancer (UC) includes carcinomas of the bladder, ureters, and renal pelvis. New treatments and biomarkers of UC emerged in this decade. To identify the key information in a vast amount of literature can be challenging. In this study, we use text mining to explore UC publications to identify important information that may lead to new research directions. Method We used topic modeling to analyze the titles and abstracts of 29,883 articles of UC from Pubmed, Web of Science, and Embase in Mar 2020. We applied latent Dirichlet allocation modeling to extract 15 topics and conducted trend analysis. Gene ontology term enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis were performed to identify UC related pathways. Results There was a growing trend regarding UC treatment especially immune checkpoint therapy but not the staging of UC. The risk factors of UC carried in different countries such as cigarette smoking in the United State and aristolochic acid in Taiwan and China. GMCSF, IL-5, Syndecan-1, ErbB receptor, integrin, c-Met, and TRAIL signaling pathways are the most relevant biological pathway associated with UC. Conclusions The risk factors of UC may be dependent on the countries and GMCSF, IL-5, Syndecan-1, ErbB receptor, integrin, c-Met, and TRAIL signaling pathways are the most relevant biological pathway associated with UC. These findings may provide further UC research directions.
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Affiliation(s)
- Hsuan-Jen Lin
- Department of Biomedical Informatics, Asia University, 500, Lioufeng Rd., Wufeng, Taichung, Taiwan.,Division of Nephrology, Asia University Hospital, Taichung, Taiwan.,Kidney Institute and Division of Nephrology, China Medical University Hospital, Taichung, Taiwan
| | - Phillip C-Y Sheu
- Department of Biomedical Informatics, Asia University, 500, Lioufeng Rd., Wufeng, Taichung, Taiwan.,Department of Electrical Engineering and Computer Science, University of California, Irvine, 5200 Engineering Hall, Irvine, CA, 92697, USA
| | - Jeffrey J P Tsai
- Department of Biomedical Informatics, Asia University, 500, Lioufeng Rd., Wufeng, Taichung, Taiwan
| | - Charles C N Wang
- Department of Biomedical Informatics, Asia University, 500, Lioufeng Rd., Wufeng, Taichung, Taiwan
| | - Che-Yi Chou
- Division of Nephrology, Asia University Hospital, Taichung, Taiwan. .,Kidney Institute and Division of Nephrology, China Medical University Hospital, Taichung, Taiwan. .,Department of Post-baccalaureate Veterinary Medicine, Asia University, Taichung, Taiwan. .,Department of internal medicine, Asia University Hospital, Taichung, 413, Taiwan.
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26
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Foysal MJ, Momtaz F, Kawsar AQMR, Rahman MM, Gupta SK, Tay ACY. Next-generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis). Lett Appl Microbiol 2019; 70:173-180. [PMID: 31782823 DOI: 10.1111/lam.13256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 10/25/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022]
Abstract
Bacterial communities strongly influence the digestion, health and immune status of fish. This study investigates the microbial distribution of the anterior, middle and distal gut sections of three economically important carp species in Bangladesh, rohu, catla and mrigal (commonly known as Indian major carps), using 16S rRNA-based Illumina sequencing technology. The alpha-diversity measurement with one-way ANOVA indicated high species richness, Shannon and Simpson indices in the middle and distal gut, while the anterior gut of IMCs had the lowest diversity. At the phylum level, there was high abundance of Proteobacteria in the GITs of rohu and mrigal, whereas Fusobacteria was dominant in the anterior and middle guts of catla. At the genus level, diverse microbial communities were identified across the three GIT sections, with six indicator genera found in rohu, catla and mrigal, as revealed by linear discriminant analysis (LDA) at a 0·05 level of significance. Of the 218 genera identified, only 33 were common across the anterior, middle and distal guts of all three species. Bacterial diversity was significantly higher (P < 0·05) in mrigal, followed by catla and rohu, respectively. Alongside the common bacteria Aeromonas, Enterobacter and Serratia, the overwhelming abundance of Cetobacterium, Shewanella and Plesiomonas warrants further investigation. SIGNIFICANCE AND IMPACT OF THE STUDY: This study investigates the microbial communities of the gastrointestinal tracts (GITs) of three Indian major carp (IMC) species-rohu, catla and mrigal, obtained from a polyculture pond under the same feeding regime. Diverse microbial communities were found, with significantly different relative abundances and diversities of phyla and genera. The results provide valuable information on GIT microbial communities that may be useful for nutrition and health management in IMCs.
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Affiliation(s)
- M J Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - F Momtaz
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - A Q M R Kawsar
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - M M Rahman
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - S K Gupta
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - A C Y Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
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27
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Lőrincz ÁM, Bartos B, Szombath D, Szeifert V, Timár CI, Turiák L, Drahos L, Kittel Á, Veres DS, Kolonics F, Mócsai A, Ligeti E. Role of Mac-1 integrin in generation of extracellular vesicles with antibacterial capacity from neutrophilic granulocytes. J Extracell Vesicles 2019; 9:1698889. [PMID: 31853340 PMCID: PMC6913618 DOI: 10.1080/20013078.2019.1698889] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 10/01/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022] Open
Abstract
Production of extracellular vesicles (EVs) involved in intercellular communication is a common capacity of most cell types. Upon encountering opsonized microorganisms, neutrophilic granulocytes release EVs that compromise bacterial growth. We carried out a systematic investigation of the involvement of potential opsonin receptors in EV-generation from human and murine neutrophils. Applying flow cytometric, proteomic and functional analysis as well as using genetically modified mice, we demonstrate that formation of antibacterial EVs depends upon stimulation of the multifunctional Mac-1 integrin complex, also called as complement receptor 3 (CR3), whereas activation of immunoglobulin binding Fc receptors or pattern recognition receptors alone or in combination is ineffective. Mac-1/CR3 stimulation and downstream tyrosine kinase signalling affect both the numbers, the cargo content and the antibacterial capacity of the produced vesicles. In contrast, Mac-1/CR3 signalling is not required for spontaneous EV formation, clearly indicating the existence of separate molecular pathways in EV biogenesis. We propose that EVs are “tailor-made” with different composition and functional properties depending on the environmental circumstances.
