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Saranya G, Viswanathan P. Identification of renal protective gut microbiome derived-metabolites in diabetic chronic kidney disease: An integrated approach using network pharmacology and molecular docking. Saudi J Biol Sci 2024; 31:104028. [PMID: 38854894 PMCID: PMC11154206 DOI: 10.1016/j.sjbs.2024.104028] [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: 02/26/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 06/11/2024] Open
Abstract
Metabolites from the gut microbiota define molecules in the gut-kidney cross talks. However, the mechanistic pathway by which the kidneys actively sense gut metabolites and their impact on diabetic chronic kidney disease (DCKD) remains unclear. This study is an attempt to investigate the gut microbiome metabolites, their host targeting genes, and their mechanistic action against DCKD. Gut microbiome, metabolites, and host targets were extracted from the gutMgene database and metabolites from the PubChem database. DCKD targets were identified from DisGeNET, GeneCard, NCBI, and OMIM databases. Computational examination such as protein-protein interaction networks, enrichment pathway, identification of metabolites for potential targets using molecular docking, hubgene-microbes-metabolite-samplesource-substrate (HMMSS) network architecture were executed using Network analyst, ShinyGo, GeneMania, Cytoscape, Autodock tools. There were 574 microbial metabolites, 2861 DCKD targets, and 222 microbes targeting host genes. After screening, we obtained 27 final targets, which are used for computational examination. From enrichment analysis, we found NF-ΚB1, AKT1, EGFR, JUN, and RELA as the main regulators in the DCKD development through mitogen activated protein kinase (MAPK) pathway signalling. The (HMMSS) network analysis found F.prausnitzi, B.adolescentis, and B.distasonis probiotic bacteria that are found in the intestinal epithelium, colonic region, metabolize the substrates like tryptophan, other unknown substrates might have direct interaction with the NF-kB1 and epidermal growth factor receptor (EGFR) targets. On docking of these target proteins with 3- Indole propionic acid (IPA) showed high binding energy affinity of -5.9 kcal/mol and -7.4kcal/mol. From this study we identified, the 3 IPA produced by F. prausnitzi A2-165 was found to have renal sensing properties inhibiting MAPK/NF-KB1 inflammatory pathway and would be useful in treating CKD in diabetics.
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Affiliation(s)
- G.R. Saranya
- Renal Research Lab, Pearl Research Park, School of Bioscience and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - Pragasam Viswanathan
- Renal Research Lab, Pearl Research Park, School of Bioscience and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
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Pan S, Jiang SS, Li R, Tian B, Huang CY, Wang R, Li YY, Zhu H, Yuan YF, Hu X. Hong Guo Ginseng Guo (HGGG) protects against kidney injury in diabetic nephropathy by inhibiting NLRP3 inflammasome and regulating intestinal flora. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155861. [PMID: 39024672 DOI: 10.1016/j.phymed.2024.155861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/09/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Diabetic nephropathy (DN) is one of the most serious complications of diabetes which leads to end-stage renal failure and approximately one-third of patients need dialysis. There is still a lack of effective and specific treatment for DN. Searching new drugs from natural foods is an alternative approach to treat diabetes and its complications. Hong Guo Ginseng Guo (HGGG), a berry with palatability and nutritional benefits, has exhibited medicinal properties to mitigate the progression of DN. PURPOSE This study investigates the effects of HGGG on streptozotocin (STZ)-induced diabetic nephropathy (DN) in rats and elucidates the mechanisms underlying its reno-protective and diabetes management benefits. METHODS The LC-MS spectra method identified the primary ingredients in HGGG. To induce DN, male Sprague-Dawley (SD) rats received a single intraperitoneal injection of 75 mg/kg STZ. Over an eight-week treatment period, we assessed biochemical parameters including blood glucose, urine albumin-to-creatinine ratio (UACR), blood urea nitrogen (BUN), and urine N-acetyl-beta-d-glucosaminidase (NAG). Tissue pathology was examined using Masson's trichrome, Periodic Acid-Schiff (PAS), and Hematoxylin-Eosin (H&E) stains. We analyzed pro-inflammatory mediators and tissue fibrosis extent using Western blotting and immunohistochemistry. Gut microbiota composition was characterized via 16S rDNA sequencing. RESULTS Seventeen chemical compounds were identified, with lobetyolin, luteolin, and rutin highlighted as the primary active elements. HGGG extract appeared to confer renal protection, demonstrated by improvements in UACR, BUN, and urine NAG levels. The reno protective effects in HGGG-treated DN rats were linked to reduced renal fibrosis and inhibition of the NLRP3 inflammasome. Additionally, HGGG administration improved gut barrier integrity and altered the gut microbiota in DN rats, increasing the relative abundance of beneficial bacteria known for regulating polyamines and producing short-chain fatty acids (SCFAs), including Ruminococcus, Barnesiella_sp, Anaerovoracaceae, and Prevotellaceae_NK3B31. Meanwhile, treatment with HGGG decreasing the presence of Oscillospira, potential pathogens responsible for producing lipopolysaccharide (LPS). CONCLUSION HGGG has potential as a beneficial fruit for managing diabetes and its associated complications through modulation of the gut microbiota.
