201
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Khezri A, Narud B, Stenseth EB, Johannisson A, Myromslien FD, Gaustad AH, Wilson RC, Lyle R, Morrell JM, Kommisrud E, Ahmad R. DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation. BMC Genomics 2019; 20:897. [PMID: 31775629 PMCID: PMC6880426 DOI: 10.1186/s12864-019-6307-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the swine artificial insemination industry to assess sperm DNA integrity. Recently, in some elite Norwegian Landrace boars (boars with excellent field fertility records), a higher level of sperm DFI has been observed. In order to obtain a better understanding of this, and to study the complexity of sperm DNA integrity, liquid preserved semen samples from elite boars with contrasting DFI levels were examined for protamine deficiency, thiol profile and disulphide bonds. Additionally, the DNA methylation profiles of the samples were determined by reduced representation bisulphite sequencing (RRBS). RESULTS In this study, different traits related to sperm DNA integrity were investigated (n = 18 ejaculates). Upon liquid storage, the levels of total thiols and disulphide bonds decreased significantly, while the DFI and protamine deficiency level increased significantly. The RRBS results revealed similar global patterns of low methylation from semen samples with different levels of DFI (low, medium and high). Differential methylation analyses indicated that the number of differentially methylated cytosines (DMCs) increased in the low-high compared to the low-medium and the medium-high DFI groups. Annotating the DMCs with gene and CpG features revealed clear differences between DFI groups. In addition, the number of annotated transcription starting sites (TSS) and associated pathways in the low-high comparison was greater than the other two groups. Pathway analysis showed that genes (based on the closest TSS to DMCs) corresponding to low-high DFI comparison were associated with important processes such as membrane function, metabolic cascade and antioxidant defence system. CONCLUSION To our knowledge, this is the first study evaluating DNA methylation in boar sperm cells with different levels of DFI. The present study shows that sperm cells with varying levels of DNA fragmentation exhibit similar global methylation, but different site-specific DNA methylation signatures. Moreover, with increasing DNA fragmentation in spermatozoa, there is an increase in the number of potentially affected downstream genes and their respective regulatory pathways.
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Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Else-Berit Stenseth
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Anders Johannisson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Ann Helen Gaustad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Topigs Norsvin, Hamar, Norway
| | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Jane M Morrell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.
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202
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Tvarijonaviciute A, Martinez-Lozano N, Rios R, Marcilla de Teruel MC, Garaulet M, Cerón JJ. Saliva as a non-invasive tool for assessment of metabolic and inflammatory biomarkers in children. Clin Nutr 2019; 39:2471-2478. [PMID: 31787367 DOI: 10.1016/j.clnu.2019.10.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Epidemiological studies in school-age children are challenging, particularly those that aim to analyse metabolic markers on blood samples obtained via invasive and stressful procedures. The objective of this paper is to evaluate the use of saliva, as a non-invasive tool in epidemiological studies performed in school-age children, to capture metabolic changes associated with body mass index (BMI), dietary characteristics and physical activity in both boys and girls. METHODS This is an observational study in which healthy children of ages between 8 and 12 years (n = 129, 60 girls and 69 boys) from three schools in a Mediterranean area of Spain were included. A panel of biomarkers was measured in serum and saliva and correlated with BMI, dietary characteristics and physical activity. RESULTS Significant positive correlation between serum and salivary levels were detected for CRP (r = 0.770) in all included children, and boys (r = 0.805) and girls (r = 0.775) separately (P < 0.001, in all cases) and for insulin in girls (r = 0.442; P < 0.05). Among all studied salivary biomarkers, insulin was significantly correlated with the three factors studied: positively with BMI and negatively with dietary characteristics (intake and composition) and physical activity (P < 0.05). Obesity and diet composition were both positively associated to pro-inflammatory biomarkers, CRP and IL1b; while diet composition shared with physical activity levels the correlation with IL6 (positive with energy, fat, carbohydrate and saturated fatty acid intake, and negative with cholesterol intake and average physical activity in boys), NGF and glucose (in both cases correlations were negative with diet composition and physical activity variables) (P < 0.05, in all cases). Sex differences were detected in serum glucose and TNFα. CONCLUSIONS Biomarkers in saliva are able to capture differences in BMI, dietary characteristics and physical activity levels in school-age children. Saliva may potentially constitute a useful non-invasive and stress-free tool to evaluate metabolic markers of inflammation and/or metabolism related to BMI and lifestyle in a sex-dependent manner.
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Affiliation(s)
- Asta Tvarijonaviciute
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), University of Murcia, Murcia, Spain.
| | | | | | | | - Marta Garaulet
- Department of Physiology, University of Murcia, IMIB-Arrixaca, Murcia, Spain.
| | - Jose J Cerón
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), University of Murcia, Murcia, Spain.
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203
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Based on Integrated Bioinformatics Analysis Identification of Biomarkers in Hepatocellular Carcinoma Patients from Different Regions. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1742341. [PMID: 31886176 PMCID: PMC6925735 DOI: 10.1155/2019/1742341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023]
Abstract
Accumulating statistics have shown that liver cancer causes the second highest mortality rate of cancer-related deaths worldwide, of which 80% is hepatocellular carcinoma (HCC). Given the underlying molecular mechanism of HCC pathology is not fully understood yet, identification of reliable predictive biomarkers is more applicable to improve patients' outcomes. The results of principal component analysis (PCA) showed that the grouped data from 1557 samples in Gene Expression Omnibus (GEO) came from different populations, and the mean tumor purity of tumor tissues was 0.765 through the estimate package in R software. After integrating the differentially expressed genes (DEGs), we finally got 266 genes. Then, the protein-protein interaction (PPI) network was established based on these DEGs, which contained 240 nodes and 1747 edges. FOXM1 was the core gene in module 1 and highly associated with FOXM1 transcription factor network pathway, while FTCD was the core gene in module 2 and was enriched in the metabolism of amino acids and derivatives. The expression levels of hub genes were in line with The Cancer Genome Atlas (TCGA) database. Meanwhile, there were certain correlations among the top ten genes in the up- and downregulated DEGs. Finally, Kaplan–Meier curves and receiver operating characteristic (ROC) curves were plotted for the top five genes in PPI. Apart from CDKN3, the others were closely concerned with overall survival. In this study, we detected the potential biomarkers and their involved biological processes, which would provide a new train of thought for clinical diagnosis and treatment.
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204
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Naderi-Meshkin H, Lai X, Amirkhah R, Vera J, Rasko JEJ, Schmitz U. Exosomal lncRNAs and cancer: connecting the missing links. Bioinformatics 2019; 35:352-360. [PMID: 30649349 DOI: 10.1093/bioinformatics/bty527] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 06/28/2018] [Indexed: 12/13/2022] Open
Abstract
Motivation Extracellular vesicles (EVs), including exosomes and microvesicles, are potent and clinically valuable tools for early diagnosis, prognosis and potentially the targeted treatment of cancer. The content of EVs is closely related to the type and status of the EV-secreting cell. Circulating exosomes are a source of stable RNAs including mRNAs, microRNAs and long non-coding RNAs (lncRNAs). Results This review outlines the links between EVs, lncRNAs and cancer. We highlight communication networks involving the tumor microenvironment, the immune system and metastasis. We show examples supporting the value of exosomal lncRNAs as cancer biomarkers and therapeutic targets. We demonstrate how a system biology approach can be used to model cell-cell communication via exosomal lncRNAs and to simulate effects of therapeutic interventions. In addition, we introduce algorithms and bioinformatics resources for the discovery of tumor-specific lncRNAs and tools that are applied to determine exosome content and lncRNA function. Finally, this review provides a comprehensive collection and guide to databases for exosomal lncRNAs. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hojjat Naderi-Meshkin
- Stem Cells & Regenerative Medicine Research Group, Academic Center for Education, Culture Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran.,Nastaran Center for Cancer Prevention, Mashhad, Iran
| | - Xin Lai
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Raheleh Amirkhah
- Nastaran Center for Cancer Prevention, Mashhad, Iran.,Reza Institute of Cancer Bioinformatics and Personalized Medicine, Mashhad, Iran
| | - Julio Vera
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, Australia.,Sydney Medical School, University of Sydney, Camperdown, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, Australia.,Sydney Medical School, University of Sydney, Camperdown, Australia
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205
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Qi L, Zhou B, Chen J, Hu W, Bai R, Ye C, Weng X, Zheng S. Significant prognostic values of differentially expressed-aberrantly methylated hub genes in breast cancer. J Cancer 2019; 10:6618-6634. [PMID: 31777591 PMCID: PMC6856906 DOI: 10.7150/jca.33433] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/31/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction: Abnormal status of gene expression plays an important role in tumorigenesis, progression and metastasis of breast cancer. Mechanisms of gene silence or activation were varied. Methylation of genes may contribute to alteration of gene expression. This study aimed to identify differentially expressed hub genes which may be regulated by DNA methylation and evaluate their prognostic value in breast cancer by bioinformatic analysis. Methods: GEO2R was used to obtain expression microarray data from GSE54002, GSE65194 and methylation microarray data from GSE20713, GSE32393. Differentially expressed-aberrantly methylated genes were identified by FunRich. Biological function and pathway enrichment analysis were conducted by DAVID. PPI network was constructed by STRING and hub genes was sorted by Cytoscape. Expression and DNA methylation of hub genes was validated by UALCAN and MethHC. Clinical outcome analysis of hub genes was performed by Kaplan Meier-plotter database for breast cancer. IHC was performed to analyze protein levels of EXO1 and Kaplan-Meier was used for survival analysis. Results: 677 upregulated-hypomethylated and 361 downregulated-hypermethylated genes were obtained from GSE54002, GSE65194, GSE20713 and GSE32393 by GEO2R and FunRich. The most significant biological process, cellular component, molecular function enriched and pathway for upregulated-hypomethylated genes were viral process, cytoplasm, protein binding and cell cycle respectively. For downregulated-hypermethylated genes, the result was peptidyl-tyrosine phosphorylation, plasma membrane, transmembrane receptor protein tyrosine kinase activity and Rap1 signaling pathway (All p< 0.05). 12 hub genes (TOP2A, MAD2L1, FEN1, EPRS, EXO1, MCM4, PTTG1, RRM2, PSMD14, CDKN3, H2AFZ, CCNE2) were sorted from 677 upregulated-hypomethylated genes. 4 hub genes (EGFR, FGF2, BCL2, PIK3R1) were sorted from 361 downregulated-hypermethylated genes. Differential expression of 16 hub genes was validated in UALCAN database (p<0.05). 7 in 12 upregulated-hypomethylated and 2 in 4 downregulated-hypermethylated hub genes were confirmed to be significantly hypomethylated or hypermethylated in breast cancer using MethHC database (p<0.05). Finally, 12 upregulated hub genes (TOP2A, MAD2L1, FEN1, EPRS, EXO1, MCM4, PTTG1, RRM2, PSMD14, CDKN3, H2AFZ, CCNE2) and 3 downregulated genes (FGF2, BCL2, PIK3R1) contributed to significant unfavorable clinical outcome in breast cancer (p<0.05). High expression level of EXO1 protein was significantly associated with poor OS in breast cancer patients (p=0.03). Conclusion: Overexpression of TOP2A, MAD2L1, FEN1, EPRS, EXO1, MCM4, PTTG1, RRM2, PSMD14, CDKN3, H2AFZ, CCNE2 and downregulation of FGF2, BCL2, PIK3R1 might serve as diagnosis and poor prognosis biomarkers in breast cancer by more research validation. EXO1 was identified as an individual unfavorable prognostic factor. Methylation might be one of the major causes leading to abnormal expression of those genes. Functional analysis and pathway enrichment analysis of those genes would provide novel ideas for breast cancer research.
