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Song Z, Wang Y, Lin P, Yang K, Jiang X, Dong J, Xie S, Rao R, Cui L, Liu F, Huang X. Identification of key modules and driving genes in nonalcoholic fatty liver disease by weighted gene co-expression network analysis. BMC Genomics 2023; 24:414. [PMID: 37488473 PMCID: PMC10364401 DOI: 10.1186/s12864-023-09458-3] [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: 09/07/2022] [Accepted: 06/16/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is characterized by excessive liver fat deposition, and progresses to liver cirrhosis, and even hepatocellular carcinoma. However, the invasive diagnosis of NAFLD with histopathological evaluation remains risky. This study investigated potential genes correlated with NAFLD, which may serve as diagnostic biomarkers and even potential treatment targets. METHODS The weighted gene co-expression network analysis (WGCNA) was constructed based on dataset E-MEXP-3291. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to evaluate the function of genes. RESULTS Blue module was positively correlated, and turquoise module negatively correlated with the severity of NAFLD. Furthermore, 8 driving genes (ANXA9, FBXO2, ORAI3, NAGS, C/EBPα, CRYAA, GOLM1, TRIM14) were identified from the overlap of genes in blue module and GSE89632. And another 8 driving genes were identified from the overlap of turquoise module and GSE89632. Among these driving genes, C/EBPα (CCAAT/enhancer binding protein α) was the most notable. By validating the expression of C/EBPα in the liver of NAFLD mice using immunohistochemistry, we discovered a significant upregulation of C/EBPα protein in NAFLD. CONCLUSION we identified two modules and 16 driving genes associated with the progression of NAFLD, and confirmed the protein expression of C/EBPα, which had been paid little attention to in the context of NAFLD, in the present study. Our study will advance the understanding of NAFLD. Moreover, these driving genes may serve as biomarkers and therapeutic targets of NAFLD.
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Affiliation(s)
- Zhengmao Song
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China
| | - Yun Wang
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China
| | - Pingli Lin
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China
| | - Kaichun Yang
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China
| | - Xilin Jiang
- Zhongshan Hospital, Xiamen University, Xiamen, China
- School of Medicine, Xiamen University, Xiamen, China
| | - Junchen Dong
- School of Medicine, Xiamen University, Xiamen, China
| | - Shangjin Xie
- Xiang'an Hospital, Xiamen University, Xiamen, China
| | - Rong Rao
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China.
| | - Lishan Cui
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China.
| | - Feng Liu
- The Fifth Hospital of Xiamen & Xiamen University, Xiamen, China.
- Xiang'an Hospital, Xiamen University, Xiamen, China.
| | - Xuefeng Huang
- Zhongshan Hospital, Xiamen University, Xiamen, China.
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Emamat H, Ghalandari H, Totmaj AS, Tangestani H, Hekmatdoost A. Calcium to magnesium intake ratio and non-alcoholic fatty liver disease development: a case-control study. BMC Endocr Disord 2021; 21:51. [PMID: 33736626 PMCID: PMC7972345 DOI: 10.1186/s12902-021-00721-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. Adoption of sedentary life style and westernized diet are shown to be associated with development of NAFLD. Since previous studies suggested that calcium (Ca) to magnesium (Mg) ratio intake is associated with some chronic diseases including dyslipidemia and insulin resistance, we designed this study to find any possible association between this ratio and NAFLD development. METHODS The NAFLD was diagnosed using Fibroscan according to a CAP cut-off value of 263 dB/m. Dietary intakes of one hundred and ninety-six patients with incident NAFLD diagnosis, and eight hundred and three controls without NAFLD were assessed using a valid food frequency questionnaire (FFQ). Dietary nutrients were calculated using Nutritionist IV software. RESULTS Age of the study population (57 % female) was 43.2 ± 14.1 years. In addition, energy-adjusted daily calcium to magnesium intake ratio was 2.34 ± 0.57 and 2.73 ± 0.69 for control and case groups, respectively. In the multivariable-adjusted model, after adjustment for potential confounding variables; including, age, gender, BMI, alcohol consumption, smoking, diabetes, physical activity, energy, dietary fiber, carbohydrate, fat, and protein intakes, participants in the third (Q3) and fourth (Q4) quartile of Ca/Mg ratio intake had a greater development of incidental NAFLD compared to the lowest quartile (Q1) [(OR = 2.86; 95 % CI: 1.20-6.81), (P-value = 0.017) and (OR = 5.97; 95 % CI: 2.54-14.01), (P-value < 0.001) for Q3 and Q4 compared to the Q1, respectively]. Moreover, energy-adjusted Ca to Mg intake ratio was positively correlated with plasma level of ALT (r = 0.18; P = 0.01); contrarily, it had no correlation with plasma levels of AST. CONCLUSIONS The current study revealed that higher dietary Ca to Mg intake ratio is associated with a greater development of NAFLD. Further interventional studies are needed to confirm the causal relationship of the Ca/Mg ratio intake and development of NAFLD.
