Information theory-based analysis of CYP2C19, CYP2D6 and CYP3A5 splicing mutations.

Several mutations are known or suspected to affect mRNA splicing of CYP2C19, CYP2D6 and CYP3A5 genes; however, little experimental evidence exists to support these conclusions. The present study applies mathematical models that measure changes in information content of splice sites in these genes to demonstrate the relationship between the predicted phenotypes of these variants to the corresponding genotypes. Based on information analysis, the CYP2C19*2 variant activates a new cryptic site 40 nucleotides downstream of the natural splice site. CYP2C19*7 abolishes splicing at the exon 5 donor site. The CYP2D6*4 allele similarly inactivates splicing at the acceptor site of exon 4 and activates a new cryptic site one nucleotide downstream of the natural acceptor. CYP2D6*11 inactivates the acceptor site of exon 2. The CYP3A5*3 allele activates a new cryptic site 236 nucleotides upstream of the exon 4 natural acceptor site. CYP3A5*5 inactivates the exon 5 donor site and CYP3A5*6 strengthens a site upstream of the natural donor site, resulting in skipping of exon 7. Other previously described missense and nonsense mutations at terminal codons of exons in these genes affected splicing. CYP2D6*8 and CYP2D6*14 both decrease the strength of the exon 3 donor site, producing transcripts lacking this exon. The results of information analysis are consistent with the poor metabolizer phenotypes observed in patients with these mutations, and illustrate the potential value of these mathematical models to quantitatively evaluate the functional consequences of new mutations suspected of altering mRNA splicing.

[1]  R. Preisig,et al.  Pharmacogenetics of mephenytoin: A new drug hydroxylation polymorphism in man , 2004, European Journal of Clinical Pharmacology.

[2]  U. Meyer,et al.  The human CYP2D locus associated with a common genetic defect in drug oxidation: a G1934----A base change in intron 3 of a mutant CYP2D6 allele results in an aberrant 3' splice recognition site. , 1990, American journal of human genetics.

[3]  T. D. Schneider,et al.  Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. , 1992, Journal of molecular biology.

[4]  J. Nicklas,et al.  Mutations that alter RNA splicing of the human HPRT gene: a review of the spectrum. , 1998, Mutation research.

[5]  D. Nebert,et al.  Characterization of the common genetic defect in humans deficient in debrisoquine metabolism , 1988, Nature.

[6]  J. Goldstein,et al.  A multifamily study on the relationship between CYP2C19 genotype and s-mephenytoin oxidation phenotype. , 1995, Pharmacogenetics.

[7]  T. D. Schneider,et al.  Information analysis of human splice site mutations , 1998, Human mutation.

[8]  T. D. Schneider,et al.  Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. , 1997, Nucleic acids research.

[9]  R. Skoda,et al.  The human debrisoquine 4-hydroxylase (CYP2D) locus: sequence and identification of the polymorphic CYP2D6 gene, a related gene, and a pseudogene. , 1989, American journal of human genetics.

[10]  P K Rogan,et al.  Redundant designations of BRCA1 intron 11 splicing mutation; c. 4216‐2A>G; IVS11‐2A>G; L78833, 37698, A>G , 2000, Human mutation.

[11]  P K Rogan,et al.  Organization of the ABCR gene: analysis of promoter and splice junction sequences. , 1998, Gene.

[12]  M H Tarbit,et al.  Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: structural studies on specific CYP2D6 substrate metabolism. , 1997, Xenobiotica; the fate of foreign compounds in biological systems.

[13]  T. D. Schneider,et al.  The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function. , 2002, Nucleic acids research.

[14]  S. Sviri,et al.  Phenotypic‐genotypic analysis of CYP2C19 in the Jewish Israeli population , 1999, Clinical pharmacology and therapeutics.

[15]  M. Eichelbaum,et al.  Assessment of the predictive power of genotypes for the in-vivo catalytic function of CYP2D6 in a German population. , 1998, Pharmacogenetics.

[16]  P K Rogan,et al.  Autosomal dominant zonular cataract with sutural opacities is associated with a splice mutation in the betaA3/A1-crystallin gene. , 1998, Molecular vision.