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Affiliation(s)
- Lina Qi
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Biting Zhou
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Jiani Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Rui Bai
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Chenyang Ye
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Xingyue Weng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
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206
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Saribas AS, Datta PK, Safak M. A comprehensive proteomics analysis of JC virus Agnoprotein-interacting proteins: Agnoprotein primarily targets the host proteins with coiled-coil motifs. Virology 2019; 540:104-118. [PMID: 31765920 DOI: 10.1016/j.virol.2019.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 11/29/2022]
Abstract
JC virus (JCV) Agnoprotein (Agno) plays critical roles in successful completion of the viral replication cycle. Understanding its regulatory roles requires a complete map of JCV-host protein interactions. Here, we report the first Agno interactome with host cellular targets utilizing "Two-Strep-Tag" affinity purification system coupled with mass spectroscopy (AP/MS). Proteomics data revealed that Agno primarily targets 501 cellular proteins, most of which contain "coiled-coil" motifs. Agno-host interactions occur in several cellular networks including those involved in protein synthesis and degradation; and cellular transport; and in organelles, including mitochondria, nucleus and ER-Golgi network. Among the Agno interactions, Rab11B, Importin and Crm-1 were first validated biochemically and further characterization was done for Crm-1, using a HIV-1 Rev-M10-like Agno mutant (L33D + E34L), revealing the critical roles of L33 and E34 residues in Crm-1 interaction. This comprehensive proteomics data provides new foundations to unravel the critical regulatory roles of Agno during the JCV life cycle.
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Affiliation(s)
- A Sami Saribas
- Department of Neuroscience, Laboratory of Molecular Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Prasun K Datta
- Department of Neuroscience, Laboratory of Molecular Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Mahmut Safak
- Department of Neuroscience, Laboratory of Molecular Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
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207
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Proteomic profiling of peritoneal dialysis effluent-derived extracellular vesicles: a longitudinal study. J Nephrol 2019; 32:1021-1031. [DOI: 10.1007/s40620-019-00658-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/30/2019] [Indexed: 01/09/2023]
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208
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Álvarez JV, Bravo SB, García-Vence M, De Castro MJ, Luzardo A, Colón C, Tomatsu S, Otero-Espinar FJ, Couce ML. Proteomic Analysis in Morquio A Cells Treated with Immobilized Enzymatic Replacement Therapy on Nanostructured Lipid Systems. Int J Mol Sci 2019; 20:ijms20184610. [PMID: 31540344 PMCID: PMC6769449 DOI: 10.3390/ijms20184610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/07/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022] Open
Abstract
Morquio A syndrome, or mucopolysaccharidosis type IVA (MPS IVA), is a lysosomal storage disease due to mutations in the N-acetylgalactosamine-6-sulfatase (GALNS) gene. Systemic skeletal dysplasia and the related clinical features of MPS IVA are due to disruption of cartilage and its extracellular matrix, leading to an imbalance of growth. Enzyme replacement therapy (ERT) with recombinant human GALNS, alpha elosulfase, provides a systemic treatment. However, this therapy has a limited impact on skeletal dysplasia because the infused enzyme cannot penetrate cartilage and bone. Therefore, an alternative therapeutic approach to reach the cartilage is an unmet challenge. We have developed a new drug delivery system based on a nanostructure lipid carrier with the capacity to immobilize enzymes used for ERT and to target the lysosomes. This study aimed to assess the effect of the encapsulated enzyme in this new delivery system, using in vitro proteomic technology. We found a greater internalization of the enzyme carried by nanoparticles inside the cells and an improvement of cellular protein routes previously impaired by the disease, compared with conventional ERT. This is the first qualitative and quantitative proteomic assay that demonstrates the advantages of a new delivery system to improve the MPS IVA ERT.
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Affiliation(s)
- J Víctor Álvarez
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Campus Vida, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain.
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
- Skeletal Dysplasia Lab Nemours Biomedical Research Nemours/Alfred I. duPont Hospital for Children, 1600 Rockland Road, Wilmington, DE 19803, USA.
| | - Susana B Bravo
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostea, Spain.
| | - María García-Vence
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostea, Spain.
| | - María J De Castro
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
| | - Asteria Luzardo
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Sciences, Campus de Lugo, University of Santiago de Compostela, 27002 Lugo, Spain.
- Paraquasil Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain.
| | - Cristóbal Colón
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
| | - Shunji Tomatsu
- Skeletal Dysplasia Lab Nemours Biomedical Research Nemours/Alfred I. duPont Hospital for Children, 1600 Rockland Road, Wilmington, DE 19803, USA.
| | - Francisco J Otero-Espinar
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Campus Vida, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain.
- Paraquasil Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain.
| | - María L Couce
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
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209
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Zhou J, Hui X, Mao Y, Fan L. Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis. Biosci Rep 2019; 39:BSR20190625. [PMID: 31311829 PMCID: PMC6680377 DOI: 10.1042/bsr20190625] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/01/2019] [Accepted: 07/12/2019] [Indexed: 01/18/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a class of the commonest malignant carcinomas. The present study aimed to elucidate the potential biomarker and prognostic targets in PDAC. The array data of GSE41368, GSE43795, GSE55643, and GSE41369 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and differentially expressed microRNAs (DEmiRNAs) in PDAC were obtained by using GEO2R, and overlapped DEGs were acquired with Venn Diagrams. Functional enrichment analysis of overlapped DEGs and DEmiRNAs was conducted with Metascape and FunRich, respectively. The protein-protein interaction (PPI) network of overlapped DEGs was constructed by STRING and visualized with Cytoscape. Overall survival (OS) of DEmiRNAs and hub genes were investigated by Kaplan-Meier (KM) plotter (KM plotter). Transcriptional data and correlation analyses among hub genes were verified through GEPIA and Human Protein Atlas (HPA). Additionally, miRNA targets were searched using miRTarBase, then miRNA-DEG regulatory network was visualized with Cytoscape. A total of 32 DEmiRNAs and 150 overlapped DEGs were identified, and Metascape showed that DEGs were significantly enriched in cellular chemical homeostasis and pathways in cancer, while DEmiRNAs were mainly enriched in signal transduction and Glypican pathway. Moreover, seven hub genes with a high degree, namely, V-myc avian myelocytomatosis viral oncogene homolog (MYC), solute carrier family 2 member 1 (SLC2A1), PKM, plasminogen activator, urokinase (PLAU), peroxisome proliferator activated receptor γ (PPARG), MET proto-oncogene, receptor tyrosine kinase (MET), and integrin subunit α 3 (ITGA3), were identified and found to be up-regulated between PDAC and normal tissues. miR-135b, miR-221, miR-21, miR-27a, miR-199b-5p, miR-143, miR-196a, miR-655, miR-455-3p, miR-744 and hub genes predicted poor OS of PDAC. An integrative bioinformatics analysis identified several hub genes that may serve as potential biomarkers or targets for early diagnosis and precision target treatment of PDAC.
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Affiliation(s)
- Jun Zhou
- Department of General Ward 1, Zhejiang Hospital of Lingyin District, Zhejiang, China
| | - Xiaoliang Hui
- Department of General Ward 1, Zhejiang Hospital of Lingyin District, Zhejiang, China
| | - Ying Mao
- Department of General Ward 1, Zhejiang Hospital of Lingyin District, Zhejiang, China
| | - Liya Fan
- Department of Gastroenterology, Zhejiang Hospital of Sandun District, Zhejiang, China
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210
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Zhao K, Bleackley M, Chisanga D, Gangoda L, Fonseka P, Liem M, Kalra H, Al Saffar H, Keerthikumar S, Ang CS, Adda CG, Jiang L, Yap K, Poon IK, Lock P, Bulone V, Anderson M, Mathivanan S. Extracellular vesicles secreted by Saccharomyces cerevisiae are involved in cell wall remodelling. Commun Biol 2019; 2:305. [PMID: 31428693 PMCID: PMC6688994 DOI: 10.1038/s42003-019-0538-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are membranous vesicles that are released by cells. In this study, the role of the Endosomal Sorting Complex Required for Transport (ESCRT) machinery in the biogenesis of yeast EVs was examined. Knockout of components of the ESCRT machinery altered the morphology and size of EVs as well as decreased the abundance of EVs. In contrast, strains with deletions in cell wall biosynthesis genes, produced more EVs than wildtype. Proteomic analysis highlighted the depletion of ESCRT components and enrichment of cell wall remodelling enzymes, glucan synthase subunit Fks1 and chitin synthase Chs3, in yeast EVs. Interestingly, EVs containing Fks1 and Chs3 rescued the yeast cells from antifungal molecules. However, EVs from fks1∆ or chs3∆ or the vps23∆chs3∆ double knockout strain were unable to rescue the yeast cells as compared to vps23∆ EVs. Overall, we have identified a potential role for yeast EVs in cell wall remodelling.
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Affiliation(s)
- Kening Zhao
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Mark Bleackley
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - David Chisanga
- 2Department of Computer Science and Information Technology, La Trobe University, Melbourne, VIC 3086 Australia
| | - Lahiru Gangoda
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Pamali Fonseka
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Michael Liem
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Hina Kalra
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Haidar Al Saffar
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Shivakumar Keerthikumar
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
- 3Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- 4Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ching-Seng Ang
- 5Bio21 Institute, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Christopher G Adda
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Lanzhou Jiang
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Kuok Yap
- 6ARC Centre of Excellence in Plant Cell Walls and Adelaide Glycomics, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Ivan K Poon
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Peter Lock
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Vincent Bulone
- 6ARC Centre of Excellence in Plant Cell Walls and Adelaide Glycomics, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Marilyn Anderson
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Suresh Mathivanan
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
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211
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Oliveira KMC, Barker JH, Berezikov E, Pindur L, Kynigopoulos S, Eischen-Loges M, Han Z, Bhavsar MB, Henrich D, Leppik L. Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model. Sci Rep 2019; 9:11433. [PMID: 31391536 PMCID: PMC6685943 DOI: 10.1038/s41598-019-47389-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/19/2022] Open
Abstract
Different species respond differently to severe injury, such as limb loss. In species that regenerate, limb loss is met with complete restoration of the limbs’ form and function, whereas in mammals the amputated limb’s stump heals and scars. In in vitro studies, electrical stimulation (EStim) has been shown to promote cell migration, and osteo- and chondrogenesis. In in vivo studies, after limb amputation, EStim causes significant new bone, cartilage and vessel growth. Here, in a rat model, the stumps of amputated rat limbs were exposed to EStim, and we measured extracellular matrix (ECM) deposition, macrophage distribution, cell proliferation and gene expression changes at early (3 and 7 days) and later stages (28 days). We found that EStim caused differences in ECM deposition, with less condensed collagen fibrils, and modified macrophage response by changing M1 to M2 macrophage ratio. The number of proliferating cells was increased in EStim treated stumps 7 days after amputation, and transcriptome data strongly supported our histological findings, with activated gene pathways known to play key roles in embryonic development and regeneration. In conclusion, our findings support the hypothesis that EStim shifts injury response from healing/scarring towards regeneration. A better understanding of if and how EStim controls these changes, could lead to strategies that replace scarring with regeneration.
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Affiliation(s)
- K M C Oliveira
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - J H Barker
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - L Pindur
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany.,Department of Plastic, Hand and Reconstructive Surgery, BG Trauma Center Frankfurt am Main gGmbH, Frankfurt am Main, Germany
| | - S Kynigopoulos
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - M Eischen-Loges
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - Z Han
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - M B Bhavsar
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - D Henrich
- Department of Trauma, Hand and Reconstructive Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - L Leppik
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany.
