Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models

[1]  P. Woods Digging deeper , 2018, Nature Astronomy.

[2]  S. Glaser,et al.  Pathogenesis of Kupffer Cells in Cholestatic Liver Injury. , 2016, The American journal of pathology.

[3]  H. Rosen,et al.  Free Fatty Acids Differentially Downregulate Chemokines in Liver Sinusoidal Endothelial Cells: Insights into Non-Alcoholic Fatty Liver Disease , 2016, PloS one.

[4]  Murugesan V. S. Rajaram,et al.  Scavenger receptor B1, the HDL receptor, is expressed abundantly in liver sinusoidal endothelial cells , 2016, Scientific Reports.

[5]  P. Rajagopalan,et al.  Designing a fibrotic microenvironment to investigate changes in human liver sinusoidal endothelial cell function. , 2015, Acta biomaterialia.

[6]  L. DeLeve Liver sinusoidal endothelial cells in hepatic fibrosis , 2015, Hepatology.

[7]  H. Kalbitzer,et al.  Formation of Fenestrae in Murine Liver Sinusoids Depends on Plasmalemma Vesicle-Associated Protein and Is Required for Lipoprotein Passage , 2014, PloS one.

[8]  M. Toribio,et al.  Intravenous Immunoglobulin Promotes Antitumor Responses by Modulating Macrophage Polarization , 2014, The Journal of Immunology.

[9]  N. Zelcer,et al.  The UPS and downs of cholesterol homeostasis. , 2014, Trends in biochemical sciences.

[10]  Z. Halpern,et al.  Infiltrating Monocyte-Derived Macrophages and Resident Kupffer Cells Display Different Ontogeny and Functions in Acute Liver Injury , 2014, The Journal of Immunology.

[11]  R. Medzhitov,et al.  Tissue-Specific Signals Control Reversible Program of Localization and Functional Polarization of Macrophages , 2014, Cell.

[12]  Alberto Mantovani,et al.  Macrophage plasticity and polarization in liver homeostasis and pathology , 2014, Hepatology.

[13]  Jun Li,et al.  Macrophage polarization and function with emphasis on the evolving roles of coordinated regulation of cellular signaling pathways. , 2014, Cellular signalling.

[14]  Susanne Bartels,et al.  Endothelial Cell-Derived Angiopoietin-2 Controls Liver Regeneration as a Spatiotemporal Rheostat , 2014, Science.

[15]  D. Adams,et al.  Paracrine Signals From Liver Sinusoidal Endothelium Regulate Hepatitis C Virus Replication , 2013, Hepatology.

[16]  T. M. Murali,et al.  Summarizing cellular responses as biological process networks , 2013, BMC Systems Biology.

[17]  L. Tucker-Kellogg,et al.  The CD47-binding peptide of thrombospondin-1 induces defenestration of liver sinusoidal endothelial cells , 2013, Liver international : official journal of the International Association for the Study of the Liver.

[18]  T. Murali,et al.  Designing a multicellular organotypic 3D liver model with a detachable, nanoscale polymeric Space of Disse. , 2013, Tissue engineering. Part C, Methods.

[19]  Andrew J. Brown,et al.  Controlling Cholesterol Synthesis beyond 3-Hydroxy-3-methylglutaryl-CoA Reductase (HMGCR)* , 2013, The Journal of Biological Chemistry.

[20]  L. DeLeve,et al.  Liver sinusoidal endothelial cells and liver regeneration. , 2013, The Journal of clinical investigation.

[21]  A. Stahl,et al.  SLC27 fatty acid transport proteins. , 2013, Molecular aspects of medicine.

[22]  T. V. van Berkel,et al.  Nuclear receptor atlas of female mouse liver parenchymal, endothelial, and Kupffer cells. , 2013, Physiological genomics.

[23]  Laura J. Dixon,et al.  Kupffer cells in the liver. , 2013, Comprehensive Physiology.

[24]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[25]  W. Ouwehand,et al.  Reactome – a curated knowledgebase of biological pathways: megakaryocytes and platelets , 2012, Journal of thrombosis and haemostasis : JTH.

[26]  Olivier Elemento,et al.  Efficient Direct Reprogramming of Mature Amniotic Cells into Endothelial Cells by ETS Factors and TGFβ Suppression , 2012, Cell.

