The AmpliChip CYP450 genotyping test: Integrating a new clinical tool

The AmpliChip CYP450 Test, which analyzes patient genotypes for cytochrome P450 (CYP) genes CYP2D6 and CYP2C19, is a major step toward introducing personalized prescribing into the clinical environment. Interest in adverse drug reactions (ADRs), the genetic revolution, and pharmacogenetics have converged with the introduction of this tool, which is anticipated to be the first of a new wave of such tools to follow over the next 5-10 years. The AmpliChip CYP450 Test is based on microarray technology, which combines hybridization in precise locations on a glass microarray and a fluorescent labeling system. It classifies individuals into two CYP2C19 phenotypes (extensive metabolizers [EMs] and poor metabolizers [PMs]) by testing three alleles, and into four CYP2D6 phenotypes (ultrarapid metabolizers [UMs], EMs, intermediate metabolizers [IMs], and PMs) by testing 27 alleles, including seven duplications. CYP2D6 is a metabolic enzyme with four activity levels (or phenotypes): UMs with unusually high activity; normal subjects, known as EMs; IMs with low activity; and PMs with no CYP2D6 activity (7% of Caucasians and 1-3% in other ethnic groups). Levels of evidence for the association between CYP2D6 PMs and ADRs are relatively reasonable and include systematic reviews of case-control studies of some typical antipsychotics and tricyclic antidepressants (TCAs). Evidence for other phenotypes is considerably more limited. The CYP2D6 PM phenotype may be associated with risperidone ADRs and discontinuation due to ADRs. Venlafaxine, aripiprazole, duloxetine, and atomoxetine are newer drugs metabolized by CYP2D6 but studies of the clinical relevance of CYP2D6 genotypes are needed. Non-psychiatric drugs metabolized by CYP2D6 include metoprolol, tamoxifen, and codeine-like drugs. CYP2C19 PMs (3-4% of Caucasians and African Americans, and 14-21% of Asians) may require dose adjustment for some TCAs, moclobemide, and citalopram. Other drugs metabolized by CYP2C19 are diazepam and omeprazole. The future of pharmacogenetics depends on the ability to overcome serious obstacles, including the difficulties of conducting and publishing studies in light of resistance from grant agencies, pharmaceutical companies, and some scientific reviewers. Assuming more studies are published, pharmacogenetic clinical applications may be compromised by economic factors and the lack of physician education. The combination of a US FDA-approved test, such as the AmpliChip CYP450 Test, and an FDA definition of CYP2D6 as a 'valid biomarker' makes CYP2D6 genotyping a prime candidate to be the first successful pharmacogenetic test in the clinical environment. One can use microarray technology to test for hundreds of single nucleotide polymorphisms (SNPs) but, taking into account the difficulties for single gene approaches such as CYP2D6, it is unlikely that very complex pharmacogenetic approaches will reach the clinical market in the next 5-10 years.     

A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations

MOTIVATION: The identification of signatures of positive selection can provide important insights into recent evolutionary history in human populations. Current methods mostly rely on allele frequency determination or focus on one or a small number of candidate chromosomal regions per study. With the availability of large-scale genotype data, efficient approaches for an unbiased whole genome scan are becoming necessary. METHODS: We have developed a new method, the whole genome long-range haplotype test (WGLRH), which uses genome-wide distributions to test for recent positive selection. Adapted from the long-range haplotype (LRH) test, the WGLRH test uses patterns of linkage disequilibrium (LD) to identify regions with extremely low historic recombination. Common haplotypes with significantly longer than expected ranges of LD given their frequencies are identified as putative signatures of recent positive selection. In addition, we have also determined the ancestral alleles of SNPs by genotyping chimpanzee and gorilla DNA, and have identified SNPs where the non-ancestral alleles have risen to extremely high frequencies in human populations, termed 'flipped SNPs'. Combining the haplotype test and the flipped SNPs determination, the WGLRH test serves as an unbiased genome-wide screen for regions under putative selection, and is potentially applicable to the study of other human populations. RESULTS: Using WGLRH and high-density oligonucleotide arrays interrogating 116 204 SNPs, we rapidly identified putative regions of positive selection in three populations (Asian, Caucasian, African-American), and extended these observations to a fourth population, Yoruba, with data obtained from the International HapMap consortium. We mapped significant regions to annotated genes. While some regions overlap with genes previously suggested to be under positive selection, many of the genes have not been previously implicated in natural selection and offer intriguing possibilities for further study. AVAILABILITY: the programs for the WGLRH algorithm are freely available and can be downloaded at http://www.affymetrix.com/support/supplement/WGLRH_program.zip.     

