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Detailed Characterization of Small Extracellular Vesicles from Different Cell Types Based on Tetraspanin Composition by ExoView R100 Platform. Int J Mol Sci 2022; 23:ijms23158544. [PMID: 35955677 PMCID: PMC9369185 DOI: 10.3390/ijms23158544] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
Small extracellular vesicles (sEV) hold enormous potential as biomarkers, drug carriers, and therapeutic agents. However, due to previous limitations in the phenotypic characterization of sEV at the single vesicle level, knowledge of cell type-specific sEV signatures remains sparse. With the introduction of next-generation sEV analysis devices, such as the single-particle interferometric reflectance imaging sensor (SP-IRIS)-based ExoView R100 platform, single sEV analyses are now possible. While the tetraspanins CD9, CD63, and CD81 were generally considered pan-sEV markers, it became clear that sEV of different cell types contain several combinations and amounts of these proteins on their surfaces. To gain better insight into the complexity and heterogeneity of sEV, we used the ExoView R100 platform to analyze the CD9/CD63/CD81 phenotype of sEV released by different cell types at a single sEV level. We demonstrated that these surface markers are sufficient to distinguish cell-type-specific sEV phenotypes. Furthermore, we recognized that tetraspanin composition in some sEV populations does not follow a random pattern. Notably, the tetraspanin distribution of sEV derived from mesenchymal stem cells (MSCs) alters depending on cell culture conditions. Overall, our data provide an overview of the cell-specific characteristics of sEV populations, which will increase the understanding of sEV physiology and improve the development of new sEV-based therapeutic approaches.
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2
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Elsayed AK, Vimalraj S, Nandakumar M, Abdelalim EM. Insulin resistance in diabetes: The promise of using induced pluripotent stem cell technology. World J Stem Cells 2021; 13:221-235. [PMID: 33815671 PMCID: PMC8006014 DOI: 10.4252/wjsc.v13.i3.221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/07/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
Insulin resistance (IR) is associated with several metabolic disorders, including type 2 diabetes (T2D). The development of IR in insulin target tissues involves genetic and acquired factors. Persons at genetic risk for T2D tend to develop IR several years before glucose intolerance. Several rodent models for both IR and T2D are being used to study the disease pathogenesis; however, these models cannot recapitulate all the aspects of this complex disorder as seen in each individual. Human pluripotent stem cells (hPSCs) can overcome the hurdles faced with the classical mouse models for studying IR. Human induced pluripotent stem cells (hiPSCs) can be generated from the somatic cells of the patients without the need to destroy a human embryo. Therefore, patient-specific hiPSCs can generate cells genetically identical to IR individuals, which can help in distinguishing between genetic and acquired defects in insulin sensitivity. Combining the technologies of genome editing and hiPSCs may provide important information about the genetic factors underlying the development of different forms of IR. Further studies are required to fill the gaps in understanding the pathogenesis of IR and diabetes. In this review, we summarize the factors involved in the development of IR in the insulin-target tissues leading to diabetes. Also, we highlight the use of hPSCs to understand the mechanisms underlying the development of IR.
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Affiliation(s)
- Ahmed K Elsayed
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | | | - Manjula Nandakumar
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Essam M Abdelalim
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
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3
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Larsen LE, Smith MA, Abbey D, Korn A, Reeskamp LF, Hand NJ, Holleboom AG. Hepatocyte-like cells derived from induced pluripotent stem cells: A versatile tool to understand lipid disorders. Atherosclerosis 2020; 303:8-14. [PMID: 32460140 DOI: 10.1016/j.atherosclerosis.2020.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/19/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Dyslipidemias are strongly linked to the development of atherosclerotic cardiovascular disease. Most dyslipidemias find their origin in the liver. In recent years, the differentiation of induced pluripotent stem cells (iPSCs) into hepatocyte-like cells has provided a versatile platform for the functional study of various dyslipidemias, both rare genetic dyslipidemia as well as common lipid disorders associated with insulin resistance or non-alcoholic fatty liver disease. In addition, iPSC-derived hepatocytes can serve as a cell model for developing novel lipid lowering therapies and have the potential of regenerative medicine. This review provides an overview of these developments.