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212
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Surman M, Hoja-Łukowicz D, Szwed S, Kędracka-Krok S, Jankowska U, Kurtyka M, Drożdż A, Lityńska A, Stępień E, Przybyło M. An Insight into the Proteome of Uveal Melanoma-Derived Ectosomes Reveals the Presence of Potentially Useful Biomarkers. Int J Mol Sci 2019; 20:ijms20153789. [PMID: 31382537 PMCID: PMC6695883 DOI: 10.3390/ijms20153789] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/29/2022] Open
Abstract
Cancer cells are known to release extracellular vesicles that often promote disease development and progression. The present study investigated the protein content and glycosylation pattern of ectosomes released in vitro by a human primary uveal melanoma Mel202 cell line. Ectosomes released by Mel202 cells were isolated from conditioned media using sequential centrifugation, and a nano-LC-MS/MS approach was used to determine their protein content. Subsequently, proteins from ectosomes, the whole cell extracts, and the membrane fractions were probed with a panel of lectins using Western blotting and flow cytometry to reveal characteristic glycan structures. As many as 2527 unique proteins were identified, and many of them are known to be involved in cancer cell proliferation and altered metabolism, tumor invasion, metastasis, or drug resistance. Lectin-based studies revealed a distinct glycosylation pattern between Mel202-derived ectosomes and the parental cell membranes. Selective enrichment of ectosomal proteins with bisected complex type N-glycans and α2,6-linked sialic acids may be significant for ectosome formation and sequestration. Differences in the surface glycosylation of Mel202 cells and ectosomes supports recent findings that the budding of ectosomes occurs within strictly determined fragments of the plasma membrane, and thus ectosomes contain a unique protein and glycan composition.
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Affiliation(s)
- Magdalena Surman
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Dorota Hoja-Łukowicz
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sabina Szwed
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sylwia Kędracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Urszula Jankowska
- Laboratory of Proteomics and Mass Spectrometry, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Magdalena Kurtyka
- Laboratory of Proteomics and Mass Spectrometry, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Anna Drożdż
- Department of Medical Physics, M. Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 Kraków, Poland
| | - Anna Lityńska
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Ewa Stępień
- Department of Medical Physics, M. Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 Kraków, Poland
| | - Małgorzata Przybyło
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland.
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213
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Deng JL, Xu YH, Wang G. Identification of Potential Crucial Genes and Key Pathways in Breast Cancer Using Bioinformatic Analysis. Front Genet 2019; 10:695. [PMID: 31428132 PMCID: PMC6688090 DOI: 10.3389/fgene.2019.00695] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/02/2019] [Indexed: 01/10/2023] Open
Abstract
Background: The molecular mechanism of tumorigenesis remains to be fully understood in breast cancer. It is urgently required to identify genes that are associated with breast cancer development and prognosis and to elucidate the underlying molecular mechanisms. In the present study, we aimed to identify potential pathogenic and prognostic differentially expressed genes (DEGs) in breast adenocarcinoma through bioinformatic analysis of public datasets. Methods: Four datasets (GSE21422, GSE29431, GSE42568, and GSE61304) from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) dataset were used for the bioinformatic analysis. DEGs were identified using LIMMA Package of R. The GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses were conducted through FunRich. The protein-protein interaction (PPI) network of the DEGs was established through STRING (Search Tool for the Retrieval of Interacting Genes database) website, visualized by Cytoscape and further analyzed by Molecular Complex Detection (MCODE). UALCAN and Kaplan–Meier (KM) plotter were employed to analyze the expression levels and prognostic values of hub genes. The expression levels of the hub genes were also validated in clinical samples from breast cancer patients. In addition, the gene-drug interaction network was constructed using Comparative Toxicogenomics Database (CTD). Results: In total, 203 up-regulated and 118 down-regulated DEGs were identified. Mitotic cell cycle and epithelial-to-mesenchymal transition pathway were the major enriched pathways for the up-regulated and down-regulated genes, respectively. The PPI network was constructed with 314 nodes and 1,810 interactions, and two significant modules are selected. The most significant enriched pathway in module 1 was the mitotic cell cycle. Moreover, six hub genes were selected and validated in clinical sample for further analysis owing to the high degree of connectivity, including CDK1, CCNA2, TOP2A, CCNB1, KIF11, and MELK, and they were all correlated to worse overall survival (OS) in breast cancer. Conclusion: These results revealed that mitotic cell cycle and epithelial-to-mesenchymal transition pathway could be potential pathways accounting for the progression in breast cancer, and CDK1, CCNA2, TOP2A, CCNB1, KIF11, and MELK may be potential crucial genes. Further, it could be utilized as new biomarkers for prognosis and potential new targets for drug synthesis of breast cancer.
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Affiliation(s)
- Jun-Li Deng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Yun-Hua Xu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
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214
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Liao Y, Yin G, Wang X, Zhong P, Fan X, Huang C. Identification of candidate genes associated with the pathogenesis of small cell lung cancer via integrated bioinformatics analysis. Oncol Lett 2019; 18:3723-3733. [PMID: 31516585 PMCID: PMC6732946 DOI: 10.3892/ol.2019.10685] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/05/2019] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of small cell lung cancer (SCLC), a highly metastatic malignant tumor, remains unclear. In the present study, important genes and pathways that are involved in the pathogenesis of SCLC were identified. The following four datasets were downloaded from the Gene Expression Omnibus: GSE60052, GSE43346, GSE15240 and GSE6044. The differentially expressed genes (DEGs) between the SCLC samples and the normal samples were analyzed using R software. The limma package was used for every dataset. The RobustRankAggreg package was used to integrate the DEGs from the four datasets. Functional and pathway enrichment analyses were conducted using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases with FunRich software and R software, respectively. In addition, the protein-protein interaction (PPI) network of the DEGs was constructed using the STRING database and Cytoscape software. Hub genes and significant modules were identified using Molecular Complex Detection in Cytoscape software. Finally, the expression values of hub genes were determined using the Oncomine online database. In total, 412 DEGs were identified following the integration of the four datasets, with 146 upregulated genes and 266 downregulated genes. The upregulated DEGs were primarily enriched in the cell cycle, cell division and microtubule binding. The downregulated DEGs were primarily enriched in the complement and coagulation cascades, the cytokine-mediated signaling pathway and protein binding. Eight hub genes and 1 significant module correlated to the cell cycle pathway were identified based on a subset of the PPI network. Finally, five hub genes were identified as highly expressed in SCLC tissue compared with normal tissue. The cell cycle pathway may be the pathway most closely associated with the pathogenesis of SCLC. NDC80, BUB1B, PLK1, CDC20 and MAD2L1 should be the focus of follow-up studies regarding the diagnosis and treatment of SCLC.
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Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Guofang Yin
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Xue Wang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Ping Zhong
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Xianming Fan
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Chengliang Huang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
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215
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Zhu J, Zhang X, Ai L, Yuan R, Ye J. Clinicohistopathological implications of MMP/VEGF expression in retinoblastoma: a combined meta-analysis and bioinformatics analysis. J Transl Med 2019; 17:226. [PMID: 31311559 PMCID: PMC6636009 DOI: 10.1186/s12967-019-1975-3] [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: 01/08/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND No in-depth systematic evidence is available for assessing retinoblastoma malignancy and eligibility for subsequent treatment. METHODS The Cochrane Library, EMBASE, PubMed, Web of Science, and China Biology Medicine databases were searched, and 16 studies comprising 718 retinoblastoma patients were included. Pooled odds ratios (ORs) and summary correlation coefficients (r) with 95% confidence intervals (CIs) in random-effects, fixed-effects or quality-effects models were calculated using Review Manager 5.3 and MetaXL. GO functional annotation and KEGG pathway analysis were performed using the GO and STRING databases. RESULTS We observed significant associations between high levels of MMP-1 (OR, 4.21; 95% CI 1.86-9.54), MMP-2 (OR, 11.18; 95% CI 4.26-29.30), MMP-9 (OR, 10.41, 95% CI 4.26-25.47), and VEGF (OR, 8.09; 95% CI 4.03-16.20) with tumor invasion; high levels of MMP-1 (OR, 3.58; 95% CI 1.48-8.71), MMP-2 (OR, 2.96; 95% CI 1.32-6.64), MMP-9 (OR, 5.49; 95% CI 3.55-8.48) and VEGF (OR, 5.30; 95% CI 2.93-9.60) with poor differentiation; and overexpression of MMP-9 (OR, 5.17; 95% CI 2.85-9.38) with advanced clinical stages. Moreover, MMP-9 and VEGF expression were positively correlated (r, 0.61; 95% CI 0.38-0.77). Multiple GO terms were enriched associated with MMP-1, MMP-2, MMP-9 and VEGF, and they are closely associated with pathways, proteoglycans and microRNAs related to cancer. CONCLUSIONS MMP-1, MMP-2, MMP-9 and VEGF play important roles in the development and progression of retinoblastoma. High levels of MMP-1, MMP-2, MMP-9 and VEGF are credible implications for increased malignancy, thus the need for more aggressive treatments.
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Affiliation(s)
- Jingyi Zhu
- Department of Ophthalmology and Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Xi Zhang
- Department of Ophthalmology and Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liqianyu Ai
- Department of Ophthalmology and Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Rongdi Yuan
- Department of Ophthalmology, Xinqiao Hospital, Army Medical University, Chongqing, 400042, China.
| | - Jian Ye
- Department of Ophthalmology and Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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216
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Cai W, Ding X, Li J, Li Z. Methylation analysis highlights novel prognostic criteria in human-metastasized melanoma. J Cell Biochem 2019; 120:11990-12001. [PMID: 30861178 DOI: 10.1002/jcb.28484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 01/24/2023]
Abstract
Melanoma accounts for 90% of the deaths associated with cutaneous neoplasms, and the 5-year survival rate of patients with the advanced stage is about 20%. Many mechanisms are involved in melanoma progression, but dynamic epigenetic changes are likely to be critical contributors, especially for DNA methylation. However, we know little about the methylation events involved in melanoma lymph node metastasis (LNM), a deficit that is of particular concern because it has a growing incidence and mortality. To identify DNA methylated-associated changes involved in the formation of metastatic melanoma, we explored the different methylated genes (DMGs) between primary and LNM melanoma by Illumina Human Methylation 450 K BeadArray GSE44661. By integrating DNA methylation and messenger RNA expression data from The Cancer Genome Atlas database, we identified these DNA methylation biomarkers. Pathway analysis highlighted these DMGs, which were closely related to the carcinogenesis of melanoma, such as cell cycle regulation and RNA transcription process. Furthermore, according to the univariate and multivariate Cox regression analysis, we constructed a four-DMG prognostic signature model, which could precisely predict the outcome of melanoma in a more exact way. In summary, this four-DMG based risk score model successfully predicts the survival of melanoma. It is independent of other clinical characteristics and is good for prognosis prediction.
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Affiliation(s)
- Weiyang Cai
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoxia Ding
- Department of Dermatology and Venereology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jingjing Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhiming Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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217
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Adaptive immune stimuli altered the cargo proteins of exosomes released by supraneural myeloid body cells in Lampetra japonica. Mol Immunol 2019; 111:64-72. [DOI: 10.1016/j.molimm.2019.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/20/2023]
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218
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Mechanism Investigation of Tagetes patula L. against Chronic Nonbacterial Prostatitis by Metabolomics and Network Pharmacology. Molecules 2019; 24:molecules24122266. [PMID: 31216740 PMCID: PMC6630244 DOI: 10.3390/molecules24122266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 11/16/2022] Open
Abstract
The major objective of this study was to investigate the anti-chronic nonbacterial prostatitis (CNP) mechanism of T. patula by metabolomics and network pharmacology. The study demonstrated that the flavonoids and polysaccharides of T. patula could alleviate prostatitis by improving the level of DHT, reducing the secretion of PSA and TNF-α. Besides, both could enhance Na+/K+-ATPase activity, decrease the O2 consumption, CO2 production, heat production, energy expenditure of rats and promote respiratory exchange ratio of rats. Up to 28 potential biomarkers and 8 key metabolic pathways related to the treatment of CNP were elucidated by the metabolomics analysis, including phenylalanine metabolism, taurine and hypotaurine metabolism, tryptophan metabolism etc. Network pharmacology prediction also reflected the potential mechanism was associated with tryptophan metabolism and energy pathway. Generally, the potential anti-CNP mechanism of flavonoids and polysaccharides of T. patula might be through reducing the expression of inflammation factors, adjusting the level of hormone and regulating the amino acid metabolism, energy metabolism and glucose and lipid metabolism.
