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Newman NK, Macovsky MS, Rodrigues RR, Bruce AM, Pederson JW, Padiadpu J, Shan J, Williams J, Patil SS, Dzutsev AK, Shulzhenko N, Trinchieri G, Brown K, Morgun A. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nat Protoc 2024; 19:1750-1778. [PMID: 38472495 DOI: 10.1038/s41596-024-00960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/29/2023] [Indexed: 03/14/2024]
Abstract
We present Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that offers a holistic view of biological systems by integrating data from multiple cohorts and diverse omics types. TkNA helps to decipher key players and mechanisms governing host-microbiota (or any multi-omic data) interactions in specific conditions or diseases. TkNA reconstructs a network that represents a statistical model capturing the complex relationships between different omics in the biological system. It identifies robust and reproducible patterns of fold change direction and correlation sign across several cohorts to select differential features and their per-group correlations. The framework then uses causality-sensitive metrics, statistical thresholds and topological criteria to determine the final edges forming the transkingdom network. With the subsequent network's topological features, TkNA identifies nodes controlling a given subnetwork or governing communication between kingdoms and/or subnetworks. The computational time for the millions of correlations necessary for network reconstruction in TkNA typically takes only a few minutes, varying with the study design. Unlike most other multi-omics approaches that find only associations, TkNA focuses on establishing causality while accounting for the complex structure of multi-omic data. It achieves this without requiring huge sample sizes. Moreover, the TkNA protocol is user friendly, requiring minimal installation and basic familiarity with Unix. Researchers can access the TkNA software at https://github.com/CAnBioNet/TkNA/ .
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Affiliation(s)
- Nolan K Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | | | - Richard R Rodrigues
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Amanda M Bruce
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jacob W Pederson
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Jyothi Padiadpu
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jigui Shan
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua Williams
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sankalp S Patil
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Amiran K Dzutsev
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Natalia Shulzhenko
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Kevin Brown
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
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Alajoleen RM, Oakland DN, Estaleen R, Shakeri A, Lu R, Appiah M, Sun S, Neumann J, Kawauchi S, Cecere TE, McMillan RP, Reilly CM, Luo XM. Tlr5 deficiency exacerbates lupus-like disease in the MRL/ lpr mouse model. Front Immunol 2024; 15:1359534. [PMID: 38352866 PMCID: PMC10862078 DOI: 10.3389/fimmu.2024.1359534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Leaky gut has been linked to autoimmune disorders including lupus. We previously reported upregulation of anti-flagellin antibodies in the blood of lupus patients and lupus-prone mice, which led to our hypothesis that a leaky gut drives lupus through bacterial flagellin-mediated activation of toll-like receptor 5 (TLR5). Methods We created MRL/lpr mice with global Tlr5 deletion through CRISPR/Cas9 and investigated lupus-like disease in these mice. Result Contrary to our hypothesis that the deletion of Tlr5 would attenuate lupus, our results showed exacerbation of lupus with Tlr5 deficiency in female MRL/lpr mice. Remarkably higher levels of proteinuria were observed in Tlr5 -/- MRL/lpr mice suggesting aggravated glomerulonephritis. Histopathological analysis confirmed this result, and Tlr5 deletion significantly increased the deposition of IgG and complement C3 in the glomeruli. In addition, Tlr5 deficiency significantly increased renal infiltration of Th17 and activated cDC1 cells. Splenomegaly and lymphadenopathy were also aggravated in Tlr5-/- MRL/lpr mice suggesting impact on lymphoproliferation. In the spleen, significant decreased frequencies of regulatory lymphocytes and increased germinal centers were observed with Tlr5 deletion. Notably, Tlr5 deficiency did not change host metabolism or the existing leaky gut; however, it significantly reshaped the fecal microbiota. Conclusion Global deletion of Tlr5 exacerbates lupus-like disease in MRL/lpr mice. Future studies will elucidate the underlying mechanisms by which Tlr5 deficiency modulates host-microbiota interactions to exacerbate lupus.
