@article{FiedlerHirschElHajjetal.2019,
  author    = {Fiedler, David and Hirsch, Daniela and El Hajj, Nady and Yang, Howard H. and Hu, Yue and Sticht, Carsten and Nanda, Indrajit and Belle, Sebastian and Rueschoff, Josef and Lee, Maxwell P. and Ried, Thomas and Haaf, Thomas and Gaiser, Timo},
  title     = {Genome-wide DNA methylation analysis of colorectal adenomas with and without recurrence reveals an association between cytosine-phosphate-guanine methylation and histological subtypes},
  series = {Genes, Chromosomes and Cancer},
  volume    = {58},
  journal   = {Genes, Chromosomes and Cancer},
  number    = {11},
  doi       = {10.1002/gcc.22787},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212676},
  pages     = {783 -- 797},
  year      = {2019},
  abstract  = {Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development, which may result in colorectal cancer (CRC). Although gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and nonrecurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set of formalin-fixed paraffin-embedded colorectal low-grade adenomas (n = 72) consisting of primary adenomas without and with recurrence (n = 59), recurrent adenomas (n = 10), and normal mucosa specimens (n = 3). We aimed to unveil differentially methylated CpG positions (DMPs) across the methylome comparing not only primary adenomas without recurrence vs primary adenomas with recurrence but also primary adenomas vs recurrent adenomas using the Illumina Human Methylation 450K BeadChip array. Unsupervised hierarchical clustering exhibited a significant association of methylation patterns with histological adenoma subtypes. No significant DMPs were identified comparing primary adenomas with and without recurrence. Despite that, a total of 5094 DMPs (false discovery rate <0.05; fold change >10\%) were identified in the comparisons of recurrent adenomas vs primary adenomas with recurrence (674; 98\% hypermethylated), recurrent adenomas vs primary adenomas with and without recurrence (241; 99\% hypermethylated) and colorectal adenomas vs normal mucosa (4179; 46\% hypermethylated). DMPs in cytosine-phosphate-guanine (CpG) islands were frequently hypermethylated, whereas open sea- and shelf-regions exhibited hypomethylation. Gene ontology analysis revealed enrichment of genes associated with the immune system, inflammatory processes, and cancer pathways. In conclusion, our methylation data could assist in establishing a more robust and reproducible histological adenoma classification, which is a prerequisite for improving surveillance guidelines.},
  language  = {en}
}
@article{MaierhoferFlunkertDittrichetal.2017,
  author    = {Maierhofer, Anna and Flunkert, Julia and Dittrich, Marcus and M{\"u}ller, Tobias and Schindler, Detlev and Nanda, Indrajit and Haaf, Thomas},
  title     = {Analysis of global DNA methylation changes in primary human fibroblasts in the early phase following X-ray irradiation},
  series = {PLoS ONE},
  volume    = {12},
  journal   = {PLoS ONE},
  number    = {5},
  doi       = {10.1371/journal.pone.0177442},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170895},
  pages     = {e0177442},
  year      = {2017},
  abstract  = {Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant. Similarly, bisulfite pyrosequencing of interspersed LINE-1 repeats and centromeric α-satellite DNA did not detect significant methylation differences between irradiated and non-irradiated cultures. Methylation of interspersed ALU repeats appeared to be slightly increased (one percentage point; p = 0.01) at 6 h after irradiation with 4 Gy. Single-cell analysis showed comparable variations in repeat methylation among individual cells in both irradiated and control cultures. Radiation-induced changes in global repeat methylation, if any, were much smaller than methylation variation between different fibroblast strains. Interestingly, α-satellite DNA methylation positively correlated with gestational age. Finally, 450K methylation arrays mainly targeting genes and CpG islands were used for global DNA methylation analysis. There were no detectable methylation differences in genic (promoter, 5' UTR, first exon, gene body, 3' UTR) and intergenic regions between irradiated and control fibroblast cultures. Although we cannot exclude minor effects, i.e. on individual CpG sites, collectively our data suggest that global DNA methylation remains rather stable in irradiated normal body cells in the early phase of DNA damage response.},
  language  = {en}
}