Germline Variant in DPYD Enhancer Regulates Expression and Alters Sensitivity to Anti-Cancer Drug 5-Fluorouracil

Core Concepts

A common germline variant (rs4294451) located within a novel enhancer region for the anti-cancer drug metabolism gene DPYD controls its transcription and alters cellular sensitivity to the chemotherapeutic 5-fluorouracil.

Abstract

The study identified a novel cis enhancer region (E9) located approximately 9 kb upstream of the DPYD gene that regulates its expression. Using reporter assays, CRISPR genome editing, and human liver samples, the authors demonstrated that the genotype status of the common germline variant rs4294451 within the E9 enhancer controls DPYD transcription and alters cellular sensitivity to the anti-cancer drug 5-fluorouracil (5-FU).

The variant genotype (A allele) was associated with reduced recruitment of the transcription factor CEBPB to the E9 enhancer, decreased interactions between the enhancer and DPYD promoter, and lower DPYD expression. Cells carrying the A allele showed increased sensitivity to 5-FU compared to those with the reference T allele.

The authors provide mechanistic insights into how a regulatory genetic variant can impact drug metabolism and sensitivity, offering a potential biomarker for predicting 5-FU toxicity risk and resistance. The findings suggest that the rs4294451 variant, which is more common in individuals of African ancestry, could contribute to racial disparities in colorectal cancer outcomes with 5-FU-based therapies.

Stats

Cells homozygous for the rs4294451 A allele had an IC50 of 9.1 μM 5-FU, while cells homozygous for the T allele had an IC50 of 95.0 μM.
Cells heterozygous for rs4294451 A/T had an intermediate IC50 of 29.9 μM 5-FU.

Quotes

"Cells homozygous for the reference T allele showed significantly higher CEBPB occupancy at both E9 and the DPYD promoter than A/T or A/A cells."
"CEBPB knockdown significantly reduced the IC50 for 5-FU in rs4294451 T/T cells, but not in rs4294451 A/A cells."

Key Insights Distilled From

Germline cis variant determines epigenetic regulation of the anti-cancer drug metabolism gene dihydropyrimidine dehydrogenase (DPYD)

by Zhang,T., Am... at www.biorxiv.org 11-05-2023

https://www.biorxiv.org/content/10.1101/2023.11.01.565230v2

Deeper Inquiries

How might the rs4294451 variant interact with other known DPYD variants to modulate 5-FU toxicity and resistance?

The rs4294451 variant, located within the enhancer region of the DPYD gene, plays a crucial role in regulating DPYD expression. This variant can interact with other known DPYD variants, such as c.85T>C and c.496A>G, to modulate 5-FU toxicity and resistance. The rs4294451 variant affects the binding of transcription factors like CEBPB to the enhancer region, leading to altered DPYD expression. Variants in the coding region of DPYD, like c.85T>C and c.496A>G, are in linkage disequilibrium with rs4294451, suggesting that the regulatory effects of rs4294451 can impact the overall DPD activity. Therefore, the interplay between rs4294451 and other DPYD variants can influence the risk of severe 5-FU toxicity and the development of resistance to 5-FU therapy.

What other transcription factors or epigenetic regulators might be involved in the genotype-dependent control of DPYD expression?

In addition to CEBPB, other transcription factors and epigenetic regulators may be involved in the genotype-dependent control of DPYD expression. Some potential candidates include FOXA1, FOXA2, JUND, MYBL2, and HNF4A, as these factors have been shown to bind to the enhancer region of DPYD. These transcription factors can interact with the enhancer region and modulate DPYD expression in a genotype-dependent manner. Furthermore, epigenetic modifications such as histone acetylation and methylation can also influence the accessibility of the enhancer region and regulate DPYD expression. Understanding the comprehensive network of transcription factors and epigenetic regulators involved in the regulatory axis of DPYD will provide valuable insights into the mechanisms underlying 5-FU toxicity and resistance.

Could targeting the CEBPB-DPYD regulatory axis be a strategy to overcome 5-FU resistance in colorectal and other cancers?

Targeting the CEBPB-DPYD regulatory axis could be a promising strategy to overcome 5-FU resistance in colorectal and other cancers. By modulating the activity of CEBPB, which regulates DPYD expression through the enhancer region, it may be possible to alter the sensitivity of cancer cells to 5-FU. Inhibiting CEBPB or disrupting its binding to the enhancer region could lead to decreased DPYD expression, potentially increasing the efficacy of 5-FU treatment. Additionally, targeting other components of the regulatory axis, such as epigenetic modifiers that control the chromatin state of the enhancer region, could also be explored as a therapeutic approach to sensitize cancer cells to 5-FU. Further research into the specific mechanisms of the CEBPB-DPYD regulatory axis and its role in 5-FU resistance will be essential for the development of targeted therapies in cancer treatment.