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Affiliation(s)
- Razan M. Alajoleen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - David N. Oakland
- Graduate Program of Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
| | - Rana Estaleen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Aida Shakeri
- Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ran Lu
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Michael Appiah
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sha Sun
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
| | - Jonathan Neumann
- Transgenic Mouse Facility, University of California, Irvine, Irvine, CA, United States
| | - Shimako Kawauchi
- Transgenic Mouse Facility, University of California, Irvine, Irvine, CA, United States
| | - Thomas E. Cecere
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ryan P. McMillan
- Department of Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Christopher M. Reilly
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States
| | - Xin M. Luo
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Wu Y, Xin M, Pham Q, Gao Y, Huang H, Jiang X, Li RW, Yu L, Luo Y, Wang J, Wang TTY. Red Cabbage Modulates Composition and Co-Occurrence Networks of Gut Microbiota in a Rodent Diet-Induced Obesity Model. Foods 2023; 13:85. [PMID: 38201113 PMCID: PMC10778922 DOI: 10.3390/foods13010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Red cabbage (RC), a cruciferous vegetable rich in various bioactive substances, can significantly reduce the risk factors of several non-communicable diseases, but the mechanism underlying the biological effects of RC remains unclear. Furthermore, mechanisms that operate through the regulation of gut microbiota also are not known. Given the relationships between diet, gut microbiota, and health, a diet-induced mice obesity model was used to elucidate the influence of RC on gut microbial composition and bacteria-bacteria interactions in mice. After 24 h of dietary intervention, a high-fat (HF) diet with the intake of RC led to increased Firmicutes/Bacteroidetes (F/B) ratios in the feces of mice. RC also reduced the relative abundance of Bifidobacteria, Lactobacillus, and Akkermansia muciniphila in mice fed a low-fat (LF) diet. After 8-weeks of dietary intervention, RC significantly changed the structure and the ecological network of the gut microbial community. Particularly, RC inhibited an HF-diet-induced increase in AF12 in mice, and this genus was positively correlated with body weight, low-density lipoprotein level, and fecal bile acid of mice. Unclassified Clostridiales, specifically increased via RC consumption, were also found to negatively correlate with hepatic free cholesterol levels in mice. Overall, our results demonstrated that RC modulating gut microbial composition and interactions are associated with the attenuation of HF-diet-induced body weight gain and altered cholesterol metabolism in mice.
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Affiliation(s)
- Yanbei Wu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Mengmeng Xin
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Quynhchi Pham
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA;
| | - Yu Gao
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Haiqiu Huang
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA (X.J.); (L.Y.)
| | - Xiaojing Jiang
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA (X.J.); (L.Y.)
| | - Robert W. Li
- Animal Parasitic Diseases Laboratory, BARC, ARS, USDA, Beltsville, MD 20705, USA;
| | - Liangli Yu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA (X.J.); (L.Y.)
| | - Yaguang Luo
- Food Quality Laboratory, BARC, ARS, USDA, Beltsville, MD 20705, USA;
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Thomas T. Y. Wang
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA;
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Padiadpu J, Garcia‐Jaramillo M, Newman NK, Pederson JW, Rodrigues R, Li Z, Singh S, Monnier P, Trinchieri G, Brown K, Dzutsev AK, Shulzhenko N, Jump DB, Morgun A. Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis. EMBO Mol Med 2023; 15:e18367. [PMID: 37859621 PMCID: PMC10630881 DOI: 10.15252/emmm.202318367] [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: 07/19/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Clinical and preclinical studies established that supplementing diets with ω3 polyunsaturated fatty acids (PUFA) can reduce hepatic dysfunction in nonalcoholic steatohepatitis (NASH) but molecular underpinnings of this action were elusive. Herein, we used multi-omic network analysis that unveiled critical molecular pathways involved in ω3 PUFA effects in a preclinical mouse model of western diet induced NASH. Since NASH is a precursor of liver cancer, we also performed meta-analysis of human liver cancer transcriptomes that uncovered betacellulin as a key EGFR-binding protein upregulated in liver cancer and downregulated by ω3 PUFAs in animals and humans with NASH. We then confirmed that betacellulin acts by promoting proliferation of quiescent hepatic stellate cells, inducing transforming growth factor-β2 and increasing collagen production. When used in combination with TLR2/4 agonists, betacellulin upregulated integrins in macrophages thereby potentiating inflammation and fibrosis. Taken together, our results suggest that suppression of betacellulin is one of the key mechanisms associated with anti-inflammatory and anti-fibrotic effects of ω3 PUFA on NASH.
