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The Role of Alternative Splicing Factors hnRNP G and Fox-2 in the Progression and Prognosis of Esophageal Cancer. DISEASE MARKERS 2022; 2022:3043737. [DOI: 10.1155/2022/3043737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/10/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022]
Abstract
Aim. Alternative splicing (AS) has been widely demonstrated in the occurrence and progression of many cancers. Nevertheless, the involvement of cancer-associated splicing factors in the development of esophageal carcinoma (ESCA) remains to be explored. Method. RNA-Seq data and the corresponding clinical information of the ESCA cohort were downloaded from The Cancer Genome Atlas database. Bioinformatics methods were used to further analyzed the differently expressed AS (DEAS) events and their splicing network. Kaplan–Meier, Cox regression, and unsupervised cluster analyses were used to assess the association between AS events and clinical characteristics of ESCA patients. The splicing factors screened out were verified in vitro at the cellular level. Results. A total of 50,342 AS events were identified, of which 3,988 were DEAS events and 46 of these were associated with overall survival (OS) of ESCA patients, with a 5-year OS rate of 0.941. By constructing a network of AS events with survival-related splicing factors, the AS factors related to prognosis can be further identified. In vitro experiments and database analysis confirmed that the high expression of hnRNP G in ESCA is related to the high invasion ability of ESCA cells and the poor prognosis of ESCA patients. In contrast, the low expression of fox-2 in esophageal cancer is related to a better prognosis. Conclusion. ESCA-associated AS factors hnRNP G and Fox-2 are of great value in deciphering the underlying mechanisms of AS in ESCA and providing clues for therapeutic goals for further validation.
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Li X, Cao X, Li J, Niu Q, Mo Y, Xiao L. Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration-rehydration responses in Physcomitrium and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:953459. [PMID: 36262662 PMCID: PMC9574186 DOI: 10.3389/fpls.2022.953459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.
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Wu L, Chen Y, Wan L, Wen Z, Liu R, Li L, Song Y, Wang L. Identification of unique transcriptomic signatures and key genes through RNA sequencing and integrated WGCNA and PPI network analysis in HIV infected lung cancer. Cancer Med 2022; 12:949-960. [PMID: 35608130 PMCID: PMC9844649 DOI: 10.1002/cam4.4853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 01/26/2023] Open
Abstract
With the widespread use of highly active antiretroviral therapy (HARRT), the survival time of AIDS patients has been greatly extended. However, the incidence of lung cancer in HIV-infected patients is increasing and has become a major problem threatening the survival of AIDS patients. The aim of this study is to use Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene analysis to find possible key genes involved in HIV-infected lung cancer. In this study, using lung tissue samples from five pairs of HIV-infected lung cancer patients, second-generation sequencing was performed and transcriptomic data were obtained. A total of 132 HIV-infected lung cancer-related genes were screened out by WGCNA and differential gene expression analysis methods. Based on gene annotation analysis, these genes were mainly enriched in mitosis-related functions and pathways. In addition, in protein-protein interaction (PPI) analysis, a total of 39 hub genes were identified. Among them, five genes (ASPM, CDCA8, CENPF, CEP55, and PLK1) were present in both three hub gene lists (intersection gene, DEGs, and WCGNA module) suggesting that these five genes may become key genes involved in HIV-infected lung cancer.