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Affiliation(s)
- Shu Pan
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China
| | - Shan-Shan Jiang
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China
| | - Rui Li
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Bei Tian
- Guizhou Innovation Agriculture Development Co., Ltd., Tongren, 554300, China
| | - Chun-Yue Huang
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Rong Wang
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China
| | - Yue-Yue Li
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China
| | - Hui Zhu
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China
| | - Yong-Fang Yuan
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China.
| | - Xiao Hu
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China.
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Fang Y, Zhang Y, Liu Q, Zheng Z, Ren C, Zhang X. Assessing the causal relationship between gut microbiota and diabetic nephropathy: insights from two-sample Mendelian randomization. Front Endocrinol (Lausanne) 2024; 15:1329954. [PMID: 38562415 PMCID: PMC10982433 DOI: 10.3389/fendo.2024.1329954] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Background The causal association between gut microbiota (GM) and the development of diabetic nephropathy (DN) remains uncertain. We sought to explore this potential association using two-sample Mendelian randomization (MR) analysis. Methods Genome-wide association study (GWAS) data for GM were obtained from the MiBioGen consortium. GWAS data for DN and related phenotypes were collected from the FinngenR9 and CKDGen databases. The inverse variance weighted (IVW) model was used as the primary analysis model, supplemented by various sensitivity analyses. Heterogeneity was assessed using Cochran's Q test, while horizontal pleiotropy was evaluated through MR-Egger regression and the MR-PRESSO global test. Reverse MR analysis was conducted to identify any reverse causal effects. Results Our analysis identified twenty-five bacterial taxa that have a causal association with DN and its related phenotypes (p < 0.05). Among them, only the g_Eubacterium_coprostanoligenes_group showed a significant causal association with type 1 DN (p < Bonferroni-adjusted p-value). Our findings remained consistent regardless of the analytical approach used, with all methods indicating the same direction of effect. No evidence of heterogeneity or horizontal pleiotropy was observed. Reverse MR analysis did not reveal any causal associations. Conclusions This study established a causal association between specific GM and DN. Our findings contribute to current understanding of the role of GM in the development of DN, offering potential insights for the prevention and treatment strategies for this condition.
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Affiliation(s)
- Yipeng Fang
- Laboratory of Molecular Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | | | - Qian Liu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Zenan Zheng
- Shantou University Medical College, Shantou, Guangdong, China
| | - Chunhong Ren
- International Medical Service Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xin Zhang
- Laboratory of Molecular Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
- Engineering Research Center of Key Technique for Biotherapy of Guangdong, Shantou, Guangdong, China
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Guo M, Fang L, Chen M, Shen J, Tan Z, He W. Dysfunction of cecal microbiota and CutC activity in mice mediating diarrhea with kidney-yang deficiency syndrome. Front Microbiol 2024; 15:1354823. [PMID: 38500584 PMCID: PMC10944907 DOI: 10.3389/fmicb.2024.1354823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
Objective Previous studies have indicated that diarrhea with kidney-yang deficiency syndrome leads to a disorder of small intestine contents and mucosal microbiota. However, the relationship of TMA-lyase (CutC) activity and TMAO with diarrhea with kidney-yang deficiency syndrome remains unexplored. Therefore, this study explores the relationship between cecal microbiota and choline TMA-lyase (CutC) activity, as well as the correlation between trimethylamine oxide (TMAO), inflammatory index, and CutC activity. Method Twenty SPF-grade male KM mice were randomly divided into the normal group (CN) and the diarrhea model group (CD). Diarrhea mouse models were established by adenine combined with Folium sennae administration. CutC activity, TMAO, interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) levels were detected, and the cecal content microbiota was sequenced. Result After 14 days, diarrhea occurred in the CD group. Compared with the CN group, there was no significant change in the activity of CutC in the small intestine of the CD group, while the activity of CutC in the cecum was significantly increased, and the levels of TMAO, IL-6, and TNF-α showed a significant increase. The Chao1 index, Observed_species index, Shannon index, and Simpson index all exhibited a decreasing trend. The main changes at the bacterial genus level were Alistipes, Enterorhabdus, Desulfovibrio, Bacteroides, Candidatus_Saccharimonas, and [Ruminococcus]_torques_group. The results of LEfSe analysis, random forest analysis and ROC curve analysis revealed Paludicola, Blautia, Negativibacillus, Paraprevotella, Harryflintia, Candidatus_Soleaferrea, Anaerotruncus, Oscillibacter, Colidextribacter, [Ruminococcus]_torques_group, and Bacteroides as characteristic bacteria in the CD group. Correlation analysis showed a significant negative correlation between cecal CutC activity and Ligilactobacillus, and a significant positive correlation with Negativibacillus and Paludicola. The level of TMAO was significantly positively correlated with CutC activity and IL-6. Conclusion Diarrhea with kidney-yang deficiency syndrome significantly affects the physiological status, digestive enzyme activity, CutC activity, TMAO levels, and inflammatory response in mice. Additionally, there are changes in the composition and function of cecal microbiota, indicating an important impact of diarrhea with kidney-yang deficiency syndrome on the host intestinal microbiota balance. The occurrence of diarrhea with kidney-yang deficiency syndrome may be associated with dysbiosis of intestinal microbiota, increased CutC activity, elevated TMAO levels, and heightened inflammatory factor levels.