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Grants
- 1398/10129 Student Research Committee, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
- 1398/10129 Student Research Committee, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
- 1398/10129 Student Research Committee, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
- 1398/10129 Student Research Committee, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
- 1398/10129 Student Research Committee, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
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Affiliation(s)
- Hadi Emamat
- Student Research Committee, Department of Clinical Nutrition and Dietetics, Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghalandari
- Department of Clinical Nutrition and Dietetics, Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, ShahidBeheshti University of Medical Sciences, 19395 - 4741, No 7, West Arghavan St., Farahzadi Blvd, 1981619573, Tehran, Iran
| | - Ali Saneei Totmaj
- Department of nutrition, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Hadith Tangestani
- Department of Nutrition, Persian Gulf Tropical Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Azita Hekmatdoost
- Department of Clinical Nutrition and Dietetics, Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, ShahidBeheshti University of Medical Sciences, 19395 - 4741, No 7, West Arghavan St., Farahzadi Blvd, 1981619573, Tehran, Iran.
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Liu Q, Cai BY, Zhu LX, Xin X, Wang X, An ZM, Li S, Hu YY, Feng Q. Liraglutide modulates gut microbiome and attenuates nonalcoholic fatty liver in db/db mice. Life Sci 2020; 261:118457. [PMID: 32961235 DOI: 10.1016/j.lfs.2020.118457] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/06/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
AIMS Liraglutide, a glucagon-like peptide-1(GLP-1) analog, is effective for the treatment of type II diabetes and nonalcoholic fatty liver disease (NAFLD). It was proved that gut microbiome plays a role in the development of NAFLD. This study aims to observe the therapeutic effect of liraglutide on nonalcoholic fatty liver (NAFL) in mice and effect on the gut microbial community. MAIN METHODS The db/db mice were used as the NAFL model, and lactulose was used as the positive control drug. Hepatic triglyceride, liver histopathology, and indices of glucolipid metabolism, including fasting blood glucose, fasting insulin, insulin resistance index and blood lipids were evaluated after treatment of liraglutide or lactulose for four weeks. The colonic microbiome of the mice was analyzed by 16S rRNA gene sequencing. KEY FINDINGS Liraglutide significantly reduced the hepatic triglyceride (TG) content, alanine aminotransferase (ALT) activity, fasting blood glucose, insulin resistance and serum low density lipoprotein (LDL) in the db/db mice. In terms of hepatic pathologies, hepatic steatosis was significantly improved after liraglutide treating. Microbiome analysis revealed that liraglutide significantly increased the abundance of Akkermansia, Romboutsia, norank_f_Bacteroidales_S24-7_group, and decreased the abundance of Klebsiella, Anaerotruncus, Bacteroides, Lachnospiraceae_UCG-001, Lachnospiraceae_NK4A136_group, Ruminiclostridium, uncultured_f__Ruminococcaceae, and Desulfovibrio. SIGNIFICANCE The results of the present study suggested that liraglutide had a certain therapeutic effect on fatty liver in db/db mice and had an impact on the composition of the intestinal microflora, especially some bacteria related to glucolipid metabolism and intestinal inflammation. Affecting gut microbiome might be a potential mechanism of liraglutide in treating NAFL.