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Affiliation(s)
| | | | - Nolan K Newman
- College of PharmacyOregon State UniversityCorvallisORUSA
| | - Jacob W Pederson
- Carlson College of Veterinary MedicineOregon State UniversityCorvallisORUSA
| | - Richard Rodrigues
- College of PharmacyOregon State UniversityCorvallisORUSA
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Zhipeng Li
- Carlson College of Veterinary MedicineOregon State UniversityCorvallisORUSA
| | - Sehajvir Singh
- College of PharmacyOregon State UniversityCorvallisORUSA
| | - Philip Monnier
- College of PharmacyOregon State UniversityCorvallisORUSA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Kevin Brown
- College of PharmacyOregon State UniversityCorvallisORUSA
- School of Chemical, Biological, and Environmental EngineeringOregon State UniversityCorvallisORUSA
| | - Amiran K Dzutsev
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Natalia Shulzhenko
- Carlson College of Veterinary MedicineOregon State UniversityCorvallisORUSA
| | - Donald B Jump
- Nutrition Program, School of Biological and Population Health Sciences, Linus Pauling InstituteOregon State UniversityCorvallisORUSA
| | - Andrey Morgun
- College of PharmacyOregon State UniversityCorvallisORUSA
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Oktaviono YH, Lamara AD, Tri Saputra PB, Arnindita JN, Pasahari D, Saputra ME, Made Adnya Suasti N. The roles of trimethylamine-N-oxide in atherosclerosis and its potential therapeutic aspect: A literature review. BIOMOLECULES & BIOMEDICINE 2023; 23:936-948. [PMID: 37337893 PMCID: PMC10655873 DOI: 10.17305/bb.2023.8893] [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: 02/09/2023] [Revised: 05/21/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023]
Abstract
Current research supports the evidence that the gut microbiome (GM), which consist of gut microbiota and their biologically active metabolites, is associated with atherosclerosis development. Trimethylamine-N-oxide (TMAO), a metabolite produced by the GM through trimethylamine (TMA) oxidation, significantly enhances the formation and vulnerability of atherosclerotic plaques. TMAO promotes inflammation and oxidative stress in endothelial cells, leading to vascular dysfunction and plaque formation. Dimethyl-1-butanol (DMB), iodomethylcholine (IMC) and fluoromethylcholine (FMC) have been recognized for their ability to reduce plasma TMAO by inhibiting trimethylamine lyase, a bacterial enzyme involved in the choline cleavage anaerobic process, thus reducing TMA formation. Conversely, indole-3-carbinol (I3C) and trigonelline inhibit TMA oxidation by inhibiting flavin-containing monooxygenase-3 (FMO3), resulting in reduced plasma TMAO. The combined use of inhibitors of choline trimethylamine lyase and flavin-containing monooxygenase-3 could provide novel therapeutic strategies for cardiovascular disease prevention by stabilizing existing atherosclerotic plaques. This review aims to present the current evidence of the roles of TMA/TMAO in atherosclerosis as well as its potential therapeutic prevention aspects.
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Affiliation(s)
- Yudi Her Oktaviono
- Department of Cardiology and Vascular Medicine, General Hospital Dr. Soetomo, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Ariikah Dyah Lamara
- Department of Cardiology and Vascular Medicine, General Hospital Dr. Soetomo, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Pandit Bagus Tri Saputra
- Department of Cardiology and Vascular Medicine, General Hospital Dr. Soetomo, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | | | - Diar Pasahari
- Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Mahendra Eko Saputra
- Department of Cardiology and Vascular Medicine, General Hospital Dr. Soetomo, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
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Newman NK, Zhang Y, Padiadpu J, Miranda CL, Magana AA, Wong CP, Hioki KA, Pederson JW, Li Z, Gurung M, Bruce AM, Brown K, Bobe G, Sharpton TJ, Shulzhenko N, Maier CS, Stevens JF, Gombart AF, Morgun A. Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome. MICROBIOME 2023; 11:208. [PMID: 37735685 PMCID: PMC10512512 DOI: 10.1186/s40168-023-01637-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/01/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND The gut microbiota contributes to macrophage-mediated inflammation in adipose tissue with consumption of an obesogenic diet, thus driving the development of metabolic syndrome. There is a need to identify and develop interventions that abrogate this condition. The hops-derived prenylated flavonoid xanthohumol (XN) and its semi-synthetic derivative tetrahydroxanthohumol (TXN) attenuate high-fat diet-induced obesity, hepatosteatosis, and metabolic syndrome in C57Bl/6J mice. This coincides with a decrease in pro-inflammatory gene expression in the gut and adipose tissue, together with alterations in the gut microbiota and bile acid composition. RESULTS In this study, we integrated and interrogated multi-omics data from different organs with fecal 16S rRNA sequences and systemic metabolic phenotypic data using a Transkingdom Network Analysis. By incorporating cell type information from single-cell RNA-seq data, we discovered TXN attenuates macrophage inflammatory processes in adipose tissue. TXN treatment also reduced levels of inflammation-inducing microbes, such as Oscillibacter valericigenes, that lead to adverse metabolic phenotypes. Furthermore, in vitro validation in macrophage cell lines and in vivo mouse supplementation showed addition of O. valericigenes supernatant induced the expression of metabolic macrophage signature genes that are downregulated by TXN in vivo. CONCLUSIONS Our findings establish an important mechanism by which TXN mitigates adverse phenotypic outcomes of diet-induced obesity and metabolic syndrome. TXN primarily reduces the abundance of pro-inflammatory gut microbes that can otherwise promote macrophage-associated inflammation in white adipose tissue. Video Abstract.