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Affiliation(s)
- Ákos M Lőrincz
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Balázs Bartos
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Dávid Szombath
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | | | - Csaba I Timár
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Science, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Science, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Kittel
- Experimental Research Institute of Hungarian Academy of Sciences, Budapest, Hungary
| | - Dániel S Veres
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ferenc Kolonics
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Attila Mócsai
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Erzsébet Ligeti
- Department of Physiology, Semmelweis University, Budapest, Hungary
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28
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Figliolini F, Ranghino A, Grange C, Cedrino M, Tapparo M, Cavallari C, Rossi A, Togliatto G, Femminò S, Gugliuzza MV, Camussi G, Brizzi MF. Extracellular Vesicles From Adipose Stem Cells Prevent Muscle Damage and Inflammation in a Mouse Model of Hind Limb Ischemia: Role of Neuregulin-1. Arterioscler Thromb Vasc Biol 2019; 40:239-254. [PMID: 31665908 DOI: 10.1161/atvbaha.119.313506] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Critical hindlimb ischemia is a severe consequence of peripheral artery disease. Surgical treatment does not prevent skeletal muscle impairment or improve long-term patient outcomes. The present study investigates the protective/regenerative potential and the mechanism of action of adipose stem cell-derived extracellular vesicles (ASC-EVs) in a mouse model of hindlimb ischemia. Approach and Results: We demonstrated that ASC-EVs exert a protective effect on muscle damage by acting both on tissue microvessels and muscle cells. The genes involved in muscle regeneration were up-regulated in the ischemic muscles of ASC-EV-treated animals. MyoD expression has also been confirmed in satellite cells. This was followed by a reduction in muscle function impairment in vivo. ASC-EVs drive myoblast proliferation and differentiation in the in vitro ischemia/reoxygenation model. Moreover, ASC-EVs have shown an anti-apoptotic effect both in vitro and in vivo. Transcriptomic analyses have revealed that ASC-EVs carry a variety of pro-angiogenic mRNAs, while proteomic analyses have demonstrated an enrichment of NRG1 (neuregulin 1). A NRG1 blocking antibody used in vivo demonstrated that NRG1 is relevant to ASC-EV-induced muscle protection, vascular growth, and recruitment of inflammatory cells. Finally, bioinformatic analyses on 18 molecules that were commonly detected in ASC-EVs, including mRNAs and proteins, confirmed the enrichment of pathways involved in vascular growth and muscle regeneration/protection. CONCLUSIONS This study demonstrates that ASC-EVs display pro-angiogenic and skeletal muscle protective properties that are associated with their NRG1/mRNA cargo. We, therefore, propose that ASC-EVs are a useful tool for therapeutic angiogenesis and muscle protection.
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Affiliation(s)
- Federico Figliolini
- From the 2i3T Scarl University of Turin (F.F., M.C., C.C.), University of Turin, Italy
| | - Andrea Ranghino
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Cristina Grange
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Massimo Cedrino
- From the 2i3T Scarl University of Turin (F.F., M.C., C.C.), University of Turin, Italy
| | - Marta Tapparo
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Claudia Cavallari
- From the 2i3T Scarl University of Turin (F.F., M.C., C.C.), University of Turin, Italy
| | - Andrea Rossi
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Gabriele Togliatto
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Saveria Femminò
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Maria Vittoria Gugliuzza
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Giovanni Camussi
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
| | - Maria Felice Brizzi
- Department of Medical Sciences (A. Ranghino, C.G., M.T., A. Rossi, G.T., S.F., M.V.G., G.C., M.F.B.), University of Turin, Italy
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Huang R, Wang K, Gao L, Gao W. TIMP1 Is A Potential Key Gene Associated With The Pathogenesis And Prognosis Of Ulcerative Colitis-Associated Colorectal Cancer. Onco Targets Ther 2019; 12:8895-8904. [PMID: 31802901 PMCID: PMC6826183 DOI: 10.2147/ott.s222608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is the third most frequently diagnosed cancer worldwide. As a high-risk factor for CRC, ulcerative colitis (UC) has been demonstrated to lead to epithelial dysplasia, DNA damage, and eventually cancer. There are approximately 18% of patients with UC may develop CRC. Patients and methods The gene expression profiles were retrieved from the Gene Expression Omnibus. The Database for Annotation, Visualization and Integrated Discovery was employed to conduct gene annotations. Protein-protein interaction network was constructed by the Search Tool for the Retrieval of Interacting Genes, and further analysed by the Molecular Complex Detection. The correlation between TIMP1 and prognosis was evaluated by the Gene Expression Profiling Interactive Analysis. To predict the potential functions of TIMP1, the GeneMANIA, Coremine, and FunRich were employed. After transfection with small interfering RNA targeting TIMP1, cell proliferation, migration, and apoptosis were determined by CCK-8, scratch wound, and Annexin V-FITC/PI assays, respectively. Results TIMP1, consistently overexpressed in the initiation and progression of UC-associated CRC (ucaCRC), was identified to be a potential biomarker for the prognosis of patients with CRC. Experimental results showed knockdown of TIMP1 could increase the migration, while did not affect the proliferation and apoptosis of RKO cells. The role of TIMP1 in the malignant transformation of ucaCRC was confirmed by using the protein/gene interactions and biological process annotation and validated by analysing the transcription factors targeting TIMP1. Conclusion TIMP1 is consistently upregulated in the pathological process of ucaCRC and can be a potential biomarker for the worse prognosis of CRC.