[27]  Cunshuan Xu,et al.  Characterization of transcriptional profiling of Kupffer cells during liver regeneration in rats , 2012, Cell biology international.

[28]  G. Kanel,et al.  Role of differentiation of liver sinusoidal endothelial cells in progression and regression of hepatic fibrosis in rats. , 2012, Gastroenterology.

[29]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[30]  T. Wynn,et al.  Protective and pathogenic functions of macrophage subsets , 2011, Nature Reviews Immunology.

[31]  Laura E. Nagy,et al.  Molecular Pathology of Liver Diseases , 2011 .

[32]  P. Rajagopalan,et al.  Engineered three-dimensional liver mimics recapitulate critical rat-specific bile acid pathways. , 2011, Tissue engineering. Part A.

[33]  Cunshuan Xu,et al.  Analysis of time-course gene expression profiles of sinusoidal endothelial cells during liver regeneration in rats , 2011, Molecular and Cellular Biochemistry.

[34]  Christopher D. Lasher,et al.  Discovering Networks of Perturbed Biological Processes in Hepatocyte Cultures , 2011, PloS one.

[35]  P. Rajagopalan,et al.  3D Hepatic Cultures Simultaneously Maintain Primary Hepatocyte and Liver Sinusoidal Endothelial Cell Phenotypes , 2010, PloS one.

[36]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[37]  M. Lazar,et al.  Endogenous Ligands for Nuclear Receptors: Digging Deeper* , 2010, The Journal of Biological Chemistry.

[38]  S. Goerdt,et al.  Liver sinusoidal endothelium: A microenvironment‐dependent differentiation program in rat including the novel junctional protein liver endothelial differentiation‐associated protein‐1 , 2010, Hepatology.

[39]  T M Murali,et al.  A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures. , 2010, Tissue engineering. Part C, Methods.

[40]  Richey M. Davis,et al.  The design of in vitro liver sinusoid mimics using chitosan-hyaluronic acid polyelectrolyte multilayers. , 2010, Tissue engineering. Part A.

[41]  M. Daemen,et al.  Equivalence testing in microarray analysis: similarities in the transcriptome of human atherosclerotic and nonatherosclerotic macrophages. , 2010, Physiological genomics.

[42]  Gary D Bader,et al.  NetPath: a public resource of curated signal transduction pathways , 2010, Genome Biology.

[43]  H. R. Payne,et al.  L-FABP directly interacts with PPAR&agr; in cultured primary hepatocytes , 2009, Journal of Lipid Research.

[44]  S. Bhatia,et al.  Microenvironmental regulation of the sinusoidal endothelial cell phenotype in vitro , 2009, Hepatology.

[45]  Simon Kasif,et al.  Biological Process Linkage Networks , 2009, PloS one.

[46]  T. Hibi,et al.  Caveolin‐1 and Rac regulate endothelial capillary‐like tubular formation and fenestral contraction in sinusoidal endothelial cells , 2009, Liver international : official journal of the International Association for the Study of the Liver.

[47]  Johan Auwerx,et al.  Targeting bile-acid signalling for metabolic diseases , 2008, Nature Reviews Drug Discovery.

[48]  Pankaj Agarwal,et al.  A global pathway crosstalk network , 2008, Bioinform..

[49]  M. Hashizume,et al.  Defective endothelial nitric oxide synthase signaling is mediated by rho‐kinase activation in rats with secondary biliary cirrhosis , 2008, Hepatology.

[50]  C. Glass,et al.  Anti-inflammatory actions of PPAR ligands: new insights on cellular and molecular mechanisms. , 2007, Trends in immunology.

[51]  Stephen F Badylak,et al.  Maintenance of hepatic sinusoidal endothelial cell phenotype in vitro using organ-specific extracellular matrix scaffolds. , 2007, Tissue engineering.

[52]  Luke P. Lee,et al.  An artificial liver sinusoid with a microfluidic endothelial-like barrier for primary hepatocyte culture. , 2007, Biotechnology and bioengineering.

[53]  S. Strom,et al.  Gene expression profiling and differentiation assessment in primary human hepatocyte cultures, established hepatoma cell lines, and human liver tissues. , 2007, Toxicology and applied pharmacology.

[54]  Mehmet Toner,et al.  Polyelectrolyte nano-scaffolds for the design of layered cellular architectures. , 2006, Tissue engineering.