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Affiliation(s)
- N K Newman
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Y Zhang
- School of Biological and Population Health Sciences, Nutrition Program, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- Present address: Oregon Health & Science University, Portland, OR, USA
| | - J Padiadpu
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - C L Miranda
- Department of Pharmaceutical Sciences, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - A A Magana
- Department of Chemistry, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - C P Wong
- School of Biological and Population Health Sciences, Nutrition Program, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - K A Hioki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
- Present address: UMASS, Amherst, MA, USA
| | - J W Pederson
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Z Li
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - M Gurung
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Present address: Children Nutrition Center, USDA, Little Rock, AR, USA
| | - A M Bruce
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - K Brown
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
- Chemical, Biological & Environmental Engineering, Oregon State University, Corvallis, OR, USA
| | - G Bobe
- Department of Animal Sciences, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - T J Sharpton
- Department of Microbiology, Department of Statistics, Oregon State University, Corvallis, OR, USA
| | - N Shulzhenko
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.
| | - C S Maier
- Department of Chemistry, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - J F Stevens
- Department of Pharmaceutical Sciences, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - A F Gombart
- Department of Biochemistry and Biophysics, Linus Pauling Institute, Corvallis, OR, USA.
| | - A Morgun
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
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Kim S, Li H, Jin Y, Armad J, Gu H, Mani S, Cui JY. Maternal PBDE exposure disrupts gut microbiome and promotes hepatic proinflammatory signaling in humanized PXR-transgenic mouse offspring over time. Toxicol Sci 2023; 194:209-225. [PMID: 37267213 PMCID: PMC10375318 DOI: 10.1093/toxsci/kfad056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Developmental exposure to the persistent environmental pollutant, polybrominated diphenyl ethers (PBDEs), is associated with increased diabetes prevalence. The microbial tryptophan metabolite, indole-3-propionic acid (IPA), is associated with reduced risk of type 2 diabetes and lower-grade inflammation and is a pregnane X receptor (PXR) activator. To explore the role of IPA in modifying the PBDE developmental toxicity, we orally exposed humanized PXR-transgenic (hPXR-TG) mouse dams to vehicle, 0.1 mg/kg/day DE-71 (an industrial PBDE mixture), DE-71+IPA (20 mg/kg/day), or IPA, from 4 weeks preconception to the end of lactation. Pups were weaned at 21 days of age and IPA supplementation continued in the corresponding treatment groups. Tissues were collected at various ages until 6 months of age (n = 5 per group). In general, the effect of maternal DE-71 exposure on the gut microbiome of pups was amplified over time. The regulation of hepatic cytokines and prototypical xenobiotic-sensing transcription factor target genes by DE-71 and IPA was age- and sex-dependent, where DE-71-mediated mRNA increased selected cytokines (Il10, Il12p40, Il1β [both sexes], and [males]). The hepatic mRNA of the aryl hydrocarbon receptor (AhR) target gene Cyp1a2 was increased by maternal DE-71 and DE-71+IPA exposure at postnatal day 21 but intestinal Cyp1a1 was not altered by any of the exposures and ages. Maternal DE-71 exposure persistently increased serum indole, a known AhR ligand, in age- and sex-dependent manner. In conclusion, maternal DE-71 exposure produced a proinflammatory signature along the gut-liver axis, including gut dysbiosis, dysregulated tryptophan microbial metabolism, attenuated PXR signaling, and elevated AhR signaling in postweaned hPXR-TG pups over time, which was partially corrected by IPA supplementation.
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Affiliation(s)
- Sarah Kim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Hao Li
- Departments of Medicine, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, Florida 34987-2352, USA
| | - Jasmine Armad
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, Florida 34987-2352, USA
| | - Sridhar Mani
- Departments of Medicine, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Julia Y Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
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Bloemendaal M, Veniaminova E, Anthony DC, Gorlova A, Vlaming P, Khairetdinova A, Cespuglio R, Lesch KP, Arias Vasquez A, Strekalova T. Serotonin Transporter (SERT) Expression Modulates the Composition of the Western-Diet-Induced Microbiota in Aged Female Mice. Nutrients 2023; 15:3048. [PMID: 37447374 PMCID: PMC10346692 DOI: 10.3390/nu15133048] [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: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Background. The serotonin transporter (SERT), highly expressed in the gut and brain, is implicated in metabolic processes. A genetic variant of the upstream regulatory region of the SLC6A4 gene encoding SERT, the so-called short (s) allele, in comparison with the long (l) allele, results in the decreased function of this transporter, altered serotonergic regulation, an increased risk of psychiatric pathology and type-2 diabetes and obesity, especially in older women. Aged female mice with the complete (Sert-/-: KO) or partial (Sert+/-: HET) loss of SERT exhibit more pronounced negative effects following their exposure to a Western diet in comparison to wild-type (Sert+/+: WT) animals. Aims. We hypothesized that these effects might be mediated by an altered gut microbiota, which has been shown to influence serotonin metabolism. We performed V4 16S rRNA sequencing of the gut microbiota in 12-month-old WT, KO and HET female mice that were housed on a control or Western diet for three weeks. Results. The relative abundance of 11 genera was increased, and the abundance of 6 genera was decreased in the Western-diet-housed mice compared to the controls. There were correlations between the abundance of Streptococcus and Ruminococcaceae_UCG-014 and the expression of the pro-inflammatory marker Toll-like-Receptor 4 (Tlr4) in the dorsal raphe, as well as the expression of the mitochondrial activity marker perixome-proliferator-activated-receptor-cofactor-1b (Ppargc1b) in the prefrontal cortex. Although there was no significant impact of genotype on the microbiota in animals fed with the Control diet, there were significant interactions between diet and genotype. Following FDR correction, the Western diet increased the relative abundance of Intestinimonas and Atopostipes in the KO animals, which was not observed in the other groups. Erysipelatoclostridium abundance was increased by the Western diet in the WT group but not in HET or KO animals. Conclusions. The enhanced effects of a challenge with a Western diet in SERT-deficient mice include the altered representation of several gut genera, such as Intestinimonas, Atopostipes and Erysipelatoclostridium, which are also implicated in serotonergic and lipid metabolism. The manipulation of these genera may prove useful in individuals with the short SERT allele.
