Tania N. Fabo, Robin M. Meyers, Evin Padhi, Laura N. Kellman, Yang Zhao et al.
Interactions between genetic variants and environmental factors influence malignancy risk, including for colorectal cancer (CRC). Prevalent CRC susceptibility loci reside predominantly in noncoding regulatory DNA where they may interact with dietary influences to dysregulate expression of specific genes predisposing to neoplasia. The impacts of CRC protective and risk dietary metabolites, butyrate and deoxycholic acid, were thus studied on the transcription-directing activity of 3703 regulatory CRC-associated variants via massively parallel reporter assays (MPRA) in human colonic cells. 1595 variant-dietary metabolite interactions were identified, pointing to dysregulation of MED13L, NKD2, and several modulators of Wnt/β-catenin signaling in potential CRC gene-environment interactions (GxE). Opposing impacts of butyrate and deoxycholic acid were also uncovered, indicating dietary influences may converge on common CRC risk loci and nominating FOSL1 and SP1 as mediators of these opposing responses. Coupling MPRA to relevant environmental factors offers an approach to extend insight into GxE in common human cancers.
Tania N. Fabo, Robin M. Meyers, Evin Padhi, Laura N. Kellman, Yang Zhao, Soumya Kundu, David L. Reynolds, Ziwei Chen, Xue Yang, Lisa Ko, Ibtihal Elfaki, Stephen B. Montgomery, Paul A. Khavari. Interactions Between Dietary Metabolites and Regulatory Risk Variants for Human Colon Cancer. 2025-09-08. https://doi.org/10.1101/2025.09.05.674475
A soft/random-barcoded lentiviral MPRA library tested 3,703 CRC-associated variants in 200-bp GRCh38 contexts in forward and reverse-complement orientations, alongside enhancer and transcription-factor motif controls. HCT116 cells were exposed to sodium butyrate or DCA for 6 or 24 h with vehicle controls, and the released table reports orientation-specific variant allelic, treatment, and interaction effects.
A hard-barcoded lentiviral MPRA library tested 1,595 CRC-associated variants in 155-bp GRCh38 genomic contexts, with 10 barcodes per allelic fragment. Primary human colonic epithelial cells were exposed to sodium butyrate or deoxycholic acid (DCA) alongside vehicle controls, and the released table reports fragment-level allelic, treatment, and interaction effects.
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