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Li F, Gong X, Zhou Y, Geng Q, Jiang Y, Yao L, Qu M, Tan Z. Integrated evidence of transcriptional, metabolic, and intestinal microbiota changes in Ruditapes philippinarum due to perfluorooctanoic acid-induced immunotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170341. [PMID: 38272093 DOI: 10.1016/j.scitotenv.2024.170341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Perfluorooctanoic acid (PFOA) is a toxic pollutant that bioaccumulates and is a significant public health concern due to its ubiquitous and persistent occurrence in global environments. Few studies have evaluated the adverse effects of PFOA on immune system, and this is particularly true for mollusks. Here, the PFOA-associated effects on immune system were evaluated in Ruditapes philippinarum using integrated analysis of metabolomes, microbiomes, and transcriptomes, providing evidence for possible mechanisms related to immunotoxicity. PFOA exposure caused clear variation in several important metabolites related to immune regulatory function within the haemolyph from R. philippinarum, while also altering key metabolic pathways, including those of lipids, unsaturated fatty acids (UFAs), and bile acids (BAs). After exposure to PFOAs, intestinal bacterial communities also clearly changed, with the predominant microflora becoming Mycoplasma and Bacteroidetes that are related to intestinal inflammation. Molecular analyses provided consistent results, wherein the expression of immune-related genes was significantly altered. Integration of the multi-'omics' analyses suggested that the TLR/MyD88/NF-kB pathway, along with PI3K-Akt-mTOR pathway, PPAR-mediated lipid metabolism and the autophagy signaling pathway, likely play important roles in initiating immunotoxic effects in R. philippinarum after PFOA exposure. These results provide further evidence that PFOA exposure can lead to immunologic dysfunction and also provide new insights into the mechanisms of PFAS alteration of bivalve immune function.
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Affiliation(s)
- Fengling Li
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Xiuqiong Gong
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Yang Zhou
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Qianqian Geng
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Yanhua Jiang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Lin Yao
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Meng Qu
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Zhijun Tan
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China; Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, People's Republic of China.
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2
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Perelo LW, Gabernet G, Straub D, Nahnsen S. How tool combinations in different pipeline versions affect the outcome in RNA-seq analysis. NAR Genom Bioinform 2024; 6:lqae020. [PMID: 38456178 PMCID: PMC10919883 DOI: 10.1093/nargab/lqae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/07/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Data analysis tools are continuously changed and improved over time. In order to test how these changes influence the comparability between analyses, the output of different workflow options of the nf-core/rnaseq pipeline were compared. Five different pipeline settings (STAR+Salmon, STAR+RSEM, STAR+featureCounts, HISAT2+featureCounts, pseudoaligner Salmon) were run on three datasets (human, Arabidopsis, zebrafish) containing spike-ins of the External RNA Control Consortium (ERCC). Fold change ratios and differential expression of genes and spike-ins were used for comparative analyses of the different tools and versions settings of the pipeline. An overlap of 85% for differential gene classification between pipelines could be shown. Genes interpreted with a bias were mostly those present at lower concentration. Also, the number of isoforms and exons per gene were determinants. Previous pipeline versions using featureCounts showed a higher sensitivity to detect one-isoform genes like ERCC. To ensure data comparability in long-term analysis series it would be recommendable to either stay with the pipeline version the series was initialized with or to run both versions during a transition time in order to ensure that the target genes are addressed the same way.
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Affiliation(s)
- Louisa Wessels Perelo
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
- M3 Research Center, Faculty of Medicine, University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
- Department of Computer Science, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
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3
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Tan S, Wang W, Jie W, Liu J. FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species. Comput Struct Biotechnol J 2022; 20:3676-3684. [PMID: 35891795 PMCID: PMC9293738 DOI: 10.1016/j.csbj.2022.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food industry. Furthermore, there is a lack of online platform to analyze users’ new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, including gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, co-expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample information, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.