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219
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Tanwar VS, Zhang X, Jagannathan L, Jose CC, Cuddapah S. Cadmium exposure upregulates SNAIL through miR-30 repression in human lung epithelial cells. Toxicol Appl Pharmacol 2019; 373:1-9. [PMID: 30998937 PMCID: PMC6547378 DOI: 10.1016/j.taap.2019.04.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 12/25/2022]
Abstract
Cadmium (Cd) is a known human lung carcinogen. In addition, Cd exposure is associated with several lung diseases including emphysema, chronic obstructive pulmonary disease (COPD), asthma and fibrosis. Although earlier studies have identified several processes dysregulated by Cd exposure, the underlying mechanisms remain unclear. Here, we examined the transcriptome of lung epithelial cells exposed to Cd to understand the molecular basis of Cd-induced diseases. Computational analysis of the transcriptome predicted a significant number of Cd-upregulated genes to be targets of miR-30 family miRNAs. Experimental validation showed downregulation of all the miR-30 family members in Cd exposed cells. We found SNAIL, an EMT master regulator, to be the most upregulated among the miR-30 targets. Furthermore, we found decrease in the levels of epithelial marker E- cadherin (CDH1) and increase in the levels of mesenchymal markers, ZEB1 and vimentin. This suggested induction of EMT in Cd exposed cells. Luciferase reporter assays showed that miR-30 repressed SNAIL by directly targeting its 3' UTR. Over expression of miR-30e and transfection of miR-30e mimics reduced Cd-induced SNAIL upregulation. Our results suggest that miR-30 negatively regulates SNAIL in lung epithelial cells and that Cd-induced downregulation of miR-30 relieves this repression, resulting in SNAIL upregulation and EMT induction. EMT plays a major role in many diseases associated with Cd exposure including fibrosis, COPD, and cancer and metastasis. Therefore, our identification of miR-30 downregulation in Cd exposed cells and the consequent activation of SNAIL provides important mechanistic insights into lung diseases associated with Cd exposure.
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Affiliation(s)
- Vinay Singh Tanwar
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Lakshmanan Jagannathan
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Cynthia C Jose
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA.
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220
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An T, Qin S, Sun D, Huang Y, Hu Y, Li S, Zhang H, Li B, Situ B, Lie L, Wu Y, Zheng L. Unique Protein Profiles of Extracellular Vesicles as Diagnostic Biomarkers for Early and Advanced Non‐Small Cell Lung Cancer. Proteomics 2019; 19:e1800160. [DOI: 10.1002/pmic.201800160] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/10/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Taixue An
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Sihua Qin
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Division of Laboratory MedicineZhujiang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Dehua Sun
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Yiyao Huang
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Yanwei Hu
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Shaopeng Li
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Han Zhang
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Bo Li
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Bo Situ
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Linmiao Lie
- Molecular Immunology InstituteSouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Yingsong Wu
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical University Guangzhou 510515 Guangdong P. R. China
| | - Lei Zheng
- Department of Laboratory MedicineNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic BiosensorsNanfang HospitalSouthern Medical University Guangzhou 510515 Guangdong P. R. China
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221
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Ma Q, Xu Y, Liao H, Cai Y, Xu L, Xiao D, Liu C, Pu W, Zhong X, Guo X. Identification and validation of key genes associated with non-small-cell lung cancer. J Cell Physiol 2019; 234:22742-22752. [PMID: 31127628 DOI: 10.1002/jcp.28839] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein-protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.
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Affiliation(s)
- Qiang Ma
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yuan Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Hebin Liao
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Yan Cai
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lei Xu
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Dan Xiao
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Chang Liu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Wenjie Pu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
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222
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Fel A, Lewandowska AE, Petrides PE, Wiśniewski JR. Comparison of Proteome Composition of Serum Enriched in Extracellular Vesicles Isolated from Polycythemia Vera Patients and Healthy Controls. Proteomes 2019; 7:proteomes7020020. [PMID: 31064135 PMCID: PMC6631625 DOI: 10.3390/proteomes7020020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 12/16/2022] Open
Abstract
Extracellular vesicles (EVs), e.g., exosomes and microvesicles, are one of the main networks of intercellular communication. In myeloproliferative neoplasms, such as polycythemia vera (PV), excess of EVs originating from overabundant blood cells can directly contribute to thrombosis through their procoagulant activity. However, the proteomic composition of these vesicles in PV patients has not been investigated before. In this work, we examined the proteomic composition of serum EVs of PV patients in comparison to healthy controls. We processed EV-enriched serum samples using the Multiple Enzyme Filter Aided Sample Preparation approach (MED-FASP), conducted LC-MS/MS measurements on a Q-Exactive HF-X mass spectrometer, and quantitatively analyzed the absolute concentrations of identified proteins by the Total Protein Approach (TPA). Thirty-eight proteins were present at statistically significant different concentrations between PV patients’ study group and healthy controls’ group. The main protein components deregulated in PV were primarily related to excessive amounts of cells, increased platelet activation, elevated immune and inflammatory response, and high concentrations of procoagulant and angiogenic agents. Our study provides the first quantitative analysis of the serum EVs’ proteome in PV patients. This new knowledge may contribute to a better understanding of the secondary systemic effects of PV disease and further development of diagnostic or therapeutic procedures.
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Affiliation(s)
- Anna Fel
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland.
| | - Aleksandra E Lewandowska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland.
| | - Petro E Petrides
- Hematology Oncology Center and Ludwig Maximilians University of Munich Medical School, Zweibrückenstraße 2, 80331 Munich, Germany.
| | - Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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223
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Ludwig S, Marczak L, Sharma P, Abramowicz A, Gawin M, Widlak P, Whiteside TL, Pietrowska M. Proteomes of exosomes from HPV(+) or HPV(-) head and neck cancer cells: differential enrichment in immunoregulatory proteins. Oncoimmunology 2019; 8:1593808. [PMID: 31143515 PMCID: PMC6527282 DOI: 10.1080/2162402x.2019.1593808] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/20/2019] [Accepted: 02/28/2019] [Indexed: 12/12/2022] Open
Abstract
Human papillomavirus (HPV) is an etiologic factor in head and neck squamous cell carcinoma (HNSCC). HPV(+) cancers respond favorably to therapy potentially due to more robust anti-tumor immune responses. We hypothesized that tumor-derived exosomes (TEX) produced by HPV(+) or HPV(-) HNSCCs differentially modulate anti-tumor immune responses. Proteomes of exosomes from HPV(+) and HPV(-) HNSCC cell lines were compared in search for proteins putatively involved in the communication with immune system. TEX were isolated from supernatants of HPV(+) (SCC-2, SCC-47, and SCC-90) or HPV(-) (PCI-13 and PCI-30) cells by size exclusion chromatography. A comparison of proteome profiles was performed by high-resolution mass spectrometry. The presence and biological activity of selected immunoregulatory proteins were validated by flow cytometry and co-incubation assays. Exosomes produced by SCC-90 and PCI-30 cells contained 711 proteins, including 80 proteins specific for HPV(+) exosomes and 77 specific for HPV(-) exosomes, associated with similar GO terms such as regulation of cell growth, metabolism, communication, and cellular signaling. Search for proteins localized in the membrane and involved in immune regulation identified a few proteins detected specifically in HPV(+) or HPV(-) exosomes. Only HPV(+) exosomes were enriched in immune effector cell-related CD47 and CD276 antigens; only HPV(-) exosomes contained tumor-protective/growth-promoting antigens, MUC-1 and HLA-DA. Flow cytometry and Western blots confirmed the reciprocal presence/paucity of these proteins in a whole panel of tumor cells and corresponding exosomes. The differential content of protein cargos in HPV(+) and HPV(-) exosomes might contribute to the disparity in immune responses that characterize HPV(+) and HPV(-) HNSCC.
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Affiliation(s)
- Sonja Ludwig
- Department of Otolaryngology, University of Duisburg-Essen, Essen, Germany.,Department of Pathology, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Lukasz Marczak
- Laboratory of Mass Spectrometry, European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Priyanka Sharma
- Department of Pathology, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Agata Abramowicz
- Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Marta Gawin
- Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Piotr Widlak
- Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Theresa L Whiteside
- Department of Pathology, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Departments of Immunology and Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Monika Pietrowska
- Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
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224
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Fonseka P, Liem M, Ozcitti C, Adda CG, Ang CS, Mathivanan S. Exosomes from N-Myc amplified neuroblastoma cells induce migration and confer chemoresistance to non-N-Myc amplified cells: implications of intra-tumour heterogeneity. J Extracell Vesicles 2019; 8:1597614. [PMID: 31007876 PMCID: PMC6461098 DOI: 10.1080/20013078.2019.1597614] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 02/18/2019] [Accepted: 03/18/2019] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma accounts for 15% of childhood cancer mortality. Amplification of the oncogene N-Myc is a well-established poor prognostic marker for neuroblastoma. Whilst N-Myc amplification status strongly correlates with higher tumour aggression and resistance to treatment, the role of N-Myc in the aggressiveness of the disease is poorly understood. Exosomes are released by many cell types including cancer cells and are implicated as key mediators in cell-cell communication via the transfer of molecular cargo. Hence, characterising the exosomal protein components from N-Myc amplified and non-amplified neuroblastoma cells will improve our understanding on their role in the progression of neuroblastoma. In this study, a comparative proteomic analysis of exosomes isolated from cells with varying N-Myc amplification status was performed. Label-free quantitative proteomic profiling revealed 968 proteins that are differentially abundant in exosomes released by the neuroblastoma cells. Gene ontology-based analysis highlighted the enrichment of proteins involved in cell communication and signal transduction in N-Myc amplified exosomes. Treatment of SH-SY5Y cells with N-Myc amplified SK-N-BE2 cell-derived exosomes increased the migratory potential, colony forming abilities and conferred resistance to doxorubicin induced apoptosis. Incubation of exosomes from N-Myc knocked down SK-N-BE2 cells abolished the transfer of resistance to doxorubicin induced apoptosis. These findings suggest that exosomes could play a pivotal role in N-Myc-driven aggressive neuroblastoma and transfer of chemoresistance between cells. Abbreviations: RNA = ribonucleic acid; DNA = deoxyribonucleic acid; FCS = foetal calf serum; NTA = nanoparticle tracking analysis; LC-MS = liquid chromatography–mass spectrometry; KD = knockdown; LTQ = linear trap quadropole; TEM = transmission electron microscopy
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Affiliation(s)
- Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Michael Liem
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Cemil Ozcitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Christopher G Adda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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225
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Sacca PA, Mazza ON, Scorticati C, Vitagliano G, Casas G, Calvo JC. Human Periprostatic Adipose Tissue: Secretome from Patients With Prostate Cancer or Benign Prostate Hyperplasia. Cancer Genomics Proteomics 2019; 16:29-58. [PMID: 30587498 DOI: 10.21873/cgp.20110] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND/AIM Periprostatic adipose tissue (PPAT) directs tumour behaviour. Microenvironment secretome provides information related to its biology. This study was performed to identify secreted proteins by PPAT, from both prostate cancer and benign prostate hyperplasia (BPH) patients. PATIENTS AND METHODS Liquid chromatography-mass spectrometry-based proteomic analysis was performed in PPAT-conditioned media (CM) from patients with prostate cancer (CMs-T) (stage T3: CM-T3, stage T2: CM-T2) or benign disease (CM-BPH). RESULTS The highest number and diversity of proteins was identified in CM-T3. Locomotion was the biological process mainly associated to CMs-T and reproduction to CM-T3. Immune responses were enriched in CMs-T. Extracellular matrix and structural proteins were associated to CMs-T. CM-T3 was enriched in proteins with catalytic activity and CM-T2 in proteins with defense/immunity activity. Metabolism and energy pathways were enriched in CM-T3 and those with immune system functions in CMs-T. Transport proteins were enriched in CM-T2 and CM-BPH. CONCLUSION Proteins and pathways reported in this study could be useful to distinguish stages of disease and may become targets for novel therapies.
