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Wernberg CW, Ravnskjaer K, Lauridsen MM, Thiele M. The Role of Diagnostic Biomarkers, Omics Strategies, and Single-Cell Sequencing for Nonalcoholic Fatty Liver Disease in Severely Obese Patients. J Clin Med 2021; 10:930. [PMID: 33804302 PMCID: PMC7957539 DOI: 10.3390/jcm10050930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/29/2022] Open
Abstract
Liver disease due to metabolic dysfunction constitute a worldwide growing health issue. Severe obesity is a particularly strong risk factor for non-alcoholic fatty liver disease, which affects up to 93% of these patients. Current diagnostic markers focus on the detection of advanced fibrosis as the major predictor of liver-related morbidity and mortality. The most accurate diagnostic tools use elastography to measure liver stiffness, with diagnostic accuracies similar in normal-weight and severely obese patients. The effectiveness of elastography tools are however hampered by limitations to equipment and measurement quality in patients with very large abdominal circumference and subcutaneous fat. Blood-based biomarkers are therefore attractive, but those available to date have only moderate diagnostic accuracy. Ongoing technological advances in omics technologies such as genomics, transcriptomics, and proteomics hold great promise for discovery of biomarkers and increased pathophysiological understanding of non-alcoholic liver disease and steatohepatitis. Very recent developments have allowed for single-cell sequencing and cell-type resolution of gene expression and function. In the near future, we will therefore likely see a multitude of breakthrough biomarkers, developed from a deepened understanding of the biological function of individual cell types in the healthy and injured liver.
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Affiliation(s)
- Charlotte W. Wernberg
- Department of Gastroenterology and Hepatology, Hospital Southwest of Jutland, 6700 Esbjerg, Denmark; (C.W.W.); (M.M.L.)
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of Southern Denmark, 5230 Odense, Denmark;
| | - Kim Ravnskjaer
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of Southern Denmark, 5230 Odense, Denmark;
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Mette M. Lauridsen
- Department of Gastroenterology and Hepatology, Hospital Southwest of Jutland, 6700 Esbjerg, Denmark; (C.W.W.); (M.M.L.)
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of Southern Denmark, 5230 Odense, Denmark;
| | - Maja Thiele
- Center for Functional Genomics and Tissue Plasticity (ATLAS), University of Southern Denmark, 5230 Odense, Denmark;
- Center for Liver Research, Department of Hepatology and Gastroenterology, Odense University Hospital, 5000 Odense, Denmark
- Institute for Clinical Research, University of Southern Denmark, 5230 Odense, Denmark
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Zhang C, Bjornson E, Arif M, Tebani A, Lovric A, Benfeitas R, Ozcan M, Juszczak K, Kim W, Kim JT, Bidkhori G, Ståhlman M, Bergh P, Adiels M, Turkez H, Taskinen M, Bosley J, Marschall H, Nielsen J, Uhlén M, Borén J, Mardinoglu A. The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease. Mol Syst Biol 2020; 16:e9495. [PMID: 32337855 PMCID: PMC7184219 DOI: 10.15252/msb.209495] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase dramatically, and there is no approved medication for its treatment. Recently, we predicted the underlying molecular mechanisms involved in the progression of NAFLD using network analysis and identified metabolic cofactors that might be beneficial as supplements to decrease human liver fat. Here, we first assessed the tolerability of the combined metabolic cofactors including l-serine, N-acetyl-l-cysteine (NAC), nicotinamide riboside (NR), and l-carnitine by performing a 7-day rat toxicology study. Second, we performed a human calibration study by supplementing combined metabolic cofactors and a control study to study the kinetics of these metabolites in the plasma of healthy subjects with and without supplementation. We measured clinical parameters and observed no immediate side effects. Next, we generated plasma metabolomics and inflammatory protein markers data to reveal the acute changes associated with the supplementation of the metabolic cofactors. We also integrated metabolomics data using personalized genome-scale metabolic modeling and observed that such supplementation significantly affects the global human lipid, amino acid, and antioxidant metabolism. Finally, we predicted blood concentrations of these compounds during daily long-term supplementation by generating an ordinary differential equation model and liver concentrations of serine by generating a pharmacokinetic model and finally adjusted the doses of individual metabolic cofactors for future human clinical trials.