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Affiliation(s)
- Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wencai Jie
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinding Liu
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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4
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Blüthner E, Pape UF, Blumenstein I, Wichmann J, Tacke F, Moosburner S. SARS-CoV-2 Antibody Prevalence in Adult Patients with Short Bowel Syndrome - A German Multicenter Cross-Sectional Study. JPEN J Parenter Enteral Nutr 2022; 46:1404-1411. [PMID: 35616296 PMCID: PMC9347527 DOI: 10.1002/jpen.2410] [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: 03/21/2022] [Revised: 04/27/2022] [Accepted: 05/23/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Not all patients suffer from a severe course of SARS-CoV-2 infection, demanding a definition of groups at risk. Short bowel syndrome (SBS) has been assumed to be a risk factor, due to the complexity of disease, the need for interdisciplinary care and frequent contact with caretakers. We aimed to establish data on the course of infection and prevalence of SARS-CoV-2 seropositivity in SBS patients in Germany. METHODS From January 2021 until January 2022 a total of 119 patients from three different tertiary care centers with SBS were included. All patients received an antibody test against the nucleocapsid (N) antigen and were asked to fill out a questionnaire, which included frequency of contact with medical personnel, risk behavior and worries. RESULTS 67% of SBS patients received parenteral nutrition with a median of 6 days per week. The seroprevalence of SARS-CoV-2 antibodies was 7.6% (n=9). Seven patients with positive antibodies had COVID-19 with a mild course. None of the patients were hospitalized or needed further treatment. There was no difference in willingness to take risks in SARS-CoV-2 antibody positive and negative patients (p=0.61). Patients were predominantly worried about the economy (61%) and transmitting COVID-19 (52%), less frequent (26%) about receiving insufficient medical treatment. CONCLUSION These are the first clinical results concerning SARS-CoV-2 seropositivity and COVID-19 disease in patients with SBS. The seropositivity is comparable to national data, which we attribute to increased risk awareness and avoidance. Further studies are warranted to investigate effects of COVID-19 infection in SBS patients. CLINICAL RELEVANCY STATEMENT Patients with short bowel syndrome are proposed to be a group at high-risk for a severe course of COVID-19. This multicenter cross-sectional study analyzes the prevalence of antibodies against the nucleocapsid (N) antigen in patients with short bowel syndrome, their risk behavior and frequency of contact with medical personnel. The overall SARS-CoV-2 seropositivity in short bowel syndrome patient was comparable to national data, possibly attributed to increased risk awareness and avoidance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Elisabeth Blüthner
- Charité - Universitätsmedizin Berlin, Department of Hepatology and Gastroenterology, Campus Charité Mitte and Campus Virchow-Klinikum, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin and Berlin Institute of Health.,BIH Charité Clinician Scientist Program, Berlin Institute of Health (BIH), Berlin, Germany
| | | | | | | | - Frank Tacke
- Charité - Universitätsmedizin Berlin, Department of Hepatology and Gastroenterology, Campus Charité Mitte and Campus Virchow-Klinikum, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin and Berlin Institute of Health
| | - Simon Moosburner
- BIH Charité Clinician Scientist Program, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Department of Surgery, Campus Charité Mitte
- Campus Virchow-Klinikum, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin and Berlin Institute of Health
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5
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Wang Y, Zheng L, Zhou Z, Yao D, Huang Y, Liu B, Duan Y, Li Y. Review article: insights into the bile acid-gut microbiota axis in intestinal failure-associated liver disease-redefining the treatment approach. Aliment Pharmacol Ther 2022; 55:49-63. [PMID: 34713470 DOI: 10.1111/apt.16676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/04/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Intestinal failure-associated liver disease (IFALD) increases mortality of patients with intestinal failure (IF), but lacks effective prevention or treatment approaches. Bile acids, gut microbiota and the host have close and complex interactions, which play a central role in modulating host immune and metabolic homeostasis. Increasing evidence suggests that derangement of the bile acid-gut microbiota (BA-GM) axis contributes to the development of IFALD. AIMS To review the BA-GM axis in the pathogenesis and clinical applications of IFALD, and to explore future directions for effective disease management. METHODS We conducted a literature search on bile acid and gut microbiota in IF and liver diseases. RESULTS The BA-GM axis demonstrates a unique IF signature manifesting as an increase in primary-to-secondary bile acids ratio, disturbed enterohepatic circulation, blunted bile acid signalling pathways, gut microbial dysbiosis, and altered microbial metabolic outputs. Bile acids and gut microbiota shape the compositional and functional alterations of each other in IF; collaboratively, they promote immune dysfunction and metabolic aberration in the liver. Diagnostic markers and treatments targeting the BA-GM axis showed promising potential in the management of IFALD. CONCLUSIONS Bile acids and gut microbiota play a central role in the development of IFALD and make attractive biomarkers as well as therapeutic targets. A multitarget, individualised therapy aiming at different parts of the BA-GM axis may provide optimal clinical benefits and requires future investigation.
