Multi-omics characterization of inflammatory bowel disease-induced hyperplasia/dysplasia in the rag2-/-/il10-/-mouse model

Qiyuan Han, Thomas J.Y. Kono, Charles G. Knutson, Nicola M. Parry, Christopher L. Seiler, James G. Fox, Steven R. Tannenbaum, Natalia Y. Tretyakova

Research output: Contribution to journalArticlepeer-review


Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.

Original languageEnglish (US)
Article number364
Pages (from-to)1-21
Number of pages21
JournalInternational journal of molecular sciences
Issue number1
StatePublished - Jan 1 2021

Bibliographical note

Funding Information:
Funding: This study was supported by grant from the National Cancer Institute (R01 CA-095039 to N.Y.T.). Q.H is partially supported by Faculty Research Development Grant from the University of Minnesota Academic Health Center.


  • Colorectal cancer
  • Dysplasia
  • Hydroxymethylome
  • Hyperplasia
  • Inflammatory bowel disease
  • Methylome
  • Multi omics analysis and integration
  • Transcriptome

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