[55]  Neil Kaplowitz,et al.  Liver biology and pathobiology , 2006, Hepatology.

[56]  Thomas Ragg,et al.  The RIN: an RNA integrity number for assigning integrity values to RNA measurements , 2006, BMC Molecular Biology.

[57]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  T. Hibi,et al.  Tumour necrosis factor α signalling through activation of Kupffer cells plays an essential role in liver fibrosis of non-alcoholic steatohepatitis in mice , 2005, Gut.

[59]  Crispin J. Miller,et al.  Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis , 2005, Bioinform..

[60]  J. Guan,et al.  FAK-mediated src phosphorylation of endophilin A2 inhibits endocytosis of MT1-MMP and promotes ECM degradation. , 2005, Developmental cell.

[61]  B. Rozell,et al.  Human sterol 12α-hydroxylase (CYP8B1) is mainly expressed in hepatocytes in a homogenous pattern , 2005, Histochemistry and Cell Biology.

[62]  J. Berger,et al.  PPARs: therapeutic targets for metabolic disease. , 2005, Trends in pharmacological sciences.

[63]  Robert Tibshirani,et al.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd Edition , 2001, Springer Series in Statistics.

[64]  G. Kullak-Ublick,et al.  Coordinate transcriptional regulation of bile acid homeostasis and drug metabolism. , 2005, Archives of biochemistry and biophysics.

[65]  S. Sugano,et al.  Serial analysis of gene expression in sinusoidal endothelial cells from normal and injured mouse liver. , 2004, Biochemical and biophysical research communications.

[66]  R. McCuskey,et al.  Rat liver sinusoidal endothelial cell phenotype is maintained by paracrine and autocrine regulation. , 2004, American journal of physiology. Gastrointestinal and liver physiology.

[67]  M. Rao,et al.  PPARalpha in the pathogenesis of fatty liver disease. , 2004, Hepatology.

[68]  J. Reddy,et al.  PPARα in the pathogenesis of fatty liver disease , 2004 .

[69]  Sangeeta N Bhatia,et al.  Exploring interactions between rat hepatocytes and nonparenchymal cells using gene expression profiling , 2004, Hepatology.

[70]  H. Ishii,et al.  Rho modulates hepatic sinusoidal endothelial fenestrae via regulation of the actin cytoskeleton in rat endothelial cells , 2004, Laboratory Investigation.

[71]  R. DeMatteo,et al.  Liver Sinusoidal Endothelial Cells Are Insufficient to Activate T Cells , 2004, The Journal of Immunology.

[72]  G. Barish,et al.  PPARs and the complex journey to obesity , 2004, Nature Medicine.

[73]  A. Kashuba,et al.  Kupffer cell-mediated IL-2 suppression of CYP3A activity in human hepatocytes. , 2004, Drug metabolism and disposition: the biological fate of chemicals.

[74]  A. Stahl A current review of fatty acid transport proteins (SLC27) , 2004, Pflügers Archiv.

[75]  G. Shulman,et al.  Liver fatty acid‐binding protein is required for high rates of hepatic fatty acid oxidation but not for the action of PPAR‐α in fasting mice , 2004, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[76]  P. Ferré,et al.  The biology of peroxisome proliferator-activated receptors: relationship with lipid metabolism and insulin sensitivity. , 2004, Diabetes.

[77]  S. Kersten,et al.  Peroxisome proliferator-activated receptor α target genes , 2004, Cellular and Molecular Life Sciences CMLS.

[78]  M. Gillespie Mitochondrial Fatty Acid Beta-Oxidation , 2003 .

[79]  Eric R. Ziegel,et al.  The Elements of Statistical Learning , 2003, Technometrics.

[80]  Silvio Albertini,et al.  Gene expression in two hepatic cell lines, cultured primary hepatocytes, and liver slices compared to the in vivo liver gene expression in rats: possible implications for toxicogenomics use of in vitro systems. , 2003, Toxicological sciences : an official journal of the Society of Toxicology.

[81]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[82]  B. Staels,et al.  Bile acids induce the expression of the human peroxisome proliferator-activated receptor alpha gene via activation of the farnesoid X receptor. , 2003, Molecular endocrinology.

[83]  P. Allavena,et al.  Macrophage polarization: tumor-associated macrophages as a paradigm for polarized M2 mononuclear phagocytes. , 2002, Trends in immunology.

