906 Variations Among 27 Genes Encoding Cytochrome P450 (CYP) Enzymes and Aldehyde Dehydrogenases (Aldhs) in the Japanese Population
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B.J Hum Jochimsen Genet et(2002) al.: Stetteria 47:419–444 hydrogenophila © Jpn Soc Hum Genet and Springer-Verlag4600/419 2002 ORIGINAL ARTICLE Susumu Saito · Aritoshi Iida · Akihiro Sekine Chie Ogawa · Saori Kawauchi · Shoko Higuchi Machi Ohno · Yusuke Nakamura 906 variations among 27 genes encoding cytochrome P450 (CYP) enzymes and aldehyde dehydrogenases (ALDHs) in the Japanese population Received: April 23, 2002 / Accepted: April 25, 2002 Abstract We screened DNAs from 48 Japanese individuals steroid hormones and xenobiotics, including various car- for single-nucleotide polymorphisms (SNPs) in genes en- cinogens and toxins (Denison and Whitlock 1995; Nelson et coding 13 cytochrome P450 (CYP) enzymes and 14 alde- al. 1996). CYP genes are classified into different families hyde dehydrogenases (ALDHs) by directly sequencing and subfamilies on the basis of sequence similarities. their entire genomic regions except for repetitive elements. Polymorphisms have been reported in CYP1A1, This approach identified 810 SNPs and 96 insertion/deletion CYP1A2, and CYP1B1 genes [Human Cytochrome polymorphisms among the 27 genes. Of the 810 SNPs, 229 P450 (CYP) Allele Nomenclature Committee, http:// were identified among the CYP genes and 581 in the ALDH www.imm.ki.se/CYPalleles/]. These three genes are genes; of the total, 48 SNPs were located in 5Ј flanking inducible by exposure to agents such as 2,3,7,8- regions, 619 in introns, 91 in exons, and 52 in 3Ј flanking tetrachlorodibenzo-p-dioxin (dioxin; Jaiswal et al. 1985, regions. These variants should contribute to studies 1987; Sutter et al. 1994) Two polymorphisms in the designed to investigate possible correlations between CYP1A1 gene, a T-to-C polymorphism in the 3Ј-noncoding genotypes and phenotypes of disease susceptibility or region and an A-to-G polymorphism (Ile462Val) in exon 7, responsiveness to drug therapy. appear to be associated with susceptibility to lung cancer (Spurr et al. 1987; Hayashi et al. 1991). For its part, Key words Single-nucleotide polymorphism (SNP) · Cyto- CYP1A2 is expressed in human liver but expression levels chrome P450 (CYP) · Aldehyde dehydrogenase (ALDH) · vary significantly from one individual to another (Butler et Steroid and xenobiotic receptor/pregnenolone X receptor al. 1992). An SNP in its 5Ј flanking region affects inducibil- (SXR/PXR) · Nuclear receptor · Xenobiotic response ity of this enzyme (Nakajima et al. 1999). Another SNP, in element · Dioxin-responsive enhancer intron 1, was associated with high catalytic activity when subjects were exposed to tobacco smoke (Sachse et al. 1999). Introduction As for CYP1B1, a C-to-G polymorphism (Leu432Val) in exon 3 has been associated with estrogen receptor-positive and progesterone receptor-positive breast cancers in Cau- Cytochrome P450 (CYP) enzymes belong to a superfamily casian patients, as well as with prostate cancers in other of hemoproteins that play central roles in the oxidative racial groups (Bailey et al. 1998; Stoilov et al. 1998; Tang et metabolism of numerous endogenous substrates such as al. 2000). Another polymorphism in this gene, Ala119Ser in exon 2, appears to influence susceptibility to breast cancer and squamous cell carcinoma of the lung in Japanese populations (Watanabe et al. 2000). Mutations in the CYP1B1 gene are responsible for primary congenital glau- coma (Bejjani et al. 1998; Stoilov et al. 1998; Plasilova et al. S. Saito · A. Iida · A. Sekine · C. Ogawa · S. Kawauchi · S. Higuchi · M. Ohno · Y. Nakamura 1999). Laboratory for Genotyping, SNP Research Center, Institute of Members of the CYP3A subfamily are the most abun- Physical and Chemical Research, Tokyo, Japan dantly expressed CYPs in human liver and small intestine Y. Nakamura (*) (Cholerton et al. 1992). Four CYP3A genes, CYP3A4, Laboratory of Molecular Medicine, Human Genome Center, CYP3A5, CYP3A7, and CYP3A43, have been described in Institute of Medical Science, The University of Tokyo, 4-6-1 humans (Nelson et al. 1996; Finta and Zaphiropoulos 2000; Shirokanedai, Minato-ku, Tokyo 108-8639, Japan Tel. ϩ81-3-5449-5372; Fax ϩ81-3-5449-5433 Domanski et al. 2001; Westlind et al. 2001), and polymor- e-mail: [email protected] phisms have been reported in the first three of those genes 420 [Human Cytochrome P450 (CYP) Allele Nomenclature The ALDH1 subfamily consists of five genes, Committee, http://www.imm.ki.se/CYPalleles/]. CYP3A4 is ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, and most abundant in adult liver (Wrighton and Stevens. 