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Affiliation(s)
- Lars E Larsen
- Department of Experimental Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Mikhaila A Smith
- Departments of Genetics and Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Deepti Abbey
- Departments of Genetics and Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Amber Korn
- Department of Experimental Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands; Department of Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Laurens F Reeskamp
- Department of Experimental Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands; Department of Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Nicholas J Hand
- Departments of Genetics and Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA.
| | - Adriaan G Holleboom
- Department of Experimental Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands; Department of Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands.
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4
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Baranova A, Maltseva D, Tonevitsky A. Adipose may actively delay progression of NAFLD by releasing tumor-suppressing, anti-fibrotic miR-122 into circulation. Obes Rev 2019; 20:108-118. [PMID: 30248223 DOI: 10.1111/obr.12765] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common liver pathology. Here we propose tissue-cooperative, homeostatic model of NAFLD. During early stages of NAFLD the intrahepatic production of miR-122 falls, while the secretion of miRNA-containing exosomes by adipose increases. Bloodstream carries exosome to the liver, where their miRNA cargo is released to regulate their intrahepatic targets. When the deterioration of adipose catches up with the failing hepatic parenchyma, the external supply of liver-supporting miRNAs gradually tapers off, leading to the fibrotic decompensation of the liver and an increase in hepatic carcinogenesis. This model may explain paradoxical observations of the disease-associated decrease in intrahepatic production of certain miRNAs with an increase in their levels in serum. Infusions of miR-122 and, possibly, some other miRNAs may be efficient for preventing NAFLD-associated hepatocellular carcinoma. The best candidates for exosome-wrapped miRNA producer are adipose tissue-derived mesenchymal stem cells (MSCs), known for their capacity to shed large amounts of exosomes into the media. Notably, MSC-derived exosomes with no specific loading are already tested in patients with liver fibrosis. Carrier exosomes may be co-manufactured along with their cargo. Exosome-delivered miRNA cocktails may augment functioning of human organs suffering from a variety of chronic diseases.
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Affiliation(s)
- A Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, USA.,Research Center for Medical Genetics, Moscow, Russia
| | - D Maltseva
- Department of Fundamental Medicine, School of Biomedicine, Far Eastern Federal University (FEFU), Vladivostok, Russia.,Scientific Research Center Bioclinicum (SRC Bioclinicum), Moscow, Russia
| | - A Tonevitsky
- Scientific Research Center Bioclinicum (SRC Bioclinicum), Moscow, Russia.,Higher School of Economics, Moscow, Russia
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5
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Wu T, Li K, Yi D, Wang L, Zhao D, Lv Y, Zhang L, Chen H, Ding B, Hou Y, Wu G. Dietary Supplementation with Trihexanoin Enhances Intestinal Function of Weaned Piglets. Int J Mol Sci 2018; 19:ijms19103277. [PMID: 30360365 PMCID: PMC6213997 DOI: 10.3390/ijms19103277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 12/01/2022] Open
Abstract
Trihexanoin is a short-chain triglyceride (SCT). Many studies have reported that SCTs play important roles in the maintenance of intestinal epithelial structure and function. The present work was to investigate the effects of trihexanoin on growth performance, carbohydrate and fat metabolism, as well as intestinal morphology and function in weaned piglets. Twenty weaned piglets (21 ± 2 d) were randomly allocated to one of two treatment groups: The control group (basal diet supplemented with 0.5% soya oil); the TH group (basal diet supplemented with 0.5% trihexanoin). Dietary trihexanoin supplementation significantly reduced diarrhea rate; increased the concentrations of LDL, HDL and total protein in plasma; decreased cholesterol concentrations and glutamyl transpeptidase activity in plasma; improved intestinal morphologic structure; altered the mRNA levels and abundances of proteins related to glycogen and fat metabolism, mucosal barrier function, antioxidant capacity and water transport capacity; and altered the community of intestinal microflora. These results indicate that dietary trihexanoin supplementation could reduce diarrhea, regulate carbohydrate and fat metabolism, exert beneficial effects on the intestinal mucosal barrier, protect the intestinal mucosa from injuries, improve intestinal transport and absorption, and enhance antioxidant capacity. In conclusion, dietary supplementation with 0.5% trihexanoin improves the intestinal function and health of weaned piglets.
