Aging, Environment, & DiseaseDNA Methylation and Hydroxymethylation

How Environment Shapes Our Epigenome

How Environment Shapes Our EpigenomeGlobal mapping of the human epigenome has revealed that normal somatic cells exhibit their own unique DNA methylation patterns1. This tissue-specific methylome is established during development and faithfully maintained through subsequent cell divisions, in a process mediated by the enzymes DNMT1 and DNMT3A6. In recent years, there has been a growing interest in the influence of environmental factors in the establishment and maintenance of DNA methylation4.  Many studies have implicated environmental exposure in promoting DNA methylation changes – thereby contributing to alterations in cellular phenotype and disease susceptibility2,8. The reliance of these studies on large epidemiological approaches and in vitro models, however, limits our ability to determine the direct causal relationship between the environment and the human epigenome.

In our study, we used a novel in vivo human neobladder model to examine the relationship between the epigenome of normal, differentiated cells and their local tissue environment7. The neobladder was constructed from a small intestine segment of bladder cancer patients undergoing radical cystectomy.  In this procedure, the small intestine was reshaped into a bladder-like reservoir and reconnected to the genitourinary system – while maintaining the tissue’s original blood supply – resulting in dramatic morphological changes as a consequence of exposing the tissue to a foreign bladder environment. We collected fresh small intestine tissues, as well as neobladder urine sediments containing intestinal epithelial cells, and subsequently monitored global DNA methylation changes in the neobladder.

One of the challenges of performing epigenetic analyses on human tissues is the heterogeneity of the samples. In our model system specifically, we were concerned about the presence of contaminating white blood cells, which may be voided along with the intestinal cells in the neobladder urine specimens due to inflammation that often occurs in the early stage of surgery. We circumvented this challenge by measuring the tissue-specific DNA methylation pattern of inflammatory cells, which was distinct from the intestinal epithelial cells. Using a combination of pyrosequencing and a bioinformatic approach, we systematically removed neobladder samples containing significant proportion of inflammatory cells from our analysis in order to ensure that the changes we detected in the neobladder were not due to a heterogeneous cell mixture5.

We observed that, in the neobladder, changes in DNA methylation occurs in a time-dependent manner. A group of intestine specifically-unmethylated probes gain methylation at the average rate of 4.9% per year while a group of non-tissue specifically-methylated probes lose methylation at the comparable rate of 4.4% per year- exceeding the age-driven rate of methylation changes in normal cells by 15 fold. We annotated each methylation probe with its functional chromatin state by segmenting the genome based on the enrichment of combinatorial histone marks3. Strikingly, we found that the subset of probes that gain methylation was enriched for enhancers that were located near genes expressed specifically in the small intestine. This increase of methylation in intestine-specific enhancers suggests a loss of intestine-specific epigenetic landscape in the neobladder, presumably due to the lack of necessary environmental signals required in order to maintain the intestine-specific epigenome.

In contrast, the subset of probes that lost methylation in the neobladder was enriched for non-tissue specific transcribed regions. Unlike promoter methylation, which is associated with gene silencing, the presence of DNA methylation in transcribed regions has been linked with increased gene expression. The loss of DNA methylation in these probes thus suggests the down-regulation of non-tissue specific genes in response to the drastic changes in the local tissue environment.

Overall, our study demonstrates that changes in physiological environment may epigenetically reprogram normal differentiated cells and, importantly, reveals unexpected dependency on signals from the local tissue environment during the maintenance of normal human methylome. Better understanding of the specific signals and mechanisms involved in this epigenetic reprogramming is critical in order to understand how alterations in local tissue environments may contribute to disease development.

 

References:

Lay FD, Triche TJ Jr, Tsai YC, Su SF, Martin SE, Daneshmand S, Skinner EC, Liang G, Chihara Y, & Jones PA (2014). Reprogramming of the human intestinal epigenome by surgical tissue transposition. Genome research, 24 (4), 545-53 PMID: 24515120

Brena RM, Huang TH, & Plass C (2006). Toward a human epigenome. Nature genetics, 38 (12), 1359-60 PMID: 17133218

Cortessis VK, Thomas DC, Levine AJ, Breton CV, Mack TM, Siegmund KD, Haile RW, & Laird PW (2012). Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Human genetics, 131 (10), 1565-89 PMID: 22740325

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, & Bernstein BE (2011). Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473 (7345), 43-9 PMID: 21441907

Feil R, & Fraga MF (2012). Epigenetics and the environment: emerging patterns and implications. Nature reviews. Genetics, 13 (2), 97-109 PMID: 22215131

Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, & Kelsey KT (2012). DNA methylation arrays as surrogate measures of cell mixture distribution. BMC bioinformatics, 13 PMID: 22568884

Jones PA, & Liang G (2009). Rethinking how DNA methylation patterns are maintained. Nature reviews. Genetics, 10 (11), 805-11 PMID: 19789556

Lay FD, Triche TJ Jr, Tsai YC, Su SF, Martin SE, Daneshmand S, Skinner EC, Liang G, Chihara Y, & Jones PA (2014). Reprogramming of the human intestinal epigenome by surgical tissue transposition. Genome research, 24 (4), 545-53 PMID: 24515120

Walker CL, & Ho SM (2012). Developmental reprogramming of cancer susceptibility. Nature reviews. Cancer, 12 (7), 479-86 PMID: 22695395

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