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Affiliation(s)
- Ru Huang
- Department of Heart Failure, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Kaijing Wang
- Department of Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Lei Gao
- Department of Heart Failure, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Wei Gao
- Department of Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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30
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Foysal MJ, Nguyen TTT, Chaklader MR, Siddik MAB, Tay CY, Fotedar R, Gupta SK. Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron ( Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum. PeerJ 2019; 7:e7553. [PMID: 31523510 PMCID: PMC6716501 DOI: 10.7717/peerj.7553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022] Open
Abstract
This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet, Bangladesh
| | - Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Muhammad A B Siddik
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.,Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Sanjay Kumar Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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31
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Wang CCN, Li CY, Cai JH, Sheu PCY, Tsai JJP, Wu MY, Li CJ, Hou MF. Identification of Prognostic Candidate Genes in Breast Cancer by Integrated Bioinformatic Analysis. J Clin Med 2019; 8:jcm8081160. [PMID: 31382519 PMCID: PMC6723760 DOI: 10.3390/jcm8081160] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is one of the most common malignancies. However, the molecular mechanisms underlying its pathogenesis remain to be elucidated. The present study aimed to identify the potential prognostic marker genes associated with the progression of breast cancer. Weighted gene coexpression network analysis was used to construct free-scale gene coexpression networks, evaluate the associations between the gene sets and clinical features, and identify candidate biomarkers. The gene expression profiles of GSE48213 were selected from the Gene Expression Omnibus database. RNA-seq data and clinical information on breast cancer from The Cancer Genome Atlas were used for validation. Four modules were identified from the gene coexpression network, one of which was found to be significantly associated with patient survival time. The expression status of 28 genes formed the black module (basal); 18 genes, dark red module (claudin-low); nine genes, brown module (luminal), and seven genes, midnight blue module (nonmalignant). These modules were clustered into two groups according to significant difference in survival time between the groups. Therefore, based on betweenness centrality, we identified TXN and ANXA2 in the nonmalignant module, TPM4 and LOXL2 in the luminal module, TPRN and ADCY6 in the claudin-low module, and TUBA1C and CMIP in the basal module as the genes with the highest betweenness, suggesting that they play a central role in information transfer in the network. In the present study, eight candidate biomarkers were identified for further basic and advanced understanding of the molecular pathogenesis of breast cancer by using co-expression network analysis.
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Affiliation(s)
- Charles C N Wang
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 413, Taiwan
| | - Chia Ying Li
- Department of Surgery, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung 402, Taiwan
| | - Jia-Hua Cai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 413, Taiwan
| | - Phillip C-Y Sheu
- Department of EECS and BME, University of California, Irvine, CA 92697, USA
| | - Jeffrey J P Tsai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 413, Taiwan
| | - Meng-Yu Wu
- Department of Emergency Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
- Department of Emergency Medicine, School of Medicine, Tzu Chi University, Hualien 970, Taiwan
| | - Chia-Jung Li
- Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan.
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Ming-Feng Hou
- Division of Breast Surgery, Department of Surgery, Center for Cancer Research,Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung 807, Taiwan.
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- National Sun Yat-Sen University-Kaohsiung Medical University Joint Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- National Chiao Tung University-Kaohsiung Medical University Joint Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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Liu D, Huo Y, Chen S, Xu D, Yang B, Xue C, Fu L, Bu L, Song S, Mei C. Identification of Key Genes and Candidated Pathways in Human Autosomal Dominant Polycystic Kidney Disease by Bioinformatics Analysis. Kidney Blood Press Res 2019; 44:533-552. [DOI: 10.1159/000500458] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022] Open
Abstract
Background/Aims: Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic form of kidney disease. High-throughput microarray analysis has been applied for elucidating key genes and pathways associated with ADPKD. Most genetic profiling data from ADPKD patients have been uploaded to public databases but not thoroughly analyzed. This study integrated 2 human microarray profile datasets to elucidate the potential pathways and protein-protein interactions (PPIs) involved in ADPKD via bioinformatics analysis in order to identify possible therapeutic targets. Methods: The kidney tissue microarray data of ADPKD patients and normal individuals were searched and obtained from NCBI Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified, and enriched pathways and central node genes were elucidated using related websites and software according to bioinformatics analysis protocols. Seven DEGs were validated between polycystic kidney disease and control kidney samples by quantitative real-time polymerase chain reaction. Results: Two original human microarray datasets, GSE7869 and GSE35831, were integrated and thoroughly analyzed. In total, 6,422 and 1,152 DEGs were extracted from GSE7869 and GSE35831, respectively, and of these, 561 DEGs were consistent between the databases (291 upregulated genes and 270 downregulated genes). From 421 nodes, 34 central node genes were obtained from a PPI network complex of DEGs. Two significant modules were selected from the PPI network complex by using Cytotype MCODE. Most of the identified genes are involved in protein binding, extracellular region or space, platelet degranulation, mitochondrion, and metabolic pathways. Conclusions: The DEGs and related enriched pathways in ADPKD identified through this integrated bioinformatics analysis provide insights into the molecular mechanisms of ADPKD and potential therapeutic strategies. Specifically, abnormal decorin expression in different stages of ADPKD may represent a new therapeutic target in ADPKD, and regulation of metabolism and mitochondrial function in ADPKD may become a focus of future research.
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Zandonadi FS, Castañeda Santa Cruz E, Korvala J. New SDC function prediction based on protein-protein interaction using bioinformatics tools. Comput Biol Chem 2019; 83:107087. [PMID: 31351242 DOI: 10.1016/j.compbiolchem.2019.107087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/13/2019] [Accepted: 06/23/2019] [Indexed: 12/11/2022]
Abstract
The precise roles for SDC have been complex to specify. Assigning and reanalyzing protein and peptide identification to novel protein functions is one of the most important challenges in postgenomic era. Here, we provide SDC molecular description to support, contextualize and reanalyze the corresponding protein-protein interaction (PPI). From SDC-1 data mining, we discuss the potential of bioinformatics tools to predict new biological rules of SDC. Using these methods, we have assembled new possibilities for SDC biology from PPI data, once, the understanding of biology complexity cannot be capture from one simple question.