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Affiliation(s)
- Yaoxuan Wang
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Lei Zheng
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Zhiyuan Zhou
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Danhua Yao
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Yuhua Huang
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Bin Liu
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Yantao Duan
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Yousheng Li
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
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6
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Keskus AG, Tombaz M, Arici BI, Dincaslan FB, Nabi A, Shehwana H, Konu O. Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease. Genome 2021; 65:57-74. [PMID: 34606733 DOI: 10.1139/gen-2021-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human Angiotensin I Converting Enzyme 2 (ACE2) plays an essential role in blood pressure regulation and SARS-CoV-2 entry. ACE2 has a highly conserved, one-to-one ortholog (ace2) in zebrafish, which is an important model for human diseases. However, the zebrafish ace2 expression profile has not yet been studied during early development, between genders, across different genotypes, or in disease. Moreover, a network-based meta-analysis for the extraction of functionally enriched pathways associated with differential ace2 expression is lacking in the literature. Herein, we first identified significant development-, tissue-, genotype-, and gender-specific modulations in ace2 expression via meta-analysis of zebrafish Affymetrix transcriptomics datasets (ndatasets = 107); and the correlation analysis of ace2 meta-differential expression profile revealed distinct positively and negatively correlated local functionally enriched gene networks. Moreover, we demonstrated that ace2 expression was significantly modulated under different physiological and pathological conditions related to development, tissue, gender, diet, infection, and inflammation using additional RNA-seq datasets. Our findings implicate a novel translational role for zebrafish ace2 in organ differentiation and pathologies observed in the intestines and liver.
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Affiliation(s)
- Ayse Gokce Keskus
- Interdisciplinary Program in Neuroscience, Bilkent University, Ankara, Turkey
| | - Melike Tombaz
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Burcin Irem Arici
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | | | - Afshan Nabi
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey
| | - Huma Shehwana
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Ozlen Konu
- Interdisciplinary Program in Neuroscience, Bilkent University, Ankara, Turkey.,Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey
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7
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Courtney CM, Onufer EJ, McDonald KG, Steinberger AE, Sescleifer AM, Seiler KM, Tecos ME, Newberry RD, Warner BW. Small Bowel Resection Increases Paracellular Gut Barrier Permeability via Alterations of Tight Junction Complexes Mediated by Intestinal TLR4. J Surg Res 2021; 258:73-81. [PMID: 33002664 PMCID: PMC7937530 DOI: 10.1016/j.jss.2020.08.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/22/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Short bowel syndrome resulting from small bowel resection (SBR) is associated with significant morbidity and mortality. Many adverse sequelae including steatohepatitis and bacterial overgrowth are thought to be related to increased bacterial translocation, suggesting alterations in gut permeability. We hypothesized that after intestinal resection, the intestinal barrier is altered via toll-like receptor 4 (TLR4) signaling at the intestinal level. METHODS B6 and intestinal-specific TLR4 knockout (iTLR4 KO) mice underwent 50% SBR or sham operation. Transcellular permeability was evaluated by measuring goblet cell associated antigen passages via two-photon microscopy. Fluorimetry and electron microscopy evaluation of tight junctions (TJ) were used to assess paracellular permeability. In parallel experiments, single-cell RNA sequencing measured expression of intestinal integral TJ proteins. Western blot and immunohistochemistry confirmed the results of the single-cell RNA sequencing. RESULTS There were similar number of goblet cell associated antigen passages after both SBR and sham operation (4.5 versus 5.0, P > 0.05). Fluorescein isothiocyanate-dextran uptake into the serum after massive SBR was significantly increased compared with sham mice (2.13 ± 0.39 ng/μL versus 1.62 ± 0.23 ng/μL, P < 0.001). SBR mice demonstrated obscured TJ complexes on electron microscopy. Single-cell RNA sequencing revealed a decrease in TJ protein occludin (21%) after SBR (P < 0.05), confirmed with immunostaining and western blot analysis. The KO of iTLR4 mitigated the alterations in permeability after SBR. CONCLUSIONS Permeability after SBR is increased via changes at the paracellular level. However, these alterations were prevented in iTLR4 mice. These findings suggest potential protein targets for restoring the intestinal barrier and obviating the adverse sequelae of short bowel syndrome.
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Affiliation(s)
- Cathleen M Courtney
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri
| | - Emily J Onufer
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri
| | - Keely G McDonald
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Allie E Steinberger
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri
| | - Anne M Sescleifer
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri
| | - Kristen M Seiler
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri
| | - Maria E Tecos
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri
| | - Rodney D Newberry
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Brad W Warner
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, Missouri.
