1
|
Sun X, Han B, Han Q, Yu Q, Wang S, Feng J, Feng T, Li X, Zhang S, Li H. Similarity of Chinese and Pakistani oral microbiome. Antonie Van Leeuwenhoek 2024; 117:38. [PMID: 38372789 DOI: 10.1007/s10482-024-01933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Oral microbiota is vital for human health and can be affected by various factors (i.e. diets, ethnicity). However, few studies have compared oral microbiota of individuals from different nationalities in the same environment. Here, we explored the assembly and interaction of oral microbial communities of Chinese and Pakistanis in one university. Firmicutes and Proteobacteria were the predominant microorganisms in the oral cavity of Chinese and Pakistanis. Streptococcus and Neisseria were the dominant genera of China, while Streptococcus and Haemophilus were the dominant genera of Pakistanis. In addition, the oral community membership and structure were not influenced by season, Chinese/Pakistani student and gender, reflecting the stability of the human oral microbiome. The beta diversity of oral microbiomes between Chinese and Pakistanis significantly differed in winter, but not in spring. The alpha diversity of Chinese students and Pakistani students was similar. Moreover, oral microbial community of both Chinese and Pakistani students was mainly driven by stochastic processes. The microbial network of Chinese was more complexity and stability than that of Pakistanis. Our study uncovers the characteristics of human oral microbiota, which is of great significance for oral and human health.
Collapse
Affiliation(s)
- Xiaofang Sun
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Binghua Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jie Feng
- Department of Digestive, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Tianshu Feng
- School of Public Health, Peking University, Beijing, 100871, China
| | - Xiaoshan Li
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou, 404120, China
| | - Shiheng Zhang
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou, 404120, China.
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
2
|
Changes in metabolic profiling of whiteleg shrimp (Penaeus vannamei) under hypoxic stress. J Invertebr Pathol 2022; 193:107798. [PMID: 35843291 DOI: 10.1016/j.jip.2022.107798] [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: 03/28/2022] [Revised: 06/13/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022]
Abstract
Hypoxia is a common concern in shrimp aquaculture, affecting growth and survival. Although recent studies have revealed important insights into hypoxia in shrimp and crustaceans, knowledge gaps remain regarding this stressor at the molecular level. In the present study, a gas chromatography-mass spectrometry (GC-MS)-based metabolomics approach was employed to characterize the metabolic signatures and pathways underlying responses of Pacific white shrimp (Penaeus vannamei) to hypoxia and to identify associated candidate biomarkers. We compared metabolite profiles of shrimp haemolymph before (0 h) and after exposure to hypoxia (1 & 2 h). Dissolved oxygen levels were maintained above 85 % saturation in the control and before hypoxia, and 15 % saturation in the hypoxic stress treatment. Results showed 44 metabolites in shrimp haemolymph that were significantly different between before and after hypoxia exposure. These metabolites were energy-related metabolites (e.g., intermediates of citric acid cycle, lactic acid, alanine), fatty acids and amino acids. Pathway analysis revealed 17 pathways that were significantly affected by hypoxia. The changes in metabolites and pathways indicate a shift from aerobic to anaerobic metabolism, disturbance in amino acid metabolism, osmoregulation, oxidative damage and Warburg effect-like response caused by hypoxic stress. Among the altered metabolites, lactic acid was most different between before and after hypoxia exposure and had the highest accurate value for biomarker identification. Future investigations may validate this molecule as a stress biomarker in aquaculture. This study contributes to a better understanding of hypoxia in shrimp and crustaceans at the metabolic level and provides a base for future metabolomics investigations on hypoxia.
