Abstract B19: Colonic transcriptional response to 1,25(OH)2 vitamin D in African and European Americans
Authors: Kupfer Sonia , Mapes Brandon , Nakagome Shigeki , Witonsky David , Rienzo Anna Di 
Published: May 2016

Abstract
Background: 1,25(OH)2 vitamin D (1,25vitD) is a steroid hormone with anti-cancer effects that functions through direct transcriptional mechanisms. In colorectal cancer (CRC), 1,25vitD is thought to play a protective role; however, it is not known to what extent inter–ethnic differences in transcriptional response could underlie differences in disease susceptibility in African-Americans (AA) whose incidence of CRC is the highest in the US. To study differences in short-term transcriptional response in the colon, we have optimized an ex vivo culture system using colonic biopsies obtained during colonoscopy, thereby eliminating a number of confounders. We use this system to study transcriptional responses between ethnicities.
Methods: Healthy subjects (n=69; 34 in discovery cohort & 35 in replication cohort) undergoing colonoscopy were consented and colonic biopsies were obtained at the rectosigmoid junction. Two colonic biopsies each were treated with 0.1μM 1,25vitD or vehicle control (EtOH) and incubated for 6 hours at 37°C. For the discovery cohort, RNA from two treatment replicates was pooled and hybridized to Illumina Human HT-12 expression chips. Transcriptional response was analyzed using the packages LUMI and LIMMA in R adjusting for covariates and multiple testing. For the replication cohort, expression for select genes was performed using quantitative real-time PCR. In silico analysis was done to identify vitamin D receptor (VDR) binding peaks using ChIP-sequence data from LS180 cell lines.
Results: In the discovery cohort, 16 AA and 18 European Americans (EA) were included. As proof of concept, the top two significantly up-regulated genes were CD14 (p=1.15x10-25) and CYP24A1 (p=7.65x10-23). There were 10 genes that showed significantly different responses to 1,25vitD between AA and EA including UPP1, UCKL1, ZSWIM4, ERCC1, MFSDA2, EPHA2, CLRN3, KIAA1324, TRIP8 and WDR55. In the replication cohort, 20 AA and 15 EA were included. Of 5 genes tested to date, 3 genes (UPP1, ERCC1 & ZSWIM4) showed evidence of replication with similar direction and effect sizes as the discovery cohort. Two genes (UCKL1 & UPP1) have VDR binding peaks within an intron (UCKL1) or 21kb downstream (UPP1). Within these peaks, there are SNPs with allele frequency differences between Africans and Europeans. In particular, the UCKL1 SNP rs58190754 that is located within the DR3 binding motif and is predicted to be functionally significant for VDR binding has an allele frequency of 10% in YRI & AA and &lt;1% in Europeans.
Conclusions: Using short-term ex vivo culture of primary colonic tissue, we found significantly up- and down-regulated genes in response to 1,25vitD including a number of established 1,25vitD targets. There were 10 genes with significantly different transcriptional responses to 1,25vitD treatment between AA and EA of which 3 genes have been replicated in preliminary work. Two genes (UPP1 & UCKL1) harbor VDR binding peaks with candidate SNPs that could be functionally relevant for gene expression differences between populations. These genes are involved in pyrimidine salvage and could have a role in cancer susceptibility. Future work will genotype SNPs and determine whether genotype predicts expression. In addition, functional assays of pyrimidine salvage are being tested. Finally, replication of additional genes is ongoing. Further studies of these genes may reveal important pathways underlying CRC disparities.
Citation Format: Sonia Kupfer, Brandon Mapes, Shigeki Nakagome, David Witonsky, Anna Di Rienzo. Colonic transcriptional response to 1,25(OH)2 vitamin D in African and European Americans. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr B19.