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8
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Maselli KM, Levin G, Gee KM, Leeflang EJ, Carreira ACO, Sogayar MC, Grikscheit TC. R-Spondin1 enhances wnt signaling and decreases weight loss in short bowel syndrome zebrafish. Biochem Biophys Rep 2021; 25:100874. [PMID: 33437880 PMCID: PMC7788494 DOI: 10.1016/j.bbrep.2020.100874] [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: 10/15/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
Background R-spondins, including R-spondin 1 (RSPO1), are a family of Wnt ligands that help to activate the canonical Wnt/β-catenin pathway, which is critical for intestinal epithelial cell proliferation and maintenance of intestinal stem cells. This proliferation underpins the epithelial expansion, or intestinal adaptation (IA), that occurs following massive bowel resection and short bowel syndrome (SBS). The purpose of this study was to identify if recombinant human RSPO1 (rhRSPO1) could be serially administered to SBS zebrafish to enhance cellular proliferation and IA. Methods Adult male zebrafish were assigned to four groups: sham + PBS, SBS + PBS, sham + rhRSPO1, and SBS + rhRSPO1. Sham fish had a laparotomy alone. SBS fish had a laparotomy with distal intestinal ligation and creation of a proximal stoma. Fish were weighed at initial surgery and then weekly. rhRSPO1 was administered post-operatively following either a one- or two-week dosing schedule with either 3 or 5 intraperitoneal injections, respectively. Fish were harvested at 7 or 14 days with intestinal segments collected for analysis. Results Repeated intraperitoneal injection of rhRSPO1 was feasible and well tolerated. At 7 days, intestinal epithelial proliferation was increased by rhRSPO1. At 14 days, SBS + rhRSPO1 fish lost significantly less weight than SBS + PBS fish. Measurements of intestinal surface area were not increased by rhRSPO1 administration but immunofluorescent staining for β-catenin and gene expression for cyclin D1 was increased. Conclusions Intraperitoneal injection of rhRSPO1 decreased weight loss in SBS zebrafish with increased β-catenin + cells and cyclin D1 expression at 14 days, indicating improved weight maintenance might result from increased activation of the canonical Wnt pathway. rhRSPO1 decreased weight loss in SBS zebrafish. rhRSPO1 increased intestinal cell epithelial proliferation at 7 days. rhRSPO1 increased β-catenin + cells at 14 days in the intestine of SBS zebrafish. rhRSPO1 increased cyclin D1 expression at 14 days in the intestine of SBS zebrafish.
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Affiliation(s)
- Kathryn M Maselli
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Gabriel Levin
- Cell and Molecular Therapy Center (NUCEL), School of Medicine, University of São Paulo, São Paulo, SP, Brazil.,Interunits Graduate Program in Biotechnology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Kristin M Gee
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Elisabeth J Leeflang
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Ana Claudia O Carreira
- Cell and Molecular Therapy Center (NUCEL), School of Medicine, University of São Paulo, São Paulo, SP, Brazil.,Interunits Graduate Program in Biotechnology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo (FMVZ-USP), São Paulo, SP, Brazil
| | - Mari Cleide Sogayar
- Cell and Molecular Therapy Center (NUCEL), School of Medicine, University of São Paulo, São Paulo, SP, Brazil.,Interunits Graduate Program in Biotechnology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Tracy C Grikscheit
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
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9
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Thänert R, Thänert A, Ou J, Bajinting A, Burnham CAD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G, Warner BW. Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Gut Microbes 2021; 13:1940792. [PMID: 34264786 PMCID: PMC8284144 DOI: 10.1080/19490976.2021.1940792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 02/08/2023] Open
Abstract
Surgical removal of the intestine, lifesaving in catastrophic gastrointestinal disorders of infancy, can result in a form of intestinal failure known as short bowel syndrome (SBS). Bloodstream infections (BSIs) are a major challenge in pediatric SBS management. BSIs require frequent antibiotic therapy, with ill-defined consequences for the gut microbiome and childhood health. Here, we combine serial stool collection, shotgun metagenomic sequencing, multivariate statistics and genome-resolved strain-tracking in a cohort of 19 patients with surgically-induced SBS to show that antibiotic-driven intestinal dysbiosis in SBS enriches for persistent intestinal colonization with BSI causative pathogens in SBS. Comparing the gut microbiome composition of SBS patients over the first 4 years of life to 19 age-matched term and 18 preterm controls, we find that SBS gut microbiota diversity and composition was persistently altered compared to controls. Commensals including Ruminococcus, Bifidobacterium, Eubacterium, and Clostridium species were depleted in SBS, while pathobionts (Enterococcus) were enriched. Integrating clinical covariates with gut microbiome composition in pediatric SBS, we identified dietary and antibiotic exposures as the main drivers of these alterations. Moreover, antibiotic resistance genes, specifically broad-spectrum efflux pumps, were at a higher abundance in SBS, while putatively beneficial microbiota functions, including amino acid and vitamin biosynthesis, were depleted. Moreover, using strain-tracking we found that the SBS gut microbiome harbors BSI causing pathogens, which can persist intestinally throughout the first years of life. The association between antibiotic-driven gut dysbiosis and enrichment of intestinal pathobionts isolated from BSI suggests that antibiotic treatment may predispose SBS patients to infection. Persistence of pathobionts and depletion of beneficial microbiota and functionalities in SBS highlights the need for microbiota-targeted interventions to prevent infection and facilitate intestinal adaptation.