[84]  T. Yoshioka,et al.  A highly specific isolation of rat sinusoidal endothelial cells by the immunomagnetic bead method using SE-1 monoclonal antibody. , 2002, Journal of hepatology.

[85]  W. Wahli,et al.  The peroxisome proliferator‐activated receptor α regulates amino acid metabolism , 2001, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[86]  T. K. Baker,et al.  Temporal gene expression analysis of monolayer cultured rat hepatocytes. , 2001, Chemical research in toxicology.

[87]  H. Lodish,et al.  Fatty acid transport proteins: a current view of a growing family , 2001, Trends in Endocrinology & Metabolism.

[88]  T. Pineau,et al.  Long-chain fatty acids regulate liver carnitine palmitoyltransferase I gene (L-CPT I) expression through a peroxisome-proliferator-activated receptor alpha (PPARalpha)-independent pathway. , 2001, The Biochemical journal.

[89]  A. Minnich,et al.  A potent PPARα agonist stimulates mitochondrial fatty acid β-oxidation in liver and skeletal muscle , 2001 .

[90]  M. Hunt,et al.  The Peroxisome Proliferator-activated Receptor α (PPARα) Regulates Bile Acid Biosynthesis* , 2000, The Journal of Biological Chemistry.

[91]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[92]  J. Chiang,et al.  Peroxisome proliferator-activated receptor alpha (PPARalpha) and agonist inhibit cholesterol 7alpha-hydroxylase gene (CYP7A1) transcription. , 2000, Journal of lipid research.

[93]  J. Kinet,et al.  Signalling through the high-affinity IgE receptor FcεRI , 1999, Nature.

[94]  M L Yarmush,et al.  Effect of cell–cell interactions in preservation of cellular phenotype: cocultivation of hepatocytes and nonparenchymal cells , 1999, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[95]  W. Hsueh,et al.  Peroxisome proliferator-activated receptor activators target human endothelial cells to inhibit leukocyte-endothelial cell interaction. , 1999, Arteriosclerosis, thrombosis, and vascular biology.

[96]  J. Reddy,et al.  Peroxisomal and Mitochondrial Fatty Acid β-Oxidation in Mice Nullizygous for Both Peroxisome Proliferator-activated Receptor α and Peroxisomal Fatty Acyl-CoA Oxidase , 1999, The Journal of Biological Chemistry.

[97]  P. Libby,et al.  PPARα Activators Inhibit Cytokine-Induced Vascular Cell Adhesion Molecule-1 Expression in Human Endothelial Cells , 1999 .

[98]  J. Lehmann,et al.  Bile acids: natural ligands for an orphan nuclear receptor. , 1999, Science.

[99]  M. Shibuya,et al.  Expressions of vascular endothelial growth factor in nonparenchymal as well as parenchymal cells in rat liver after necrosis. , 1999, Biochemical and biophysical research communications.

[100]  H. Lodish,et al.  A family of fatty acid transporters conserved from mycobacterium to man. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[101]  J. Chiang Regulation of bile acid synthesis. , 1998, Frontiers in bioscience : a journal and virtual library.

[102]  M. L. Le Beau,et al.  Human mitochondrial enoyl-CoA hydratase gene (ECHS1): structural organization and assignment to chromosome 10q26.2-q26.3. , 1997, Genomics.

[103]  J. McGarry,et al.  The mitochondrial carnitine palmitoyltransferase system. From concept to molecular analysis. , 1997, European journal of biochemistry.

[104]  J. Vamecq,et al.  Peroxisome proliferators and peroxisome proliferator activated receptors (PPARs) as regulators of lipid metabolism. , 1997, Biochimie.

[105]  J. Rosenfeld,et al.  A Direct Role for Sterol Regulatory Element Binding Protein in Activation of 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase Gene (*) , 1996, The Journal of Biological Chemistry.

[106]  P. Meier Molecular mechanisms of hepatic bile salt transport from sinusoidal blood into bile. , 1995, The American journal of physiology.

[107]  C. Felder Muscarinic acetylcholine receptors: signal transduction through multiple effectors , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[108]  A. Mahfoudi,et al.  Fatty acids and retinoids control lipid metabolism through activation of peroxisome proliferator-activated receptor-retinoid X receptor heterodimers. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[109]  D. Russell Cholesterol biosynthesis and metabolism , 1992, Cardiovascular Drugs and Therapy.