Collapse
|
3
|
Nguyen TV, Alfaro A, Frost E, Chen D, Beale DJ, Mundy C. Investigating the biochemical effects of heat stress and sample quenching approach on the metabolic profiling of abalone (Haliotis iris). Metabolomics 2021; 18:7. [PMID: 34958425 DOI: 10.1007/s11306-021-01862-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Ocean temperatures have been consistently increasing due to climate change, and the frequency of heatwave events on shellfish quality is a growing concern worldwide. Typically, shellfish growing areas are in remote or difficult to access locations which makes in-field sampling and sample preservation of shellfish heat stress difficult. As such, there is a need to investigate in-field sampling approaches that facilitate the study of heat stress in shellfish. OBJECTIVES This study aims to apply a gas chromatography-mass spectrometry (GC-MS) based metabolomics approach to examine molecular mechanisms of heat stress responses in shellfish using abalone as a model, and compare the effects of different quenching protocols on abalone metabolic profiles. METHODS Twenty adult Haliotis iris abalone were exposed to two temperatures (14 °C and 24 °C) for 24 h. Then, haemolymph and muscle tissues of each animal were sampled and quenched with 4 different protocols (liquid nitrogen, dry ice, cold methanol solution and normal ice) which were analyzed via GC-MS for central carbon metabolites. RESULTS The effects of different quenching protocols were only observed in muscle tissues in which the cold methanol solution and normal ice caused some changes in the observed metabolic profiles, compared to dry ice and liquid nitrogen. Abalone muscle tissues were less affected by thermal stress than haemolymph. There were 10 and 46 compounds significantly influenced by thermal stress in muscle and haemolymph, respectively. The changes of these metabolite signatures indicate oxidative damage, disturbance of amino acid and fatty acid metabolism, and a shift from aerobic metabolism to anaerobic pathways. CONCLUSIONS The study provided insights into the heat response of abalone, which could be useful for understanding the effects of marine heatwaves and summer mortality events on abalone. Dry ice appeared to be a suitable protocol, and safer in-field alternative to liquid nitrogen, for quenching of abalone tissues.
Collapse
Affiliation(s)
- Thao V Nguyen
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Andrea Alfaro
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Emily Frost
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Donglin Chen
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecoscience Precinct, Dutton Park, QLD, Australia
| | - Craig Mundy
- IMAS Fisheries and Aquaculture Centre, College of Science and Engineering, University of Tasmania, Taroona, TAS, Australia
| |
Collapse
|
4
|
Li S, Alfaro AC, Nguyen TV, Young T, Lulijwa R. An integrated omics approach to investigate summer mortality of New Zealand Greenshell™ mussels. Metabolomics 2020; 16:100. [PMID: 32915338 DOI: 10.1007/s11306-020-01722-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Green-lipped mussels, commercially known as Greenshell™ mussels (Perna canaliculus Gmelin 1791), contribute > $300 million to New Zealand's aquaculture exports. However, mortalities during summer months and potential pathogenic outbreaks threaten the industry. Thermal stress mechanisms and immunological responses to pathogen infections need to be understood to develop health assessment strategies and early warning systems. METHODS P. canaliculus were collected during a mortality event at a commercial aquaculture farm in Firth of Thames, New Zealand. Gill tissues from six healthy and six unhealthy mussels were excised and processed for metabolomic (GC-MS) and label-free proteomic (LC-MS) profiling. Univariate analyses were conducted separately on each data layer, with data being integrated via sparse multiple discriminative canonical correlation analysis. Pathway enrichment analysis was used to probe coordinated changes in functionally related metabolite sets. RESULTS Findings revealed disruptions of the tricarboxylic acid (TCA) cycle and fatty acid metabolism in unhealthy mussels. Metabolomics analyses also indicated oxidative stress in unhealthy mussels. Proteomics analyses identified under-expression of proteins associated with cytoskeleton structure and regulation of cilia/flagellum in gill tissues of unhealthy mussels. Integrated omics revealed a positive correlation between Annexin A4 and CCDC 150 and saturated fatty acids, as well as a negative correlation between 2-aminoadipic acid and multiple cytoskeletal proteins. CONCLUSIONS Our study demonstrates the ability of using integrative omics to reveal metabolic perturbations and protein structural changes in the gill tissues of stressed P. canaliculus and provides new insight into metabolite and protein interactions associated with incidences of summer mortality in this species.
Collapse
Affiliation(s)
- Siming Li
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Thao V Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Ronald Lulijwa
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| |
Collapse
|
5
|
Ding Y, Wang X, Pan J, Ji M, Luo Z, Zhao P, Zhang Y, Wang G. Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development. Arch Med Sci 2020; 16:177-188. [PMID: 32051722 PMCID: PMC6963149 DOI: 10.5114/aoms.2020.91290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/01/2017] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Aberrant expression of long non-coding RNAs (lncRNAs) has been implicated in various diseases, including cancer. However, little is known about lncRNAs in human brain gliomas. MATERIAL AND METHODS We examined lncRNA profiles from three glioma specimens using lncRNA expression profiling microarrays. Quantitative real-time RT-PCR was used to analyze the differential expression of raw intensities of lncRNA expression in glioma and peritumoral tissues. RESULTS We found 4858 lncRNAs to be differentially expressed between tumor tissue and peritumoral tissue. Of these, 2845 lncRNAs were up-regulated (fold change > 3.0) and 2013 were down-regulated (fold change < 1/3). A total of 4084 messenger RNAs were also differentially expressed, including 2280 up-regulated transcripts (fold change > 3.0) and 1804 that were down-regulated (fold change < 1/3). Consistent with the microarray data, qPCR confirmed differential expression of these 6 lncRNAs (ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc003qmb.2) between tumor and peritumoral tissue. We next established co-expression networks of differentially expressed lncRNAs and mRNAs. Many mRNAs, such as LOC729991, NUDCD1, SHC3, PDGFA, and MDM2, and lncRNAs, such as ENST00000425922, ENST00000455568, uc002ukz.1, ENST00000502715, and NR_027873, have been shown to play important roles in glioma development. Consistent with this, pathway analysis revealed that "GLIOMA" (KEGG Pathway ID: hsa05214) was significantly enriched in tumor tissue. CONCLUSIONS Our data suggest that altered expression of lncRNAs may be a critical determinant of tumorigenesis in glioma patients.