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Affiliation(s)
- Tao Wu
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Kang Li
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Dan Yi
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Lei Wang
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Di Zhao
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Yang Lv
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Lin Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Hongbo Chen
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Binying Ding
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Yongqing Hou
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Guoyao Wu
- Engineering Research Center of Feed Protein Resources on Agricultural By-products, Ministry of Education, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
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Aguayo-Orozco A, Bois FY, Brunak S, Taboureau O. Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity. Front Genet 2018; 9:396. [PMID: 30279702 PMCID: PMC6153316 DOI: 10.3389/fgene.2018.00396] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) represents a wide spectrum of disease, ranging from simple fatty liver through steatosis with inflammation and necrosis to cirrhosis. One of the most challenging problems in biomedical research and within the chemical industry is to understand the underlying mechanisms of complex disease, and complex adverse outcome pathways (AOPs). Based on a set of 28 steatotic chemicals with gene expression data measured on primary hepatocytes at three times (2, 8, and 24 h) and three doses (low, medium, and high), we identified genes and pathways, defined as molecular initiating events (MIEs) and key events (KEs) of steatosis using a combination of a time series and pathway analyses. Among the genes deregulated by these compounds, the study highlighted OSBPL9, ALDH7A1, MYADM, SLC51B, PRDX6, GPAT3, TMEM135, DLGDA5, BCO2, APO10LA, TSPAN6, NEURL1B, and DUSP1. Furthermore, pathway analysis indicated deregulation of pathways related to lipid accumulation, such as fat digestion and absorption, linoleic and linolenic acid metabolism, calcium signaling pathway, fatty acid metabolism, peroxisome, retinol metabolism, and steroid metabolic pathways in a time dependent manner. Such transcription profile analysis can help in the understanding of the steatosis evolution over time generated by chemical exposure.
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Affiliation(s)
- Alejandro Aguayo-Orozco
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederic Yves Bois
- Institut National de l'Environnement Industriel et des Risques (INERIS), Unité Modèles pour l'Ecotoxicologie et la Toxicologie (METO), Verneuil en Halatte, France
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Olivier Taboureau
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,UMRS 973 INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
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7
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Boeckmans J, Natale A, Buyl K, Rogiers V, De Kock J, Vanhaecke T, Rodrigues RM. Human-based systems: Mechanistic NASH modelling just around the corner? Pharmacol Res 2018; 134:257-267. [PMID: 29964161 DOI: 10.1016/j.phrs.2018.06.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023]
Abstract
Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by excessive triglyceride accumulation in the liver accompanied by inflammation, cell stress and apoptosis. It is the tipping point to the life-threatening stages of non-alcoholic fatty liver disease (NAFLD). Despite the high prevalence of NASH, up to five percent of the global population, there are currently no approved drugs to treat this disease. Animal models, mostly based on specific diets and genetic modifications, are often employed in anti-NASH drug development. However, due to interspecies differences and artificial pathogenic conditions, they do not represent the human situation accurately and are inadequate for testing the efficacy and safety of potential new drugs. Human-based in vitro models provide a more legitimate representation of the human NASH pathophysiology and can be used to investigate the dysregulation of cellular functions associated with the disease. Also in silico methodologies and pathway-based approaches using human datasets, may contribute to a more accurate representation of NASH, thereby facilitating the quest for new anti-NASH drugs. In this review, we describe the molecular components of NASH and how human-based tools can contribute to unraveling the pathogenesis of this disease and be used in anti-NASH drug development. We also propose a roadmap for the development and application of human-based approaches for future investigation of NASH.