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Affiliation(s)
- Mirjam Bloemendaal
- Departments of Psychiatry & Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (P.V.); (A.A.V.)
| | - Ekaterina Veniaminova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
| | | | - Anna Gorlova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
| | - Priscilla Vlaming
- Departments of Psychiatry & Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (P.V.); (A.A.V.)
| | - Adel Khairetdinova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
| | - Raymond Cespuglio
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
- Neuroscience Research Center of Lyon, Claude-Bernard Lyon-1 University, 69500 Bron, France
| | - Klaus Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, 97080 Würzburg, Germany; (K.P.L.); (T.S.)
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Alejandro Arias Vasquez
- Departments of Psychiatry & Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (P.V.); (A.A.V.)
| | - Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, 97080 Würzburg, Germany; (K.P.L.); (T.S.)
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, 6229 HX Maastricht, The Netherlands
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9
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Newman NK, Macovsky M, Rodrigues RR, Bruce AM, Pederson JW, Patil SS, Padiadpu J, Dzutsev AK, Shulzhenko N, Trinchieri G, Brown K, Morgun A. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529449. [PMID: 36865280 PMCID: PMC9980039 DOI: 10.1101/2023.02.22.529449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Technological advances have generated tremendous amounts of high-throughput omics data. Integrating data from multiple cohorts and diverse omics types from new and previously published studies can offer a holistic view of a biological system and aid in deciphering its critical players and key mechanisms. In this protocol, we describe how to use Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that can perform meta-analysis of cohorts and detect master regulators among measured parameters that govern pathological or physiological responses of host-microbiota (or any multi-omic data) interactions in a particular condition or disease. TkNA first reconstructs the network that represents a statistical model capturing the complex relationships between the different omics of the biological system. Here, it selects differential features and their per-group correlations by identifying robust and reproducible patterns of fold change direction and sign of correlation across several cohorts. Next, a causality-sensitive metric, statistical thresholds, and a set of topological criteria are used to select the final edges that form the transkingdom network. The second part of the analysis involves interrogating the network. Using the network's local and global topology metrics, it detects nodes that are responsible for control of given subnetwork or control of communication between kingdoms and/or subnetworks. The underlying basis of the TkNA approach involves fundamental principles including laws of causality, graph theory and information theory. Hence, TkNA can be used for causal inference via network analysis of any host and/or microbiota multi-omics data. This quick and easy-to-run protocol requires very basic familiarity with the Unix command-line environment.
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Affiliation(s)
- Nolan K Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Matthew Macovsky
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Richard R Rodrigues
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Amanda M Bruce
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jacob W Pederson
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Sankalp S Patil
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jyothi Padiadpu
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Amiran K Dzutsev
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Natalia Shulzhenko
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kevin Brown
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
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10
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Hiéronimus L, Huaux F. B-1 cells in immunotoxicology: Mechanisms underlying their response to chemicals and particles. FRONTIERS IN TOXICOLOGY 2023; 5:960861. [PMID: 37143777 PMCID: PMC10151831 DOI: 10.3389/ftox.2023.960861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Since their discovery nearly 40 years ago, B-1 cells have continued to challenge the boundaries between innate and adaptive immunity, as well as myeloid and lymphoid functions. This B-cell subset ensures early immunity in neonates before the development of conventional B (B-2) cells and respond to immune injuries throughout life. B-1 cells are multifaceted and serve as natural- and induced-antibody-producing cells, phagocytic cells, antigen-presenting cells, and anti-/pro-inflammatory cytokine-releasing cells. This review retraces the origin of B-1 cells and their different roles in homeostatic and infectious conditions before focusing on pollutants comprising contact-sensitivity-inducing chemicals, endocrine disruptors, aryl hydrocarbon receptor (AHR) ligands, and reactive particles.