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Affiliation(s)
- Cheng Zhang
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
- School of Pharmaceutical SciencesZhengzhou UniversityZhengzhouChina
| | - Elias Bjornson
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University Hospital GothenburgGothenburgSweden
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Muhammad Arif
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Abdellah Tebani
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Alen Lovric
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
- Present address:
Division of Clinical PhysiologyDepartment of Laboratory MedicineKarolinska InstitutetKarolinska University HospitalStockholmSweden
- Present address:
Unit of Clinical PhysiologyKarolinska University HospitalStockholmSweden
| | - Rui Benfeitas
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
- Present address:
Science for Life LaboratoryDepartment of Biochemistry and BiophysicsNational Bioinformatics Infrastructure Sweden (NBIS)Stockholm UniversityStockholmSweden
| | - Mehmet Ozcan
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Kajetan Juszczak
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Woonghee Kim
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Jung Tae Kim
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Gholamreza Bidkhori
- Centre for Host‐Microbiome InteractionsFaculty of Dentistry, Oral & Craniofacial SciencesKing's College LondonLondonUK
| | - Marcus Ståhlman
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University Hospital GothenburgGothenburgSweden
| | - Per‐Olof Bergh
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University Hospital GothenburgGothenburgSweden
| | - Martin Adiels
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University Hospital GothenburgGothenburgSweden
| | - Hasan Turkez
- Department of Medical BiologyFaculty of MedicineAtatürk UniversityErzurumTurkey
| | - Marja‐Riitta Taskinen
- Research Programs Unit, Diabetes and ObesityDepartment of Internal MedicineHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | | | - Hanns‐Ulrich Marschall
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University Hospital GothenburgGothenburgSweden
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Mathias Uhlén
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
| | - Jan Borén
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University Hospital GothenburgGothenburgSweden
| | - Adil Mardinoglu
- Science for Life LaboratoryKTH—Royal Institute of TechnologyStockholmSweden
- Centre for Host‐Microbiome InteractionsFaculty of Dentistry, Oral & Craniofacial SciencesKing's College LondonLondonUK
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Mato JM, Alonso C, Noureddin M, Lu SC. Biomarkers and subtypes of deranged lipid metabolism in non-alcoholic fatty liver disease. World J Gastroenterol 2019; 25:3009-3020. [PMID: 31293337 PMCID: PMC6603806 DOI: 10.3748/wjg.v25.i24.3009] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/06/2019] [Accepted: 05/18/2019] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a heterogeneous and complex disease that is imprecisely diagnosed by liver biopsy. NAFLD covers a spectrum that ranges from simple steatosis, nonalcoholic steatohepatitis (NASH) with varying degrees of fibrosis, to cirrhosis, which is a major risk factor for hepatocellular carcinoma. Lifestyle and eating habit changes during the last century have made NAFLD the most common liver disease linked to obesity, type 2 diabetes mellitus and dyslipidemia, with a global prevalence of 25%. NAFLD arises when the uptake of fatty acids (FA) and triglycerides (TG) from circulation and de novo lipogenesis saturate the rate of FA β-oxidation and very-low density lipoprotein (VLDL)-TG export. Deranged lipid metabolism is also associated with NAFLD progression from steatosis to NASH, and therefore, alterations in liver and serum lipidomic signatures are good indicators of the disease’s development and progression. This review focuses on the importance of the classification of NAFLD patients into different subtypes, corresponding to the main alteration(s) in the major pathways that regulate FA homeostasis leading, in each case, to the initiation and progression of NASH. This concept also supports the targeted intervention as a key approach to maximize therapeutic efficacy and opens the door to the development of precise NASH treatments.
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Affiliation(s)
- José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, Derio 48160, Bizkaia, Spain
| | - Cristina Alonso
- OWL Metabolomics, Technology Park of Bizkaia, Derio 48160, Bizkaia, Spain
| | - Mazen Noureddin
- Division of Digestive and Liver Diseases, Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Shelly C Lu
- Division of Digestive and Liver Diseases, Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
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The OMICs Window into Nonalcoholic Fatty Liver Disease (NAFLD). Metabolites 2019; 9:metabo9020025. [PMID: 30717274 PMCID: PMC6409793 DOI: 10.3390/metabo9020025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/26/2019] [Accepted: 01/30/2019] [Indexed: 12/17/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common cause of hepatic abnormalities worldwide. Nonalcoholic steatohepatitis (NASH) is part of the spectrum of NAFLD and leads to progressive liver disease, such as cirrhosis and hepatocellular carcinoma. In NASH patient, fibrosis represents the major predictor of liver-related mortality; therefore, it is important to have an early and accurate diagnosis of NASH. The current gold standard for the diagnosis of NASH is still liver biopsy. The development of biomarkers able to predict disease severity, prognosis, as well as response to therapy without the need for a biopsy is the focus of most up-to-date genomic, transcriptomic, proteomic, and metabolomic research. In the future, patients might be diagnosed and treated according to their molecular signatures. In this short review, we discuss how information from genomics, proteomics, and metabolomics contribute to the understanding of NAFLD pathogenesis.
