Functional relevance of epigenetic modifications in inflammatory bowel disease Dissertation in fulfilment of the requirements for the degree “Dr. rer. nat.” of the Faculty of Mathematics and Natural Sciences at Kiel University submitted by Zhe Feng Kiel, 2013 First referee: Prof. Dr. Dr. Thomas C.G. Bosch . Second referee: Prof. Dr. Philip Rosenstiel . Date of the oral examination: 17.06.2013 . Approved for publication: ........................................................... Signed: Prof. Dr. Wolfgang J. Duschl, Dean ........................................................... "I only know that I know nothing." (Socrates) To my parents Parts of this thesis have been published in Genome Research. Häsler R, Feng Z, Bäckdahl L, Spehlmann ME, Franke A, Teschendorff A, Rakyan VK, Down TA, Wilson GA, Feber A, Beck S, Schreiber S, Rosenstiel P. A functional methylome map of ulcerative colitis. Genome Res. 2012 Nov;22(11):2130-7. doi: 10.1101/gr.138347.112. Epub 2012 Jul 23. The final version of this publication can be found in the appendix (Page 120-127). Table of Contents Table of Contents 1 INTRODUCTION ..................................................................................................................................... 4 1.1 Ulcerative colitis: a multifactorial induced complex disorder ................................................................. 4 1.1.1 Epidemiology of ulcerative colitis ......................................................................................................... 5 1.1.2 Clinical phenotype of ulcerative colitis ................................................................................................. 6 1.1.3 Epithelial barrier dysfunction and autoimmunity ................................................................................. 7 1.1.4 Immunological aspects of UC ................................................................................................................ 8 1.1.5 Genetic background of UC .................................................................................................................... 9 1.1.6 Environmental factors ......................................................................................................................... 10 1.2 Epigenetic regulation in UC .................................................................................................................... 11 1.2.1 Epigenitic mechanisms ........................................................................................................................ 13 1.2.2 DNA methylation patterns .................................................................................................................. 14 1.2.3 Non-coding RNA and other epigenetic mechanisms ........................................................................... 16 1.2.4 Epigenetics and environment .............................................................................................................. 17 1.2.5 Twin studies ........................................................................................................................................ 18 1.3 Hypothesis and Aims of the study .......................................................................................................... 19 2 MATERIALS AND METHODS .......................................................................................................... 20 2.1 Patient group composition and sample preparation ............................................................................. 20 2.1.1 Patient Recruitment ............................................................................................................................ 20 2.1.2 Samples storage and preparation ....................................................................................................... 21 2.1.3 RNA extraction from biopsy ................................................................................................................ 22 2.1.4 DNA extraction from biopsies ............................................................................................................. 22 2.2 Genome-wide scanning of the transcriptional and methylational profiling ......................................... 24 2.2.1 Genome-wide Transcriptome Profiling (Layer I) ................................................................................. 24 2.2.2 Genome-wide Quantification of Differentially Methylated Regions (Layer II) .................................... 25 1 Table of Contents 2.2.3 Genome-wide Quantification of individual Methylation Variable Positions (Layer III) ...................... 27 2.3 Merging of the transcriptional and methylational data (from Layer I,II & III) ...................................... 29 2.4 Validation of the transcriptional and methylational candidates .......................................................... 29 2.4.1 Validation of differential mRNA expression via Real-Time PCR .......................................................... 30 2.4.2 Validation of differential DNAm via Pyrosequencing .......................................................................... 32 2.5 Gene Ontology analysis .......................................................................................................................... 34 2.6 Chromatin- immunoprecipitation following quantitative real-time PCR ............................................. 34 2.6.1 Preparation of samples and control DNA ........................................................................................... 34 2.6.2 Immunoprecipitation of 5-hydroxymethylcytidine enriched DNA fragments .................................... 35 2.6.3 Examination of 5-hydroxymethylcytidine enrichment via qRT PCR .................................................... 35 3 RESULTS .................................................................................................................................................. 37 3.1 Genome-wide profiling of transcription and DNA methylation in ulcerative colitis ............................ 37 3.1.1 Genome-wide transcriptome profiling (Layer I) ................................................................................. 37 3.1.2 Genome-wide methylome profiling (Layer II and layer III) ................................................................. 37 3.1.3 Genome-wide quantification of individual methylated variable positions (Layer III) ......................... 37 3.1.4 Merging of the transcriptional and methylational data (from Layer I,II & III) .................................... 38 3.1.5 Intra-class correlations of the three-layer dataset ............................................................................. 40 3.1.6 Overview: genomic location of the different methylation in ulcerative colitis .................................. 41 3.1.7 Principle component analysis of the significant candidates ............................................................... 41 3.1.8 Correlation between the expressional and methylational data (in cis) .............................................. 42 3.1.9 Gene ontology (GO) analysis of the disease relevant processes ........................................................ 43 3.2 Validation of selected candidate transcripts under potential epigenetic control ................................ 44 3.3 Potential new finding of the DNA hydroxymethylation in the acute inflammation ............................ 49 4 DISCUSSION ........................................................................................................................................... 52 4.1 Genetics and epigenetics in the pathogenesis of ulcerative colitis ...................................................... 52 2 Table of Contents 4.2 Environment and epigenetics in the pathogenesis of ulcerative colitis ................................................ 56 4.3 Ulcerative colitis: a complex epigenetic disorder .................................................................................. 57 4.4 Genome-wide patterns of hypomethylation are a prominent motive in UC ........................................ 59 4.5 DNA demethylation in chronic and acute colitis .................................................................................... 60 4.5.1 Passive mechanisms of DNA demethylation are potentially absent in UC ......................................... 62 4.5.2 Demethylation in mammalian cells: a multi-step process .................................................................. 62 4.5.3 The APOBEC Family: Mediators of 5-mC or 5-hmC Deamination ....................................................... 63 4.5.4 Reduced BER activity may lead to carcinogenesis of UC ..................................................................... 64 4.6 Concluding remarks and future studies ................................................................................................. 66 5 SUMMARY ............................................................................................................................................... 67 6 ZUSAMMENFASSUNG ........................................................................................................................ 68 7 REFERENCES ......................................................................................................................................... 69 8 APPENDIX ..............................................................................................................................................