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11
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Bouranis JA, Beaver LM, Jiang D, Choi J, Wong CP, Davis EW, Williams DE, Sharpton TJ, Stevens JF, Ho E. Interplay between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach. Nutrients 2022; 15:nu15010042. [PMID: 36615700 PMCID: PMC9824405 DOI: 10.3390/nu15010042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Brassica vegetables contain a multitude of bioactive compounds that prevent and suppress cancer and promote health. Evidence suggests that the gut microbiome may be essential in the production of these compounds; however, the relationship between specific microbes and the abundance of metabolites produced during cruciferous vegetable digestion are still unclear. We utilized an ex vivo human fecal incubation model with in vitro digested broccoli sprouts (Broc), Brussels sprouts (Brus), a combination of the two vegetables (Combo), or a negative control (NC) to investigate microbial metabolites of cruciferous vegetables. We conducted untargeted metabolomics on the fecal cultures by LC-MS/MS and completed 16S rRNA gene sequencing. We identified 72 microbial genera in our samples, 29 of which were significantly differentially abundant between treatment groups. A total of 4499 metabolomic features were found to be significantly different between treatment groups (q ≤ 0.05, fold change > 2). Chemical enrichment analysis revealed 45 classes of compounds to be significantly enriched by brassicas, including long-chain fatty acids, coumaric acids, and peptides. Multi-block PLS-DA and a filtering method were used to identify microbe−metabolite interactions. We identified 373 metabolites from brassica, which had strong relationships with microbes, such as members of the family Clostridiaceae and genus Intestinibacter, that may be microbially derived.
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Affiliation(s)
- John A. Bouranis
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Laura M. Beaver
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
| | - Jaewoo Choi
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Carmen P. Wong
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Edward W. Davis
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - David E. Williams
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Thomas J. Sharpton
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Jan F. Stevens
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Emily Ho
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Correspondence:
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12
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Mousa WK, Chehadeh F, Husband S. Microbial dysbiosis in the gut drives systemic autoimmune diseases. Front Immunol 2022; 13:906258. [PMID: 36341463 PMCID: PMC9632986 DOI: 10.3389/fimmu.2022.906258] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/20/2022] [Indexed: 09/29/2023] Open
Abstract
Trillions of microbes survive and thrive inside the human body. These tiny creatures are crucial to the development and maturation of our immune system and to maintain gut immune homeostasis. Microbial dysbiosis is the main driver of local inflammatory and autoimmune diseases such as colitis and inflammatory bowel diseases. Dysbiosis in the gut can also drive systemic autoimmune diseases such as type 1 diabetes, rheumatic arthritis, and multiple sclerosis. Gut microbes directly interact with the immune system by multiple mechanisms including modulation of the host microRNAs affecting gene expression at the post-transcriptional level or production of microbial metabolites that interact with cellular receptors such as TLRs and GPCRs. This interaction modulates crucial immune functions such as differentiation of lymphocytes, production of interleukins, or controlling the leakage of inflammatory molecules from the gut to the systemic circulation. In this review, we compile and analyze data to gain insights into the underpinning mechanisms mediating systemic autoimmune diseases. Understanding how gut microbes can trigger or protect from systemic autoimmune diseases is crucial to (1) tackle these diseases through diet or lifestyle modification, (2) develop new microbiome-based therapeutics such as prebiotics or probiotics, (3) identify diagnostic biomarkers to predict disease risk, and (4) observe and intervene with microbial population change with the flare-up of autoimmune responses. Considering the microbiome signature as a crucial player in systemic autoimmune diseases might hold a promise to turn these untreatable diseases into manageable or preventable ones.
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Affiliation(s)
- Walaa K. Mousa
- Biology Department, Whitman College, Walla Walla, WA, United States
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Fadia Chehadeh
- Biology Department, Whitman College, Walla Walla, WA, United States
| | - Shannon Husband
- Biology Department, Whitman College, Walla Walla, WA, United States
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13
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Wu J, Pang T, Lin Z, Zhao M, Jin H. The key player in the pathogenesis of environmental influence of systemic lupus erythematosus: Aryl hydrocarbon receptor. Front Immunol 2022; 13:965941. [PMID: 36110860 PMCID: PMC9468923 DOI: 10.3389/fimmu.2022.965941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
The aryl hydrocarbon receptor was previously known as an environmental receptor that modulates the cellular response to external environmental changes. In essence, the aryl hydrocarbon receptor is a cytoplasmic receptor and transcription factor that is activated by binding to the corresponding ligands, and they transmit relevant information by binding to DNA, thereby activating the transcription of various genes. Therefore, we can understand the development of certain diseases and discover new therapeutic targets by studying the regulation and function of AhR. Several autoimmune diseases, including systemic lupus erythematosus (SLE), have been connected to AhR in previous studies. SLE is a classic autoimmune disease characterized by multi-organ damage and disruption of immune tolerance. We discuss here the homeostatic regulation of AhR and its ligands among various types of immune cells, pathophysiological roles, in addition to the roles of various related cytokines and signaling pathways in the occurrence and development of SLE.
