# Role of the microbiota in DNA methylation and CRC development

> **NIH NIH R01** · CORIELL INSTITUTE FOR MEDICAL RESEARCH · 2020 · $600,157

## Abstract

The colonic microbiome has been implicated in colorectal cancer (CRC) pathogenesis but the exact mechanisms
underlying these observations remain incompletely understood. We have observed striking associations
between specific host microbes and aberrant DNA methylation in CRC. For example, Fusobacterium species
are substantially enriched in cancers affected by the CpG Island Methylator Phenotype (CIMP). Preliminary data
based on sequencing and qPCR validation also show enrichment of bacteria that have been linked to disease
in humans or mouse models (E.coli sp., Klebsiella sp. etc.). High levels of these pathogenic bacteria are
associated with recurrences in CIMP+ colon cancers. This unexpected link between colonic microbiota and
epigenetic control was also seen in an analysis of DNA methylation genome wide in the colonic mucosa of germ
free (GF) mice compared to conventionalized mice, where we found that reintroduction of bacteria led to
hypermethylation of normally unmethylated CpG island sites (the main anomaly seen in CIMP+ cases). Thus,
our preliminary data support a new hypothesis, that the GI microbiota affects colonic neoplasia through
inducing or modulating aberrant DNA methylation and epigenetic control. Mechanistically, we propose that
multiple parallel mechanisms may be contributing to this link including DNA damage associated recruitment of
silencing complexes, and metabolic disturbances whereby bacteria secrete metabolites and/or toxins that diffuse
into colonic epithelial cells and affect DNA methylation directly (e.g. 2-hydroxyglutarate [2-HG], which inhibits the
TET DNA demethylase enzymes) or indirectly (e.g. butyrate, which is known to modulate epigenetics through
inhibition of histone deacetylases). To test these hypotheses, we propose three specific aims: (1) Define the
microbiome across the spectrum of CIMP+ tumors. We will use 16S RNA genomic sequencing in an
extensive tumor (cancer, precursors and adjacent normal) set simultaneously characterized for CIMP, mutations
and gene expression. (2) Impact of CIMP+ associated bacteria on tumorigenesis and DNA methylation in
mice. GF Il10-/-;Apcmin/+ mice will be colonized with bacterial candidates (e.g. E.coli, F.nucleatum, K.pneumonia)
and tumor incidence, severity, survival as well as DNA methylation and gene expression in normal and tumor
tissues will be evaluated. We will also test whether drugs targeting DNA methylation are effective in prevention
of bacteria-associated tumorigenesis. (3) Study metabolites by which bacteria influence DNA methylation
profiles. We will use metabolomics on cultures of bacteria associated with CIMP and on lysates from CIMP+
and CIMP- cancers to identify metabolites that potentially modulate DNA methylation. These (e.g. 2HG, butyrate)
will be tested for effects on DNA methylation (in cell culture and in GF mice) and tumorigenesis (in mice). The
proposed research tests a new mechanism for microbiome-associated tumorigenesis and has important
implicat...

## Key facts

- **NIH application ID:** 9828596
- **Project number:** 5R01CA214005-04
- **Recipient organization:** CORIELL INSTITUTE FOR MEDICAL RESEARCH
- **Principal Investigator:** Jean-Pierre J. Issa
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $600,157
- **Award type:** 5
- **Project period:** 2017-12-15 → 2022-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9828596

## Citation

> US National Institutes of Health, RePORTER application 9828596, Role of the microbiota in DNA methylation and CRC development (5R01CA214005-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9828596. Licensed CC0.

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