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Affiliation(s)
- Joost Boeckmans
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Alessandra Natale
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Karolien Buyl
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Vera Rogiers
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Joery De Kock
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Tamara Vanhaecke
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Robim M Rodrigues
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
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8
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Hosoya M, Czysz K. Translational Prospects and Challenges in Human Induced Pluripotent Stem Cell Research in Drug Discovery. Cells 2016; 5:cells5040046. [PMID: 28009813 PMCID: PMC5187530 DOI: 10.3390/cells5040046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/27/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Despite continuous efforts to improve the process of drug discovery and development, achieving success at the clinical stage remains challenging because of a persistent translational gap between the preclinical and clinical settings. Under these circumstances, the discovery of human induced pluripotent stem (iPS) cells has brought new hope to the drug discovery field because they enable scientists to humanize a variety of pharmacological and toxicological models in vitro. The availability of human iPS cell-derived cells, particularly as an alternative for difficult-to-access tissues and organs, is increasing steadily; however, their use in the field of translational medicine remains challenging. Biomarkers are an essential part of the translational effort to shift new discoveries from bench to bedside as they provide a measurable indicator with which to evaluate pharmacological and toxicological effects in both the preclinical and clinical settings. In general, during the preclinical stage of the drug development process, in vitro models that are established to recapitulate human diseases are validated by using a set of biomarkers; however, their translatability to a clinical setting remains problematic. This review provides an overview of current strategies for human iPS cell-based drug discovery from the perspective of translational research, and discusses the importance of early consideration of clinically relevant biomarkers.
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Affiliation(s)
- Masaki Hosoya
- Integrated Technology Research Laboratories, Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Katherine Czysz
- Integrated Technology Research Laboratories, Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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9
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Characterization of iPSCs derived from dermal fibroblasts from a healthy 19year old female. Stem Cell Res 2016; 17:597-599. [PMID: 27934589 DOI: 10.1016/j.scr.2016.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/18/2016] [Indexed: 11/20/2022] Open
Abstract
Primary fibroblasts from a healthy 19years old female were reprogrammed by transduction of retroviruses OCT4, SOX2, c-MYC and KLF4. iPSCs were characterized by immunocytochemistry, embryonic body-formation, DNA-fingerprint and karyotype analysis and comparative transcriptome analyses with the human embryonic stem cell line H1 revealed a Pearsons correlation coefficient of 0.8952.
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10
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Graffmann N, Ring S, Kawala MA, Wruck W, Ncube A, Trompeter HI, Adjaye J. Modeling Nonalcoholic Fatty Liver Disease with Human Pluripotent Stem Cell-Derived Immature Hepatocyte-Like Cells Reveals Activation of PLIN2 and Confirms Regulatory Functions of Peroxisome Proliferator-Activated Receptor Alpha. Stem Cells Dev 2016; 25:1119-33. [PMID: 27308945 PMCID: PMC4971413 DOI: 10.1089/scd.2015.0383] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD/steatosis) is a metabolic disease characterized by the incorporation of fat into hepatocytes. In this study, we developed an in vitro model for NAFLD based on hepatocyte-like cells (HLCs) differentiated from human pluripotent stem cells. We induced fat storage in these HLCs and detected major expression changes of metabolism-associated genes, as well as an overall reduction of liver-related microRNAs. We observed an upregulation of the lipid droplet coating protein Perilipin 2 (PLIN2), as well as of numerous genes of the peroxisome proliferator-activated receptor (PPAR) pathway, which constitutes a regulatory hub for metabolic processes. Interference with PLIN2 and PPARα resulted in major alterations in gene expression, especially affecting lipid, glucose, and purine metabolism. Our model recapitulates many metabolic changes that are characteristic for NAFLD. It permits the dissection of disease-promoting molecular pathways and allows us to investigate the influences of distinct genetic backgrounds on disease progression.