Evolution of enzyme superfamilies

Enzyme evolution is often constrained by aspects of catalysis. Sets of homologous proteins that catalyze different overall reactions but share an aspect of catalysis, such as a common partial reaction, are called mechanistically diverse superfamilies. The common mechanistic steps and structural characteristics of several of these superfamilies, including the enolase, Nudix, amidohydrolase, and haloacid dehalogenase superfamilies have been characterized. In addition, studies of mechanistically diverse superfamilies are helping to elucidate mechanisms of functional diversification, such as catalytic promiscuity. Understanding how enzyme superfamilies evolve is vital for accurate genome annotation, predicting protein functions, and protein engineering.     

Contrasting demographies and persistence of rare annual plants in highly variable environments

Spatial and temporal variation in critical life history traits differ markedly between two co-occurring, rare and endangered annual plants, Gilia tenuiflora arenaria and Chorizanthe pungens pungens, that have restricted, but overlapping geographic distributions in coastal habitats of central California, USA. Environmental variation was extreme during the 6-year study (1997–2002), with the greatest differences between an intense wet, warm El Niño year (1998), followed by a very dry, cool La Niña (1999). Both species have similar increases in adult survival and seed set with wetter, warmer weather in spring, but they differed in other traits: more Gilia germinated in years with high rainfall and temperature, while more Chorizanthe germinated in dry, cooler years; Gilia abundance increased with the number of years since the previous large El Niño event, while Chorizanthe abundance declined; and Gilia abundance was independent of the previous year’s seed set, while Chorizanthe density was directly related to the previous year’s seed set. The strong negative associations of Chorizanthe abundance with warm, wet weather and with time since the previous El Niño probably reflect the particular sequence of annual weather patterns from 1997 through 2002, especially the extremes in 1998 and 1999. Since it germinates readily in most years under a wide range of winter conditions and does not develop a long-lived seed bank, Chorizanthe seedling abundance reflects recent additions and depletions of its seed bank, rather than prevailing weather, per se. In contrast, Gilia seeds may remain in the seed bank for many years, until relatively rare winter conditions trigger significant germination. These species-specific demographies enhance persistence and coexistence of these species, but the mechanisms differ from each other and from those described for annuals in other highly variable environments.     

Genotoxicity and transmission electron microscopy studies of molybdocene dichloride

The cytotoxic effects of molybdocene dichloride (Cp(2)MoCl(2)) were investigated in V79 Chinese hamster lung cells using the micronucleus assay. Cp(2)MoCl(2) produced significant genotoxic damage whereby 0.2micronuclei/1000 binucleated cells were induced per muM of Cp(2)MoCl(2). Transmission electron microscopic analysis of thin-sectioned cells treated with Cp(2)MoCl(2) (300microM) showed distinct morphological alterations of the nuclei, condensation of chromatin, and a high incidence of polynucleated cells. Implications for the mechanism of antitumor action of molybdocene dichloride are discussed.     

Microarray analysis of Bacillus cereus group virulence factors

Bacillus cereus, B. thuringiensis and B. anthracis are closely related medically and economically important bacterial species that belong to the B. cereus group. Members of the B. cereus group carry genes encoding several important virulence factors, including enterotoxins, phospholipases and exotoxins. Since it is difficult to differentiate among B. cereus group members, and because Bacillus virulence factors are very important for pathogenesis, we explored the use of microarray-based detection of virulence factor genes as a tool for strain identification and for determining virulence. Our method requires an initial multiplex PCR amplification step, followed by identification of the PCR amplicons by hybridization to an oligonucleotide microarray containing genes for all three types of Bacillus virulence factors including B. anthracis virulence factors. The DNA chip described here contains 21 identical arrays used for analysis of seven samples in triplicates. Using the arrays, we found that virulence factors are present in several combinations in the strains analyzed. This work also demonstrates the potential of oligonucleotide microarrays for medical, food safety and biodefense analysis of microbial pathogens.     

The Effects of Gibberellin4+7 on the Vase Life and Flower Quality of Alstroemeria Cut Flowers

Leaf yellowing is a major problem in Alstroemeria and absence of leaf senescence symptoms is an important quality attribute. Two Alstroemeria cultivars ‘Yellow King’ and ‘Marina’ were sourced from a commercial farm and harvested when sepals began to reflex. Stems were re-cut under water and kept in vase solutions of gibberellin A₄₊₇ (0, 2.5, 5.0, 7.5, 10.0, 12.5 or 15.0 mg l⁻¹ [Provide^r]). Treatments and cultivars were combined in a factorial fashion and arranged in a completely randomised design. Application of GA₄₊₇ in the holding solution at 2.5–10.0 mg l⁻¹ significantly delayed the onset of leaf senescence by around 7 days and significantly increased days to 50% petal fall by ca. 2 days. Additionally, these GA₄₊₇ concentrations resulted in higher retention of leaf nitrogen, leaf chlorophyll and also increased leaf water content, while reducing leaf dry weight, all relative to untreated controls. Cultivar ‘Yellow King’ had significantly longer vase life and a better retention of leaf quality than ‘Marina’. Our results suggest that a concentration of 10 mg l⁻¹ GA₄₊₇ can be used to prolong vase life, delay leaf senescence and enhance post-harvest quality of Alstroemeria cut flowers during their transport to market.     