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Affiliation(s)
- Flávia S Zandonadi
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Departamento de Química Analítica, Universidade de Campinas, UNICAMP, Campinas, SP, Brazil.
| | - Elisa Castañeda Santa Cruz
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Departamento de Química Analítica, Universidade de Campinas, UNICAMP, Campinas, SP, Brazil
| | - Johanna Korvala
- Cancer and Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, University of Oulu, Oulu, Finland
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34
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Liu YR, Hu Y, Zeng Y, Li ZX, Zhang HB, Deng JL, Wang G. Neurexophilin and PC-esterase domain family member 4 (NXPE4) and prostate androgen-regulated mucin-like protein 1 (PARM1) as prognostic biomarkers for colorectal cancer. J Cell Biochem 2019; 120:18041-18052. [PMID: 31297877 DOI: 10.1002/jcb.29107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022]
Abstract
Owing to the high morbidity and mortality, novel biomarkers in the occurrence and development of colorectal cancer (CRC) are needed nowadays. In this study, the CRC-related datasets were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. After screening the differentially expressed genes (DEGs) in R software, a total of 238 upregulated and 199 downregulated DEGs were revealed simultaneously. Then the Kaplan-Meier survival analysis and Cox regression analysis were used to reveal the prognostic function of these DEGs. Neurexophilin and PC-esterase domain family member 4 (NXPE4) and prostate androgen-regulated mucin-like protein 1 (PARM1) were two outstanding independent overall survival (OS) and relapse-free survival (RFS) prognostic genes of CRC in TCGA database. We next verified the expression of NXPE4 and PARM1 messenger RNA (mRNA) levels were significantly lower in CRC tumor tissue than in the adjacent noncancerous tissue in our clinical samples, and NXPE4 mRNA expression level was related to the tumor location and tumor size, while PARM1 was related to tumor location, lymph nodes metastasis, and tumor size. This study demonstrated that NXPE4 and PARM1 might be two potential novel prognostic biomarkers for CRC.
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Affiliation(s)
- Ya-Rui Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Yang Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Ying Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Zhi-Xing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Hai-Bo Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Jun-Li Deng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, P. R. China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, P.R. China
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Chen WX, Xu LY, Cheng L, Qian Q, He X, Peng WT, Zhu YL. Bioinformatics analysis of dysregulated microRNAs in exosomes from docetaxel-resistant and parental human breast cancer cells. Cancer Manag Res 2019; 11:5425-5435. [PMID: 31354350 PMCID: PMC6579872 DOI: 10.2147/cmar.s201335] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Resistance to docetaxel is a major obstacle to effective treatment of breast cancer. Exosomal microRNAs (miRNAs) have recently been introduced in cell-to-cell transmission of chemoresistance between heterogeneous populations of tumor cells with diverse drug sensitivity. However, a systematic evaluation of the exosomal miRNA signature remains largely unclear. Method: miRNA expression profiles in exosomes from docetaxel-resistant (D/exo) and parental sensitive breast cancer cells (S/exo) were assessed using microarray. Bioinformatics analysis was performed to predict target genes of the dysregulated miRNAs and to uncover their potential roles in chemoresistance formation. Signaling pathways, gene ontology terms, transcription factors, protein-protein interactions, and hub genes were also constructed. Results: The selected exosomal miRNAs could modulate target genes responsible for MAPK, TGF-beta, Wnt, mTOR, and PI3K/Akt signaling pathways. Function enrichment analysis revealed the involvement of target genes in transcription regulation, protein phosphorylation, kinase activity, and protein binding. Enriched transcription factors including SP1, SP4, and EGR1 were obtained and a protein-protein interaction network was established. The hub genes for up-expressed and down-expressed exosomal miRNAs such as CCND1 and PTEN were identified. Conclusion: This bioinformatics study provides a comprehensive view of the function of dysregulated exosomal miRNAs, and may help us to understand exosome-mediated resistance transmission and overcome docetaxel resistance in future breast cancer therapy.
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Affiliation(s)
- Wei-Xian Chen
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China.,Department of Post-doctoral Working Station, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
| | - Ling-Yun Xu
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
| | - Lin Cheng
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
| | - Qi Qian
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
| | - Xiao He
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
| | - Wen-Ting Peng
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
| | - Yu-Lan Zhu
- Department of Breast Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, People's Republic of China
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Foysal MJ, Fotedar R, Tay CY, Gupta SK. Dietary supplementation of black soldier fly ( Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron ( Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets. PeerJ 2019; 7:e6891. [PMID: 31149398 PMCID: PMC6534111 DOI: 10.7717/peerj.6891] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/01/2019] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet, Bangladesh
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Sanjay Kumar Gupta
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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Liu T, You X, Sui J, Shen B, Zhang Y, Zhang XM, Yang S, Yao YZ, Yang F, Yin LH, Pu YP, Liang GY. Prognostic value of a two-microRNA signature for papillary thyroid cancer and a bioinformatic analysis of their possible functions. J Cell Biochem 2019; 120:7185-7198. [PMID: 30390338 DOI: 10.1002/jcb.27993] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Recent scientific evidence has suggested that microRNAs (miRNAs) play an important role in papillary thyroid cancer (PTC). In the current study, we aim to identify a miRNA-related signature as the sensitive and novel prognostic biomarkers. METHODS We performed a comprehensive analysis of the data downloaded from the Cancer Genome Atlas (TCGA) database. The association between survival outcome and miRNA was assessed by the univariate and multivariate Cox proportional hazards model. The risk score model was built to evaluate the predicting value of miRNA signature. The potential biofunctions and transcription factors of target miRNAs were investigated through bioinformatic analysis. The result was verified by the quantitative real-time polymerase chain reaction (qRT-PCR) in 32 pairs of PTC and adjacent nontumor tissues. In addition, the results were verified by other cohorts from gene expression omnibus (GEO) as detected by microarrays. RESULTS A total of 1030 miRNAs were identified from the TCGA database. Thirty-six key intersection miRNAs were obtained. The associations between clinical features and key miRNAs were evaluated. Eventually, a two-miRNA signature (hsa-miR-181a-2-3p and hsa-miR-138-1-3p) was identified. The power of the miRNA prognostic signature was effective. In total, we identified 202 genes that were associated with 2 miRNAs above, and the top 10 enriched transcript factors that highly related with the target miRNAs were explored. The qRT-PCR and GEO data validation were consistent with bioinformatics results. CONCLUSIONS A tumor-specific miRNA signature was identified, and the joint prognostic power was evaluated, which may be potential biomarkers for prognosis of PTC. IMPACT The two-miRNA signature could become the potential prognostic indicator of PTC in the future.