[110]  J. Patrick,et al.  Calcium modulation and high calcium permeability of neuronal nicotinic acetylcholine receptors , 1992, Neuron.

[111]  J. Spitzer,et al.  Glutamine and fatty acid oxidation are the main sources of energy for Kupffer and endothelial cells. , 1991, The American journal of physiology.

[112]  M. Milanick Na-Ca exchange: evidence against a ping-pong mechanism and against a Ca pool in ferret red blood cells. , 1991, The American journal of physiology.

[113]  R. Tompkins,et al.  Long‐Term in Vitro Function of Adult Hepatocytes in a Collagen Sandwich Configuration , 1991, Biotechnology progress.

[114]  H. Schulz,et al.  Beta oxidation of fatty acids. , 1991, Biochimica et biophysica acta.

[115]  R. Busse,et al.  Calcium‐dependent nitric oxide synthesis in endothelial cytosol is mediated by calmodulin , 1990, FEBS letters.

[116]  R. Tompkins,et al.  Hepatocyte function and extracellular matrix geometry: long‐term culture in a sandwich configuration , 1989, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[117]  B. Fleshler,et al.  The Liver: Biology and Pathobiology , 1983 .

[118]  J. Kane,et al.  Fatty acid binding protein. Isolation from rat liver, characterization, and immunochemical quantification. , 1982, The Journal of biological chemistry.

[119]  G. Mannaerts,et al.  Mitochondrial and peroxisomal fatty acid oxidation in liver homogenates and isolated hepatocytes from control and clofibrate-treated rats. , 1979, The Journal of biological chemistry.

[120]  P. Lazarow Rat liver peroxisomes catalyze the beta oxidation of fatty acids. , 1978, The Journal of biological chemistry.

[121]  L. D. Wright Biosynthesis of Isoprenoid Compounds , 1961 .

[122]  C. W. Greene,et al.  THE FEDERATION OF AMERICAN SOCIETIES FOR EXPERIMENTAL BIOLOGY. , 1917, Science.

[123]  S. Bhatia,et al.  Hepatic tissue engineering , 2020, Principles of Tissue Engineering.

[124]  Gunther Hartmann,et al.  Virally infected mouse liver endothelial cells trigger CD8+ T-cell immunity. , 2010, Gastroenterology.

[125]  Piero Rinaldo,et al.  Fatty acid oxidation disorders. , 2002, Annual review of physiology.

[126]  D. Vance,et al.  Biochemistry.of.Lipids,.Lipoproteins.and.Membranes,.4th.edition , 2002 .

[127]  M. Hunt,et al.  The peroxisome proliferator-activated receptor alpha (PPARalpha) regulates bile acid biosynthesis. , 2000, The Journal of biological chemistry.

[128]  P. Edwards,et al.  Sterols and isoprenoids: signaling molecules derived from the cholesterol biosynthetic pathway. , 1999, Annual review of biochemistry.

[129]  P. Edwards,et al.  Signaling molecules derived from the cholesterol biosynthetic pathway. , 1997, Sub-cellular biochemistry.

[130]  J. Ravetch Fc receptors. , 1997, Current opinion in immunology.

[131]  M L Yarmush,et al.  Culture matrix configuration and composition in the maintenance of hepatocyte polarity and function. , 1996, Biomaterials.

[132]  W. Wahli,et al.  Differential expression of peroxisome proliferator-activated receptors (PPARs): tissue distribution of PPAR-alpha, -beta, and -gamma in the adult rat. , 1996, Endocrinology.

[133]  A. DeFranco,et al.  Transmembrane signaling by antigen receptors of B and T lymphocytes. , 1995, Current opinion in cell biology.

[134]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[135]  J. Kinet,et al.  Fc receptors. , 1991, Annual review of immunology.

[136]  J. McGarry,et al.  Regulation of hepatic fatty acid oxidation and ketone body production. , 1980, Annual review of biochemistry.

[137]  A Karlin,et al.  Nicotinic acetylcholine receptors. , 1977 .

[138]  B. Endoplasmic CHOLESTEROL biosynthesis. , 1957, Nutrition reviews.

[139]  T. Pineau,et al.  Long-chain fatty acids regulate liver carnitine palmitoyltransferase I gene (L-CPT I ) expression through a peroxisome-proliferator-activated receptor α (PPARα)-independent pathway , 2022 .