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Affiliation(s)
- Qian Liu
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China; Baoshan District Hospital of Integrated Traditional Chinese Medicine of Shanghai, Shanghai 201900, China
| | - Bei-Yu Cai
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China
| | - Li-Xin Zhu
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 510655, China
| | - Xin Xin
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China
| | - Xin Wang
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China
| | - Zi-Ming An
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China
| | - Shuang Li
- Baoshan District Hospital of Integrated Traditional Chinese Medicine of Shanghai, Shanghai 201900, China.
| | - Yi-Yang Hu
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China.
| | - Qin Feng
- Shuguang Hospital Affliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203,China.
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Sanz‐Garcia C, McMullen MR, Chattopadhyay S, Roychowdhury S, Sen G, Nagy LE. Nontranscriptional Activity of Interferon Regulatory Factor 3 Protects Mice From High-Fat Diet-Induced Liver Injury. Hepatol Commun 2019; 3:1626-1641. [PMID: 31832571 PMCID: PMC6887899 DOI: 10.1002/hep4.1441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/26/2019] [Indexed: 12/17/2022] Open
Abstract
Interferon regulatory factor 3 (IRF3) has both transcriptional and nontranscriptional functions. Transcriptional activity is dependent on serine phosphorylation of IRF3, while transcription-independent IRF3-mediated apoptosis requires ubiquitination. IRF3 also binds to inhibitor of nuclear factor kappa B kinase (IKKβ) in the cytosol, restricting nuclear translocation of p65. IRF3-deficient mice are highly sensitive to high-fat diet (HFD)-induced liver injury; however, it is not known if transcriptional and/or nontranscriptional activity of IRF3 confers protection. Using a mouse model only expressing nontranscriptional functions of IRF3 (Irf3 S1/S1), we tested the hypothesis that nontranscriptional activity of IRF3 protects mice from HFD-induced liver injury. C57BL/6, Irf3 -/-, and Irf3 S1/S1 mice were fed an HFD for 12 weeks. In C57BL/6 mice, the HFD increased expression of interferon (IFN)-dependent genes, despite a decrease in IRF3 protein in the liver. The HFD had no impact on IFN-dependent gene expression Irf3 -/- or Irf3 S1/S1 mice, both lacking IRF3 transcriptional activity. Liver injury, apoptosis, and fibrosis were exacerbated in Irf3 -/- compared to C57BL/6 mice following the HFD; this increase was ameliorated in Irf3 S1/S1 mice. Similarly, expression of inflammatory cytokines as well as numbers of neutrophils and infiltrating monocytes was increased in Irf3 -/- mice compared to C57BL/6 and Irf3 S1/S1 mice. While the HFD increased the ubiquitination of IRF3, a response associated with IRF3-mediated apoptosis, in Irf3 S1/S1 mice, protection from liver injury was not due to differences in apoptosis of hepatocytes or immune cells. Instead, protection from HFD-induced liver injury in Irf3 S1/S1 mice was primarily associated with retardation of nuclear translocation of p65 and decreased expression of nuclear factor kappa B (NFκB)-dependent inflammatory cytokines. Conclusion: Taken together, these data identify important contributions of the nontranscriptional function of IRF3, likely by reducing NFκB signaling, in dampening the hepatic inflammatory environment in response to an HFD.
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Affiliation(s)
- Carlos Sanz‐Garcia
- Department of Inflammation and ImmunityLerner Research InstituteCleveland ClinicClevelandOH
| | - Megan R. McMullen
- Department of Inflammation and ImmunityLerner Research InstituteCleveland ClinicClevelandOH
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and ImmunologyUniversity of Toledo College of Medicine and Life SciencesToledoOH
| | - Sanjoy Roychowdhury
- Department of Inflammation and ImmunityLerner Research InstituteCleveland ClinicClevelandOH
- Department of Molecular MedicineCase Western Reserve UniversityClevelandOH
| | - Ganes Sen
- Department of Inflammation and ImmunityLerner Research InstituteCleveland ClinicClevelandOH
- Department of Molecular MedicineCase Western Reserve UniversityClevelandOH
| | - Laura E. Nagy
- Department of Inflammation and ImmunityLerner Research InstituteCleveland ClinicClevelandOH
- Department of Molecular MedicineCase Western Reserve UniversityClevelandOH
- Gastroenterology and HepatologyLerner Research InstituteCleveland ClinicClevelandOH
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Fu S, Zhang L, Lv J, Zhu B, Wang W, Wang X. Two main stream methods analysis and visual 3D genome architecture. Semin Cell Dev Biol 2019; 90:43-53. [DOI: 10.1016/j.semcdb.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 01/07/2023]
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Lv J, Bhatia M, Wang X. Roles of Mitochondrial DNA in Energy Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1038:71-83. [PMID: 29178070 DOI: 10.1007/978-981-10-6674-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Mitochondria are independent double-membrane organelles responsible for energy production, specifically by completing oxidative phosphorylation. Mitochondria are essential to regulate energy metabolism, signaling pathways, and cell death. Mitochondrial DNA (mtDNA) can be altered by metabolic disorders, oxidative stress, or inflammation in the progression and development of various diseases. In this chapter, we overview the role of mtDNA in energy metabolism and the diseases that are associated with mtDNA abnormality, with a special focus on the major factors which regulate the mechanism of mtDNA in metabolism.
