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Evidence for genetic heterogeneity in familial Wilms' tumor.

Wilms' tumor (WT), a childhood kidney cancer, occurs both sporadically and, less frequently, in a familial context. Genetic linkage studies of several large WT families have excluded the one cloned WT gene, WT1, as the locus responsible for familial predisposition. These data demonstrate the existence of a familial predisposition gene distinct from WT1 and, more broadly, imply that the genetic etiology of WT is heterogenous. However, it has been unknown whether the predisposition observed in large WT families is also heterogenous or perhaps is due to mutations at a single locus. Recently, examination of a large French-Canadian WT family has demonstrated genetic linkage to 17q12-q21. We report here the results from a genetic linkage study of six WT pedigrees. Analyses of genotype data from eight loci within the 17q12-q21 region in these families resulted in cumulative lod scores of <-4.0 through the region, thereby excluding linkage. The ability to rule out the 17q region as the site of a predisposition gene in several of these pedigrees individually demonstrates the existence of more than one gene that predisposes to WT in large pedigrees and again emphasizes that the etiology of WT is genetically heterogenous.

Adult↗

Gene x environment interaction and cognitive performance: animal studies on the role of corticosterone.

A fundamental question in the neurobiology of cognition is how stress and glucocorticoids modify learning and memory processes. Why some individuals develop cognitive deficits after stress, while other individuals improve in cognitive performance under similar adverse conditions is still unresolved. To address these questions we focus on those issues. First, corticosterone, which appears to be the preferred glucocorticoid for the rodent and human brain, acts via brain mineralocorticoid (MR) and glucocorticoid receptors (GR) on the expression of networks of corticosteroid-responsive genes. Different effects are achieved by MR and GR activation. Second, the experimental context that determines the timing and the consequences of corticosterone action during the various stages of information processing is reviewed. Third, the genetic context and the environmental context are investigated. Using apolipoprotein E knockout (apoE0/0) mice we show that apoE (apoE4 is a genetic risk factor for Alzheimer's disease) is a candidate gene with an important function in shaping the cognitive outcome (genotype x environment interaction).

Animals↗

Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids.

Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.

Chloroplasts↗

Application of Bayesian inference using Gibbs sampling to item-response theory modeling of multi-symptom genetic data.

Several "genetic" item-response theory (IRT) models are fitted to the responses of 1086 adolescent female twins to the 33 multi-category item Mood and Feeling Questionnaire relating to depressive symptomatology in adolescence. A Markov-chain Monte Carlo (MCMC) algorithm is used within a Bayesian framework for inference using Gibbs sampling, implemented in the program WinBUGS 1.4. The final model incorporated separate genetic and non-shared environmental traits ("A and E") and item-specific genetic effects. Simpler models gave markedly poorer fit to the observations judged by the deviance information criterion (DIC). The common genetic factor showed major loadings on melancholic items, while the environmental factor loaded most highly on items relating to self-deprecation. The MCMC approach provides a convenient and flexible alternative to Maximum Likelihood for estimating the parameters of IRT models for relatively large numbers of items in a genetic context. Additional benefits of the IRT approach are discussed including the estimation of latent trait scores, including genetic factor scores, and their sampling errors.

Adolescent↗

Association of the organic cation transporter OCTN genes with Crohn's disease in the Spanish population.

The SLC22A4 and SLC22A5 genes within the IBD5 risk locus encode the organic cation transporters OCTN1 and OCTN2. Two variants, 1672C>T in SLC22A4 and -207G>C in SLC22A5, were shown to alter these genes' functions and were identified as genetic susceptibility factors for Crohn's disease (CD). We pursued to check both putative etiologic variants in an independent population through a case-control study with 309 Spanish CD patients and 408 ethnically matched healthy subjects. Both polymorphisms were found in partial linkage disequilibrium (D'=0.86). The separate analysis of each OCTN variant evidenced no association. However, when the simultaneous presence of mutant variants in both genes was analyzed, an effect on CD susceptibility was observed (P=0.026, odds ratio (OR) (95% confidence interval (CI))=1.59 (1.03-2.45)). The previously described predisposition conferred by the 5q31-risk haplotype increased in the absence of the etiologic 1672T and -207C alleles (P=0.0006, OR (95% CI)=10.14 (1.97-98.04)). Moreover, the risk contributed by these polymorphisms was higher in the IBD5 wild-type population (P=0.003, OR (95% CI)=2.65 (1.32-5.35)), arguing against the exclusive etiological role of the OCTN variants. The haplotype pattern inferred led to the consideration of these variants as susceptibility markers only in a defined genetic context. Our data support the interpretation of the 1672C>T SLC22A4 and -207G>C SLC22A5 polymorphisms as genetic markers of susceptibility/protection haplotypes.