Collapse
Affiliation(s)
- Yi Ding
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Xinfa Wang
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Junchen Pan
- Department of Neurosurgery, Nanjing BenQ hospital, Nanjing, China
| | - Minjun Ji
- Department of Neurosurgery, Nanjing Medical University, Nanjing, China
| | - Zhengxiang Luo
- Department of Neurosurgery, Nanjing Brian Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Penglai Zhao
- Department of Neurosurgery, Nanjing Brian Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yansong Zhang
- Department of Neurosurgery, Nanjing Brian Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Gang Wang
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
6
|
Nguyen TV, Alfaro AC, Young T, Green S, Zarate E, Merien F. Itaconic acid inhibits growth of a pathogenic marine Vibrio strain: A metabolomics approach. Sci Rep 2019; 9:5937. [PMID: 30976014 PMCID: PMC6459830 DOI: 10.1038/s41598-019-42315-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/29/2019] [Indexed: 01/28/2023] Open
Abstract
The antimicrobial role of itaconic acid (ITA) has been recently discovered in mammalian cells. In our previous studies, we discovered that marine molluscs biosynthesise substantial quantities of ITA when exposed to marine pathogens, but its antimicrobial function to Vibrio bacteria is currently unknown. Thus, in this study, we used an untargeted gas chromatography-mass spectrometry (GC-MS) platform to identify metabolic changes of Vibrio sp. DO1 (V. corallyliticus/neptunius-like isolate) caused by ITA exposure. Vibrio sp. DO1 was cultured in Luria-Bertani broth supplemented with 3 mM sodium acetate and with different concentrations of ITA (0, 3 and 6 mM) for 24 h. The results showed that ITA completely inhibited Vibrio sp. growth at 6 mM and partially inhibited the bacterial growth at 3 mM. A principal component analysis (PCA) revealed a clear separation between metabolite profiles of Vibrio sp. DO1 in the 3 mM ITA treatment and the control, which were different in 25 metabolites. Among the altered metabolites, the accumulation of glyoxylic acid and other metabolites in glyoxylate cycle (cis-aconitic acid, isocitric acid and fumaric acid) together with the increase of isocitrate lyase (ICL) activity in the 3 mM ITA treatment compared to the control suggest that ITA inhibited Vibrio sp. growth via disruption of central carbon metabolism.
Collapse
Affiliation(s)
- Thao Van Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand.
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Saras Green
- Mass Spectrometry Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Erica Zarate
- Mass Spectrometry Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Fabrice Merien
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| |
Collapse
|
7
|
Liu X, Wang X, Chen Z, Ye J, Liao Y, Zhang W, Chang J, Xu F. De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L. PLANT CELL REPORTS 2019; 38:101-116. [PMID: 30430213 DOI: 10.1007/s00299-018-2352-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
Analysis of terpenoids content, transcriptome from Chamaemelum nobile showed that the content of the terpenoids in the roots was the highest and key genes involved in the terpenoids synthesis pathway were identified. Chamaemelum nobile is a widely used herbaceous medicinal plant rich in volatile oils, mainly composed of terpenoids. It is widely used in food, cosmetics, medicine, and other fields. In this study, we analyzed the transcriptome and the content and chemical composition of the terpenoids in different organs of C. nobile. Gas chromatography-mass spectrometry analysis showed that the total content of the terpenoids among C. nobile organs was highest in the roots, followed by the flowers. Illumina HiSeq 2500 high-throughput sequencing technology was used to sequence the transcripts of roots, stems, leaves, and flowers of C. nobile. We obtained 139,757 unigenes using the Trinity software assembly. A total of 887 unigenes were annotated to secondary metabolism. In total, 55,711 differentially expressed genes were screened among different organs of C. nobile. We identified 16 candidate genes that may be involved in the terpenoid biosynthesis from C. nobile and analyzed their expression patterns using real-time PCR. Results showed that the expression pattern of these genes was tissue-specific and had significant differential expression levels in different organs of C. nobile. Among these genes, 13 were expressed in roots with the highest levels. Furthermore, the transcript levels of these 13 genes were positively correlated with the content of α-pinene, β-phellandrene, 1,8-cineole, camphor, α-terpineol, carvacrol, (E,E)-farnesol and chamazulene, suggesting that these 13 genes may be involved in the regulation of the synthesis of the volatile terpenoids. These results laid the foundation for the subsequent improvement of C. nobile quality through genetic engineering.
