Ethanol exposure drives colon location specific cell composition changes in a normal colon crypt 3D organoid model

Matthew Devall,Jeroen R. Huyghe,Christopher H. Dampier,Lucas T. Jennelle,Jennifer Bryant,Sarah J. Plummer,Stephen Eaton,Ulrike Peters,Steven M. Powell,Graham Casey

doi:10.1038/s41598-020-80240-1

Abstract

Alcohol is a consistently identified risk factor for colon cancer. However, the molecular mechanism underlying its effect on normal colon crypt cells remains poorly understood. We employed RNA-sequencing to asses transcriptomic response to ethanol exposure (0.2% vol:vol) in 3D organoid lines derived from healthy colon (n = 34). Paired regression analysis identified 2,162 differentially expressed genes in response to ethanol. When stratified by colon location, a far greater number of differentially expressed genes were identified in organoids derived from the left versus right colon, many of which corresponded to cell-type specific markers. To test the hypothesis that the effects of ethanol treatment on colon organoid populations were in part due to differential cell composition, we incorporated external single cell RNA-sequencing data from normal colon biopsies to estimate cellular proportions following single cell deconvolution. We inferred cell-type-specific changes, and observed an increase in transit amplifying cells following ethanol exposure that was greater in organoids from the left than right colon, with a concomitant decrease in more differentiated cells. If this occurs in the colon following alcohol consumption, this would lead to an increased zone of cells in the lower crypt where conditions are optimal for cell division and the potential to develop mutations.

Highlights

While a growing number of inherited genetic variants have been associated with colorectal cancer (CRC) risk in recent years[1,2], environmental factors, such as alcohol consumption have been strongly implicated[3]
Substantial differences in transcriptomic responses were observed between 3D organoids derived from the left and right colon
We measured the effect of ethanol exposure on global gene expression profiles of colon organoids derived from normal colon crypts, and identified 2,162 significant differentially expressed genes (DEGs)

Summary

Introduction

While a growing number of inherited genetic variants have been associated with colorectal cancer (CRC) risk in recent years[1,2], environmental factors, such as alcohol consumption have been strongly implicated[3]. Alcohol consumption has been associated with increased risk for cancers of the left colon and rectum in males[7], while other studies have indicated increased risk for tumors of the left colon in regular alcohol drinkers across g enders[8,9] This implies that colon location should be a relevant factor to consider when assessing the effects of alcohol exposure in normal colon crypt epithelial cells. Ethanol exposure led to an increase in overall number of proliferative transit amplifying cells at the expense of differentiated cells, in the left colon This result has important implications for cancer risk as it suggests that alcohol consumption could lead to an increased zone of cells in the lower part of the crypt in the colon, where conditions are optimal for cell division and the potential to develop mutations. These results provide important insight into the molecular basis for the observed differential effect of alcohol consumption on risk for different locations of the colon

Methods

Results

Conclusion