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14
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Wang Z, Li F, Liu J, Luo Y, Guo H, Yang Q, Xu C, Ma S, Chen H. Intestinal Microbiota - An Unmissable Bridge to Severe Acute Pancreatitis-Associated Acute Lung Injury. Front Immunol 2022; 13:913178. [PMID: 35774796 PMCID: PMC9237221 DOI: 10.3389/fimmu.2022.913178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022] Open
Abstract
Severe acute pancreatitis (SAP), one of the most serious abdominal emergencies in general surgery, is characterized by acute and rapid onset as well as high mortality, which often leads to multiple organ failure (MOF). Acute lung injury (ALI), the earliest accompanied organ dysfunction, is the most common cause of death in patients following the SAP onset. The exact pathogenesis of ALI during SAP, however, remains unclear. In recent years, advances in the microbiota-gut-lung axis have led to a better understanding of SAP-associated lung injury (PALI). In addition, the bidirectional communications between intestinal microbes and the lung are becoming more apparent. This paper aims to review the mechanisms of an imbalanced intestinal microbiota contributing to the development of PALI, which is mediated by the disruption of physical, chemical, and immune barriers in the intestine, promotes bacterial translocation, and results in the activation of abnormal immune responses in severe pancreatitis. The pathogen-associated molecular patterns (PAMPs) mediated immunol mechanisms in the occurrence of PALI via binding with pattern recognition receptors (PRRs) through the microbiota-gut-lung axis are focused in this study. Moreover, the potential therapeutic strategies for alleviating PALI by regulating the composition or the function of the intestinal microbiota are discussed in this review. The aim of this study is to provide new ideas and therapeutic tools for PALI patients.
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Affiliation(s)
- Zhengjian Wang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fan Li
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jin Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yalan Luo
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Haoya Guo
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Qi Yang
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Caiming Xu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Shurong Ma
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Shurong Ma, ; Hailong Chen,
| | - Hailong Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Shurong Ma, ; Hailong Chen,
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15
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Martens PJ, Centelles-Lodeiro J, Ellis D, Cook DP, Sassi G, Verlinden L, Verstuyf A, Raes J, Mathieu C, Gysemans C. High Serum Vitamin D Concentrations, Induced via Diet, Trigger Immune and Intestinal Microbiota Alterations Leading to Type 1 Diabetes Protection in NOD Mice. Front Immunol 2022; 13:902678. [PMID: 35784365 PMCID: PMC9241442 DOI: 10.3389/fimmu.2022.902678] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The hormonally-active form of vitamin D, 1,25-dihydroxyvitamin D3, can modulate both innate and adaptive immunity, through binding to the nuclear vitamin D receptor expressed in most immune cells. A high dose of regular vitamin D protected non-obese diabetic (NOD) mice against type 1 diabetes (T1D), when initiated at birth and given lifelong. However, considerable controversy exists on the level of circulating vitamin D (25-hydroxyvitamin D3, 25(OH)D3) needed to modulate the immune system in autoimmune-prone subjects and protect against T1D onset. Here, we evaluated the impact of two doses of dietary vitamin D supplementation (400 and 800 IU/day), given to female NOD mice from 3 until 25 weeks of age, on disease development, peripheral and gut immune system, gut epithelial barrier function, and gut bacterial taxonomy. Whereas serum 25(OH)D3 concentrations were 2.6- (400 IU/day) and 3.9-fold (800 IU/day) higher with dietary vitamin D supplementation compared to normal chow (NC), only the 800 IU/day vitamin D-supplemented diet delayed and reduced T1D incidence compared to NC. Flow cytometry analyses revealed an increased frequency of FoxP3+ Treg cells in the spleen of mice receiving the 800 IU/day vitamin D-supplemented diet. This vitamin D-induced increase in FoxP3+ Treg cells, also expressing the ecto-5’-nucleotidase CD73, only persisted in the spleen of mice at 25 weeks of age. At this time point, the frequency of IL-10-secreting CD4+ T cells was also increased in all studied immune organs. High-dose vitamin D supplementation was unable to correct gut leakiness nor did it significantly modify the increased gut microbial diversity and richness over time observed in NOD mice receiving NC. Intriguingly, the rise in alpha-diversity during maturation occurred especially in mice not progressing to hyperglycaemia. Principal coordinates analysis identified that both diet and disease status significantly influenced the inter-individual microbiota variation at the genus level. The abundance of the genera Ruminoclostridium_9 and Marvinbryantia gradually increased or decreased, respectively in faecal samples of mice on the 800 IU/day vitamin D-supplemented diet compared to mice on the 400 IU/day vitamin D-supplemented diet or NC, irrespective of disease outcome. In summary, dietary vitamin D reduced T1D incidence in female NOD mice at a dose of 800, but not of 400, IU/day, and was accompanied by an expansion of Treg cells in various lymphoid organs and an altered intestinal microbiota signature.