Collapse
Affiliation(s)
- Xiaomeng Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaohui Wang
- Enshi Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Zexiong Chen
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jie Chang
- Hubei Collaborative Innovation Center of Targeted Antitumor Drug, Jingchu University of Technology, Jingmen, 448000, Hubei, China
- College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, 448000, Hubei, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| |
Collapse
|
8
|
Nguyen TV, Alfaro AC, Merien F, Young T, Grandiosa R. Metabolic and immunological responses of male and female new Zealand Greenshell™ mussels (Perna canaliculus) infected with Vibrio sp. J Invertebr Pathol 2018; 157:80-89. [PMID: 30110610 DOI: 10.1016/j.jip.2018.08.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/09/2018] [Accepted: 08/12/2018] [Indexed: 12/20/2022]
Abstract
Massive mortalities due to pathogens are routinely reported in bivalve cultivation that have significant economic consequences for the global aquaculture industry. However, host-pathogen interactions and infection mechanisms that mediate these interactions are poorly understood. In addition, gender-specific immunological responses have been reported for some species, but the reasons for such differences have not been elucidated. In this study, we used a GC/MS-based metabolomics platform and flow cytometry approach to characterize metabolic and immunological responses in haemolymph of male and female mussels (Perna canaliculus) experimentally infected with Vibrio sp. Sex-based differences in immunological responses were identified, with male mussels displaying higher mortality, oxidative stress and apoptosis after pathogen exposure. However, central metabolic processes appeared to be similar between sexes at 24 h post injection with Vibrio sp. DO1. Significant alterations in relative levels of 37 metabolites were detected between infected and uninfected mussels. These metabolites are involved in major perturbations on the host's innate immune system. In addition, there were alterations of seven metabolites in profiles of mussels sampled on the second day and mussels that survived six days after exposure. These metabolites include itaconic acid, isoleucine, phenylalanine, creatinine, malonic acid, glutaric acid and hydroxyproline. Among these, itaconic acid has the potential to be an important biomarker for Vibrio sp. DO1 infection. These findings provide new insights on the mechanistic relationship between a bivalve host and a pathogenic bacterium and highlight the need to consider host sex as a biological variable in future immunological studies.
Collapse
Affiliation(s)
- Thao V Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.
| | - Fabrice Merien
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Roffi Grandiosa
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| |
Collapse
|
9
|
Nguyen TV, Alfaro AC, Young T, Ravi S, Merien F. Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:396-409. [PMID: 29611031 DOI: 10.1007/s10126-018-9804-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Vibrio coralliilyticus is a bacterial pathogen which can affect a range of marine organisms, such as corals, fish and shellfish, with sometimes devastating consequences. However, little is known about the mechanisms involved in the host-pathogen interaction, especially within molluscan models. We applied gas chromatography-mass spectrometry (GC-MS)-based metabolomics to characterize the physiological responses in haemolymph of New Zealand Greenshell™ mussels (Perna canaliculus) injected with Vibrio sp. DO1 (V. coralliilyticus/neptunius-like isolate). Univariate data analyses of metabolite profiles in Vibrio-exposed mussels revealed significant changes in 22 metabolites at 6 h post-infection, compared to non-exposed mussels. Among them, 10 metabolites were up-regulated, while 12 metabolites were down-regulated in infected mussels. Multivariate analyses showed a clear distinction between infected and non-infected mussels. In addition, secondary pathway analyses indicated perturbations of the host innate immune system following infection, including oxidative stress, inflammation and disruption of the TCA cycle, change in amino acid metabolism and protein synthesis. These findings provide new insights into the pathogenic mechanisms of Vibrio infection of mussels and demonstrate our ability to detect detailed and rapid host responses from haemolymph samples using a metabolomics approach.