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Affiliation(s)
- Tong Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Xin You
- Department of General Surgery, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Jing Sui
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Bo Shen
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China
| | - Yan Zhang
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China
| | - Xiao-Mei Zhang
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China
| | - Sheng Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Yong-Zhong Yao
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Fei Yang
- Department of Occupational and Environmental Health, School of Public Health, Central South University, Changsha, Hunan, China
| | - Li-Hong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Yue-Pu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Ge-Yu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
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Xiong Y, Liu L, Xia Y, Qi Y, Chen Y, Chen L, Zhang P, Kong Y, Qu Y, Wang Z, Lin Z, Chen X, Xiang Z, Wang J, Bai Q, Zhang W, Yang Y, Guo J, Xu J. Tumor infiltrating mast cells determine oncogenic HIF-2α-conferred immune evasion in clear cell renal cell carcinoma. Cancer Immunol Immunother 2019; 68:731-741. [PMID: 30758643 PMCID: PMC11028303 DOI: 10.1007/s00262-019-02314-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 02/07/2019] [Indexed: 01/16/2023]
Abstract
PURPOSE Hypoxia-inducible factor 2α (HIF-2α) overexpression leads to activation of angiogenic pathways. However, little is known about the association between HIF-2α expression and anti-tumor immunity in clear cell renal cell carcinoma (ccRCC). We aimed to explore how HIF-2α influenced the microenvironment and the underlying mechanisms. EXPERIMENTAL DESIGN We immunohistochemically evaluated immune cells infiltrations and prognostic value of HIF-2α expression in a retrospective Zhongshan Hospital cohort of 280 ccRCC patients. Fresh tumor samples, non-tumor tissues and autologous peripheral blood for RT-PCR, ELISA and flow cytometry analyses were collected from patients who underwent nephrectomy in Zhongshan Hospital from September 2017 to April 2018. The TCGA KIRC cohort and SATO cohort were assessed to support our findings. RESULTS We demonstrated that ccRCC patients with HIF-2αhigh tumors exhibited reduced overall survival (p = 0.025) and recurrence-free survival (p < 0.001). Functions of CD8+ T cells were impaired in HIF-2αhigh patients. In ccRCC patients, HIF-2α induced the expression of stem cell factor (SCF), which served as chemoattractant for mast cells. Tumor infiltrating mast cells impaired anti-tumor immunity partly by secreting IL-10 and TGF-β. HIF-2α mRNA level adversely associated with immunostimulatory genes expression in KIRC and SATO cohorts. CONCLUSIONS HIF-2α contributed to evasion of anti-tumor immunity via SCF secretion and subsequent recruitment of mast cells in ccRCC patients.
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Affiliation(s)
- Ying Xiong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Liu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Xia
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yangyang Qi
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yifan Chen
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peipei Zhang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunyi Kong
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yang Qu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zewei Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiyuan Lin
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiang Chen
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhuoyi Xiang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Bai
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuanfeng Yang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
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Hurwitz SN, Meckes DG. Extracellular Vesicle Integrins Distinguish Unique Cancers. Proteomes 2019; 7:proteomes7020014. [PMID: 30979041 PMCID: PMC6630702 DOI: 10.3390/proteomes7020014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 12/16/2022] Open
Abstract
The proteomic profile of extracellular vesicles (EVs) has been of increasing interest, particularly in understanding cancer growth, drug resistance, and metastatic behavior. Emerging data suggest that cancer-derived EVs carry an array of oncogenic cargo, including certain integrin proteins that may, in turn, promote cell detachment, migration, and selection of future metastatic sites. We previously reported a large comparison of secreted vesicle protein cargo across sixty diverse human cancer cell lines. Here, we analyze the distinct integrin profiles of these cancer EVs. We further demonstrate the enrichment of integrin receptors in cancer EVs compared to vesicles secreted from benign epithelial cells. The total EV integrin levels, including the quantity of integrins α6, αv, and β1 correlate with tumor stage across a variety of epithelial cancer cells. In particular, integrin α6 also largely reflects breast and ovarian progenitor cell expression, highlighting the utility of this integrin protein as a potential circulating biomarker of certain primary tumors. This study provides preliminary evidence of the value of vesicle-associated integrin proteins in detecting the presence of cancer cells and prediction of tumor stage. Differential expression of integrins across cancer cells and selective packaging of integrins into EVs may contribute to further understanding the development and progression of tumor growth and metastasis across a variety of cancer types.
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Affiliation(s)
- Stephanie N Hurwitz
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA.
| | - David G Meckes
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA.
