Detection of an Endogenous Urinary Biomarker Associated With CYP2D6 Activity Using Global Metabolomics

Jessica Tay-Sontheimer; Laura M Shireman; Richard P Beyer; Taurence Senn; Daniela Witten; Robin E Pearce; Andrea Gaedigk; Cletus L Gana Fomban; Justin D Lutz; Nina Isoherranen; Kenneth E Thummel; Oliver Fiehn; J Steven Leeder; Yvonne S Lin


Pharmacogenomics. 2014;15(16):1947-1962. 

In This Article

Abstract and Introduction


Aim We sought to discover endogenous urinary biomarkers of human CYP2D6 activity.

Patients & Methods Healthy pediatric subjects (n = 189) were phenotyped using dextromethorphan and randomized for candidate biomarker selection and validation. Global urinary metabolomics was performed using liquid chromatography quadrupole time-of-flight mass spectrometry. Candidate biomarkers were tested in adults receiving fluoxetine, a CYP2D6 inhibitor.

Results A biomarker, M1 (m/z 444.3102) was correlated with CYP2D6 activity in both the pediatric training and validation sets. Poor metabolizers had undetectable levels of M1, whereas it was present in subjects with other phenotypes. In adult subjects, a 9.56-fold decrease in M1 abundance was observed during CYP2D6 inhibition.

Conclusion Identification and validation of M1 may provide a noninvasive means of CYP2D6 phenotyping.


In various pediatric populations, a substantial percentage (10–65%)[1] of drugs are prescribed off-label, primarily because of lack of study information in this age group.[2] Although the number of drugs with some pediatric dosing information doubled from 22% in 1975 to 41% in 2009,[3] available information remains inadequate to provide effective safety and dosing guidances for all pediatric age groups. Studies conducted in the past two decades show major deficiencies with pediatric dosing methods built on allometry.[4–8] Optimal drug safety and efficacy in this vulnerable population requires an increased understanding of the impacts of physiological maturation and genetic variation on drug-metabolizing enzymes.[9–11] One such enzyme, CYP2D6, participates in the elimination of approximately 15% of clinically used drugs metabolized by cytochrome P450s,[12] including antipsychotics and antidepressants, beta-blockers, opioid analgesics[13,14] and the antitussive dextromethorphan (DM).[15]

CYP2D6 activity is determined, in significant part, by genetic variation. More than 100 allelic variants and subvariants of this highly polymorphic enzyme are defined,[16] including gene deletions, and nonfunctional, reduced-function and multiple-copy-number alleles.[17,18] The various allele combinations result in a continuum from little or no activity and poor metabolizer (PM) phenotype, reduced function and intermediate metabolizer phenotype, 'wild-type' activity and extensive metabolizer phenotype to, in the case of gene duplications, increased CYP2D6 expression and ultrarapid metabolizer phenotype.[18–20] Gaedigk et al. proposed using these genetic factors to predict individual CYP2D6 activity scores.[19,21]

Substantial interindividual variation in CYP2D6 activity exists within each category of CYP2D6 phenotype.[21–23] Factors such as ontogeny, drug–drug interactions (DDIs), diet and disease may contribute to patient variation in drug disposition. Thus, phenotyping may be necessary to determine CYP2D6 activity when personalizing drug therapy[24] or evaluating DDIs.[25] Traditional phenotyping studies involve the administration of a probe drug or drug cocktail. The administration of such drugs to children, pregnant women and the elderly may be a concern.

Phenotyping using endogenous biomarkers is an alternative method of assessing CYP2D6 activity that may eliminate risks of exogenous drug administration in CYP2D6 DDI studies or when evaluating altered activity in special patient populations. Additionally, retrospective analyses of banked samples may be conducted without prior knowledge of an individual's CYP2D6 phenotype. If biomarker measurements from a spot urine sample could be used, that could eliminate the need for prolonged clinical visits in which the patient must provide timed sample collections. For example, CYP2D6 activity can be measured using a 4-h urine collection following DM administration. Several endogenous substrates have been proposed as CYP2D6 substrates. They include 5-methoxy-N,N-dimethyltryptamine,[26] pinoline,[27] progesterone,[28] anandamide[29,30] and a number of compounds up- or downregulated in CYP2D6-transgenic mice.[31] However, the identification and validation of endogenous biomarkers for CYP2D6 phenotyping, particularly in humans, is immature.

The goal of this study was to discover endogenous biomarkers of CYP2D6 activity. Children were phenotyped for CYP2D6 activity using a urinary dextromethorphan-to-dextrorphan metabolic ratio (DM/DX),[21,32] and a global metabolomics approach was used to detect endogenous, urinary metabolites capable of predicting DM/DX in a pediatric training set group. A targeted analytical approach was used to further analyze the relationship between a candidate biomarker and CYP2D6 activity, and these results were validated in urine from a second group of children. Furthermore, the change in metabolite levels and CYP2D6 activity was assessed in adults during CYP2D6 inhibition.