Collapse
Affiliation(s)
- Thao V Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Sridevi Ravi
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Fabrice Merien
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| |
Collapse
|
10
|
Lan YB, Huang YZ, Qu F, Li JQ, Ma LJ, Yan J, Zhou JH. Time course of global gene expression alterations in Candida albicans during infection of HeLa cells. Bosn J Basic Med Sci 2017; 17:120-131. [PMID: 28397609 DOI: 10.17305/bjbms.2017.1667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/09/2016] [Indexed: 01/21/2023] Open
Abstract
Candida albicans (C. albicans) is an opportunistic fungus that quickly adapts to various microniches. It causes candidiasis, a common fungal infection for which the pathogenic mechanism has not been elucidated yet. To explore the pathogenic mechanism of candidiasis we used several methods, including microscopic observation of morphological changes of HeLa cells and fungus, analysis of differentially expressed genes using gene chips, and a series of biological and bioinformatic analyses to explore genes that are possibly involved in the pathogenesis of C. albicans. During the C. albicans infection, significant morphological changes of the fungus were observed, and the HeLa cells were gradually destroyed. The gene chip experiments showed upregulated expression of 120 genes and downregulated expression of 178 genes. Further analysis showed that some genes may play an important role in the pathogenesis of C. albicans. Overall, morphological variation and adaptive gene expression within a particular microniche may exert important effects during C. albicans infections.
Collapse
Affiliation(s)
- Yi-Bing Lan
- Department of Gynecology, The Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | | | | | | | | | | | | |
Collapse
|
11
|
Niere F, Namjoshi S, Song E, Dilly GA, Schoenhard G, Zemelman BV, Mechref Y, Raab-Graham KF. Analysis of Proteins That Rapidly Change Upon Mechanistic/Mammalian Target of Rapamycin Complex 1 (mTORC1) Repression Identifies Parkinson Protein 7 (PARK7) as a Novel Protein Aberrantly Expressed in Tuberous Sclerosis Complex (TSC). Mol Cell Proteomics 2015; 15:426-44. [PMID: 26419955 DOI: 10.1074/mcp.m115.055079] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Indexed: 01/05/2023] Open
Abstract
Many biological processes involve the mechanistic/mammalian target of rapamycin complex 1 (mTORC1). Thus, the challenge of deciphering mTORC1-mediated functions during normal and pathological states in the central nervous system is challenging. Because mTORC1 is at the core of translation, we have investigated mTORC1 function in global and regional protein expression. Activation of mTORC1 has been generally regarded to promote translation. Few but recent works have shown that suppression of mTORC1 can also promote local protein synthesis. Moreover, excessive mTORC1 activation during diseased states represses basal and activity-induced protein synthesis. To determine the role of mTORC1 activation in protein expression, we have used an unbiased, large-scale proteomic approach. We provide evidence that a brief repression of mTORC1 activity in vivo by rapamycin has little effect globally, yet leads to a significant remodeling of synaptic proteins, in particular those proteins that reside in the postsynaptic density. We have also found that curtailing the activity of mTORC1 bidirectionally alters the expression of proteins associated with epilepsy, Alzheimer's disease, and autism spectrum disorder-neurological disorders that exhibit elevated mTORC1 activity. Through a protein-protein interaction network analysis, we have identified common proteins shared among these mTORC1-related diseases. One such protein is Parkinson protein 7, which has been implicated in Parkinson's disease, yet not associated with epilepsy, Alzheimers disease, or autism spectrum disorder. To verify our finding, we provide evidence that the protein expression of Parkinson protein 7, including new protein synthesis, is sensitive to mTORC1 inhibition. Using a mouse model of tuberous sclerosis complex, a disease that displays both epilepsy and autism spectrum disorder phenotypes and has overactive mTORC1 signaling, we show that Parkinson protein 7 protein is elevated in the dendrites and colocalizes with the postsynaptic marker postsynaptic density-95. Our work offers a comprehensive view of mTORC1 and its role in regulating regional protein expression in normal and diseased states.