Case-Control Studies↗

AGT and RH blood group polymorphisms affect blood pressure and lipids in Afro-Caribbeans.

Population blood pressure variation is most likely due to multiple genes. This is likely the reason why monogenic testing with the angiotensinogen (AGT) gene polymorphisms on chromosome 1 (1q42-43), especially M235T, has met with negative results, especially in those of African descent. The RH blood group system, also on chromosome 1 (1 p36.2-34), has likewise been associated with blood pressure variation in African-Americans and with the rise in blood pressure with age in whites. Using a random sample of the population, we investigated the combined effects of single and combined variation of the AGTN M235T and RH genotypes on blood pressure, lipids, and lipoprotein concentrations in Afro-Caribbeans aged 18-60 years from the island nation of Dominica. In monogenic analysis, AGT M235T was not associated with blood pressure. However, it was associated with HDL (MM 42+/-23, MT 44+/-12, TT 52+/-14 (P=0.002)). RH genotype was significantly associated with systolic blood pressure (P=0.006) and Apo-A (P=0.003). These effects remained after adjustment for age, gender, weight, and BMI. In the polygenetic analysis, AGT M235T and RH were significantly associated with systolic blood pressure (P=0.037; interaction effects, P=0.068). The association of the AGT M235T with blood pressure across RH blood group haplotypes was then tested. Of the five RH haplotypes available for analysis, the AGT M235T was significantly associated with blood pressure within the "D" haplotype (P=0.01). The RH blood group and gender were significantly associated with systolic blood pressure and Apo-A levels (P=0.005 and 0.012, respectively). All interactions were independent of age and weight. In conclusion, we demonstrate a significant association of AGT M235T with blood pressure and cholesterol metabolism in an Afro-Caribbean population in the "genetic context" of the RH blood group system. Further investigation of these interactions may help understand the effects of genetic factors on cardiovascular risk in African-derived and other populations.

Adult↗

Combined analysis of six lipoprotein lipase genetic variants on triglycerides, high-density lipoprotein, and ischemic heart disease: cross-sectional, prospective, and case-control studies from the Copenhagen City Heart Study.

CONTEXT: Genetic variants in lipoprotein lipase may affect triglycerides, high-density lipoprotein (HDL), and risk of ischemic heart disease (IHD). OBJECTIVE: The objective of this study was to investigate the influence of T(-93)G, G(-53)C, Asp9Asn, Gly188Glu, Asn291Ser, and Ser447Ter lipoprotein lipase genotypes on triglycerides, HDL, and IHD. DESIGN: The cross-sectional study involved 9004 adults. The prospective study consisted of 8817 adults developing 1001 IHD events over 23 yr. The case-control study involved 7818 non-IHD individuals vs. cohorts of 915 and 1062 IHD patients, respectively. SETTING: The study was performed in the Danish general population (the Copenhagen City Heart Study). PARTICIPANTS: IHD was angina pectoris or myocardial infarction. MAIN OUTCOME MEASURES: Triglycerides, HDL, and IHD were the main outcome measures. RESULTS: Cross-sectionally, triglycerides varied by genotype with 1.27 mmol/liter in women and 1.22 mmol/liter in men. HDL cholesterol varied by genotype with 0.49 mmol/liter in women and 0.60 mmol/liter in men. Prospectively, 9Asn (with -93G) heterozygotes and homozygotes combined vs. noncarriers had a hazard ratio for IHD of 1.6 [95% confidence interval (CI), 1.2-2.3]; 291Ser and 447Ter did not change IHD risk. In the case-control study, combining the cohorts of IHD patients, 9Asn (with -93G) heterozygotes and homozygotes combined vs. noncarriers had an odds ratio for IHD of 1.5 (CI, 1.2-2.1). 291Ser and 447Ter did not change IHD risk. Stratified for apolipoprotein E genotype, the odds ratios for IHD in 9Asn (with -93G) heterozygotes and homozygotes combined vs. noncarriers were 2.6 (CI, 1.2-5.5) among epsilon32 individuals and 2.4 (CI, 1.4-4.1) among epsilon43 individuals. CONCLUSIONS: Genetic variation in lipoprotein lipase is associated with differences in plasma triglycerides greater than 1 mmol/liter and differences in HDL cholesterol greater than 0.5 mmol/liter. A 1.6-fold risk of IHD in 9Asn (with -93G) heterozygotes and homozygotes combined is influenced by apolipoprotein E genotype.