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Affiliation(s)
- Liwei Wu
- Department of Thoracic SurgeryShanghai Public Health Clinical Center, Fudan University ShanghaiShanghaiChina
| | - Yongfang Chen
- Department of PharmacyShanghai Public Health Clinical CenterShanghaiChina
| | - Laiyi Wan
- Department of Thoracic SurgeryShanghai Public Health Clinical Center, Fudan University ShanghaiShanghaiChina
| | - Zilu Wen
- Department of Thoracic SurgeryShanghai Public Health Clinical Center, Fudan University ShanghaiShanghaiChina,Department of Scientific ResearchShanghai Public Health Clinical Center, Fudan UniversityShanghaiChina
| | - Rong Liu
- Department of PharmacyShanghai Public Health Clinical CenterShanghaiChina
| | - Leilei Li
- Department of Thoracic SurgeryShanghai Public Health Clinical Center, Fudan University ShanghaiShanghaiChina
| | - Yanzheng Song
- Department of Thoracic SurgeryShanghai Public Health Clinical Center, Fudan University ShanghaiShanghaiChina,TB CenterShanghai Emerging and Re‐emerging Infectious Disease Institute, Fudan UniversityShanghaiChina
| | - Lin Wang
- Department of Thoracic SurgeryShanghai Public Health Clinical Center, Fudan University ShanghaiShanghaiChina,TB CenterShanghai Emerging and Re‐emerging Infectious Disease Institute, Fudan UniversityShanghaiChina
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Anžel A, Heider D, Hattab G. MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks. Comput Struct Biotechnol J 2022; 20:1044-1055. [PMID: 35284047 PMCID: PMC8886009 DOI: 10.1016/j.csbj.2022.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
Thanks to recent advances in sequencing and computational technologies, many researchers with biological and/or medical backgrounds are now producing multiple data sets with an embedded temporal dimension. Multi-modalities enable researchers to explore and investigate different biological and physico-chemical processes with various technologies. Motivated to explore multi-omics data and time-series multi-omics specifically, the exploration process has been hindered by the separation introduced by each omics-type. To effectively explore such temporal data sets, discover anomalies, find patterns, and better understand their intricacies, expertise in computer science and bioinformatics is required. Here we present MOVIS, a modular time-series multi-omics exploration tool with a user-friendly web interface that facilitates the data exploration of such data. It brings into equal participation each time-series omic-type for analysis and visualization. As of the time of writing, two time-series multi-omics data sets have been integrated and successfully reproduced. The resulting visualizations are task-specific, reproducible, and publication-ready. MOVIS is built on open-source software and is easily extendable to accommodate different analytical tasks. An online version of MOVIS is available under https://movis.mathematik.uni-marburg.de/ and on Docker Hub (https://hub.docker.com/r/aanzel/movis).
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Affiliation(s)
- Aleksandar Anžel
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Strasse 6, Marburg 35032, Hesse, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Strasse 6, Marburg 35032, Hesse, Germany
| | - Georges Hattab
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Strasse 6, Marburg 35032, Hesse, Germany
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Li F, Meng X, Wang X, Ji C, Wu H. Graphene-triphenyl phosphate (TPP) co-exposure in the marine environment: Interference with metabolism and immune regulation in mussel Mytilus galloprovincialis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112904. [PMID: 34655885 DOI: 10.1016/j.ecoenv.2021.112904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Both immune regulation and endocrine systems are great challenges to marine organisms, and effective protocols for determining these adverse outcome pathways are limited, especially in vivo. The increasing usage of graphene nanomaterials can lead to the frequent exposure to marine organisms. Triphenyl phosphate (TPP), an organophosphate flame retardant, is frequently detected in natural environments. In this study, the combined toxic effects of co-exposure to graphene and TPP was investigated in Mytilus galloprovincialis using computational toxicology and multi-omics technology. Noticeably, graphene could disturb the membrane stability and increase the tissue accumulation of TPP. The adsorption behavior of TPP on graphene could inhibit the surface activity of graphene. In the digestive gland, transcriptomics analysis revealed the down-regulated genes in graphene + TPP treatment, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), sorbitol dehydrogenase (SORD), glutathione s-transferase mu 3 (GSTM3) and 4-aminobutyrate aminotransferase (ABAT), were mainly associated with oxidative stress and energy metabolism. Moreover, metabolic responses indicated that graphene + TPP could cause disturbances in energy metabolism and osmotic regulation marked by differentially altered ATP, glucose and taurine in mussels. These data underline the need for further knowledge on the potential interactions of nanomaterials with existing contaminants in marine organisms.
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Affiliation(s)
- Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China.
| | - Xiangjing Meng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaoqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China.