Collapse
Affiliation(s)
- Farr Niere
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas; ‖Waggoner Center for Alcohol and Addiction Research, University of Texas, Austin, Texas
| | - Sanjeev Namjoshi
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas
| | - Ehwang Song
- **Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409
| | - Geoffrey A Dilly
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas
| | - Grant Schoenhard
- ‡‡Pain Therapeutics, Inc., 7801 N Capital of Texas Hwy, #260, Austin, Texas 78731
| | - Boris V Zemelman
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas
| | - Yehia Mechref
- **Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409
| | - Kimberly F Raab-Graham
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas; ‖Waggoner Center for Alcohol and Addiction Research, University of Texas, Austin, Texas; ‡‡Pain Therapeutics, Inc., 7801 N Capital of Texas Hwy, #260, Austin, Texas 78731
| |
Collapse
|
12
|
Gu S, Li G, Zhang X, Yan J, Gao J, An X, Liu Y, Su P. Aberrant expression of long noncoding RNAs in chronic thromboembolic pulmonary hypertension. Mol Med Rep 2014; 11:2631-43. [PMID: 25522749 PMCID: PMC4337719 DOI: 10.3892/mmr.2014.3102] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 11/25/2014] [Indexed: 01/04/2023] Open
Abstract
Chronic thromboembolic pulmonary hypertension (CTEPH) is one of the primary causes of severe pulmonary hypertension. In order to identify long noncoding RNAs (lncRNAs) that may be involved in the development of CTEPH, comprehensive lncRNA and messenger RNA (mRNA) profiling of endothelial tissues from the pulmonary arteries of CTEPH patients was conducted with microarray analysis. Differential expression of 185 lncRNAs was observed in the CTEPH tissues compared with healthy control tissues. Further analysis identified 464 regulated enhancer-like lncRNAs and overlapping, antisense or nearby mRNA pairs. Coexpression networks were subsequently constructed and investigated. The expression levels of the lncRNAs, NR_036693, NR_027783, NR_033766 and NR_001284, were significantly altered. Gene ontology and pathway analysis demonstrated the potential role of lncRNAs in the regulation of central process, including inflammatory response, response to endogenous stimulus and antigen processing and presentation. The use of bioinformatics may help to uncover and analyze large quantities of data identified by microarray analyses, through rigorous experimental planning, statistical analysis and the collection of more comprehensive data regarding CTEPH. The results of the present study provided evidence which may be helpful in future studies on the diagnosis and management of CTEPH.
Collapse
Affiliation(s)
- Song Gu
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Guanghui Li
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xitao Zhang
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Jun Yan
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Jie Gao
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xiangguang An
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Yan Liu
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Pixiong Su
- Department of Cardiac Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, P.R. China
| |
Collapse
|
13
|
The noncoding RNA expression profile and the effect of lncRNA AK126698 on cisplatin resistance in non-small-cell lung cancer cell. PLoS One 2013; 8:e65309. [PMID: 23741487 PMCID: PMC3669360 DOI: 10.1371/journal.pone.0065309] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 04/29/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The efficacy of cisplatin-based chemotherapy in non-small-cell lung cancer is limited by the acquired drug resistance. Identification the RNAs related to the cisplatin resistance may help to improve clinical response rates. METHODS Microarray expression profiling of mRNAs, lncRNA and miRNA was undertaken in A549 cells and cisplatin resistant A549/CDDP cells. Differentially expressed mRNAs, lncRNAs and miRNAs, verified by realtime RT-PCR, were subjected to pathway analysis. Expression of NKD2 and β-catenin was assessed by realtime RT-PCR and western blot analysis. The effect of lncRNA AK126698 on cisplatin induced apoptosis was investigated by annexin-V/PI flow cytometry. RESULTS In total, 1471 mRNAs, 1380 lncRNAs and 25 miRNAs differentially expressed in A549/CDDP and A549 cells. Among them, 8 mRNAs, 8 lncRNAs and 5 miRNAs differentially expressed in gene chip analysis were validated. High-enrichment pathway analysis identified that some classical pathways participated in proliferation, differentiation, avoidance of apoptosis, and drug metabolism were differently expressed in these cells lines. Gene co-expression network identified many genes like FN1, CTSB, EGFR, and NKD2; lncRNAs including BX648420, ENST00000366408, and AK126698; and miRNAs such as miR-26a and let-7i potentially played a key role in cisplatin resistance. Among which, the canonical Wnt pathway was investigated because it was demonstrated to be targeted by both lncRNAs and miRNAs including lncRNA AK126698. Knockdown lncRNA AK126698 not only greatly decreased NKD2 which can negatively regulate Wnt/β-catenin signaling but also increased the accumulation and nuclear translocation of β-catenin, and significantly depressed apoptosis rate induced by cisplatin in A549 cells. CONCLUSION Cisplatin resistance in non-small-cell lung cancer cells may relate to the changes in noncoding RNAs. Among these, AK126698 appears to confer cisplatin resistance by targeting the Wnt pathway.