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Affiliation(s)
- Paula Alejandra Sacca
- Institute of Biology and Experimental Medicine (IBYME), CONICET, Buenos Aires, Argentina
| | - Osvaldo Néstor Mazza
- Department of Urology, School of Medicine, University of Buenos Aires, Clínical Hospital "José de San Martín", Buenos Aires, Argentina
| | - Carlos Scorticati
- Department of Urology, School of Medicine, University of Buenos Aires, Clínical Hospital "José de San Martín", Buenos Aires, Argentina
| | | | - Gabriel Casas
- Department of Pathology, Deutsches Hospital, Buenos Aires, Argentina
| | - Juan Carlos Calvo
- Institute of Biology and Experimental Medicine (IBYME), CONICET, Buenos Aires, Argentina.,Department of Biological Chemistry, School of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
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226
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Jeon OH, Wilson DR, Clement CC, Rathod S, Cherry C, Powell B, Lee Z, Khalil AM, Green JJ, Campisi J, Santambrogio L, Witwer KW, Elisseeff JH. Senescence cell-associated extracellular vesicles serve as osteoarthritis disease and therapeutic markers. JCI Insight 2019; 4:125019. [PMID: 30944259 DOI: 10.1172/jci.insight.125019] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/21/2019] [Indexed: 12/19/2022] Open
Abstract
Senescent cells (SnCs) are increasingly recognized as central effector cells in age-related pathologies. Extracellular vesicles (EVs) are potential cellular communication tools through which SnCs exert central effector functions in the local tissue environment. To test this hypothesis in a medical indication that could be validated clinically, we evaluated EV production from SnCs enriched from chondrocytes isolated from human arthritic cartilage. EV production increased in a dose-responsive manner as the concentration of SnCs increased. The EVs were capable of transferring senescence to nonsenescent chondrocytes and inhibited cartilage formation by non-SnCs. microRNA (miR) profiles of EVs isolated from human arthritic synovial fluid did not fully overlap with the senescent chondrocyte EV profiles. The effect of SnC clearance was tested in a murine model of posttraumatic osteoarthritis. miR and protein profiles changed after senolytic treatment but varied depending on age. In young animals, senolytic treatment altered expression of miR-34a, -30c, -125a, -24, -92a, -150, and -186, and this expression correlated with cartilage production. The primary changes in EV contents in aged mice after senolytic treatment, which only reduced pain and degeneration, were immune related. In sum, EV contents found in synovial fluid may serve as a diagnostic for arthritic disease and indicator for therapeutic efficacy of senolytic treatment.
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Affiliation(s)
- Ok Hee Jeon
- Buck Institute for Research on Aging, Novato, California, USA
| | - David R Wilson
- Translational Tissue Engineering Center, Wilmer Eye Institute, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Cristina C Clement
- Department of Pathology, Orthopedic Surgery, Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Sona Rathod
- Translational Tissue Engineering Center, Wilmer Eye Institute, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christopher Cherry
- Translational Tissue Engineering Center, Wilmer Eye Institute, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bonita Powell
- Department of Molecular and Comparative Pathobiology and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zhenghong Lee
- Department of Radiology, Case Western Reserve University, University Hospitals Bolwell, Cleveland, Ohio, USA
| | - Ahmad M Khalil
- Genetics and Genome Sciences and Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jordan J Green
- Translational Tissue Engineering Center, Wilmer Eye Institute, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, California, USA.,Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Laura Santambrogio
- Department of Pathology, Orthopedic Surgery, Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer H Elisseeff
- Translational Tissue Engineering Center, Wilmer Eye Institute, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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227
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Wu HY, Li MW, Li QQ, Pang YY, Chen G, Lu HP, Pan SL. Elevation of miR-191-5p level and its potential signaling pathways in hepatocellular carcinoma: a study validated by microarray and in-house qRT-PCR with 1,291 clinical samples. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1439-1456. [PMID: 31933962 PMCID: PMC6947072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/21/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The miR-191-5p expression has been reported to increase in hepatocellular carcinoma (HCC), but its clinical value and exact role remain to be further clarified. Thus, a comprehensive analysis was performed in the current study to explore the underlying function of miR-191-5p in HCC. METHODS HCC-related expression data were collected to conduct a thorough analysis to determine the miR-191-5p expression and its clinical significance in HCC, including microarray data from the Gene Expression Omnibus and ArrayExpress database as well as quantitative real-time polymerase chain reaction (qRT-PCR) data of 178 matched clinical samples. The underlying relationship between miR-191-5p and HCC was also explored on the basis of a series of bioinformatics analyses. RESULTS The overall pooled meta-analysis showed an overexpression of miR-191-5p in the HCC samples (SMD=0.400, 95% CI=0.139-0.663, P=0.003), consistent with the detected result of the clinical HCC samples through the qRT-PCR analysis. Higher miR-191-5p levels were correlated with advanced TNM stages (III and IV), higher pathological grades, and metastasis. Functionally, 64 potential target genes were acquired for further mechanism analysis. Two pathways (p75 neurotrophin receptor and liver kinase B1-mediated signaling pathways), which were likely modulated by miR-191-5p, were regarded to be linked to the deterioration of HCC. Early growth response 1 and UBE2D3 were identified as the most likely targets for miR-191-5p in HCC and were commonly implied in the top enriched pathways and protein-protein network. CONCLUSIONS In summary, miR-191-5p may function as a tumor promoter miRNA of HCC, and the miR-191-5p inhibitor may contribute to the targeted HCC treatment in the future.
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Affiliation(s)
- Hua-Yu Wu
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Mei-Wei Li
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Qi-Qi Li
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Yu-Yan Pang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Hui-Ping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, P. R. China
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228
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Lou W, Ding B, Xu L, Fan W. Construction of Potential Glioblastoma Multiforme-Related miRNA-mRNA Regulatory Network. Front Mol Neurosci 2019; 12:66. [PMID: 30971889 PMCID: PMC6444190 DOI: 10.3389/fnmol.2019.00066] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/28/2019] [Indexed: 12/18/2022] Open
Abstract
Background: Glioblastoma multiforme (GBM), the most common and aggressive human malignant brain tumor, is notorious for its limited treatment options and poor prognosis. MicroRNAs (miRNAs) are found to be involved in tumorigenesis of GBM. However, a comprehensive miRNA-mRNA regulatory network has still not been established. Methods: A miRNA microarray dataset (GSE90603) was obtained from GEO database. Then, we employed GEO2R tool to perform differential expression analysis. Potential transcription factors and target genes of screened differentially expressed miRNAs (DE-miRNAs) were predicted. The GBM mRNA dataset were downloaded from TCGA database for identifying differentially expressed genes (DEGs). Next, GO annotation and KEGG pathway enrichment analysis was conducted. PPI network was then established, and hub genes were identified via Cytoscape software. The expression and prognostic roles of hub genes was further evaluated. Results: Total 33 DE-miRNAs, consisting of 10 upregulated DE-miRNAs and 23 downregulated DE-miRNAs, were screened. SP1 was predicted to potentially regulate most of screened DE-miRNAs. Three thousand and twenty seven and 3,879 predicted target genes were obtained for upregulated and downregulated DE-miRNAs, respectively. Subsequently, 1,715 upregulated DEGs and 1,259 downregulated DEGs were identified. Then, 149 and 295 potential downregulated and upregulated genes commonly appeared in target genes of DE-miRNAs and DEGs were selected for GO annotation and KEGG pathway enrichment analysis. The downregulated genes were significantly enriched in cGMP-PKG signaling pathway and calcium signaling pathway whereas the upregulated genes were enriched in pathways in cancer and PI3K-Akt signaling pathway. Construction and analysis of PPI network showed that STXBP1 and TP53 were recognized as hub genes with the highest connectivity degrees. Expression analytic result of the top 20 hub genes in GBM using GEPIA database was generally identical with previous differential expression analysis for TCGA data. EGFR, PPP3CB, and MYO5A expression was significantly associated with patients' OS. Conclusions: In this study, we established a potential GBM-related miRNA-mRNA regulatory network, which explores a comprehensive understanding of the molecular mechanisms and provides key clues in seeking novel therapeutic targets for GBM. In the future, more experiments need to be performed to validate our current findings.
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Affiliation(s)
- Weiyang Lou
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Key Laboratory of Organ Transplantation, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Key Laboratory of Organ Transplantation, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Liang Xu
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Key Laboratory of Organ Transplantation, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Weimin Fan
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Key Laboratory of Organ Transplantation, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, China.,Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
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229
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Gézsi A, Kovács Á, Visnovitz T, Buzás EI. Systems biology approaches to investigating the roles of extracellular vesicles in human diseases. Exp Mol Med 2019; 51:1-11. [PMID: 30872567 PMCID: PMC6418293 DOI: 10.1038/s12276-019-0226-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane-enclosed structures secreted by cells. In the past decade, EVs have attracted substantial attention as carriers of complex intercellular information. They have been implicated in a wide variety of biological processes in health and disease. They are also considered to hold promise for future diagnostics and therapy. EVs are characterized by a previously underappreciated heterogeneity. The heterogeneity and molecular complexity of EVs necessitates high-throughput analytical platforms for detailed analysis. Recently, mass spectrometry, next-generation sequencing and bioinformatics tools have enabled detailed proteomic, transcriptomic, glycomic, lipidomic, metabolomic, and genomic analyses of EVs. Here, we provide an overview of systems biology experiments performed in the field of EVs. Furthermore, we provide examples of how in silico systems biology approaches can be used to identify correlations between genes involved in EV biogenesis and human diseases. Using a knowledge fusion system, we investigated whether certain groups of proteins implicated in the biogenesis/release of EVs were associated with diseases and phenotypes. Furthermore, we investigated whether these proteins were enriched in publicly available transcriptomic datasets using gene set enrichment analysis methods. We found associations between key EV biogenesis proteins and numerous diseases, which further emphasizes the key role of EVs in human health and disease.
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Affiliation(s)
- András Gézsi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
- MTA-SE Immune-Proteogenomics Extracellular Vesicle Research Group, Budapest, Hungary
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Árpád Kovács
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Tamás Visnovitz
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Edit I Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary.
- MTA-SE Immune-Proteogenomics Extracellular Vesicle Research Group, Budapest, Hungary.