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Affiliation(s)
- Jiapei Lv
- Zhongshan Hospital Institute of Fudan University, Shanghai Medical School, Shanghai, China
| | - Madhav Bhatia
- Department of Pathology, University of Otago, Wellington, New Zealand
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
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Abstract
OBJECTIVE Obesity and insulin resistance play important roles in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Mg intake is linked to a reduced risk of metabolic syndrome and insulin resistance; people with NAFLD or alcoholic liver disease are at high risk of Mg deficiency. The present study aimed to investigate whether Mg and Ca intakes were associated with risk of fatty liver disease and prediabetes by alcohol drinking status. DESIGN We analysed the association between Ca or Mg intake and fatty liver disease, prediabetes or both prediabetes and fatty liver disease in cross-sectional analyses. SETTING Third National Health and Nutrition Examination Survey (NHANES III) follow-up cohort of US adults. SUBJECTS Nationally representative sample of US adults in NHANES (n 13 489). RESULTS After adjusting for potential confounders, Mg intake was associated with approximately 30 % reduced odds of fatty liver disease and prediabetes, comparing the highest intake quartile v. the lowest. Mg intake may only be related to reduced odds of fatty liver disease and prediabetes in those whose Ca intake is less than 1200 mg/d. Mg intake may also only be associated with reduced odds of fatty liver disease among alcohol drinkers. CONCLUSIONS The study suggests that high intake of Mg may be associated with reduced risks of fatty liver disease and prediabetes. Further large studies, particularly prospective cohort studies, are warranted to confirm the findings.
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Zhong HH, Hu SJ, Yu B, Jiang SS, Zhang J, Luo D, Yang MW, Su WY, Shao YL, Deng HL, Hong FF, Yang SL. Apoptosis in the aging liver. Oncotarget 2017; 8:102640-102652. [PMID: 29254277 PMCID: PMC5731987 DOI: 10.18632/oncotarget.21123] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/15/2017] [Indexed: 12/11/2022] Open
Abstract
Various changes in the liver during aging can reduce hepatic function and promote liver injury. Aging is associated with high morbidity and a poor prognosis in patients with various liver diseases, including nonalcoholic fatty liver disease, hepatitis C and liver cancer, as well as with surgeries such as partial hepatectomy and liver transplantation. In addition, apoptosis increases with liver aging. Because apoptosis is involved in regeneration, fibrosis and cancer prevention during liver aging, and restoration of the appropriate level of apoptosis can alleviate the adverse effects of liver aging, it is important to understand the mechanisms underlying this process. Herein, we elaborate on the causes of apoptosis during liver aging, with a focus on oxidative stress, genomic instability, lipotoxicity, endoplasmic reticulum stress, dysregulation of nutrient sensing, and liver stem/progenitor cell activity.
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Affiliation(s)
- Hua-Hua Zhong
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Shao-Jie Hu
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Bo Yu
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Sha-Sha Jiang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Jin Zhang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Dan Luo
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Mei-Wen Yang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Wan-Ying Su
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Ya-Lan Shao
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Hao-Lin Deng
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Fen-Fang Hong
- Department of Experimental Teaching Center, Nanchang University, Nanchang 330031, China
| | - Shu-Long Yang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
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Mitochondrial DNA Methylation and Related Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:117-132. [DOI: 10.1007/978-981-10-6674-0_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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