Collapse
|
14
|
Sun Y, Yu B, Zhang K, Chen X, Chen D. Paradigm of Time-sequence Development of the Intestine of Suckling Piglets with Microarray. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:1481-92. [PMID: 25049506 PMCID: PMC4093015 DOI: 10.5713/ajas.2012.12004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 07/01/2012] [Accepted: 04/15/2012] [Indexed: 11/27/2022]
Abstract
The interaction of the genes involved in intestinal development is the molecular basis of the regulatory mechanisms of intestinal development. The objective of this study was to identify the significant pathways and key genes that regulate intestinal development in Landrace piglets, and elucidate their rules of operation. The differential expression of genes related to intestinal development during suckling time was investigated using a porcine genome array. Time sequence profiles were analyzed for the differentially expressed genes to obtain significant expression profiles. Subsequently, the most significant profiles were assayed using Gene Ontology categories, pathway analysis, network analysis, and analysis of gene co-expression to unveil the main biological processes, the significant pathways, and the effective genes, respectively. In addition, quantitative real-time PCR was carried out to verify the reliability of the results of the analysis of the array. The results showed that more than 8000 differential expression transcripts were identified using microarray technology. Among the 30 significant obtained model profiles, profiles 66 and 13 were the most significant. Analysis of profiles 66 and 13 indicated that they were mainly involved in immunity, metabolism, and cell division or proliferation. Among the most effective genes in these two profiles, CN161469, which is similar to methylcrotonoyl-Coenzyme A carboxylase 2 (beta), and U89949.1, which encodes a folate binding protein, had a crucial influence on the co-expression network.
Collapse
Affiliation(s)
- Yunzi Sun
- Animal Nutrition Institute, Sichuan Agricultural University, No.116, N Baoshan Rd, Yunyan District, Guiyang, Guizhou, 550001,
China
| | - Bing Yu
- Animal Nutrition Institute, Sichuan Agricultural University, No.116, N Baoshan Rd, Yunyan District, Guiyang, Guizhou, 550001,
China
- Key Laboratory of Animal Disease-resistant Nutrition, Ministry of Education, Yaan, Sichuan, 625004,
China
| | - Keying Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, No.116, N Baoshan Rd, Yunyan District, Guiyang, Guizhou, 550001,
China
- Key Laboratory of Animal Disease-resistant Nutrition, Ministry of Education, Yaan, Sichuan, 625004,
China
| | - Xijian Chen
- Genminix Informatics Ltd. Co., Shanghai, 200234,
China
| | - Daiwen Chen
- Animal Nutrition Institute, Sichuan Agricultural University, No.116, N Baoshan Rd, Yunyan District, Guiyang, Guizhou, 550001,
China
- Key Laboratory of Animal Disease-resistant Nutrition, Ministry of Education, Yaan, Sichuan, 625004,
China
| |
Collapse
|
15
|
Moing A, Aharoni A, Biais B, Rogachev I, Meir S, Brodsky L, Allwood JW, Erban A, Dunn WB, Kay L, de Koning S, de Vos RCH, Jonker H, Mumm R, Deborde C, Maucourt M, Bernillon S, Gibon Y, Hansen TH, Husted S, Goodacre R, Kopka J, Schjoerring JK, Rolin D, Hall RD. Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics. THE NEW PHYTOLOGIST 2011; 190:683-96. [PMID: 21275993 DOI: 10.1111/j.1469-8137.2010.03626.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• Variations in tissue development and spatial composition have a major impact on the nutritional and organoleptic qualities of ripe fleshy fruit, including melon (Cucumis melo). To gain a deeper insight into the mechanisms involved in these changes, we identified key metabolites for rational food quality design. • The metabolome, volatiles and mineral elements were profiled employing an unprecedented range of complementary analytical technologies. Fruits were followed at a number of time points during the final ripening process and tissues were collected across the fruit flesh from rind to seed cavity. Approximately 2000 metabolite signatures and 15 mineral elements were determined in an assessment of temporal and spatial melon fruit development. • This study design enabled the identification of: coregulated hubs (including aspartic acid, 2-isopropylmalic acid, β-carotene, phytoene and dihydropseudoionone) in metabolic association networks; global patterns of coordinated compositional changes; and links of primary and secondary metabolism to key mineral and volatile fruit complements. • The results reveal the extent of metabolic interactions relevant to ripe fruit quality and thus have enabled the identification of essential candidate metabolites for the high-throughput screening of melon breeding populations for targeted breeding programmes aimed at nutrition and flavour improvement.