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Affiliation(s)
- Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anna Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jocelyn Ou
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adam Bajinting
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Holly J. Engelstad
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maria E. Tecos
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - I. Malick Ndao
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carla Hall-Moore
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colleen Rouggly-Nickless
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mike A. Carl
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Deborah C. Rubin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas O. Davidson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Phillip I. Tarr
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B. Warner
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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10
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Maselli KM, Gee K, Grikscheit TC. Remnant Intestinal Length Defines Intestinal Adaptation and Hepatic Steatosis: Two Zebrafish Models. J Surg Res 2020; 255:86-95. [DOI: 10.1016/j.jss.2020.05.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/10/2020] [Accepted: 05/03/2020] [Indexed: 12/12/2022]
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11
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Channabasappa N, Girouard S, Nguyen V, Piper H. Enteral Nutrition in Pediatric Short-Bowel Syndrome. Nutr Clin Pract 2020; 35:848-854. [PMID: 32815247 DOI: 10.1002/ncp.10565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pediatric intestinal failure (IF) is the critical reduction of intestinal mass or function below the amount necessary for normal growth in children. Short-bowel syndrome (SBS) is the most common cause of IF in infants and children and is caused by intestinal resection. Enteral autonomy and freedom from parenteral nutrition is the mainstay of nutrition management in SBS. The goal is to achieve intestinal adaptation while maintaining proper growth and development. Treatment is variable, and there remains a paucity of evidence to draw well-informed conclusions for the care of individuals in this complex population. Physiological principles of enteral nutrition and practical recommendations for advancing the diet of patients with pediatric SBS are presented. Emerging trends in nutrition management, such as the growing interest in blending diets and the impact on SBS, are reviewed. Finally, the influence of the microbiome on enteral tolerance and small bowel bacterial overgrowth are considered.
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Affiliation(s)
- Nandini Channabasappa
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sara Girouard
- Department of Clinical Nutrition, Children's Health of Dallas, Dallas, Texas, USA
| | - Van Nguyen
- Department of Gastroenterology, Children's Health of Dallas, Dallas, Texas, USA
| | - Hannah Piper
- Division of Pediatric Surgery, Unversity of British Columbia, Vancouver, British Columbia, Canada
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12
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Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota. Anim Microbiome 2020; 2:26. [PMID: 33499964 PMCID: PMC7807502 DOI: 10.1186/s42523-020-00046-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. RESULTS Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. CONCLUSION As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.
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13
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Maselli KM, Gee K, Isani M, Fode A, Schall KA, Grikscheit TC. Broad-spectrum antibiotics alter the microbiome, increase intestinal fxr, and decrease hepatic steatosis in zebrafish short bowel syndrome. Am J Physiol Gastrointest Liver Physiol 2020; 319:G212-G226. [PMID: 32597709 DOI: 10.1152/ajpgi.00119.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Short bowel syndrome (SBS) is associated with changes in the intestinal microbiome and marked local and systemic inflammation. There is also a late complication of SBS, intestinal failure associated liver disease (IFALD) in which hepatic steatosis progresses to cirrhosis. Most patients with SBS arrive at massive intestinal resection after a contaminating intraabdominal catastrophe and have a history of exposure to broad-spectrum antibiotics. We therefore investigated whether the administration of broad-spectrum antibiotics in conjunction with SBS in zebrafish (ZF) would replicate these systemic effects observed in humans to identify potentially druggable targets to aid in the management of SBS and resulting IFALD. In zebrafish with SBS, broad-spectrum antibiotics altered the microbiome, decreased inflammation, and reduced the development of hepatic steatosis. After two weeks of broad-spectrum antibiotics, these fish exhibited decreased alpha diversity, with less variation in microbial community composition between SBS and sham fish. Additionally, administration of broad-spectrum antibiotics was associated with decreased expression of intestinal toll-like receptor 4 (tlr4), increased expression of the intestinal gene encoding the Farnesoid X receptor (fxr), decreased expression of downstream hepatic cyp7a1, and decreased development of hepatic steatosis. SBS in zebrafish reproducibly results in increased epithelial surface area as occurs in human patients who demonstrate intestinal adaptation, but antibiotic administration in zebrafish with SBS reduced these gains with increased cell death in the intervillus pocket that contains stem/progenitor cells. These alternate states in SBS zebrafish might direct the development of future human therapies.NEW & NOTEWORTHY In a zebrafish model that replicates a common clinical scenario, systemic effects of the administration of broad-spectrum antibiotics in a zebrafish model of SBS identified two alternate states that led to the establishment of fat accumulation in the liver or its absence. Broad-spectrum antibiotics given to zebrafish with SBS over 2 wk altered the intestinal microbiome, decreased intestinal and hepatic inflammation, and decreased hepatic steatosis.