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40
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Foysal M, Fotedar R, Gupta S, Chaklader M. Biological ball filters regulate bacterial communities in marron (
Cherax cainii
) culture system. Lett Appl Microbiol 2019; 68:455-463. [DOI: 10.1111/lam.13125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 11/28/2022]
Affiliation(s)
- M.J. Foysal
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Genetic Engineering and Biotechnology Shahjalal University of Science and Technology Sylhet Bangladesh
| | - R. Fotedar
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - S.K. Gupta
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
- ICAR‐Indian Institute of Agricultural Biotechnology Ranchi India
| | - M.R. Chaklader
- School of Molecular and Life Sciences Curtin University Bentley WA Australia
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41
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The classical NLRP3 inflammasome controls FADD unconventional secretion through microvesicle shedding. Cell Death Dis 2019; 10:190. [PMID: 30804327 PMCID: PMC6389912 DOI: 10.1038/s41419-019-1412-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022]
Abstract
Fas-associated death domain (FADD) is a key adaptor molecule involved in numerous physiological processes including cell death, proliferation, innate immunity and inflammation. Therefore, changes in FADD expression have dramatic cellular consequences. In mice and humans, FADD regulation can occur through protein secretion. However, the molecular mechanisms accounting for human FADD secretion were still unknown. Here we report that canonical, non-canonical, but not alternative, NLRP3 inflammasome activation in human monocytes/macrophages induced FADD secretion. NLRP3 inflammasome activation by the bacterial toxin nigericin led to the proinflammatory interleukin-1β (IL-1β) release and to the induction of cell death by pyroptosis. However, we showed that FADD secretion could occur in absence of increased IL-1β release and pyroptosis and, reciprocally, that IL-1β release and pyroptosis could occur in absence of FADD secretion. Especially, FADD, but not IL-1β, secretion following NLRP3 inflammasome activation required extracellular glucose. Thus, FADD secretion was an active process distinct from unspecific release of proteins during pyroptosis. This FADD secretion process required K+ efflux, NLRP3 sensor, ASC adaptor and CASPASE-1 molecule. Moreover, we identified FADD as a leaderless protein unconventionally secreted through microvesicle shedding, but not exosome release. Finally, we established human soluble FADD as a new marker of joint inflammation in gout and rheumatoid arthritis, two rheumatic diseases involving the NLRP3 inflammasome. Whether soluble FADD could be an actor in these diseases remains to be determined. Nevertheless, our results advance our understanding of the mechanisms contributing to the regulation of the FADD protein expression in human cells.
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42
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Shao YC, Nie XC, Song GQ, Wei Y, Xia P, Xu XY. Prognostic value of DKK2 from the Dickkopf family in human breast cancer. Int J Oncol 2018; 53:2555-2565. [PMID: 30320375 PMCID: PMC6203157 DOI: 10.3892/ijo.2018.4588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022] Open
Abstract
Breast cancer is one of the most frequently diagnosed types of cancer with a high mortality and malignancy rate in women worldwide. The Dickkopf (DKK) protein family, as a canonical Wnt/β-catenin pathway antagonist, has been implicated in both physiological and pathological processes. This study aimed to comprehensively characterize the prognostic value and elucidate the mechanisms of DKKs in breast cancer and its subtypes. Firstly, DKK mRNA expression and corresponding outcome were analyzed by means of the Gene Expression-Based Outcome for Breast Cancer Online (GOBO) platform based on PAM50 intrinsic breast cancer subtypes. Subsequently, we extracted breast cancer datasets from the Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) to validate the expression profile and prognostic values from the GOBO platform. Moreover, a protein-protein network was created and functional enrichment was conducted to explore the underlying mechanisms of action of the DKKs. In addition, we uncovered the genetic and epigenetic alterations of DKK2 in breast cancer. The main finding of this study was the differential roles of DKKs in the PAM50 subtypes of breast cancer analyzed. The overall trend was that a high level of DKK2 was associated with a good survival in breast cancer, although it played an opposite role in the Normal-like subtype. We also found that DKK2 carried out its functions through multiple signaling pathways, not limited to the Wnt/β-catenin cascade in breast cancer. Finally, we used our own data to validate the bioinformatics analysis data for DKK2 by RT-qPCR. Taken together, our findings suggest that DKK2 may be a potential prognostic biomarker for the Normal-like subtype of breast cancer. However, the prognostic role of DKKs in the subtypes of breast cancer still requires validation by larger sample studies in the future.
