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Dissertation Dissertation Submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the Degree of Doctor of Natural Sciences Presented by Ann-Cathrin Hofer (M.Sc.) Born in Heidelberg, Germany Oral Examination: 12th of September 2016 Regulatory T cells protect the neonatal liver and secure the hepatic circadian rhythm Referees 1st Referee: Prof. Dr. Peter Angel 2nd Referee: Dr. Markus Feuerer This dissertation was performed and written during the period from November 2012 to May 2016 in the German Cancer Research Center (DKFZ) under the supervision of Prof. Dr. Peter Angel and direct supervision of Dr. Markus Feuerer. The dissertation was submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany in June 2016. German Cancer Research Center (DKFZ) Immune Tolerance (D100) Im Neuenheimer Feld 280 69120 Heidelberg, Germany I II Confirmation Hereby, I confirm that I have written this thesis independently, using only the results of my investigation unless otherwise stated. Furthermore, I declare that I have not submitted this thesis for a degree to any other academic or similar institution. Parts of this dissertation have been submitted for publishing: Regulatory T cells protect the liver early in life and safeguard the hepatic circadian rhythm Ann-Cathrin Hofer, Thomas Hielscher, David M. Richards, Michael Delacher, Ulrike Träger, Sophia Föhr, Artyom Vlasov, Marvin Wäsch, Marieke Esser, Annette Kopp-Schneider, Achim Breiling, Frank Lyko, Ursula Klingmüller, Peter Angel, Jakub Abramson, Jeroen Krijgsveld & Markus Feuerer Parts of the experiments in this dissertation were performed in collaboration with other research groups as follows: CG methylation analysis with the 454 pyrosequencing technology: Division of Epigenetics, DKFZ, Heidelberg Dr. Achim Breiling & Prof. Dr. Frank Lyko Quantitative differential proteomics experiments: Genome Biology Unit, EMBL, Heidelberg Sophia Föhr and Dr. Jeroen Krijgsveld Bioinformatic analysis of microarray data Division of Biostatistics, DKFZ, Heidelberg Thomas Hielscher and Annette Kopp-Schneider Mdr2-/- liver microarray data Division of Signal Transduction and Growth Control, DKFZ, Heidelberg Prof. Dr. Peter Angel ____________________________ _______________________________ (Place/Date) (Signature) III IV Table of content 1 Summary ...................................................................................................... 1 2 Zusammenfassung ...................................................................................... 2 3 Introduction .................................................................................................. 3 3.1 The immune system ................................................................................................. 3 3.1.1 The innate immune response .......................................................................... 3 3.1.2 The adaptive immune response ...................................................................... 4 3.2 Regulatory T cells .................................................................................................... 6 3.2.1 Thymic-derived Treg cells ................................................................................. 7 3.2.2 Thymus-derived versus peripheral-induced Treg cells ................................. 10 3.2.3 Heterogeneity idea of Treg cell ........................................................................ 11 3.2.4 Tissue-specialized Treg cells .......................................................................... 13 3.3 Liver cells ............................................................................................................... 16 3.4 Circadian rhythm .................................................................................................... 18 3.4.1 Circadian rhythm pathway ............................................................................. 18 3.4.2 Lymphocytes and the circadian rhythm ....................................................... 22 4 Aim of study ................................................................................................23 5 Methods .......................................................................................................24 5.1 Mice ....................................................................................................................... 24 5.1.1 Keeping ........................................................................................................... 24 5.2 Tissue sample preparation ..................................................................................... 24 5.2.1 Cell depletion .................................................................................................. 24 5.2.2 Tissue isolation and sample preparation...................................................... 25 5.2.3 AutoMACS cell purification ........................................................................... 25 5.2.4 Blood samples ................................................................................................ 25 5.3 Cell culture techniques ........................................................................................... 26 5.3.1 Primary hepatocyte isolation ......................................................................... 26 5.4 Flow cytometry ....................................................................................................... 26 5.5 Fluorescence-activated cell sorting (FACS)............................................................ 27 5.5.1 In vivo proliferation assay ............................................................................. 27 V 5.6 Epigenetics ............................................................................................................ 28 5.6.1 Purification and bisulfite conversion of genomic DNA ................................ 28 5.7 Proteomics ............................................................................................................. 29 5.7.1 Protein digestion, labeling of peptides with stable isotopes (TMT) and fractionation ................................................................................................................. 29 5.7.2 LC-ESI-MS/MS analysis .................................................................................. 29 5.7.3 Protein identification and quantification ....................................................... 30 5.8 PCR techniques ..................................................................................................... 30 5.8.1 RNA isolation and cDNA synthesis ............................................................... 30 5.8.2 Quantitative real-time PCR ............................................................................. 31 5.8.3 RNA expression profiling ............................................................................... 31 5.9 Bioinformatic and statistical analysis ...................................................................... 31 5.9.1 Bioinformatic and statistical analysis of proteomic data ............................ 31 5.9.2 Bioinformatics and statistical analysis of microarray data ......................... 32 5.9.3 General statistical analysis ............................................................................ 33 6 Materials ..................................................................................................... 34 6.1 Mice ....................................................................................................................... 34 6.2 Antibodies .............................................................................................................. 35 6.3 Cytokines ............................................................................................................... 36 6.4 Kits ......................................................................................................................... 37 6.5 Bisulfite Primer ....................................................................................................... 38 6.6 Quantitative real-time PCR primer .......................................................................... 39 6.7 Reagents ................................................................................................................ 40 6.8 Plasticware and consumables ................................................................................ 42 6.9 Buffers and solutions .............................................................................................. 43 6.10 Equipment .............................................................................................................. 44 6.11 Software ................................................................................................................. 45 7 Results ........................................................................................................ 46 7.1 Hepatic regulatory T cells ....................................................................................... 46 7.2 The neonatal liver ................................................................................................... 59 7.3 Neonatal Treg cells protect homeostasis and metabolic liver function ...................... 68 VI 7.4 Treg cells influence the circadian rhythm ................................................................. 74 8 Discussion ...................................................................................................92
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