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Mardinoglu A, Boren J, Smith U, Uhlen M, Nielsen J. Systems biology in hepatology: approaches and applications. Nat Rev Gastroenterol Hepatol 2018; 15:365-377. [PMID: 29686404 DOI: 10.1038/s41575-018-0007-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Detailed insights into the biological functions of the liver and an understanding of its crosstalk with other human tissues and the gut microbiota can be used to develop novel strategies for the prevention and treatment of liver-associated diseases, including fatty liver disease, cirrhosis, hepatocellular carcinoma and type 2 diabetes mellitus. Biological network models, including metabolic, transcriptional regulatory, protein-protein interaction, signalling and co-expression networks, can provide a scaffold for studying the biological pathways operating in the liver in connection with disease development in a systematic manner. Here, we review studies in which biological network models were used to integrate multiomics data to advance our understanding of the pathophysiological responses of complex liver diseases. We also discuss how this mechanistic approach can contribute to the discovery of potential biomarkers and novel drug targets, which might lead to the design of targeted and improved treatment strategies. Finally, we present a roadmap for the successful integration of models of the liver and other human tissues with the gut microbiota to simulate whole-body metabolic functions in health and disease.
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Affiliation(s)
- Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden. .,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ulf Smith
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jens Nielsen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Benfeitas R, Uhlen M, Nielsen J, Mardinoglu A. New Challenges to Study Heterogeneity in Cancer Redox Metabolism. Front Cell Dev Biol 2017; 5:65. [PMID: 28744456 PMCID: PMC5504267 DOI: 10.3389/fcell.2017.00065] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) are important pathophysiological molecules involved in vital cellular processes. They are extremely harmful at high concentrations because they promote the generation of radicals and the oxidation of lipids, proteins, and nucleic acids, which can result in apoptosis. An imbalance of ROS and a disturbance of redox homeostasis are now recognized as a hallmark of complex diseases. Considering that ROS levels are significantly increased in cancer cells due to mitochondrial dysfunction, ROS metabolism has been targeted for the development of efficient treatment strategies, and antioxidants are used as potential chemotherapeutic drugs. However, initial ROS-focused clinical trials in which antioxidants were supplemented to patients provided inconsistent results, i.e., improved treatment or increased malignancy. These different outcomes may result from the highly heterogeneous redox responses of tumors in different patients. Hence, population-based treatment strategies are unsuitable and patient-tailored therapeutic approaches are required for the effective treatment of patients. Moreover, due to the crosstalk between ROS, reducing equivalents [e.g., NAD(P)H] and central metabolism, which is heterogeneous in cancer, finding the best therapeutic target requires the consideration of system-wide approaches that are capable of capturing the complex alterations observed in all of the associated pathways. Systems biology and engineering approaches may be employed to overcome these challenges, together with tools developed in personalized medicine. However, ROS- and redox-based therapies have yet to be addressed by these methodologies in the context of disease treatment. Here, we review the role of ROS and their coupled redox partners in tumorigenesis. Specifically, we highlight some of the challenges in understanding the role of hydrogen peroxide (H2O2), one of the most important ROS in pathophysiology in the progression of cancer. We also discuss its interplay with antioxidant defenses, such as the coupled peroxiredoxin/thioredoxin and glutathione/glutathione peroxidase systems, and its reducing equivalent metabolism. Finally, we highlight the need for system-level and patient-tailored approaches to clarify the roles of these systems and identify therapeutic targets through the use of the tools developed in personalized medicine.
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Affiliation(s)
- Rui Benfeitas
- Science for Life Laboratory, KTH Royal Institute of TechnologyStockholm, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH Royal Institute of TechnologyStockholm, Sweden
| | - Jens Nielsen
- Science for Life Laboratory, KTH Royal Institute of TechnologyStockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH Royal Institute of TechnologyStockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden
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