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Affiliation(s)
- Kathryn M Maselli
- Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, California
| | - Kristin Gee
- Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, California
| | - Mubina Isani
- Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, California
| | - Alexa Fode
- Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, California
| | - Kathy A Schall
- Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, California
| | - Tracy C Grikscheit
- Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, California.,Department of Surgery, Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California
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14
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Preterm birth and sustained inflammation: consequences for the neonate. Semin Immunopathol 2020; 42:451-468. [PMID: 32661735 PMCID: PMC7508934 DOI: 10.1007/s00281-020-00803-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022]
Abstract
Almost half of all preterm births are caused or triggered by an inflammatory process at the feto-maternal interface resulting in preterm labor or rupture of membranes with or without chorioamnionitis (“first inflammatory hit”). Preterm babies have highly vulnerable body surfaces and immature organ systems. They are postnatally confronted with a drastically altered antigen exposure including hospital-specific microbes, artificial devices, drugs, nutritional antigens, and hypoxia or hyperoxia (“second inflammatory hit”). This is of particular importance to extremely preterm infants born before 28 weeks, as they have not experienced important “third-trimester” adaptation processes to tolerate maternal and self-antigens. Instead of a balanced adaptation to extrauterine life, the delicate co-regulation between immune defense mechanisms and immunosuppression (tolerance) to allow microbiome establishment is therefore often disturbed. Hence, preterm infants are predisposed to sepsis but also to several injurious conditions that can contribute to the onset or perpetuation of sustained inflammation (SI). This is a continuing challenge to clinicians involved in the care of preterm infants, as SI is regarded as a crucial mediator for mortality and the development of morbidities in preterm infants. This review will outline the (i) role of inflammation for short-term consequences of preterm birth and (ii) the effect of SI on organ development and long-term outcome.
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15
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Grillot J, Ait S, Bergoin C, Couronne T, Blond E, Peraldi C, Barnoud D, Chambrier C, Lauverjat M. Vitamin C in Home Parenteral Nutrition: A Need for Monitoring. Nutrients 2020; 12:nu12061667. [PMID: 32503297 PMCID: PMC7352530 DOI: 10.3390/nu12061667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 11/16/2022] Open
Abstract
To date, there are no recommendations about screening plasma vitamin C concentration and adjust its supplementation in patients on long-term home parenteral nutrition (HPN). The aim of this study was to evaluate vitamin C status and determine if a commercial multivitamin preparation (CMVP) containing 125 mg of vitamin C is sufficient in stable patients on HPN. All clinically stable patients receiving HPN or an intravenous fluid infusion at least two times per week for at least 6 months, hospitalized for nutritional assessment, were retrospectively included, for a total of 186 patients. We found that 29% of the patients had vitamin C insufficiency (i.e., <25 µmol/L). In univariate analysis, C-reactive protein (CRP) (p = 0.002) and intake of only 125 mg of vitamin C (p = 0.001) were negatively associated with vitamin C levels, and duration of follow-up in our referral center (p = 0.009) was positively associated with vitamin C levels. In multivariate analysis, only CRP (p = 0.001) and intake of 125 mg of vitamin C (p < 0.0001) were independently associated with low plasma vitamin C concentration. Patients receiving only CMVP with a low plasma vitamin C level significantly received personal compounded HPN (p = 0.008) and presented an inflammatory syndrome (p = 0.002). Vitamin C insufficiency is frequent in individuals undergoing home parenteral nutrition; therefore, there is a need to monitor plasma vitamin C levels, especially in patients on HPN with an inflammatory syndrome and only on CMVP.
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Affiliation(s)
- Julienne Grillot
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, CEDEX, 69921 Oullins, France;
- Correspondence: ; Tel.: +33-478-86-39-91
| | - Sabrina Ait
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
| | - Charlotte Bergoin
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
| | - Thomas Couronne
- Department of Gastroenterology, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France;
| | - Emilie Blond
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, CEDEX, 69921 Oullins, France;
- Biochemistry Department, Lyon Sud Hospital, Hospices Civils de Lyon, F-69495 Pierre Benite, France
| | - Catherine Peraldi
- Centre Agréé de Nutrition Parentérale à Domicile, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France; (C.P.); (M.L.)
| | - Didier Barnoud
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
| | - Cécile Chambrier
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
- Centre Agréé de Nutrition Parentérale à Domicile, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France; (C.P.); (M.L.)
| | - Madeleine Lauverjat
- Centre Agréé de Nutrition Parentérale à Domicile, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France; (C.P.); (M.L.)