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Affiliation(s)
- Nina Graffmann
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Sarah Ring
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Marie-Ann Kawala
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Wasco Wruck
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Audrey Ncube
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Hans-Ingo Trompeter
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - James Adjaye
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
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11
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Wruck W, Graffmann N, Kawala MA, Adjaye J. Concise Review: Current Status and Future Directions on Research Related to Nonalcoholic Fatty Liver Disease. Stem Cells 2016; 35:89-96. [PMID: 27374784 DOI: 10.1002/stem.2454] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/27/2016] [Accepted: 06/18/2016] [Indexed: 02/06/2023]
Abstract
Considered a feature of the metabolic syndrome, nonalcoholic fatty liver disease (NAFLD), is associated with insulin resistance, type 2 diabetes, obesity and drug toxicity. Its prevalence is estimated at about 30% in western countries mainly due to sedentary life styles and high fat diets. Genome-wide association studies have identified polymorphisms in several genes, for example, PNPLA3, and TM6SF2 which confer susceptibility to NAFLD. Here, we review recent findings in the NAFLD field with a particular focus on published transcriptomics datasets which we subject to a meta-analysis. We reveal a common gene signature correlating with the progression of the disease from steatosis and steatohepatitis and reveal that lipogenic and cholesterol metabolic pathways are main actors in this signature. We propose the use of disease-in-a-dish models based on hepatocyte-like cells derived from patient-specific induced pluripotent stem cells (iPSC). These will enable investigations into the contribution of genetic background in the progression from NALFD to non-alcoholic steatohepatitis. Furthermore, an iPSC-based approach should aid in the elucidation of the function of new biomarkers, thus enabling better diagnostic tests and validation of potential drug targets. Stem Cells 2017;35:89-96.
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Affiliation(s)
- Wasco Wruck
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Nina Graffmann
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Marie-Ann Kawala
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - James Adjaye
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf, Germany
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12
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Wruck W, Kashofer K, Rehman S, Daskalaki A, Berg D, Gralka E, Jozefczuk J, Drews K, Pandey V, Regenbrecht C, Wierling C, Turano P, Korf U, Zatloukal K, Lehrach H, Westerhoff HV, Adjaye J. Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes. Sci Data 2015; 2:150068. [PMID: 26646939 PMCID: PMC4672680 DOI: 10.1038/sdata.2015.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/20/2015] [Indexed: 12/19/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its progression to more severe disease states.
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Affiliation(s)
- Wasco Wruck
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz 8036, Austria
| | - Samrina Rehman
- The Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Andriani Daskalaki
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
| | - Daniela Berg
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ewa Gralka
- Magnetic Resonance Center (CERM), University of Florence, 50019 Florence, Italy
| | - Justyna Jozefczuk
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
| | - Katharina Drews
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
| | - Vikash Pandey
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
| | - Christian Regenbrecht
- Institute for Pathology &Comprehensive Cancer Center, Cancer Stem Cell Group, Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Christoph Wierling
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, 50019 Florence, Italy
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kurt Zatloukal
- Institute of Pathology, Medical University of Graz, Graz 8036, Austria
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
| | - Hans V Westerhoff
- The Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.,Netherlands Institute for Systems Biology, VU University Amsterdam, HV NL-1081 Amsterdam, The Netherlands.,Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1018 WS Amsterdam, The Netherlands
| | - James Adjaye
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany.,Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin 14195, Germany
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13
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Westerhoff HV, Nakayama S, Mondeel TDGA, Barberis M. Systems Pharmacology: An opinion on how to turn the impossible into grand challenges. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 15:23-31. [PMID: 26464087 DOI: 10.1016/j.ddtec.2015.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 11/20/2022]
Abstract
A pharmacology that hits single disease-causing molecules with a single drug passively distributing to the target tissue, was almost ready. Such a pharmacology is not (going to be) effective however: a great many diseases are systems biology diseases; complex networks of some hundred thousand types of molecule, determine the functions that constitute human health, through nonlinear interactions. Malfunctions are caused by a variety of molecular failures at the same time; rarely the same variety in different individuals; in complex constellations of OR and AND logics. Few molecules cause disease single-handedly and few drugs will cure the disease all by themselves when dosed for a limited amount of time. We here discuss the implications that this discovery of the network nature of disease should have for pharmacology. We suggest ways in which pharmacokinetics, pharmacodynamics, but also systems biology and genomics may have to change so as better to deal with systems-biology diseases.