1992); ALDH1L1. ALDH1A1 is a cytosolic enzyme ubiquitously this enzyme metabolizes approximately 50% of the drugs in distributed in human tissues, including brain and red blood current use as well as a number of steroids, environmental cells (Yoshida 1992). Several ALDH1A1 variants have chemicals, and carcinogens (Thummel and Wilkinson 1998; been associated with various degrees of enzyme deficiency Guengerich 1999). Nonsynonymous SNPs in CYP3A4 have in the liver and red blood cells (Yoshida et al. 1989; Yoshida been identified in various ethnic populations (Sata et al. 1992). Mitochondrial ALDH1B1 is expressed in liver, kid- 2000; Dai et al. 2001; Eiselt et al. 2001; Hsieh et al. 2001; ney, muscle, heart, and placenta (Stewart et al. 1996); this Lamba et al. 2002), and Rebbeck et al. (1998) have reported enzyme may play a role in ethanol detoxification (Stewart et association between an SNP in the 5Ј flanking region of the al. 1995). Although three polymorphisms have been re- CYP3A4 gene and advanced prostate cancer. Expression ported in its coding regions, no significant difference has levels of CYP3A4, CYP3A5, and CYP3A7 vary widely been found in the allelic frequencies of those polymor- among individuals; measurements of CYP3A4 activities in phisms between alcoholic versus nonalcoholic Caucasians adults reveal 10- to 40-fold differences (de Wildt et al. (Sherman et al. 1993). ALDH1A2 is involved in retinal 1999). CYP3A5 also shows heterogeneity of expression in metabolism (Wang et al. 1996). ALDH1A3 is expressed in liver (Lown et al. 1994), and SNPs resulting in alternative salivary gland, stomach, and kidney (Hsu et al. 1994). The splicing and an absence of CYP3A5 protein have been ALDH1L1 gene encodes a 10-formyltetrahydrofolate de- found in some individuals (Kuehl et al. 2001). CYP3A7, on hydrogenase (Champion et al. 1994). the other hand, is expressed mainly in fetal liver; this ALDH2, a mitochondrial enzyme, is highly expressed in enzyme seems to disappear shortly after birth, although various tissues but predominantly in the liver (Stewart et al. some people continue to express CYP3A7 mRNA even in 1996). ALDH2 exhibits strong oxidative activity toward adulthood (Schuetz et al. 1994). acetaldehyde, and plays a major role in its detoxification Animal experiments have revealed an important role (Lindahl 1992). In oriental populations, alcohol sensitivity of CYP4B1 in mutagenic activation of procarcinogens in is associated with a genetic deficiency of ALDH2 caused by the urinary bladder (Imaoka et al. 1997). Bladder-tumor a G-to-A mutation in exon 12 (Yoshida et al. 1985). A patients, indeed, show significantly higher expression of polymorphism in the human ALDH2 promoter was re- CYP4B1 than do patients with other types of cancer cently described (Chou et al. 1999; Harada et al. 1999), but (Imaoka et al. 2000). it is not clear whether this polymorphism affects alcohol CYP4F2, CYP4F3, and CYP4F8 were originally cloned metabolism. from human neutrophils, liver, and seminal vesicle, respec- The ALDH3 subfamily consists of four genes, tively (Kikuta et al. 1993, 1994; Bylund et al. 1999). CYP4F2 ALDH3A1, ALDH3A2, ALDH3B1, and ALDH3B2. and CYP4F3 are also called leukotriene B4 (LTB4) omega- ALDH3A1 is a cytosolic enzyme highly expressed in stom- hydroxylases because they possess efficient catalytic activity ach and lung, and at low (or undetectable) levels in normal toward LTB4, an important chemotactic and chemokinetic liver (Lindahl 1992). Although a C-to-G polymorphism participant in the inflammatory response. (Pro329Ala) has been reported in Caucasian and Asian CYP27A1 (sterol 27-hydroxylase) catalyzes the first step populations (Tsukamoto et al. 1997), its biological effects in oxidation of the side chains of sterol intermediates during are currently unknown. ALDH3A2, a microsomal enzyme synthesis of bile acids (Cali and Russell 1991). Mutations in constitutively expressed in several tissues, catalyzes oxida- the CYP27A1 gene cause cerebrotendinous xanthomatosis, tion of fatty aldehydes (Rizzo and Craft 1991; Chang and a rare autosomal recessive defect of lipid storage (Cali et al. Yoshida 1997). Mutations in ALDH3A2 that cause loss of 1991). CYP27B1, also known as 25-hydroxyvitamin D3 enzymatic activity are responsible for Sjögren-Larsson syn- 1alpha-hydroxylase (1alpha-hydroxylase), catalyzes the drome (De Laurenzi et al. 1996). Hsu et al. (1997) deter- conversion of 25-hydroxyvitamin D3 to 1alpha, 25- mined the structures of the ALDH3B1 and ALDH3B2 dihydroxyvitamin D3. This enzyme plays an important role genes, but the function of neither enzyme is known at in calcium homeostasis (Takeyama et al. 1997). Mutations present. in the CYP27B1 gene cause pseudovitamin D-deficiency ALDH5A1 is highly expressed in brain as well as in rickets (Fu et al. 1997; Kitanaka et al. 1998; Wang et al. liver, pituitary, heart, and ovary (Chambliss et al. 1995). 1998). Mutations in the ALDH5A1 gene cause succinic semi- The aldehyde dehydrogenase (ALDH; EC 1.2.1.3) aldehyde dehydrogenase deficiency, a rare inborn error superfamily involves a group of NAD (P)ϩ-dependent of the neurotransmitter 4-aminobutyric acid (Chambliss et enzymes that catalyze the oxidation of a wide spectrum of al. 1998). ALDH6A1 is the only CoA-dependent dehydro- endogenous and exogenous aldehydes (Lindahl 1992). Thus genase in the ALDH family (Goodwin et al. 1989). Lin and far, 17 functional ALDH genes and three pseudogenes Napoli (2000) isolated a cDNA encoding ALDH8A1. Al- have been identified in the human genome and some lelic variants of the ALDH9A1 gene, which encodes polymorphisms have been reported already (Yoshida et al. an enzyme that catalyzes dehydrogenation of gamma- 1998; Vasiliou and Pappa 2000; Sophos et al.