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Affiliation(s)
- Mingmin Guo
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Leyao Fang
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Meili Chen
- Changsha Hospital of Traditional Chinese Medicine, Changsha, China
| | - Junxi Shen
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Zhoujin Tan
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Wenzhi He
- School of Stomatology, Hunan University of Chinese Medicine, Changsha, China
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Xiong Y, Zhu X, Luo Q. Causal relationship between gut microbiota and autoimmune thyroiditis: A mendelian study. Heliyon 2024; 10:e25652. [PMID: 38356548 PMCID: PMC10865322 DOI: 10.1016/j.heliyon.2024.e25652] [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: 09/20/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Background Autoimmune thyroiditis (AIT), also known as Hashimoto's thyroiditis (HT) or chronic lymphocytic thyroiditis, is a prevalent autoimmune disorder. Despite its high prevalence, the pathogenesis of AIT remains unclear. Previous studies have suggested a potential association between gut microbiota and AIT. However, whether this relationship is causal or coincidental remains uncertain. To address this gap in knowledge, our study aimed to investigate the potential causal association between gut microbiota and AIT using the two-sample Mendelian randomization (MR) method. Methods Summary-level gut microbiota data comprising 211 taxa (131 genera, 35 families, 20 orders, 16 classes, and 9 phyla) were obtained from the comprehensive MiBioGen study. Genetic associations with 22 gastrointestinal diseases were extracted from the UK Biobank, FinnGen study, and various extensive GWAS studies. A meticulous MR analysis was conducted to evaluate the causal relationship between genetically predicted gut microbiota and these gastrointestinal diseases. Sensitivity analyses and tests for heterogeneity were systematically performed to validate the reliability of our findings. Results Six gut microbiota species showed significant associations with AIT according to the IVW method. Among them, the following exhibited negative associations with AIT: family Alcaligenaceae, family Pasteurellaceae (ID: 3689), family Peptococcaceae, genus Lachnospira, genus Victivallis, and order Pasteurellales (ID: 3688). No evidence of pleiotropy or heterogeneity was detected. Conclusion The MR analysis uncovered a causal relationship at the genetic prediction level between specific gut microbiota and AIT. These findings offer novel insights into the mechanisms governing the development of AIT mediated by gut microbiota. This knowledge could inform the design of future interventions, potentially involving microbiome-related strategies, to address the mechanisms associated with AIT development.
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Affiliation(s)
- Yujun Xiong
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China, 100370, Beijing, China
| | - Xingyun Zhu
- Department of Endocrinology, Beijing Jishuitan Hospital, No. 31, East Xinjiekou Street, Xicheng District, 100035, Beijing, China
| | - Qingfeng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China, 100370, Beijing, China
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Yu L, Zhao Y, Zhao Y. Advances in the pharmacological effects and molecular mechanisms of emodin in the treatment of metabolic diseases. Front Pharmacol 2023; 14:1240820. [PMID: 38027005 PMCID: PMC10644045 DOI: 10.3389/fphar.2023.1240820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Rhubarb palmatum L., Polygonum multijiorum Thunb., and Polygonum cuspidatum Sieb. Et Zucc. are traditional Chinese medicines that have been used for thousands of years. They are formulated into various preparations and are widely used. Emodin is a traditional Chinese medicine monomer and the main active ingredient in Rhubarb palmatum L., Polygonum multijiorum Thunb., and Polygonum cuspidatum Sieb. Et Zucc. Modern research shows that it has a variety of pharmacological effects, including promoting lipid and glucose metabolism, osteogenesis, and anti-inflammatory and anti-autophagy effects. Research on the toxicity and pharmacokinetics of emodin can promote its clinical application. This review aims to provide a basis for further development and clinical research of emodin in the treatment of metabolic diseases. We performed a comprehensive summary of the pharmacology and molecular mechanisms of emodin in treating metabolic diseases by searching databases such as Web of Science, PubMed, ScienceDirect, and CNKI up to 2023. In addition, this review also analyzes the toxicity and pharmacokinetics of emodin. The results show that emodin mainly regulates AMPK, PPAR, and inflammation-related signaling pathways, and has a good therapeutic effect on obesity, hyperlipidemia, non-alcoholic fatty liver disease, diabetes and its complications, and osteoporosis. In addition, controlling toxic factors and improving bioavailability are of great significance for its clinical application.
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Affiliation(s)
- Linyuan Yu
- Department of Traditional Chinese Medicine, Chengdu Integrated TCM and Western Medicine Hospital, Chengdu, China
- Department of Pharmacy, Sichuan Second Hospital of TCM, Chengdu, China
| | - Yongliang Zhao
- Nursing Department, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yongli Zhao
- Department of Traditional Chinese Medicine, Chengdu Integrated TCM and Western Medicine Hospital, Chengdu, China
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