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Affiliation(s)
- Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands; Molecular Cell Physiology, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands; Manchester Centre for Integrative Systems Biology, The University of Manchester, UK.
| | - Shintaro Nakayama
- Molecular Cell Physiology, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands
| | - Thierry D G A Mondeel
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
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14
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Sahini N, Selvaraj S, Borlak J. Whole genome transcript profiling of drug induced steatosis in rats reveals a gene signature predictive of outcome. PLoS One 2014; 9:e114085. [PMID: 25470483 PMCID: PMC4254931 DOI: 10.1371/journal.pone.0114085] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/04/2014] [Indexed: 12/20/2022] Open
Abstract
Drug induced steatosis (DIS) is characterised by excess triglyceride accumulation in the form of lipid droplets (LD) in liver cells. To explore mechanisms underlying DIS we interrogated the publically available microarray data from the Japanese Toxicogenomics Project (TGP) to study comprehensively whole genome gene expression changes in the liver of treated rats. For this purpose a total of 17 and 12 drugs which are diverse in molecular structure and mode of action were considered based on their ability to cause either steatosis or phospholipidosis, respectively, while 7 drugs served as negative controls. In our efforts we focused on 200 genes which are considered to be mechanistically relevant in the process of lipid droplet biogenesis in hepatocytes as recently published (Sahini and Borlak, 2014). Based on mechanistic considerations we identified 19 genes which displayed dose dependent responses while 10 genes showed time dependency. Importantly, the present study defined 9 genes (ANGPTL4, FABP7, FADS1, FGF21, GOT1, LDLR, GK, STAT3, and PKLR) as signature genes to predict DIS. Moreover, cross tabulation revealed 9 genes to be regulated ≥10 times amongst the various conditions and included genes linked to glucose metabolism, lipid transport and lipogenesis as well as signalling events. Additionally, a comparison between drugs causing phospholipidosis and/or steatosis revealed 26 genes to be regulated in common including 4 signature genes to predict DIS (PKLR, GK, FABP7 and FADS1). Furthermore, a comparison between in vivo single dose (3, 6, 9 and 24 h) and findings from rat hepatocyte studies (2 h, 8 h, 24 h) identified 10 genes which are regulated in common and contained 2 DIS signature genes (FABP7, FGF21). Altogether, our studies provide comprehensive information on mechanistically linked gene expression changes of a range of drugs causing steatosis and phospholipidosis and encourage the screening of DIS signature genes at the preclinical stage.
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Affiliation(s)
- Nishika Sahini
- Centre for Pharmacology and Toxicology, Hannover Medical School, Hannover, Germany
| | | | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Hannover, Germany
- * E-mail:
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15
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RPPanalyzer toolbox: an improved R package for analysis of reverse phase protein array data. Biotechniques 2014; 57:125-35. [PMID: 25209047 DOI: 10.2144/000114205] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/20/2014] [Indexed: 11/23/2022] Open
Abstract
Analysis of large-scale proteomic data sets requires specialized software tools, tailored toward the requirements of individual approaches. Here we introduce an extension of an open-source software solution for analyzing reverse phase protein array (RPPA) data. The R package RPPanalyzer was designed for data preprocessing followed by basic statistical analyses and proteomic data visualization. In this update, we merged relevant data preprocessing steps into a single user-friendly function and included a new method for background noise correction as well as new methods for noise estimation and averaging of replicates to transform data in such a way that they can be used as input for a new time course plotting function. We demonstrate the robustness of our enhanced RPPanalyzer platform by analyzing longitudinal RPPA data of MET receptor signaling upon stimulation with different hepatocyte growth factor concentrations.
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