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16
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Qi D, Shi W, Black AR, Kuss MA, Pang X, He Y, Liu B, Duan B. Repair and regeneration of small intestine: A review of current engineering approaches. Biomaterials 2020; 240:119832. [PMID: 32113114 DOI: 10.1016/j.biomaterials.2020.119832] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 02/06/2023]
Abstract
The small intestine (SI) is difficult to regenerate or reconstruct due to its complex structure and functions. Recent developments in stem cell research, advanced engineering technologies, and regenerative medicine strategies bring new hope of solving clinical problems of the SI. This review will first summarize the structure, function, development, cell types, and matrix components of the SI. Then, the major cell sources for SI regeneration are introduced, and state-of-the-art biofabrication technologies for generating engineered SI tissues or models are overviewed. Furthermore, in vitro models and in vivo transplantation, based on intestinal organoids and tissue engineering, are highlighted. Finally, current challenges and future perspectives are discussed to help direct future applications for SI repair and regeneration.
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Affiliation(s)
- Dianjun Qi
- Department of General Practice, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China; Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, USA; Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Wen Shi
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, USA; Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Adrian R Black
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mitchell A Kuss
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, USA; Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Xining Pang
- Department of General Practice, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China; Department of Academician Expert Workstation and Liaoning Province Human Amniotic Membrane Dressings Stem Cells and Regenerative Medicine Engineering Research Center, Shenyang Amnion Biological Engineering Technology Research and Development Center Co., Ltd, Shenyang, Liaoning, China
| | - Yini He
- Department of General Practice, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Bing Liu
- Department of Anorectal Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Bin Duan
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, USA; Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA; Department of Surgery, University of Nebraska Medical Center, Omaha, NE, USA; Department of Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA.
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17
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Zhao C, Jia Z, Li E, Zhao X, Han T, Tian J, Li F, Zou D, Lin R. Hepatotoxicity evaluation of Euphorbia kansui on zebrafish larvae in vivo. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 62:152959. [PMID: 31132752 DOI: 10.1016/j.phymed.2019.152959] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Euphorbia kansui is effective in treating various diseases, such as ascites and edema, but its liver toxicity is a major obstacle in its wide use in the clinic. However, further investigations have suggested that Euphorbia kansui can cause liver injury. HYPOTHESIS The study aims to investigate the effect of Euphorbia kansui exposure on zebrafish, and explain the underlying toxicity mechanisms from a comprehensive perspective. STUDY DESIGN The 4dpf zebrafish larvae were exposed to Euphorbia kansui at a sub-lethal concentration. METHODS We evaluated the effect of Euphorbia kansui on the ultrastructure and function of the liver, apoptosis of liver cells by PCR and western blot, and metabolic profile by GC-MS based on sub-lethal concentrations. RESULTS Our results suggested Euphorbia kansui could lead to liver injury and significant alteration of the metabolomics of the zebrafish larvae in sub-lethal concentration conditions. It could also induce alterations in liver microstructure, hepatic function, gene expression and protein associated with the apoptosis process, as well as endogenous metabolism. KEGG pathway analysis identified some biological processes on the basis of different metabolisms and their associated processes especially for amino acid metabolism. CONCLUSION The results bring us closer to an in-depth understanding of the toxic effects of Euphorbia kansui on zebrafish liver, which will be significantly helpful in effectively guiding safer clinical application of this herb in the clinic. Furthermore, our results also showed the zebrafish model is reliable for evaluation of Euphorbia kansui extract hepatotoxicity and as a methodological reference for the evaluation of Traditional Chinese Medicine with underlying liver toxicity.
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Affiliation(s)
- Chongjun Zhao
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Higher Education Garden, Liangxiang, Fangshan District, Beijing 102488, PR China
| | - Zhe Jia
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Higher Education Garden, Liangxiang, Fangshan District, Beijing 102488, PR China
| | - Erwen Li
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Higher Education Garden, Liangxiang, Fangshan District, Beijing 102488, PR China
| | - Xia Zhao
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Higher Education Garden, Liangxiang, Fangshan District, Beijing 102488, PR China
| | - Ting Han
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Higher Education Garden, Liangxiang, Fangshan District, Beijing 102488, PR China
| | - Jinghuan Tian
- CCRF (Beijing) Incorporated, Shimao International Center Office Building One, Room, 806, Gongti North Road, Chaoyang District, Beijing, PR China
| | - Farong Li
- Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, Shanxi Normal University, Xi'an, PR China
| | - Dixin Zou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China; College of Pharmacy, Inner Mongolia Medical University, Hohhot, Inner Mongolia 010110, PR China.
| | - Ruichao Lin
- Beijing Key Laboratory for Quality Evaluation of Chinese Materia Medica, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Higher Education Garden, Liangxiang, Fangshan District, Beijing 102488, PR China.