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Daher D, Deracinois B, Courcoux P, Baniel A, Chollet S, Froidevaux R, Flahaut C. Sensopeptidomic Kinetic Approach Combined with Decision Trees and Random Forests to Study the Bitterness during Enzymatic Hydrolysis Kinetics of Micellar Caseins. Foods 2021; 10:foods10061312. [PMID: 34200404 PMCID: PMC8228083 DOI: 10.3390/foods10061312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022] Open
Abstract
Protein hydrolysates are, in general, mixtures of amino acids and small peptides able to supply the body with the constituent elements of proteins in a directly assimilable form. They are therefore characterised as products with high nutritional value. However, hydrolysed proteins display an unpleasant bitter taste and possible off-flavours which limit the field of their nutrition applications. The successful identification and characterisation of bitter protein hydrolysates and, more precisely, the peptides responsible for this unpleasant taste are essential for nutritional research. Due to the large number of peptides generated during hydrolysis, there is an urgent need to develop methods in order to rapidly characterise the bitterness of protein hydrolysates. In this article, two enzymatic hydrolysis kinetics of micellar milk caseins were performed for 9 h. For both kinetics, the optimal time to obtain a hydrolysate with appreciable organoleptic qualities is 5 h. Then, the influence of the presence or absence of peptides and their intensity over time compared to the different sensory characteristics of hydrolysates was studied using heat maps, random forests and regression trees. A total of 22 peptides formed during the enzymatic proteolysis of micellar caseins and influencing the bitterness the most were identified. These methods represent simple and efficient tools to identify the peptides susceptibly responsible for bitterness intensity and predict the main sensory feature of micellar casein enzymatic hydrolysates.
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Affiliation(s)
- Dahlia Daher
- UMR Transfrontalière 1158 BioEcoAgro, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, 59000 Lille, France; (D.D.); (B.D.); (S.C.); (R.F.)
- Ingredia S.A. 51 Av. Lobbedez-CS 60946, CEDEX, 62033 Arras, France;
| | - Barbara Deracinois
- UMR Transfrontalière 1158 BioEcoAgro, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, 59000 Lille, France; (D.D.); (B.D.); (S.C.); (R.F.)
| | - Philippe Courcoux
- Oniris, StatSC, rue de la Géraudière, 44322 Nantes, France;
- INRA USC1381, 44322 Nantes, France
| | - Alain Baniel
- Ingredia S.A. 51 Av. Lobbedez-CS 60946, CEDEX, 62033 Arras, France;
| | - Sylvie Chollet
- UMR Transfrontalière 1158 BioEcoAgro, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, 59000 Lille, France; (D.D.); (B.D.); (S.C.); (R.F.)
| | - Rénato Froidevaux
- UMR Transfrontalière 1158 BioEcoAgro, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, 59000 Lille, France; (D.D.); (B.D.); (S.C.); (R.F.)
| | - Christophe Flahaut
- UMR Transfrontalière 1158 BioEcoAgro, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, 59000 Lille, France; (D.D.); (B.D.); (S.C.); (R.F.)
- Correspondence: ; Tel.: +33-321791780
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7
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Freedman AA, Smart BP, Keenan-Devlin LS, Romero J, Franklin A, Borders A, Ernst LM, Miller GE. Time-dependent changes in placental mRNA expression after delivery due to delayed specimen collection. Am J Reprod Immunol 2021; 86:e13452. [PMID: 34014593 DOI: 10.1111/aji.13452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022] Open
Abstract
PROBLEM Current scientific guidelines recommend collecting placental specimens within two hours of delivery for gene expression analysis. However, collecting samples in a narrow time window is a challenge in the dynamic and unpredictable clinical setting, so delays in placental specimen collection are possible. The purpose of our analysis was to investigate temporal changes in placental gene expression by longitudinally sampling placentas over a 24 h period. METHOD OF STUDY Eight placentas from individuals with uncomplicated, term pregnancies delivered by scheduled cesarean section were collected and sampled following the placental delivery and again at 1, 2, 4, 6, and 24 h post-delivery. At each time point, biopsies of chorionic villous tissue were taken from 3 cotyledons to account for intra-placental heterogeneity. The 3 biopsies from each time point were pooled prior to RNA extraction. Expression of 382 mRNA transcripts was quantified using the NanoString nCounter System. Fold change values were calculated for each time point relative to delivery, and a fold change threshold of 1.25 was used to determine a meaningful change from delivery. RESULTS Based on a fold change threshold of 1.25, 84.3% of transcripts were stable for at least 1 h, 80.2% were stable for at least two hours, and 20.6% of transcripts were stable through the collection at 24 h. CONCLUSION Our results suggest that for some mRNA transcripts, expression changes as time to sample collection increases. We have developed a Web application to allow investigators to explore transcripts relevant to their research interests and to set appropriate thresholds to aid in determining whether placentas with delayed sample collection can be included in analyses (https://placentaexpression.foundationsofhealth.org/).