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230
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Grange C, Tritta S, Tapparo M, Cedrino M, Tetta C, Camussi G, Brizzi MF. Stem cell-derived extracellular vesicles inhibit and revert fibrosis progression in a mouse model of diabetic nephropathy. Sci Rep 2019; 9:4468. [PMID: 30872726 PMCID: PMC6418239 DOI: 10.1038/s41598-019-41100-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/21/2019] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) that are derived from mesenchymal stromal cells (MSCs) have been shown to reprogram injured cells by activating regenerative processes. We herein investigate the potential therapeutic effect of EVs, shed by human bone marrow MSCs and by human liver stem-like cells (HLSCs), on the progression and reversion of fibrosis in a mouse model of diabetic nephropathy, as induced by streptozotocin. After the development of nephropathy, stem cell-derived EVs were administered weekly to diabetic mice for four weeks. The stem cell-derived EV treatment, but not the fibroblast EV treatment that was used as a control, significantly ameliorated functional parameters, such as albumin/creatinine excretion, plasma creatinine and blood urea nitrogen, which are altered in diabetic mice. Moreover, the renal fibrosis that develops during diabetic nephropathy progression was significantly inhibited in stem cell EV-treated animals. A correlation was found between the down regulation of several pro-fibrotic genes in renal tissues and the anti-fibrotic effect of HLSC and MSC EVs. A comparative analysis of HLSC and MSC EV miRNA content highlighted some common and some specific patterns of miRNAs that target predicted pro-fibrotic genes. In conclusion, stem cell-derived EVs inhibit fibrosis and prevent its progression in a model of diabetes-induced chronic kidney injury.
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Affiliation(s)
- Cristina Grange
- Department of Medical Sciences, University of Turin, Turin, Italy.,Molecular Biotechnology Centre, University of Turin, Turin, Italy
| | - Stefania Tritta
- Molecular Biotechnology Centre, University of Turin, Turin, Italy
| | - Marta Tapparo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Massimo Cedrino
- Molecular Biotechnology Centre, University of Turin, Turin, Italy
| | | | - Giovanni Camussi
- Department of Medical Sciences, University of Turin, Turin, Italy. .,Molecular Biotechnology Centre, University of Turin, Turin, Italy. .,2i3T Società per la gestione dell'incubatore di imprese e per il trasferimento tecnologico Scarl, University of Turin, Turin, Italy.
| | - Maria Felice Brizzi
- Department of Medical Sciences, University of Turin, Turin, Italy. .,Molecular Biotechnology Centre, University of Turin, Turin, Italy. .,2i3T Società per la gestione dell'incubatore di imprese e per il trasferimento tecnologico Scarl, University of Turin, Turin, Italy.
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231
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Stadnicka K, Dębowska M, Dębski J, Bajek A. Secreting oviduct epithelial cells of Coturnix coturnix japonica (QOEC) and changes to their proteome after nonviral transfection. J Cell Biochem 2019; 120:12724-12739. [PMID: 30854717 DOI: 10.1002/jcb.28541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/13/2019] [Accepted: 02/21/2019] [Indexed: 02/04/2023]
Abstract
The quail oviduct (Coturnix c. japonica) is a natural candidate avian bioreactor, while the secretive quail oviduct epithelial cells (QOECs) are potential in vitro producers of recombinant proteins and vaccines. In view of the need for highly performing and transformable cell lines, QOEC may potentially act as an alternative bioreactor platform to the existing ones, for example, to the Chinese hamster ovary. The aim of this work was to characterize QOECs and their response to nucleofection with a nonviral plasmid DNA carrying the human interferon-α 2a gene (hIFNλ2a), in vitro. Primary QOEC cultures from laying quails (10-15 weeks old) were characterized by their proliferation rate, doubling time, and multilineage differentiation. Electroporation to cell nuclei (nucleofection) was used to deliver nonviral plasmid DNA containing a reporter GFP and hIFN under the ovalbumin promoter. The posttransfection analysis included polymerase chain reaction, Western blot analysis, and liquid chromatography coupled to tandem mass spectrometry. QOEC showed a typical epithelial characteristic in a primary 2D monolayer culture system and retained secretive potential up to the first passage. QOEC showed differentiation into osteoblastic lineage after stimulation. The nucleofection mean efficiency was low (2.3%). Differences of up to 10% in the proteomic profiles between nontransfected and transfected QOEC were found, the most important of these were related to the absence of keratins and cell-adhesion proteins in the transfected QOEC. Concluding, with the practical information provided here, QOEC have the potential to serve as an avian secreting cellular platform. QOEC may be further transformed to cell lineage to meet the requirement for a stable, electrocompetent, and transfectable model. The first proteomic comparison of QOEC delivered in this study showed, in the majority, a stable proteome of the nontransfected vs transfected QOEC.
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Affiliation(s)
- Katarzyna Stadnicka
- Department of Animal Biotechnology and Genetics, Faculty of Animal Breeding and Biology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Michalina Dębowska
- Department of Animal Biotechnology and Genetics, Faculty of Animal Breeding and Biology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Janusz Dębski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics-Polish Academy of Sciences, Warsaw, Poland
| | - Anna Bajek
- Department of Tissue Engineering, Nicolaus Copernicus University, Bydgoszcz, Poland
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232
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Manfredi M, Conte E, Barberis E, Buzzi A, Robotti E, Caneparo V, Cecconi D, Brandi J, Vanni E, Finocchiaro M, Astegiano M, Gariglio M, Marengo E, De Andrea M. Integrated serum proteins and fatty acids analysis for putative biomarker discovery in inflammatory bowel disease. J Proteomics 2019; 195:138-149. [DOI: 10.1016/j.jprot.2018.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
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233
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Ticket to a bubble ride: Cargo sorting into exosomes and extracellular vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140203. [PMID: 30822540 DOI: 10.1016/j.bbapap.2019.02.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) are released by cells into the extracellular milieu to facilitate intercellular communication in both physiological and pathological condition. EVs contain selective repertoires of proteins, RNAs, lipids and metabolites that moderate signalling pathways in the recipient cells. The enrichment of a particular set of proteins or RNAs within the EVs highlights the existence of specific sorting mechanisms that orchestrate the selective packaging of the cargo. The molecular machinery of cargo sorting has remained obscure over the years and functional studies are required to understand this complex mechanism. In this article, we offer a brief overview of the molecular mechanisms that are known to regulate sorting of various molecules into EVs. We also discuss how different pathways of biogenesis alter the exosomal cargo as well and the implications of the cellular state on the content of the EVs. Understanding the sorting of exosomal cargo could further be exploited in clinical settings for targeted drug delivery and to block disease progression.
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234
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Predicting MicroRNA Target Genes and Identifying Hub Genes in IIA Stage Colon Cancer Patients Using Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6341967. [PMID: 30881993 PMCID: PMC6383401 DOI: 10.1155/2019/6341967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/26/2018] [Indexed: 01/27/2023]
Abstract
Background Colon cancer is a heterogeneous disease, differing in clinical symptoms, epigenetics, and prognosis for each individual patient. Identifying the core genes is important for early diagnoses and it provides a more precise method for treating colon cancer. Materials and Methods In this study, we wanted to pinpoint these core genes so we obtained GSE101502 microRNA profiles from the GEO database, which resulted in 17 differential expressed microRNAs that were identified by GEO2R analysis. Then, 875 upregulated and 2920 downregulated target genes were predicted by FunRich. GO and KEGG pathway were used to do enrich analysis. Results GO analysis indicated that upregulated genes were significantly enriched in the regulation of cell communication and signaling and in nervous system development, while the downregulated genes were significantly enriched in nervous system development and regulation of transcription from the RNA polymerase II promoter. KEGG pathway analysis suggested that the upregulated genes were enriched in axon guidance, MAPK signaling pathway, and endocytosis, while the downregulated genes existed in pathways in cancer, focal adhesion, and PI3K-Akt signaling pathway. The top four molecules including 82 hub genes were identified from the PPI network and involved in endocytosis, spliceosome, TGF-beta signaling pathway, and lysosome. Finally, NUDT21, GNB1, CLINT1, and COL1A2 core gene were selected due to their correlation with the prognosis of IIA stage colon cancer. Conclusion this study suggested that NUDT21, GNB1, CLINT1, and COL1A2 might be the core genes for colon cancer that play an important role in the development and prognosis of IIA stage colon cancer.
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235
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Yang M, Liu J, Wang F, Tian Z, Ma B, Li Z, Wang B, Zhao W. Lysyl oxidase assists tumor‑initiating cells to enhance angiogenesis in hepatocellular carcinoma. Int J Oncol 2019; 54:1398-1408. [PMID: 30720077 DOI: 10.3892/ijo.2019.4705] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/14/2018] [Indexed: 11/06/2022] Open
Abstract
A highly tumorigenic and malignant sub‑population of HCC containing tumor‑initiating cells (TICs) are defined by high self‑renewal and sphere formation ability. Lysyl oxidase (LOX) regulates various factors involved in extracellular matrix (ECM) maintenance, migration and angiogenesis. Certain reports have demonstrated the role of LOX in ECM crosslinking, however, the cancer‑promoting effects of LOX in HCC remain unclear, and whether LOX has a role in the regulation of angiogenesis in HCC TICs has not been elucidated. In the current study, RNA sequencing using next‑generation sequencing technology and bioinformatics analyses revealed that LOX gene expression was significantly upregulated in cell spheres. Sphere cells may form tumors with more vascular enrichment compared with tumors produced from adherent cells, as observed in a mouse xenograft model. LOX expression is correlated with increased vascular endothelial growth factor (VEGF) and platelet‑derived growth factor, as demonstrated by analyses of The Cancer Genome Atlas and Gene Expression Omnibus databases. Conditioned media obtained from LOX‑overexpressing tumor cells stimulated angiogenesis via secreted VEGF and enhanced the tube formation capacity of endothelial cells. Furthermore, these functional behaviors were blocked by the LOX inhibitor β‑aminopropionitrile. These findings provide novel mechanistic insight into the pivotal role of LOX in the regulation of TICs in HCC. Combination of LOX inhibitor with sorafenib is a potentially advantageous strategy for HCC therapy.
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Affiliation(s)
- Min Yang
- Department of Gerontology, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Jingtao Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pharmacy, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Fei Wang
- Division of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 0853, Houston, TX 77030, USA
| | - Zhihua Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Central Laboratory, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Bo Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Zhongwu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Boqing Wang
- Department of Hepatopancreatobiliary Surgery, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Wei Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cell Biology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
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236
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Lane RE, Korbie D, Trau M, Hill MM. Optimizing Size Exclusion Chromatography for Extracellular Vesicle Enrichment and Proteomic Analysis from Clinically Relevant Samples. Proteomics 2019; 19:e1800156. [PMID: 30632691 DOI: 10.1002/pmic.201800156] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/12/2018] [Indexed: 01/13/2023]
Abstract
The field of extracellular vesicle (EV) research has rapidly expanded in recent years, with particular interest in their potential as circulating biomarkers. Proteomic analysis of EVs from clinical samples is complicated by the low abundance of EV proteins relative to highly abundant circulating proteins such as albumin and apolipoproteins. To overcome this, size exclusion chromatography (SEC) has been proposed as a method to enrich EVs whilst depleting protein contaminants; however, the optimal SEC parameters for EV proteomics have not been thoroughly investigated. Here, quantitative evaluation and optimization of SEC are reported for separating EVs from contaminating proteins. Using a synthetic model system followed by cell line-derived EVs, it is found that a 10 mL Sepharose 4B column in PBS produces optimal resolution of EVs from background protein. By spiking-in cancer cell-derived EVs to healthy plasma, it is shown that some cancer EV-associated proteins are detectable by nano-LC-MS/MS when as little as 1% of the total plasma EV number are derived from a cancer cell line. These results suggest that an optimized SEC and nanoLC-MS/MS workflow may be sufficiently sensitive for disease EV protein biomarker discovery from patient-derived clinical samples.