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Affiliation(s)
- Pieter-Jan Martens
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Javier Centelles-Lodeiro
- Laboratory of Molecular Bacteriology, Rega-Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Darcy Ellis
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dana Paulina Cook
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gabriele Sassi
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lieve Verlinden
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Annemieke Verstuyf
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Rega-Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Chantal Mathieu
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Conny Gysemans
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
- *Correspondence: Conny Gysemans,
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16
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Nutritional values, beneficial effects, and food applications of broccoli (Brassica oleracea var. italica Plenck). Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2021.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Fernández-Gallego N, Sánchez-Madrid F, Cibrian D. Role of AHR Ligands in Skin Homeostasis and Cutaneous Inflammation. Cells 2021; 10:cells10113176. [PMID: 34831399 PMCID: PMC8622815 DOI: 10.3390/cells10113176] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 02/07/2023] Open
Abstract
Aryl hydrocarbon receptor (AHR) is an important regulator of skin barrier function. It also controls immune-mediated skin responses. The AHR modulates various physiological functions by acting as a sensor that mediates environment–cell interactions, particularly during immune and inflammatory responses. Diverse experimental systems have been used to assess the AHR’s role in skin inflammation, including in vitro assays of keratinocyte stimulation and murine models of psoriasis and atopic dermatitis. Similar approaches have addressed the role of AHR ligands, e.g., TCDD, FICZ, and microbiota-derived metabolites, in skin homeostasis and pathology. Tapinarof is a novel AHR-modulating agent that inhibits skin inflammation and enhances skin barrier function. The topical application of tapinarof is being evaluated in clinical trials to treat psoriasis and atopic dermatitis. In the present review, we summarize the effects of natural and synthetic AHR ligands in keratinocytes and inflammatory cells, and their relevance in normal skin homeostasis and cutaneous inflammatory diseases.
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Affiliation(s)
- Nieves Fernández-Gallego
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa (IIS-IP), 28006 Madrid, Spain;
- Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Francisco Sánchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa (IIS-IP), 28006 Madrid, Spain;
- Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (F.S.-M.); (D.C.)
| | - Danay Cibrian
- Immunology Service, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa (IIS-IP), 28006 Madrid, Spain;
- Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (F.S.-M.); (D.C.)
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18
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Yang Y, Chan WK. Glycogen Synthase Kinase 3 Beta Regulates the Human Aryl Hydrocarbon Receptor Cellular Content and Activity. Int J Mol Sci 2021; 22:ijms22116097. [PMID: 34198826 PMCID: PMC8201391 DOI: 10.3390/ijms22116097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/21/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a cytosolic receptor which is involved in diverse cellular events in humans. The most well-characterized function of AHR is its ability to upregulate gene transcription after exposure to its ligands, such as environmental toxicants, dietary antioxidants, drugs, and endogenous ligands. The cellular content of AHR is partly controlled by its degradation via the ubiquitin–proteasome system and the lysosome-dependent autophagy. We used human cervical cancer (HeLa) cells to investigate how AHR undergoes protein degradation and how its activity is modulated. Since the glycogen synthase kinase 3 beta (GSK3β)-mediated phosphorylation can trigger protein degradation and substrates of GSK3β contain stretches of serine/threonine residues which can be found in AHR, we examined whether degradation and activity of AHR can be controlled by GSK3β. We observed that AHR undergoes the GSK3β-dependent, LC3-mediated lysosomal degradation without ligand treatment. The AHR can be phosphorylated in a GSK3β-dependent manner at three putative sites (S436/S440/S444, S689/S693/T697, and S723/S727/T731), which leads to lysosomal degradation of the AHR protein. Inhibition of the GSK3β activity suppresses the ligand-activated transcription of an AHR target gene in HeLa, human liver cancer (Hep3B), and human breast cancer (MCF-7) cells. Collectively, our findings support that phosphorylation of AHR by GSK3β is essential for the optimal activation of its target gene transcription and this phosphorylation may partake as an “off” switch by subjecting the receptor to lysosomal degradation.
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