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Affiliation(s)
- Alexa A Freedman
- Institute for Policy Research, Northwestern University, Evanston, IL, USA.,Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, USA
| | - Britney P Smart
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, USA
| | - Lauren S Keenan-Devlin
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of Chicago, Pritzker School of Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Janedelie Romero
- Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, USA
| | - Andrew Franklin
- Department of Pediatrics, Division of Neonatology, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ann Borders
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of Chicago, Pritzker School of Medicine, NorthShore University HealthSystem, Evanston, IL, USA.,Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Linda M Ernst
- Department of Pathology, University of Chicago Pritzker School of Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Gregory E Miller
- Institute for Policy Research, Northwestern University, Evanston, IL, USA.,Department of Psychology, Northwestern University, Evanston, IL, USA
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Zhang M, Hill JE, Alexander TW, Huang Y. The nasal viromes of cattle on arrival at western Canadian feedlots and their relationship to development of bovine respiratory disease. Transbound Emerg Dis 2020; 68:2209-2218. [PMID: 33031627 DOI: 10.1111/tbed.13873] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/03/2020] [Indexed: 01/08/2023]
Abstract
Bovine respiratory disease (BRD) has a complex pathogenesis and aetiology, being the costliest disease affecting the cattle industry in North America. In this study, we applied Nanopore-based viral metagenomic sequencing to explore the nasal virome of cattle upon arrival at feedlot and related the findings to the development of BRD. Deep nasal swabs (DNS) from 310 cattle for which BRD outcomes were known (155 cattle developed BRD within 40 days and 155 remained healthy) were included. The most prevalent virus in on-arrival samples was bovine coronavirus (BCV) (45.2%, 140/310), followed by bovine rhinitis virus B (BRBV) (21.9%, 68/310), enterovirus E (EVE) (19.6%, 60/310), bovine parainfluenza virus 3 (BPIV3) (10.3%, 32/310), ungulate tetraparvovirus 1 (UTPV1) (9.7%, 30/310) and influenza D virus (7.1%, 22/310). No relationship was found between BRD development and the number of viruses detected, the presence of any specific individual virus or combination of viruses. Bovine kobuvirus (BKV) was detected in 2.6% of animals (8/310), being the first report of this virus in Canada. Results of this study demonstrate the diversity of viruses in bovine DNS collected upon arrival at feedlot and highlights the need for further research into prediction of BRD development in the context of mixed infections.
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Affiliation(s)
- Maodong Zhang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Trevor W Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Yanyun Huang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc, Saskatoon, SK, Canada
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Liu X, Zhang L, Yang X, Zhang Y, Xu W, Zhang P, Zhao W, Peng K, Gong Y, Liu N. Simultaneous detection and quantification of 57 compounds in Spatholobi Caulis applying ultra‐fast liquid chromatography with tandem mass spectrometry. J Sep Sci 2020; 43:4247-4262. [DOI: 10.1002/jssc.202000496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Xiao‐Yan Liu
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center Peking University Beijing P. R. China
| | - Lei Zhang
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center Peking University Beijing P. R. China
| | - Xiu‐Wei Yang
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center Peking University Beijing P. R. China
| | - You‐Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center Peking University Beijing P. R. China
| | - Wei Xu
- State Key Laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center Peking University Beijing P. R. China
| | - Peng Zhang
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou P. R. China
| | - Wei Zhao
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou P. R. China