Fine Roots vs. Needles: A Comparison of 13C and 15N Dynamics in a Ponderosa Pine Forest Soil

Plant allocation patterns may affect soil C and N storage due to differences in litter quality and the depth of plant C and N inputs into the soil. We studied the dynamics of dual-labeled (¹³C/¹⁵N) Pinus ponderosa needles and fine roots placed at two soil depths (O and A horizon) in a temperate conifer forest soil during 2 y. Input of C as fine roots resulted in much more C retained in soil (70.5 ± 2.2% of applied) compared with needle C (42.9 ± 1.3% of applied) after 1.5 y. Needles showed faster mass loss, rates of soil ¹³CO₂ efflux, and more ¹⁵N immobilized into microbial biomass than did fine roots. The larger proportion of labile C compounds initially present in needles (17% more needle C was water soluble than in fine roots) likely contributed to its shorter C residence time and greater degree of transformation in the soil. A double exponential decay function best described the rate of ¹³C loss, with a smaller initial pulse of C loss from fine roots (S₁k₁) and a slower decay rate of the recalcitrant C pool for fine roots (0.03 y⁻¹) compared with (0.19 y⁻¹) for needles. Soil ¹³C respiration, representing heterotrophic respiration of litter C, was much more seasonal from the O horizon than from the A. However, offsetting seasonal patterns in ¹³C dynamics in the O horizon resulted in no net effect of soil depth on total ¹³C retention in the soil after 1.5 y for either litter. Almost 90% of applied litter N was retained in the soil after 1.5 y, independent of litter quality or soil depth. Very small amounts of ¹³C or ¹⁵N (<3% of applied) moved to the horizon above or below the placement depth (i.e., O to A or A to O). Our results suggest that plant allocation belowground to fine roots results in more C retained and less N mineralized compared with allocation aboveground to needles, primarily due to litter quality differences.     

Mechanisms and pathophysiological implications of sinusoidal endothelial cell gap formation following treatment with galactosamine/endotoxin in mice

Neutrophil extravasation from sinusoids is a critical step for acute inflammatory tissue injury. However, the role of sinusoidal endothelial cells (SECs) in this process remains unclear. Matrix metalloproteinases (MMPs) have been shown to involve gap formation in SECs in several liver diseases. Therefore, the present study examined SEC modifications elicited by galactosamine (Gal)/endotoxin (ET). Treatment of male C3Heb/FeJ mice with Gal/ET or Gal/TNF caused the formation of numerous gaps in SECs at 4 h when no neutrophil extravasation occurred. Six hours after Gal/ET or Gal/TNF treatment, blood elements started to penetrate to the extrasinusoidal space through large gaps. Treatment with ET alone caused sinusoidal neutrophil accumulation but no gap formation, neutrophil extravasation, or hemorrhage. Gal/ET treatment increased hepatic MMP-2 and MMP-9 mRNA expression (6.7- and 11-fold, respectively). Pretreatment with 2-[(4-biphenylsulfonyl) amino]-3-phenyl-propionic acid, an MMP-2/MMP-9 inhibitor (5 mg/kg), minimized gap formation after Gal/ET and Gal/TNF treatment. The MMP inhibitor reduced injury only in the Gal/ET model mainly due to reduced TNF formation. The MMP inhibitor attenuated sinusoidal neutrophil accumulation at 6 h but failed to attenuate Gal/TNF-induced liver injury at 7 h due to excessive apoptosis. These results suggest that Gal/ET or Gal/TNF activates MMPs, which are responsible for SEC gap formation. Although the initial appearance of gap formation is independent of neutrophils, the gaps allow initial contact of neutrophils with damaged hepatocytes. In addition, MMP activation promotes neutrophil accumulation in sinusoids.     

Dissociating the dual roles of apoptosis-inducing factor in maintaining mitochondrial structure and apoptosis

The mitochondrial protein apoptosis-inducing factor (AIF) translocates to the nucleus and induces apoptosis. Recent studies, however, have indicated the importance of AIF for survival in mitochondria. In the absence of a means to dissociate these two functions, the precise roles of AIF remain unclear. Here, we dissociate these dual roles using mitochondrially anchored AIF that cannot be released during apoptosis. Forebrain-specific AIF null (tel. AifDelta) mice have defective cortical development and reduced neuronal survival due to defects in mitochondrial respiration. Mitochondria in AIF deficient neurons are fragmented with aberrant cristae, indicating a novel role of AIF in controlling mitochondrial structure. While tel. AifDelta Apaf1(-/-) neurons remain sensitive to DNA damage, mitochondrially anchored AIF expression in these cells significantly enhanced survival. AIF mutants that cannot translocate into nucleus failed to induce cell death. These results indicate that the proapoptotic role of AIF can be uncoupled from its physiological function. Cell death induced by AIF is through its proapoptotic activity once it is translocated to the nucleus, not due to the loss of AIF from the mitochondria.