Collapse
Affiliation(s)
- Annick Moing
- INRA-UMR 619 Biologie du Fruit, Centre INRA de Bordeaux, Villenave d'Ornon, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
An G, Bartels J, Vodovotz Y. In Silico Augmentation of the Drug Development Pipeline: Examples from the study of Acute Inflammation. Drug Dev Res 2010; 72:187-200. [PMID: 21552346 DOI: 10.1002/ddr.20415] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The clinical translation of promising basic biomedical findings, whether derived from reductionist studies in academic laboratories or as the product of extensive high-throughput and -content screens in the biotechnology and pharmaceutical industries, has reached a period of stagnation in which ever higher research and development costs are yielding ever fewer new drugs. Systems biology and computational modeling have been touted as potential avenues by which to break through this logjam. However, few mechanistic computational approaches are utilized in a manner that is fully cognizant of the inherent clinical realities in which the drugs developed through this ostensibly rational process will be ultimately used. In this article, we present a Translational Systems Biology approach to inflammation. This approach is based on the use of mechanistic computational modeling centered on inherent clinical applicability, namely that a unified suite of models can be applied to generate in silico clinical trials, individualized computational models as tools for personalized medicine, and rational drug and device design based on disease mechanism.
Collapse
Affiliation(s)
- Gary An
- Department of Surgery, University of Chicago, Chicago, IL 60637
| | | | | |
Collapse
|
17
|
Vodovotz Y, Constantine G, Faeder J, Mi Q, Rubin J, Bartels J, Sarkar J, Squires RH, Okonkwo DO, Gerlach J, Zamora R, Luckhart S, Ermentrout B, An G. Translational systems approaches to the biology of inflammation and healing. Immunopharmacol Immunotoxicol 2010; 32:181-95. [PMID: 20170421 PMCID: PMC3134151 DOI: 10.3109/08923970903369867] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inflammation is a complex, non-linear process central to many of the diseases that affect both developed and emerging nations. A systems-based understanding of inflammation, coupled to translational applications, is therefore necessary for efficient development of drugs and devices, for streamlining analyses at the level of populations, and for the implementation of personalized medicine. We have carried out an iterative and ongoing program of literature analysis, generation of prospective data, data analysis, and computational modeling in various experimental and clinical inflammatory disease settings. These simulations have been used to gain basic insights into the inflammatory response under baseline, gene-knockout, and drug-treated experimental animals for in silico studies associated with the clinical settings of sepsis, trauma, acute liver failure, and wound healing to create patient-specific simulations in polytrauma, traumatic brain injury, and vocal fold inflammation; and to gain insight into host-pathogen interactions in malaria, necrotizing enterocolitis, and sepsis. These simulations have converged with other systems biology approaches (e.g., functional genomics) to aid in the design of new drugs or devices geared towards modulating inflammation. Since they include both circulating and tissue-level inflammatory mediators, these simulations transcend typical cytokine networks by associating inflammatory processes with tissue/organ impacts via tissue damage/dysfunction. This framework has now allowed us to suggest how to modulate acute inflammation in a rational, individually optimized fashion. This plethora of computational and intertwined experimental/engineering approaches is the cornerstone of Translational Systems Biology approaches for inflammatory diseases.
Collapse
Affiliation(s)
- Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Chen F, Zhu HH, Zhou LF, Li J, Zhao LY, Wu SS, Wang J, Liu W, Chen Z. Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model. BMC Genomics 2010; 11:240. [PMID: 20398290 PMCID: PMC2867829 DOI: 10.1186/1471-2164-11-240] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 04/15/2010] [Indexed: 11/10/2022] Open
Abstract
Background Due to the high morbidity and mortality of fulminant hepatitis, early diagnosis followed by early effective treatment is the key for prognosis improvement. So far, little is known about the gene expression changes in the early stage of this serious illness. Identification of the genes related to the very early stage of fulminant hepatitis development may provide precise clues for early diagnosis. Results Balb/C mice were used for ConA injection to induce fulminant hepatitis that was confirmed by pathological and biochemical examination. After a gene chip-based screening, the data of gene expression in the liver, was further dissected by ANOVA analysis, gene expression profiles, gene network construction and real-time RT-PCR. At the very early stage of ConA-triggered fulminant hepatitis, totally 1,473 genes with different expression variations were identified. Among these, 26 genes were finally selected for further investigation. The data from gene network analysis demonstrate that two genes, MPDZ and Acsl1, localized in the core of the network. Conclusions At the early stages of fulminant hepatitis, expression of twenty-six genes involved in protein transport, transcription regulation and cell metabolism altered significantly. These genes form a network and have shown strong correlation with fulminant hepatitis development. Our study provides several potential targets for the early diagnosis of fulminant hepatitis.
Collapse
Affiliation(s)
- Feng Chen
- State Key Laboratory of Infectious Disease Diagnosis and Treatment, First Affiliated Hospital, College of Medicine, Zhejiang University, Zhejiang, 310003, China
| | | | | | | | | | | | | | | | | |
Collapse
|