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Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer, though mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. We use human colonic organoids to profile ASA responses on genome-wide gene expression and chromatin accessibility. Human colonic organoids from one individual were cultured and treated in triplicate with 3 mM ASA or vehicle control (DMSO) for 24 h. Gene expression and chromatin accessibility were measured using RNA- and ATAC-sequencing, respectively. Differentially expressed genes were analyzed using DESeq2. Top genes were validated by qPCR. Gene set enrichment was performed by SetRank. Differentially accessible peaks were analyzed using DiffBind and edgeR. Peak annotation and differential transcription factor motifs were determined by HOMER and diffTF. The results showed robust transcriptional responses to ASA with significant enrichment for fatty acid oxidation and peroxisome proliferator-activated receptor (PPAR) signaling that were validated in independent organoid lines. A large number of differentially accessible chromatin regions were found in response to ASA with significant enrichment for Fos, Jun, and Hnf transcription factor motifs. Integrated analysis of epigenomic and genomic treatment responses highlighted gene regions that could mediate ASA’s specific effects in the colon including those involved in chemoprotection and/or toxicity. Assessment of chromatin accessibility and transcriptional responses to ASA yielded new observations about genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study colonic ASA responses between individuals and populations in future studies.

In Tibetans, noncoding alleles in EPAS1 —whose protein product hypoxia-inducible factor 2α (HIF-2α) drives the response to hypoxia—carry strong signatures of positive selection; however, their functional mechanism has not been systematically examined. Here, we report that high-altitude alleles disrupt the activity of four EPAS1 enhancers in one or more cell types. We further characterize one enhancer (ENH5) whose activity is both allele specific and hypoxia dependent. Deletion of ENH5 results in down-regulation of EPAS1 and HIF-2α targets in acute hypoxia and in a blunting of the transcriptional response to sustained hypoxia. Deletion of ENH5 in mice results in dysregulation of gene expression across multiple tissues. We propose that pleiotropic adaptive effects of the Tibetan alleles in EPAS1 underlie the strong selective signal at this gene.

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

Background: African Americans have the highest burden of colorectal cancer (CRC) in the US. Active 1,25(OH)2vitamin D (1,25vitD) protects from CRC, though the role of population differences in 1,25vitD responses to CRC disparities is unknown. To study inter-ethnic host-environment interactions in the colon, we have established human-derived colonic organoids from diverse populations. We used this approach to study differences in transcriptional and chromatin accessibility responses to 1,25vitD between Americans of African (AA) and European (EA) ancestry. Methods: Colonic organoids from 60 subjects (30 AA and 30 EA) were established. After passaging, organoids were differentiated for 24h and then treated with 100nM 1,25vitD or ethanol (vehicle control). Chromatin accessibility and gene expression were assessed at 4 and 6 hours by RNA-seq and ATAC-seq, respectively. Inter-ethnic responses were assessed using dream (Hoffman et al, 2020). Genotyping was performed using the Infinium OmniExpress-24, and ancestry was estimated using imputed genotypes. Expression quantitative trait loci (eQTL) mapping was performed using BRIdGE (Maranville et al, 2011). Results: Organoid lines from 54 subjects (28 AA and 26 EA) were included after removing 5 with inconsistent ancestry. For overall 1,25vitD response, 7816 differentially expressed protein-coding genes at a false discovery rate (FDR) Citation Format: Sonia Kupfer, David Witonsky, Jinchao Li, Margaret Bielski, Kristi Lawrence. Differences in vitamin D genomic and epigenomic responses in colonic organoids from African- and European-Americans [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-143.