[17]  U. Brinkmann,et al.  Genomic organization of the human CYP3A locus: identification of a new, inducible CYP3A gene. , 2001, Pharmacogenetics.

[18]  J. Vockley,et al.  Exon skipping in IVD RNA processing in isovaleric acidemia caused by point mutations in the coding region of the IVD gene. , 2000, American journal of human genetics.

[19]  L. Bertilsson,et al.  Pronounced differences between native Chinese and Swedish populations in the polymorphic hydroxylations of debrisoquin and S‐mephenytoin , 1992, Clinical pharmacology and therapeutics.

[20]  M. Eichelbaum,et al.  Defective N-oxidation of sparteine in man: A new pharmacogenetic defect , 1979, European Journal of Clinical Pharmacology.

[21]  G R Wilkinson,et al.  The major genetic defect responsible for the polymorphism of S-mephenytoin metabolism in humans. , 1994, The Journal of biological chemistry.

[22]  U. Meyer,et al.  Evolution of a highly polymorphic human cytochrome P450 gene cluster: CYP2D6. , 1992, Genomics.

[23]  J. Brockmöller,et al.  Cytochrome P450 2D6 variants in a Caucasian population: allele frequencies and phenotypic consequences. , 1997, American journal of human genetics.

[24]  R. Pyeritz,et al.  Splice-site mutations in atherosclerosis candidate genes: relating individual information to phenotype. , 1999, Circulation.

[25]  Ann Daly,et al.  Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression , 2001, Nature Genetics.

[26]  M. Relling,et al.  Pharmacogenomics: translating functional genomics into rational therapeutics. , 1999, Science.

[27]  Jin‐ding Huang,et al.  Genetic polymorphism of cytochrome P450 3A5 in Chinese. , 2001, Drug metabolism and disposition: the biological fate of chemicals.

[28]  P. Dayer,et al.  A novel transversion in the intron 5 donor splice junction of CYP2C19 and a sequence polymorphism in exon 3 contribute to the poor metabolizer phenotype for the anticonvulsant drug S-mephenytoin. , 1999, The Journal of pharmacology and experimental therapeutics.

[29]  Jack A. Taylor,et al.  Splice variants but not mutations of DNA polymerase beta are common in bladder cancer. , 2002, Cancer research.

[30]  T. D. Schneider,et al.  Information content of individual genetic sequences. , 1997, Journal of theoretical biology.

[31]  J. Lafitte,et al.  Polymorphism of the cytochrome P450 CYP2D6 gene in a European population: characterization of 48 mutations and 53 alleles, their frequencies and evolution. , 1997, Pharmacogenetics.

[32]  J. Lo-Guidice,et al.  A novel CYP2D6 allele with an abolished splice recognition site associated with the poor metabolizer phenotype. , 1995, Pharmacogenetics.

[33]  M. Lai,et al.  G169R mutation diminishes the metabolic activity of CYP2D6 in Chinese. , 1999, Drug metabolism and disposition: the biological fate of chemicals.

[34]  E. Skjelbo,et al.  Phenotypes and genotypes for CYP2D6 and CYP2C19 in a black Tanzanian population. , 1999, British journal of clinical pharmacology.

[35]  J. Goldstein,et al.  Biochemistry and molecular biology of the human CYP2C subfamily. , 1994, Pharmacogenetics.

[36]  P K Rogan,et al.  Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites , 1995, Human mutation.

[37]  S. Berget.  Exon Recognition in Vertebrate Splicing (*) , 1995, The Journal of Biological Chemistry.

[38]  J Deisenhofer,et al.  Structure and function of cytochromes P450: a comparative analysis of three crystal structures. , 1995, Structure.

[39]  R. Padgett,et al.  Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. , 1994, Journal of molecular biology.

[40]  Thomas D. Schneider,et al.  Rogan PK, Faux BM, Schneider TD. 1998. Information analysis of human splice site mutations. Hum Mutat 12:153–171. , 1999 .

[41]  J. Idle,et al.  POLYMORPHIC HYDROXYLATION OF DEBRISOQUINE IN MAN , 1977, The Lancet.