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18
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Isani MA, Gee K, Schall K, Schlieve CR, Fode A, Fowler KL, Grikscheit TC. Wnt signaling inhibition by monensin results in a period of Hippo pathway activation during intestinal adaptation in zebrafish. Am J Physiol Gastrointest Liver Physiol 2019; 316:G679-G691. [PMID: 30896968 DOI: 10.1152/ajpgi.00343.2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intestinal adaptation (IA) is a critical response to increase epithelial surface area after intestinal loss. Short bowel syndrome (SBS) may follow massive intestinal resection in human patients, particularly without adequate IA. We previously validated a model in zebrafish (ZF) that recapitulates key SBS pathophysiological features. Previous RNA sequencing in this model identified upregulation of genes in the Wnt and Hippo pathways. We therefore sought to identify the timeline of increasing cell proliferation and considered the signaling that might underpin the epithelial remodeling of IA in SBS. SBS was created in a ZF model as previously reported and compared with sham fish with and without exposure to monensin, an ionophore known to inhibit canonical Wnt signaling. Rescue of the monensin effects was attempted with a glycogen synthase kinase 3 inhibitor that activates wnt signaling, CHIR-99021. A timeline was constructed to identify peak cellular proliferation, and the Wnt and Hippo pathways were evaluated. Peak stem cell proliferation and morphological changes of adaptation were identified at 7 days. Wnt inhibition diminished IA at 2 wk and resulted in activation of genes of the Wnt/β-catenin and Yes-associated protein (YAP)/Hippo pathway. Increased cytoplasmic YAP was observed in monensin-treated SBS fish. Genes of the WASP-interacting protein (WIP) pathway were elevated during Wnt blockade. In conclusion, cellular proliferation and morphological changes accompany SBS even in attempted Wnt blockade. Wnt/β-catenin, YAP/Hippo pathway, and WIP pathway genes increase during early Wnt blockade. Further understanding of the effects of Wnt and YAP pathway signaling in proliferating stem cells might enrich our knowledge of targets to assist IA. NEW & NOTEWORTHY Intestinal adaptation is a critical response to increase epithelial surface area after large intestinal losses. Inhibition of Wnt/β-catenin signaling impairs intestinal adaptation in a zebrafish model of short bowel syndrome. There is a subsequent upregulation in genes of the Yes-associated protein/Hippo and WIP pathway. These may be targets for future human therapies, as patients are salvaged by the compensation of increased intestinal epithelial surface area through successful intestinal adaptation.
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Affiliation(s)
- Mubina A Isani
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California
| | - Kristin Gee
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California
| | - Kathy Schall
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California
| | - Christopher R Schlieve
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California
| | - Alexa Fode
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California
| | - Kathryn L Fowler
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California
| | - Tracy C Grikscheit
- Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles, California.,Department of Surgery, Keck School of Medicine, University of Southern California , Los Angeles, California
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19
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Visger CJ, Wong GKS, Zhang Y, Soltis PS, Soltis DE. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. AMERICAN JOURNAL OF BOTANY 2019; 106:280-291. [PMID: 30779448 DOI: 10.1002/ajb2.1239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass. KEY RESULTS In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size. CONCLUSIONS While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.
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Affiliation(s)
- Clayton J Visger
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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20
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Abstract
Short-bowel syndrome represents the most common cause of intestinal failure and occurs when the remaining intestine cannot support fluid and nutrient needs to sustain adequate physiology and development without the use of supplemental parenteral nutrition. After intestinal loss or damage, the remnant bowel undergoes multifactorial compensatory processes, termed adaptation, which are largely driven by intraluminal nutrient exposure. Previous studies have provided insight into the biological processes and mediators after resection, however, there still remains a gap in the knowledge of more comprehensive mechanisms that drive the adaptive responses in these patients. Recent data support the microbiota as a key mediator of gut homeostasis and a potential driver of metabolism and immunomodulation after intestinal loss. In this review, we summarize the emerging ideas related to host-microbiota interactions in the intestinal adaptation processes.
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Key Words
- Adaptive Responses
- CONV, conventional
- ENS, enteric nervous system
- Enteric Flora
- GF, germ-free
- GI, gastrointestinal
- GLP-2, glucagon-like peptide 2
- IBD, inflammatory bowel disease
- ICR, ileocecal resection
- IF, intestinal failure
- IL, interleukin
- Immune System
- Intestinal Failure
- Microbial Metabolites
- NEC, necrotizing enterocolitis
- PN, parenteral nutrition
- SBR, small bowel resection
- SBS, short-bowel syndrome
- SCFA, short-chain fatty acid
- SFB, segmented filamentous bacteria
- TGR5, Takeda-G-protein-receptor 5
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