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Affiliation(s)
- You-Cheng Shao
- Department of Pathophysiology, College of Basic Medicine Science, China Medical University, Shenyang, Liaoning 110122
| | - Xiao-Cui Nie
- Shenyang Maternity and Infant Hospital, Shenyang, Liaoning 110011
| | - Guo-Qing Song
- Department of Breast Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004
| | - Yan Wei
- Department of Pathophysiology, College of Basic Medicine Science, China Medical University, Shenyang, Liaoning 110122
| | - Pu Xia
- Department of Cell Biology, College of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Xiao-Yan Xu
- Department of Pathophysiology, College of Basic Medicine Science, China Medical University, Shenyang, Liaoning 110122
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43
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Wang J, Liu L, Bai Q, Ou C, Xiong Y, Qu Y, Wang Z, Xia Y, Guo J, Xu J. Tumor-infiltrating neutrophils predict therapeutic benefit of tyrosine kinase inhibitors in metastatic renal cell carcinoma. Oncoimmunology 2018; 8:e1515611. [PMID: 30546957 DOI: 10.1080/2162402x.2018.1515611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 01/15/2023] Open
Abstract
Tumor-infiltrating neutrophils (TINs) show diverse predictive effects in the context of different cancer types and therapeutic regimens. In this study we investigated their relevance with therapeutic effect of tyrosine kinase inhibitors (TKIs) in metastatic renal cell carcinoma (mRCC). Two independent datasets including 271 mRCC patients treated by TKIs or IL-2/IFN-α based immunotherapy were retrospective included, and TINs were detected by immunohistochemistry. The presence of TINs was observed in 50 (45.0%) samples of the TKI cohort and in 73 (45.6%) samples of the immunotherapy cohort. TINs were associated with shorter overall survival (HR, 1.776; 95%CI, 1.191-2.650; p = 0.004) in the TKI cohort, but not in the immunotherapy cohort (HR, 1.074; 95%CI, 0.767-1.505; p = 0.672). Multivariate Cox analysis confirmed the independent prognostic value of TINs for TKI-treated patients (HR, 2.078, 95%CI, 1.352-3.195; p = 0.001), apart from other parameters. Moreover, survival benefit of TKI therapy was superior to IL-2/IFN-α immunotherapy only among TINs-absent patients (HR, 1.561; 95%CI, 0.927-2.629; p = 0.094). Data mining in the TCGA cohort of renal cell carcinoma revealed the predominant immunosuppressive function of TINs in renal cell carcinoma. The negative correlation between TINs and intratumoral CD8+ T cells was further confirmed in the TKI cohort (p = 0.019), the immunotherapy cohort (p = 0.001) and the TCGA cohort (p < 0.001). In conclusion, the presence of TINs was an independent, unfavorable prognostic factor in TKI-treated mRCC patients. TINs could also predict therapeutic benefit of TKIs over IL-2/IFN-α immunotherapy. These findings should be further confirmed within datasets of clinical trials or prospective observational studies.
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Affiliation(s)
- Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Liu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Bai
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chenzhang Ou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ying Xiong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Qu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zewei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yu Xia
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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44
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Yan Y, Su W, Zeng S, Qian L, Chen X, Wei J, Chen N, Gong Z, Xu Z. Effect and Mechanism of Tanshinone I on the Radiosensitivity of Lung Cancer Cells. Mol Pharm 2018; 15:4843-4853. [PMID: 30216081 DOI: 10.1021/acs.molpharmaceut.8b00489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Resistance to radiotherapy is one of the main obstacles to improving cancer prognoses. To effectively destroy cancer cells, novel radiation sensitizers are needed. Recently, several natural products have been shown to exhibit promising tumor-killing properties. However, little is known about the specific mechanisms of these natural compounds on cancer treatment. In this study, after screening a high-throughput natural product library, we identified tanshinone I (Tan I) as a potential radiation sensitizer in lung cancer cells. METHODS Lung cancer radioresistant cell lines, H358-IR and H157-IR, were first established to confirm the radioresistant phenotypes. After that, a natural product library was used to screen the potential radiation sensitizer. We further examined the inhibition functions of Tan I on radioresistant cancer cells via a series of experiments. RESULTS Tan I significantly inhibited cell proliferation and clone formation, consequently enhancing radiosensitivity in radioresistant lung cancer cells, H358-IR and H157-IR. Stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics indicated that Tan I downregulates expression of pro-oncogenic protein phosphoribosyl pyrophosphate aminotransferase (PPAT) in both H358-IR and H157-IR cells. Further analysis of molecular docking showed that Tan I is well-docked into the active pocket of the structure of PPAT, serving as a potential PPAT inhibitor. CONCLUSIONS Taken together, these findings suggest that inhibition of the tumor promoter PPAT by Tan I exerts marked inhibitory effects on radioresistant lung cancer cells, improving radiation efficacy.
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45
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Hamid Z, Summa M, Armirotti A. A Swath Label-Free Proteomics insight into the Faah -/- Mouse Liver. Sci Rep 2018; 8:12142. [PMID: 30108271 PMCID: PMC6092373 DOI: 10.1038/s41598-018-30553-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Fatty acid amide hydrolase (FAAH) is an important enzyme for lipid metabolism and an interesting pharmacological target, given its role in anandamide breakdown. The FAAH−/− genotype is the most widely used mouse model to investigate the effects of a complete pharmacological inhibition of this enzyme. In this paper, we explore, by means of label-free SWATH proteomics, the changes in protein expression occurring in the liver of FAAH−/− knockout (KO) mice. We identified several altered biological processes and pathways, like fatty acid synthesis and glycolysis, which explain the observed phenotype of this mouse. We also observed the alteration of other proteins, like carboxylesterases and S-methyltransferases, apparently not immediately related to FAAH, but known to have important biological roles. Our study, reporting more than 3000 quantified proteins, offers an in-depth analysis of the liver proteome of this model.
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Affiliation(s)
- Zeeshan Hamid
- D3Validation, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova, Italy.,Scuola Superiore Sant'Anna. via Piazza Martiri della Libertà, 33, 56127, Pisa, Italy
| | - Maria Summa
- Analytical Chemistry and In-vivo Facility, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry and In-vivo Facility, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova, Italy.
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46
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You S, Gao L. Identification of NMU as a potential gene conferring alectinib resistance in non-small cell lung cancer based on bioinformatics analyses. Gene 2018; 678:137-142. [PMID: 30096454 DOI: 10.1016/j.gene.2018.08.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 12/25/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, and adjuvant targeted therapy has shown great benefits for the NSCLC patients with specific genomic mutations. Alectinib, a selective anaplastic lymphoma kinase (ALK) inhibitor, has been clinically used for the NSCLC patients with ALK-rearrangement, however, irreversible therapeutic resistance for the patients receiving alectinib treatment frequently occurs. Here we show that neuromedin U (NMU) may confer the alectinib resistance in NSCLC via multiple mechanisms based on the integrative bioinformatics analyses. Through employing the bioinformatics analyses of three microarray datasets, NMU, overexpressed in both NSCLC tissues and alectinib-resistant NSCLC cells, was initially identified as potential candidate for causing alectinib resistance in NSCLC. The resistance function of NMU in NSCLC was validated by performing protein/gene interactions and biological process annotation analyses, and further validated by analyzing the transcription factors targeting NMU mRNA. Collectively, these results indicated that NMU may confer alectinib resistance in NSCLC.