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Affiliation(s)
- Rebecca E Lane
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia 4072
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia 4072
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia 4072.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia 4072
| | - Michelle M Hill
- UQ Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Brisbane, Australia 4102.,QIMR Berghofer Medical Research Institute, Herston, Australia 4006
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237
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Zhang H, Dong S, Feng J. Epigenetic profiling and mRNA expression reveal candidate genes as biomarkers for colorectal cancer. J Cell Biochem 2019; 120:10767-10776. [PMID: 30672027 DOI: 10.1002/jcb.28368] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hui Zhang
- Department of Medical Oncology The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research Nanjing Jiangsu People's Republic of China
| | - Shuchen Dong
- Department of Medical Oncology The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research Nanjing Jiangsu People's Republic of China
| | - Jifeng Feng
- Department of Medical Oncology The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research Nanjing Jiangsu People's Republic of China
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238
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Deduction of Novel Genes Potentially Involved in Keratinocytes of Type 2 Diabetes Using Next-Generation Sequencing and Bioinformatics Approaches. J Clin Med 2019; 8:jcm8010073. [PMID: 30634634 PMCID: PMC6352191 DOI: 10.3390/jcm8010073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/04/2019] [Accepted: 01/06/2019] [Indexed: 02/06/2023] Open
Abstract
Keratinocytes constitute the major cell type of epidermis, which participates in re-epithelialization during wound repair and the immune defense response to pathogens. The aim of the current study was to explore the differentially expressed genes and novel microRNA (miRNA) regulations that are potentially involved in diabetic keratinocytes through next-generation sequencing (NGS) and bioinformatics approaches. A total of 420 differentially expressed genes between normal and diabetic keratinocytes were identified, and systematic bioinformatics analyses indicated that these differentially expressed genes were functionally enriched in interferon-alpha signaling, viral defense response, and immune response. Additionally, the potential miR-340-3p-DTX3L interaction that has been systematically validated in miRNA prediction databases was proposed to participate in the disrupted skin homeostasis, altering the defense and immune response of diabetic skin. The findings may provide new insights into understanding the pathogenesis of epidermal pathologies in diabetic patients and targeting novel molecules to advance diabetic skin care in clinical practice.
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239
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Liu F, Ma T, Zhang Y. Genome-wide identification of protein binding sites on RNAs in mammalian cells. Biochem Biophys Res Commun 2019; 508:953-958. [DOI: 10.1016/j.bbrc.2018.11.184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 11/28/2018] [Indexed: 12/15/2022]
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240
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Ali AS, Raju R, Kshirsagar R, Ivanov AR, Gilbert A, Zang L, Karger BL. Multi-Omics Study on the Impact of Cysteine Feed Level on Cell Viability and mAb Production in a CHO Bioprocess. Biotechnol J 2018; 14:e1800352. [PMID: 30485675 DOI: 10.1002/biot.201800352] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/18/2018] [Indexed: 12/12/2022]
Abstract
There is continual demand to maximize CHO cell culture productivity of a biotherapeutic while maintaining product quality. In this study, a comprehensive multi-omics analysis is performed to investigate the cellular response to the level of dosing of the amino acid cysteine (Cys) in the production of a monoclonal antibody (mAb). When Cys feed levels are insufficient, there is a significant decrease in protein titer. Multi-omics (metabolomics and proteomics, with support from RNAseq) is performed over the time course of the CHO bioprocess producing an IgG1 mAb in 5 L bioreactors. Pathway analysis reveals that insufficient levels of Cys in the feed lead to Cys depletion in the cell. This depletion negatively impacts antioxidant molecules, such as glutathione (GSH) and taurine, leading to oxidative stress with multiple deleterious cellular effects. In this paper, the resultant ER stress and subsequent apoptosis that affects cell viability and viable cell density has been considered. Key metabolic enzymes and metabolites are identified that can be potentially monitored as the process progresses and/or increased in the cell either by nutrient feeding or genetic engineering. This work reinforces the centrality of redox balance to cellular health and success of the bioprocess as well as the power of multi-omics to provide an in-depth understanding of the CHO cell biology during biopharmaceutical production.
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Affiliation(s)
- Amr S Ali
- Cell Culture Development, Biogen, Inc., Cambridge, MA, 02142, USA.,Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Ravali Raju
- Cell Culture Development, Biogen, Inc., Cambridge, MA, 02142, USA
| | | | - Alexander R Ivanov
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Alan Gilbert
- Cell Culture Development, Biogen, Inc., Cambridge, MA, 02142, USA
| | - Li Zang
- Analytical Development, Biogen, Inc., Cambridge, MA, 02142, USA
| | - Barry L Karger
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
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241
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Jiao Q, Yin RH, Zhao SJ, Wang ZY, Zhu YB, Wang W, Zheng YY, Yin XB, Guo D, Wang SQ, Zhu YX, Bai WL. Identification and molecular analysis of a lncRNA-HOTAIR transcript from secondary hair follicle of cashmere goat reveal integrated regulatory network with the expression regulated potentially by its promoter methylation. Gene 2018; 688:182-192. [PMID: 30521888 DOI: 10.1016/j.gene.2018.11.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/05/2018] [Accepted: 11/22/2018] [Indexed: 01/17/2023]
Abstract
The HOTAIR transcript is transcribed from the antisense strand within the HOXC gene cluster, and it is thought to play a role in regulating the inductive capacity of dermal papilla cells during the reconstruction of hair-follicle. In the current investigation, we firstly isolated and characterized a lncRNA-HOTAIR transcript from the secondary hair follicle of cashmere goat. Also, we analyzed its transcriptional pattern and methylation level of HOTAIR gene promoter in secondary hair follicle of cashmere goat during anagen and telogen stages. Nucleotide composition analysis indicated that the contents of Adenine (A) and Thymine (T) are higher than that of Guanine (G) and Cytosine (C) in lncRNA-HOTAIR transcript of cashmere goat with the highest frequency distribution of AG nucleotide pair (8.06%). The regulatory network analysis showed a directly or indirectly complex regulatory relationships between lncRNA-HOTAIR of cashmere goat and its potential target molecules: miRNAs, mRNAs and proteins. Also, we showed that lncRNA-HOTAIR was properly transcribed at both anagen and telogen stages of secondary hair follicle of cashmere goat with the anagen being significantly higher than telogen in its expression, which suggest that lncRNA-HOTAIR transcript might be involved in the reconstruction of secondary hair follicle with the formation and growth of cashmere fiber. Taken together with methylation analysis of HOTAIR gene promoter, our data suggest that the promoter methylation of HOTAIR gene most likely is involved in its transcriptional suppression in secondary hair follicle of cashmere goat.
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Affiliation(s)
- Qian Jiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Rong H Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Su J Zhao
- Sichuan Animal Science Academy, Chengdu 610066, PR China
| | - Ze Y Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yu B Zhu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yuan Y Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xian B Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Shi Q Wang
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Yan X Zhu
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Wen L Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China.
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242
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Abramowicz A, Marczak L, Wojakowska A, Zapotoczny S, Whiteside TL, Widlak P, Pietrowska M. Harmonization of exosome isolation from culture supernatants for optimized proteomics analysis. PLoS One 2018; 13:e0205496. [PMID: 30379855 PMCID: PMC6209201 DOI: 10.1371/journal.pone.0205496] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022] Open
Abstract
Exosomes, the smallest subset of extracellular vesicles (EVs), have recently attracted much attention in the scientific community. Their involvement in intercellular communication and molecular reprogramming of different cell types created a demand for a stringent characterization of the proteome which exosomes carry and deliver to recipient cells. Mass spectrometry (MS) has been extensively used for exosome protein profiling. Unfortunately, no standards have been established for exosome isolation and their preparation for MS, leading to accumulation of artefactual data. These include the presence of high-abundance exosome-contaminating serum proteins in culture media which mask low-abundance exosome-specific components, isolation methods that fail to yield “pure” vesicles or variability in protein solubilization protocols. There is an unmet need for the development of standards for exosome generation, harvesting, and isolation from cellular supernatants and for optimization of protein extraction methods before proteomics analysis by MS. In this communication, we illustrate the existing problems in this field and provide a set of recommendations that are expected to harmonize exosome processing for MS and provide the faithful picture of the proteomes carried by exosomes. The recommended workflow for effective and specific identification of proteins in exosomes released by the low number of cells involves culturing cells in medium with a reduced concentration of exosome-depleted serum, purification of exosomes by size-exclusion chromatography, a combination of different protein extraction method and removal of serum-derived proteins from the final dataset using an appropriate sample of cell-unexposed medium as a control. Application of this method allowed detection of >250 vesicle-specific proteins in exosomes from 10 mL of culture medium.
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Affiliation(s)
- Agata Abramowicz
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Lukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Wojakowska
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | | | - Theresa L. Whiteside
- Department of Pathology, Immunology and Otolaryngology, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Piotr Widlak
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Monika Pietrowska
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
- * E-mail:
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243
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Communication of prostate cancer cells with bone cells via extracellular vesicle RNA; a potential mechanism of metastasis. Oncogene 2018; 38:1751-1763. [PMID: 30353168 PMCID: PMC6372071 DOI: 10.1038/s41388-018-0540-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022]
Abstract
The role of extracellular vesicles (EVs) as vehicles for cell-to-cell communication between a tumour and its environment is a relatively new concept. The hypothesis that EVs may be critical in co-opting tissues by tumours to generate distant metastatic niches is particularly pertinent to prostate cancer (PCa), where metastatic-tropism to bone predominates over other tissue types. The potential role of EVs as a means of communication between PCa cells and cells of the bone stroma such as osteoblasts, is yet to be fully explored. In this study, we demonstrate that PCa cell EVs both enhance osteoblast viability and produce a significantly more supportive growth environment for PCa cells when grown in co-culture with EV-treated osteoblasts (p < 0.005). Characterisation of the RNA cargo of EVs produced by the bone-metastatic PCa cell line PC3, highlights the EV-RNA cargo is significantly enriched in genes relating to cell surface signalling, cell–cell interaction, and protein translation (p < 0.01). Using novel techniques to track RNA, we demonstrate the delivery of a set of PCa-RNAs to osteoblast via PCa-EVs and show the effect on osteoblast endogenous transcript abundance. Taken together, by using proof-of-concept studies we demonstrate for the first time the contribution of the RNA element of the PCa EV cargo, providing evidence to support PCa EV communication via RNA molecules as a potential novel route to mediate bone metastasis. We propose targeting PCa EVs could offer a potentially important preventative therapy for men at risk of metastatic PCa.
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244
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Liu J, Liu Z, Zhang X, Gong T, Yao D. Examination of the expression and prognostic significance of DLGAPs in gastric cancer using the TCGA database and bioinformatic analysis. Mol Med Rep 2018; 18:5621-5629. [PMID: 30365066 PMCID: PMC6236227 DOI: 10.3892/mmr.2018.9574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
The discs large-associated protein (DLGAP) family has been implicated in psychological and neurological diseases. However, few studies have explored the association between the expression of DLGAPs and different types of cancer. Therefore, the present study analyzed the status of DLGAPs in gastric cancer (GC) using bioinformatic tools. Analyses of data obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases revealed that there was selective upregulation of DLGAP4 and DLGAP5 expression in GC tissues when compared with normal gastric tissues. In addition, survival analysis using OncoLnc indicated that high expression of DLGAP4 was significantly correlated with shorter overall survival for all GC patients. However, Kaplan-Meier plots demonstrated that the expression of all DLGAPs, except for DLGAP3, was correlated with patient prognosis; DLGAP4 was consistently associated with GC. DLGAP4 mRNA and protein distributions were examined by reverse transcription-quantitative polymerase chain reaction and immunohistochemsitry. Furthermore, its mutation rate and associated biological processes and signaling pathways were assessed in GC with cBioPortal and FunRich analyses. Taken together, these results indicated that DLGAP4 may serve an oncogenic role in GC development and may be a monitoring target for GC prognosis.
