Elucidation of the genetic basis of the common ‘intermediate metabolizer’ phenotype for drug oxidation by CYP2D6

Abstract

A subgroup of 10-15% of Caucasians are termed phenotypical 'intermediate metabolizers' of drug substrates of CYP2D6 because they have severely impaired yet residual in-vivo function of this cytochrome P450. Genotyping based on the currently known CYP2D6 alleles does not predict this phenotype satisfactorily. A systematic sequencing strategy through 1.6 kb of the CYP2D6 5'-flanking sequence revealed six mutations of which three were exclusively associated with the functional CYP2D6*2 allele (-1496 C to G; -652 C to T; and -590 G to A), two were associated with the nonfunctional *4 and with the functional *10-alleles (-1338 C to T and -912 G to A) and one (-1147 A to G) was seen in all *2, *4 and *10-alleles investigated. The -1496 C to G mutation was found to be polymorphic within CYP2D6*2 alleles. In a family study, the wild-type CYP2D6 *2[-1496 C] and the novel variant [-1496 G] allele co-segregated with lower and higher CYP2D6 in-vivo function, respectively, as shown by phenotyping using sparteine as probe drug. In a representative population sample selected for genotypes comprising one CYP2D6*2 and one non-functional allele, the median urinary metabolic ratio (MRs) for sparteine oxidation was 4.4-fold reduced in individuals with the variant allele (*2[-1496 G], MRs = 0.53, n = 27) compared with individuals lacking the mutation (*2[-1496 C], MRs = 2.33, n = 12; P < 0.0001). The mutation -1496 C to G has an estimated frequency of approximately 20% in the general population and allows establishment of a genotype for the identification of over 60% of intermediate metabolizers in Caucasian populations.

Association of graded allele-specific changes in CYP2D6 function with imipramine dose requirement in a large group of depressed patients

“…Our findings corroborate a recent report stating that psychiatric patients genotyped homozygous or heterozygous for CYP2C19 and CYP2D6 null alleles (CYP2C19*2, and CYP2D6*3, *4, *5 and *6) were hospitalized for a longer time during treatment with psychotropic medication, as compared with subjects without these alleles. 44 The allele frequencies and prevalence of 'abnormal' CYP2D6 genotypes (that is, without functional alleles or with an elevated number of functional alleles) that we found were in agreement with the figures previously reported for Western populations, 13,22,34,35,45,46 and depressed patients in specialized psychiatric hospitals, 47,48 respectively.…”

“…This clearly indicates the importance of genotyping for the reduced-function CYP2D6 alleles *9, *10 and *41. 22,35,[39][40][41] Testing for CYP2D6 *3, *4, *5, *6, *9, *10 and *41, and gene duplication, followed by calculation of the SGD, may thus help to predict IMI metabolism for all subgroups of subjects, allowing for an alternative IMI starting dose to reach predefined IMI þ DESI plasma concentrations more quickly.…”

“…13 Therefore, a clear-cut gene-dose effect could not be established so far. 3,21 Newly identified genetic polymorphisms, encoding decreased rather than deficient alleles, such as CYP2D6*41 (which was reported to account for 60% of intermediate metabolizers), 22 may facilitate a greatly desired prediction of metabolic activity and/ or clinical outcome. So far, the potential benefit of pretherapeutic CYP2D6 genotyping has seriously been restricted to a limited fraction of patients, that is, poor and ultrarapid metabolizers only.…”

Identification and characterization of novel sequence variations in the cytochrome P4502D6 (CYP2D6) gene in African Americans

“…[25][26][27] This was primarily due to the fact that sequence data to support these investigations was limited to 1620 bp of 5 0 -flanking sequence deposited in M33388 commonly referred to as the 'Kimura sequence'. 28 Furthermore, sequence data for the CYP2D7-2D6 intergenic region were incomplete, since the 'Kimura sequence' and accession X90926 (containing partial intergenic sequence and connecting with the CYP2D7/2D8 locus sequence M33387) did not overlap.…”

High-throughput analysis of informative CYP2D6 compound haplotypes

“…The genotypic information that the protocol provides can be used in conjunction with known CYP2D6 allele frequencies in different ethnic groups as a guide to deciding which other polymorphisms should be characterized, depending on whether a study is concerned with identifying URM or IM phenotypes. For example, CYP2D6*2 alleles can be further characterized into three distinct haplotypes that confer different enzyme activities: the multiduplicated CYP2D6*2 (n) [3], CYP2D6*2 [Ϫ1496G], and CYP2D6*2 [Ϫ1496C] [48]. The multiduplicated CYP2D6*2 and variants cause the overexpression of CYP2D6 enzyme that results in the URM phenotype: CYP2D6*2 [Ϫ1496G] has several amino acid differences from the wild type (CYP2D6*1), but comparable enzyme activity; the variant with the 5Ј flanking sequence Ϫ1496C mutation in the presumed transcription initiation site causes the gene to be transcribed less efficiently and the CYP2D6*2 [Ϫ1496C]/*0 (null) genotype is believed to be responsible for at least 50 -60% of IM phenotypes in Europeans.…”