The Impact of the CYP2D6 “Enhancer” Single Nucleotide Polymorphism on CYP2D6 Activity

Abstract

rs5758550 has been associated with enhanced transcription and suggested to be a useful marker of CYP2D6 activity. As there are limited and inconsistent data regarding the utility of this distant “enhancer” single nucleotide polymorphism (SNP), our goal was to further assess the impact of rs5758550 on CYP2D6 activity toward two probe substrates, atomoxetine (ATX) and dextromethorphan (DM), using in vivo urinary metabolite (DM; n = 188) and pharmacokinetic (ATX; n = 70) and in vitro metabolite formation (ATX and DM; n = 166) data. All subjects and tissues were extensively genotyped, the “enhancer” SNP phased with established CYP2D6 haplotypes either computationally or experimentally, and the impact on CYP2D6 activity investigated using several linear models of varying complexity to determine the proportion of variability in CYP2D6 activity captured by each model. For all datasets and models, the “enhancer” SNP had no or only a modest impact on CYP2D6 activity prediction. An increased effect, when present, was more pronounced for ATX than DM suggesting potential substate‐dependency. In addition, CYP2D6*2 alleles with the “enhancer” SNP were associated with modestly higher metabolite formation rates in vitro, but not in vivo; no effect was detected for CYP2D6*1 alleles with “enhancer” SNP. In summary, it remains inconclusive whether the small effects detected in this investigation are indeed caused by the “enhancer” SNP or are rather due to its incomplete linkage with other variants within the gene. Taken together, there does not appear to be sufficient evidence to warrant the “enhancer” SNP be included in clinical CYP2D6 pharmacogenetic testing.

Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine

“…Apart from itself, rs5758550, located 115 kbp downstream of the CYP2D6 promoter, resides within a pivotal enhancer region directing CYP2D6 expression. The “enhancer” SNP was suggested to affect overall CYP2D6 mRNA expression ( Wang et al, 2015 ; Dinh et al, 2021 ). These findings provide support for our current results.…”

A frequent CYP2D6 variant promotes skipping of exon 3 and reduces CYP2D6 protein expression in human liver samples

“…However, there have been a few studies that debate the influence of rs5758550 and rs16947. For example, rs5758550 apparently does not alter CYP2D6*2 activity towards the metabolism of tamoxifen ( Sanchez-Spitman et al, 2017 ) or dextromethorphan ( Dinh et al, 2022 ) but does impact atomoxetine metabolism ( Dinh et al, 2022 ). These discrepancies may be due to a variety of reasons, including the highly polymorphic nature of CYP2D6, the small sample sizes used in the studies, the analysis methods used, and the capacity of a substrate drug to serve as a surrogate for CYPD6-specific enzyme activity and/or protein abundance.…”

“…In a recent cross-ancestry GWAS, the compensatory effect of rs5758550 on the deleterious effects of rs16947 was confirmed for CYP2D6-dependent endoxifen plasma concentration ( Khor et al, 2023 ). However, there are inconsistent results regarding the impact of rs5758550 and rs16947 on in vivo CYP2D6 protein expression/activity ( Sanchez-Spitman et al, 2017 ; Ning et al, 2018 ; Thomas et al, 2020 ; Dinh et al, 2022 ; Khor et al, 2023 ). Furthermore, overall CYP2D6 mRNA levels do not seem to correlate well with protein levels ( Ning et al, 2018 ), indicating that additional uncharacterized post-transcriptional events influence CYP2D6 expression.…”

PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting

“…Additionally, variants in regulatory regions within the extended 22q13 locus and a variant in NFIB have also been suggested to impact CYP2D6 function 16–21 . Although those within CYP2D6 may directly impact metabolic capacity, the clinical utility of variants indirectly acting on function via regulatory mechanisms has, however, not yet been demonstrated.…”

“…Additionally, variants in regulatory regions within the extended 22q13 locus and a variant in NFIB have also been suggested to impact CYP2D6 function. [16][17][18][19][20][21] Although those within CYP2D6 may directly impact metabolic capacity, the clinical utility of variants indirectly acting on function via regulatory mechanisms has, however, not yet been demonstrated. A patient may also have a rare variant(s) in the CYP2D6 gene which may not be interrogated but could conceivably impact function or variants in other genes that contribute to drug metabolism and disposition.…”