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Affiliation(s)
- Jiaxin Liu
- Department of Gerontological Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Zhao Liu
- Department of Oncological Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Xiaozhi Zhang
- Department of Radiation Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Tuotuo Gong
- Department of Radiation Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Demao Yao
- Department of Gerontological Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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245
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Ni M, Liu X, Wu J, Zhang D, Tian J, Wang T, Liu S, Meng Z, Wang K, Duan X, Zhou W, Zhang X. Identification of Candidate Biomarkers Correlated With the Pathogenesis and Prognosis of Non-small Cell Lung Cancer via Integrated Bioinformatics Analysis. Front Genet 2018; 9:469. [PMID: 30369945 PMCID: PMC6194157 DOI: 10.3389/fgene.2018.00469] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/24/2018] [Indexed: 01/10/2023] Open
Abstract
Background and Objective: Non-small cell lung cancer (NSCLC) accounts for 80-85% of all patients with lung cancer and 5-year relative overall survival (OS) rate is less than 20%, so that identifying novel diagnostic and prognostic biomarkers is urgently demanded. The present study attempted to identify potential key genes associated with the pathogenesis and prognosis of NSCLC. Methods: Four GEO datasets (GSE18842, GSE19804, GSE43458, and GSE62113) were obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between NSCLC samples and normal ones were analyzed using limma package, and RobustRankAggreg (RRA) package was used to conduct gene integration. Moreover, Search Tool for the Retrieval of Interacting Genes database (STRING), Cytoscape, and Molecular Complex Detection (MCODE) were utilized to establish protein-protein interaction (PPI) network of these DEGs. Furthermore, functional enrichment and pathway enrichment analyses for DEGs were performed by Funrich and OmicShare. While the expressions and prognostic values of top genes were carried out through Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan Meier-plotter (KM) online dataset. Results: A total of 249 DEGs (113 upregulated and 136 downregulated) were identified after gene integration. Moreover, the PPI network was established with 166 nodes and 1784 protein pairs. Topoisomerase II alpha (TOP2A), a top gene and hub node with higher node degrees in module 1, was significantly enriched in mitotic cell cycle pathway. In addition, Interleukin-6 (IL-6) was enriched in amb2 integrin signaling pathway. The mitotic cell cycle was the most significant pathway in module 1 with the highest P-value. Besides, five hub genes with high degree of connectivity were selected, including TOP2A, CCNB1, CCNA2, UBE2C, and KIF20A, and they were all correlated with worse OS in NSCLC. Conclusion: The results showed that TOP2A, CCNB1, CCNA2, UBE2C, KIF20A, and IL-6 may be potential key genes, while the mitotic cell cycle pathway may be a potential pathway contribute to progression in NSCLC. Further, it could be used as a new biomarker for diagnosis and to direct the synthesis medicine of NSCLC.
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Affiliation(s)
- Mengwei Ni
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Dan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jinhui Tian
- Evidence Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Ting Wang
- Beijing Institute of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Shuyu Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Ziqi Meng
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Kaihuan Wang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaojiao Duan
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Zhou
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaomeng Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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246
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Ju C, Li Y, Shen Y, Liu Y, Cai J, Liu N, Ma G, Tang Y. Transplantation of Cardiac Mesenchymal Stem Cell-Derived Exosomes for Angiogenesis. J Cardiovasc Transl Res 2018; 11:429-437. [PMID: 30276617 DOI: 10.1007/s12265-018-9824-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/31/2018] [Indexed: 12/25/2022]
Abstract
We demonstrated the effects of exosomes secreted by cardiac mesenchymal stem cells (C-MSC-Exo) in protecting acute ischemic myocardium from reperfusion injury. To investigate the effect of exosomes from C-MSC on angiogenesis, we injected C-MSC-Exo or PBS intramuscularly into ischemic hind limb. Blood perfusion of limb was evaluated by laser Doppler Imaging. We observed that ischemic limb treated with C-MSC-Exo exhibits improved blood perfusion compared to ischemic limb treated with PBS at 2 weeks and 1 month after induction of limb ischemia. To explore the potential mechanisms underlying C-MSC-Exo's angiogenetic effect, we performed microRNA array analysis and identify mmu-miR-7116-5p as the most abundant enriched miRNA detected in C-MSC-Exo. Bioinformatics' analysis shows that miR-7116-5p negatively regulates protein polyubiquitination. In conclusion, our study demonstrated that intramuscular delivery of C-MSC-Exo after limb ischemia improves blood perfusion, and we identified the most abundant miRNAs that are preferentially enriched in C-MSC-Exo.
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Affiliation(s)
- Chengwei Ju
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, China
| | - Youngjun Li
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, China
| | - Yan Shen
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Yutao Liu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Jingwen Cai
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Naifeng Liu
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, China
| | - Gengshan Ma
- Department of Cardiology, Zhongda Hospital, Medical School of Southeast University, Nanjing, China.
| | - Yaoliang Tang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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247
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van Herwijnen MJC, Driedonks TAP, Snoek BL, Kroon AMT, Kleinjan M, Jorritsma R, Pieterse CMJ, Hoen ENMN', Wauben MHM. Abundantly Present miRNAs in Milk-Derived Extracellular Vesicles Are Conserved Between Mammals. Front Nutr 2018; 5:81. [PMID: 30280098 PMCID: PMC6153340 DOI: 10.3389/fnut.2018.00081] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
Mammalian milk is not only a source of nutrition for the newborn, but also contains various components that regulate further development. For instance, milk is an abundant source of microRNAs (miRNAs), which are evolutionary conserved small non-coding RNAs that are involved in post-transcriptional regulation of target mRNA. MiRNAs present in milk can occur in extracellular vesicles (EVs), which are nanosized membrane vesicles released by many cell types as a means of intercellular communication. The membrane of EVs protects enclosed miRNAs from degradation and harbors molecules that allow specific targeting to recipient cells. Although several studies have investigated the miRNA content in milk EVs from individual species, little is known about the evolutionary conserved nature of EV-associated miRNAs among different species. In this study, we profiled the miRNA content of purified EVs from human and porcine milk. These data were compared to published studies on EVs from human, cow, porcine, and panda milk to assess the overlap in the top 20 most abundant miRNAs. Interestingly, several abundant miRNAs were shared between species (e.g., let-7 family members let-7a, let-7b, let-7f, and miR-148a). Moreover, these miRNAs have been implicated in immune-related functions and regulation of cell growth and signal transduction. The conservation of these miRNA among species, not only in their sequence homology, but also in their incorporation in milk EVs of several species, suggests that they are evolutionarily selected to regulate cell function in the newborn.
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Affiliation(s)
- Martijn J C van Herwijnen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Tom A P Driedonks
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Department of Biology, Science4Life Utrecht University, Utrecht, Netherlands
| | - A M Theresa Kroon
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Marije Kleinjan
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Ruurd Jorritsma
- Department of Farm Animal Health, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life Utrecht University, Utrecht, Netherlands
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Marca H M Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
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248
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Xu Y, Zhao W, Olson SD, Prabhakara KS, Zhou X. Alternative splicing links histone modifications to stem cell fate decision. Genome Biol 2018; 19:133. [PMID: 30217220 PMCID: PMC6138936 DOI: 10.1186/s13059-018-1512-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. However, their intricate interrelations and joint contributions to ESC fate decision remain unclear. RESULTS We analyze the transcriptomes and epigenomes of human ESC and five types of differentiated cells. We identify thousands of alternatively spliced exons and reveal their development and lineage-dependent characterizations. Several histone modifications show dynamic changes in alternatively spliced exons and three are strongly associated with 52.8% of alternative splicing events upon hESC differentiation. The histone modification-associated alternatively spliced genes predominantly function in G2/M phases and ATM/ATR-mediated DNA damage response pathway for cell differentiation, whereas other alternatively spliced genes are enriched in the G1 phase and pathways for self-renewal. These results imply a potential epigenetic mechanism by which some histone modifications contribute to ESC fate decision through the regulation of alternative splicing in specific pathways and cell-cycle genes. Supported by experimental validations and extended datasets from Roadmap/ENCODE projects, we exemplify this mechanism by a cell-cycle-related transcription factor, PBX1, which regulates the pluripotency regulatory network by binding to NANOG. We suggest that the isoform switch from PBX1a to PBX1b links H3K36me3 to hESC fate determination through the PSIP1/SRSF1 adaptor, which results in the exon skipping of PBX1. CONCLUSION We reveal the mechanism by which alternative splicing links histone modifications to stem cell fate decision.
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Affiliation(s)
- Yungang Xu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Scott D. Olson
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Karthik S. Prabhakara
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
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249
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Qing L, Chen H, Tang J, Jia X. Exosomes and Their MicroRNA Cargo: New Players in Peripheral Nerve Regeneration. Neurorehabil Neural Repair 2018; 32:765-776. [PMID: 30223738 PMCID: PMC6146407 DOI: 10.1177/1545968318798955] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peripheral nerve injury is a major clinical problem and often results in a poor functional recovery. Despite obvious clinical need, treatment strategies have been largely suboptimal. In the nervous system, exosomes, which are nanosized extracellular vesicles, play a critical role in mediating intercellular communication. More specifically, microRNA carried by exosomes are involved in various key processes such as nerve and vascular regeneration, and exosomes originating from Schwann cells, macrophages, and mesenchymal stem cells can promote peripheral nerve regeneration. In this review, the current knowledge of exosomes' and their miRNA cargo's role in peripheral nerve regeneration are summarized. The possible future roles of exosomes in therapy and the potential for microRNA-containing exosomes to treat peripheral nerve injuries are also discussed.
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Affiliation(s)
- Liming Qing
- Department of Hand & Microsurgery, Xiangya Hospital of
Central South University, Changsha, Hunan, 410008
- Department of Neurosurgery, University of Maryland School of
Medicine, Baltimore, MD 21201, USA
| | - Huanwen Chen
- Department of Neurosurgery, University of Maryland School of
Medicine, Baltimore, MD 21201, USA
| | - Juyu Tang
- Department of Hand & Microsurgery, Xiangya Hospital of
Central South University, Changsha, Hunan, 410008
| | - Xiaofeng Jia
- Department of Neurosurgery, University of Maryland School of
Medicine, Baltimore, MD 21201, USA
- Department of Orthopedics, University of Maryland School of
Medicine, Baltimore, MD 21201, USA
- Department of Anatomy and Neurobiology, University of Maryland
School of Medicine, Baltimore, MD 21201, USA
- Department of Biomedical Engineering, Johns Hopkins University
School of Medicine, Baltimore, MD 21205, USA
- Department of Anesthesiology and Critical Care Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Anand S, Foot N, Ang C, Gembus KM, Keerthikumar S, Adda CG, Mathivanan S, Kumar S. Arrestin‐Domain Containing Protein 1 (Arrdc1) Regulates the Protein Cargo and Release of Extracellular Vesicles. Proteomics 2018; 18:e1800266. [DOI: 10.1002/pmic.201800266] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/10/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Sushma Anand
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Natalie Foot
- Center for Cancer Biology University of South Australia and SA Pathology Adelaide South Australia 5000 Australia
| | - Ching‐Seng Ang
- Bio21 Institute University of Melbourne Victoria Melbourne 3010 Australia
| | - Kelly M. Gembus
- Center for Cancer Biology University of South Australia and SA Pathology Adelaide South Australia 5000 Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Christopher G. Adda
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Sharad Kumar
- Center for Cancer Biology University of South Australia and SA Pathology Adelaide South Australia 5000 Australia
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