| | - Kai‐Feng Peng
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou P. R. China
| | - Yun Gong
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou P. R. China
| | - Ni‐Fu Liu
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou P. R. China
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Chen SD, Pan HY, Huang JB, Liu XP, Li JH, Ho CJ, Tsai MH, Yang JL, Chen SF, Chen NC, Chuang YC. Circulating MicroRNAs from Serum Exosomes May Serve as a Putative Biomarker in the Diagnosis and Treatment of Patients with Focal Cortical Dysplasia. Cells 2020; 9:cells9081867. [PMID: 32785072 PMCID: PMC7465068 DOI: 10.3390/cells9081867] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022] Open
Abstract
Focal cortical dysplasia (FCD) is a congenital malformation of cortical development where the cortical neurons located in the brain area fail to migrate in the proper formation. Epilepsy, particularly medically refractory epilepsy, is the most common clinical presentation for all types of FCD. This study aimed to explore the expression change of circulating miRNAs in patients with FCD from serum exosomes. A total of nine patients with FCD and four healthy volunteers were enrolled in this study. The serum exosomes were isolated from the peripheral blood of the subjects. Transmission electron microscopy (TEM) was used to identify the exosomes. Both exosomal markers and neuronal markers were detected by Western blotting analysis to prove that we could obtain central nervous system-derived exosomes from the circulation. The expression profiles of circulating exosomal miRNAs were assessed using next-generation sequencing analysis (NGS). We obtained a total of 107 miRNAs with dominant fold change (>2-fold) from both the annotated 5p-arm and 3p-arm of 2780 mature miRNAs. Based on the integrated platform of HMDD v3.2, miRway DB and DIANA-miRPath v3.0 online tools, and confirmed by MiRBase analysis, four potentially predicted miRNAs from serum exosomes in patients with FCD were identified, including miR194-2-5p, miR15a-5p, miR-132-3p, and miR-145-5p. All four miRNAs presented upregulated expression in patients with FCD compared with controls. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and pathway category of four target miRNAs, we found eight possible signaling pathways that may be related to FCD. Among them, we suggest that the mTOR signaling pathway, PI3K-Akt signaling pathway, p53 signaling pathway, and cell cycle regulation and TGF-beta signaling pathway are high-risk pathways that play a crucial role in the pathogenesis of FCD and refractory epilepsy. Our results suggest that the circulating miRNAs from exosomes may provide a potential biomarker for diagnostic, prognostic, and therapeutic adjuncts in patients with FCD and refractory epilepsy.
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Affiliation(s)
- Shang-Der Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Hsiu-Yung Pan
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (H.-Y.P.); (J.-B.H.)
| | - Jyun-Bin Huang
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (H.-Y.P.); (J.-B.H.)
| | - Xuan-Ping Liu
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
| | - Jie-Hau Li
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
| | - Chen-Jui Ho
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
| | - Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Jenq-Lin Yang
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
| | - Shu-Fang Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
| | - Nai-Ching Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
| | - Yao-Chung Chuang
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Neurology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Biological Science, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Correspondence:
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11
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Li Y, Wu T, Wu C, Wang Q, Ma P, Shao Y, Yu H, Hu Y. Eugenol-loaded chitosan emulsion holds the texture of chilled hairtail (Trichiurus lepturus) better: mechanism exploration by proteomic analysis. Food Funct 2020; 11:7509-7522. [DOI: 10.1039/d0fo01135e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Eugenol-loaded chitosan emulsion (ELCE) has been proved to have an excellent antibacterial property.