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Affiliation(s)
- Shuangjie You
- Department of Heart Failure, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Lei Gao
- Department of Heart Failure, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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47
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Jiang H, Zhu R, Liu H, Bao C, Liu J, Eltahir A, Langford PR, Sun D, Liu Z, Sun C, Gu J, Han W, Feng X, Lei L. Transcriptomic analysis of porcine PBMCs in response to Actinobacillus pleuropneumoniae reveals the dynamic changes of differentially expressed genes related to immuno-inflammatory responses. Antonie van Leeuwenhoek 2018; 111:2371-2384. [DOI: 10.1007/s10482-018-1126-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/06/2018] [Indexed: 01/23/2023]
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48
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Hurwitz SN, Sun L, Cole KY, Ford CR, Olcese JM, Meckes DG. An optimized method for enrichment of whole brain-derived extracellular vesicles reveals insight into neurodegenerative processes in a mouse model of Alzheimer's disease. J Neurosci Methods 2018; 307:210-220. [PMID: 29894726 DOI: 10.1016/j.jneumeth.2018.05.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the major cause of dementia that has increased dramatically in prevalence over the past several decades. Yet many questions still surround the etiology of AD. Recently, extracellular vesicles (EVs) that transport protein, lipid, and nucleic acids from cell to cell have been implicated in the clearance and propagation of misfolded proteins. Investigation of EVs in AD progression, and their potential diagnostic utility may contribute to understanding and treating AD. However, the challenges of isolating brain-derived EVs have in part hindered these studies. NEW METHOD Here, we provide an optimized method for the enrichment of brain-derived EVs by iodixanol floatation density gradient for mass spectrometry analysis. RESULTS We demonstrate the isolation of these vesicles and the enrichment of EV proteins compared to sedimentation gradient isolation of vesicles. Moreover, comparative proteomic analysis of brain-derived EVs from healthy and AD mouse brains revealed differences in vesicular content including proteins involved in aging, immune response, and oxidation-reduction maintenance. These changes provide insight into AD-associated neurodegeneration and potential biomarkers of AD. Comparison with existing methods: Recent techniques have used sedimentation sucrose gradients to isolate EVs from brain tissue. However, here we demonstrate the advantages of floatation iodixanol density gradient isolation of small EVs, and provide evidence of EV enrichment by electron microscopy, immunoblot analysis, and quantitative mass spectrometry. CONCLUSIONS Together these findings offer a rigorous technique for enriching whole tissue-derived EVs for downstream analyses, and application of this approach to uncovering molecular changes in AD progression and other neurological conditions.
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Affiliation(s)
- Stephanie N Hurwitz
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, United States
| | - Li Sun
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, United States
| | - Kalonji Y Cole
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, United States
| | - Charles R Ford
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, United States
| | - James M Olcese
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, United States.
| | - David G Meckes
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, United States.
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49
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Yang Y, Boza-Serrano A, Dunning CJR, Clausen BH, Lambertsen KL, Deierborg T. Inflammation leads to distinct populations of extracellular vesicles from microglia. J Neuroinflammation 2018; 15:168. [PMID: 29807527 PMCID: PMC5972400 DOI: 10.1186/s12974-018-1204-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background Activated microglia play an essential role in inflammatory responses elicited in the central nervous system (CNS). Microglia-derived extracellular vesicles (EVs) are suggested to be involved in propagation of inflammatory signals and in the modulation of cell-to-cell communication. However, there is a lack of knowledge on the regulation of EVs and how this in turn facilitates the communication between cells in the brain. Here, we characterized microglial EVs under inflammatory conditions and investigated the effects of inflammation on the EV size, quantity, and protein content. Methods We have utilized western blot, nanoparticle tracking analysis (NTA), and mass spectrometry to characterize EVs and examine the alterations of secreted EVs from a microglial cell line (BV2) following lipopolysaccharide (LPS) and tumor necrosis factor (TNF) inhibitor (etanercept) treatments, or either alone. The inflammatory responses were measured with multiplex cytokine ELISA and western blot. We also subjected TNF knockout mice to experimental stroke (permanent middle cerebral artery occlusion) and validated the effect of TNF inhibition on EV release. Results Our analysis of EVs originating from activated BV2 microglia revealed a significant increase in the intravesicular levels of TNF and interleukin (IL)-6. We also observed that the number of EVs released was reduced both in vitro and in vivo when inflammation was inhibited via the TNF pathway. Finally, via mass spectrometry, we identified 49 unique proteins in EVs released from LPS-activated microglia compared to control EVs (58 proteins in EVs released from LPS-activated microglia and 37 from control EVs). According to Gene Ontology (GO) analysis, we found a large increase of proteins related to translation and transcription in EVs from LPS. Importantly, we showed a distinct profile of proteins found in EVs released from LPS treated cells compared to control. Conclusions We demonstrate altered EV production in BV2 microglial cells and altered cytokine levels and protein composition carried by EVs in response to LPS challenge. Our findings provide new insights into the potential roles of EVs that could be related to the pathogenesis in neuroinflammatory diseases. Electronic supplementary material The online version of this article (10.1186/s12974-018-1204-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiyi Yang
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Lund, Sweden.
| | - Antonio Boza-Serrano
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Lund, Sweden
| | | | - Bettina Hjelm Clausen
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,BRIGDE-Brain Research-Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kate Lykke Lambertsen
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,BRIGDE-Brain Research-Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Tomas Deierborg
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Lund, Sweden.
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50
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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