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Affiliation(s)
- Yuan Li
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
| | - Tiantian Wu
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
| | - Chunhua Wu
- College of Food Science
- Fujian Agriculture and Forestry University
- Fuzhou 350002
- China
| | - Qin Wang
- Department of Nutrition and Food Science
- College of Agriculture and Nature Resources
- University of Maryland
- College Park
- USA
| | - Peihua Ma
- Department of Nutrition and Food Science
- College of Agriculture and Nature Resources
- University of Maryland
- College Park
- USA
| | - Ying Shao
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
| | - Haixia Yu
- Ocean Research Center of Zhoushan
- Zhejiang University
- Zhoushan 316021
- China
| | - Yaqin Hu
- College of Biosystems Engineering and Food Science
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment
- Zhejiang Key Laboratory for Agro-Food Processing
- Integrated Research Base of Southern Fruit and Vegetable Preservation Technology
- Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control
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12
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Zhang M, Hill JE, Godson DL, Ngeleka M, Fernando C, Huang Y. The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada. Transbound Emerg Dis 2019; 67:924-934. [PMID: 31715071 PMCID: PMC7168541 DOI: 10.1111/tbed.13419] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]
Abstract
The aetiology and pathogenesis of bovine respiratory disease (BRD) are complex and involve the interplay of infectious agents, management and environmental factors. Previous studies of BRD focused on ante‐mortem samples from the upper respiratory tract and identified several unconventional viruses. The lung, however, is the primary location where significant BRD lesions are usually found and is a common post‐mortem diagnostic specimen. In this study, results of high‐throughput virome sequencing, bacterial culture, targeted real‐time PCR and histological examination of 130 bovine pneumonic lungs from western Canadian cattle were combined to explore associations of microorganisms with different types of pneumonia. Fibrinous bronchopneumonia (FBP) was the predominant type of pneumonia (46.2%, 60/130) and was associated with the detection of Mannheimia haemolytica. Detection of Histophilus somni and Pasteurella multocida was associated with suppurative bronchopneumonia (SBP) and concurrent bronchopneumonia and bronchointerstitial pneumonia (BP&BIP), respectively. Sixteen viruses were identified, of which bovine parvovirus 2 (BPV2) was the most prevalent (11.5%, 15/130) followed by ungulate tetraparvovirus 1 (UTPV1, 8.5%, 11/130) and bovine respiratory syncytial virus (BRSV, 8.5%, 11/130). None of these viruses, however, were significantly associated with a particular type of pneumonia. Unconventional viruses such as influenza D virus (IDV) and bovine rhinitis B virus (BRBV) were detected, although sparsely, consistent with our previous findings in upper respiratory tract samples. Taken together, our results show that while virus detection in post‐mortem lung samples is of relatively little diagnostic value, the strong associations of H. somni and M. haemolytica with SBP and FBP, respectively, indicate that histopathology can be useful in differentiating bacterial aetiologies.
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Affiliation(s)
- Maodong Zhang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dale L Godson
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc., Saskatoon, SK, Canada
| | - Musangu Ngeleka
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc., Saskatoon, SK, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yanyun Huang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc., Saskatoon, SK, Canada
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13
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Listopad SA, Norden-Krichmar TM. A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons. BMC Bioinformatics 2019; 20:595. [PMID: 31744472 PMCID: PMC6862834 DOI: 10.1186/s12859-019-3121-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/01/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Researchers commonly analyze lists of differentially expressed entities (DEEs), such as differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and differentially methylated positions/regions (DMPs/DMRs), across multiple pairwise comparisons. Large biological studies can involve multiple conditions, tissues, and timepoints that result in dozens of pairwise comparisons. Manually filtering and comparing lists of DEEs across multiple pairwise comparisons, typically done by writing custom code, is a cumbersome task that can be streamlined and standardized. RESULTS A-Lister is a lightweight command line and graphical user interface tool written in Python. It can be executed in a differential expression mode or generic name list mode. In differential expression mode, A-Lister accepts as input delimited text files that are output by differential expression tools such as DESeq2, edgeR, Cuffdiff, and limma. To allow for the most flexibility in input ID types, to avoid database installation requirements, and to allow for secure offline use, A-Lister does not validate or impose restrictions on entity ID names. Users can specify thresholds to filter the input file(s) by column(s) such as p-value, q-value, and fold change. Additionally, users can filter the pairwise comparisons within the input files by fold change direction (sign). Queries composed of intersection, fuzzy intersection, difference, and union set operations can also be performed on any number of pairwise comparisons. Thus, the user can filter and compare any number of pairwise comparisons within a single A-Lister differential expression command. In generic name list mode, A-Lister accepts delimited text files containing lists of names as input. Queries composed of intersection, fuzzy intersection, difference, and union set operations can then be performed across these lists of names. CONCLUSIONS A-Lister is a flexible tool that enables the user to rapidly narrow down large lists of DEEs to a small number of most significant entities. These entities can then be further analyzed using visualization, pathway analysis, and other bioinformatics tools.
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Affiliation(s)
- Stanislav A Listopad
- Department of Computer Science, University of California Irvine, California, USA
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