Adult↗

Selection and design of probiotics.

Over the past 5 years the probiotic field has exploded with a number of new cultures, each purported to elicit a variety of benefits. Lists of functional characteristics and benefits, in vivo, are now commonplace to any presentation on probiotics. Scientifically established health claims remain among the highest priorities to companies who seek to establish solid health benefits that will promote their particular probiotic. The scientific community faces a greater challenge and must objectively seek cause and effect relationships for many potential and currently investigated probiotic species and strain combinations. Rational selection and design of probiotics remains an important challenge and will require a platform of basic information about the physiology and genetics of candidate strains relevant to their intestinal roles, functional activities, and interactions with other resident microflora. In this context, genetic characterization of probiotic cultures is essential to unequivocally define their contributions to the intestinal microbiota and ultimately identify the genotypes that control any unique and beneficial properties. Strain selection and differentiation, based on the genetic complement and programming of a candidate probiotic, then becomes feasible. Looking ahead, it will be vital to the development of this exploding field to correlate important characteristics in probiotics with known genotypes and regulatory controls that are likely to affect functionality and beneficial outcomes, in vivo.

Base Sequence↗

Probing p53 biological functions through the use of genetically engineered mouse models.

The p53 tumor suppressor gene is rendered dysfunctional in the majority of human cancers. To model the effects of p53 dysfunction in an experimentally manipulable organismal context, genetically engineered inbred mice have been the models of choice. Transgenic and knock-out technologies have been utilized to generate an array of different p53 germ line alterations. As expected, many (though not all) of the mutant p53 mouse models are susceptible to enhanced spontaneous and carcinogen-induced tumors of a variety of types. A number of different variables affect the incidence and spectrum of tumors in p53 mutant mice. These include strain background, the nature of the p53 mutation, the presence of wild-type p53 (in addition to mutant p53), exposure to physical and chemical mutagens, or introduction of other cancer-associated genes into the mutant p53 background. In addition to their role in furthering our understanding of the mechanisms of cancer initiation and progression, these models have led to unexpected insights into p53 function in embryogenesis and aging. With the development of ever more sophisticated methods for manipulating the mouse genome, new p53 models are on the horizon, which should deliver advances that will provide not only important mechanistic insights but also discoveries of great clinical relevance.

Animals↗

Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach.

We present a new algorithm called PromoterInspector to locate eukaryotic polymase II promoter regions in large genomic sequences with a high degree of specificity. PromoterInspector focuses on the genetic context of promoters, rather than their exact location. Application of PromoterInspector can serve as a crucial pre-processing step for other methods to locate exactly, or to analyze promoters. PromoterInspector does not depend on heuristics, because it is purely based on libraries of IUPAC words extracted from training sequences by an unsupervised learning approach. We compared PromoterInspector to in silico promoter prediction tools using the sequences from the review by J.W. Fickett. PromoterInspector compared favourably on Fickett's evaluation scheme. A true positive to false positive ratio of 2.3 was obtained, surpassing the best ratio of 0.6, reported for TSSG. The application of our method to several large genomic sequences of over 1.3 million base-pairs in total resulted in even more specific predictions. The coverage of annotated promoters was comparable to other in silico promoter prediction methods, while the true positive predictions increased by up to 100% of total matches. PromoterInspector scans 100 kb in less than one minute on a workstation, and thus is especially applicable for large genome analysis. The method is available at http://genomatix.gsf. de/cgi-bin/promoterinspector/promoterinspector.pl.

3' Untranslated Regions↗

An empirical comparison of information-theoretic selection criteria for multivariate behavior genetic models.

Information theory provides an attractive basis for statistical inference and model selection. However, little is known about the relative performance of different information-theoretic criteria in covariance structure modeling, especially in behavioral genetic contexts. To explore these issues, information-theoretic fit criteria were compared with regard to their ability to discriminate between multivariate behavioral genetic models under various model, distribution, and sample size conditions. Results indicate that performance depends on sample size, model complexity, and distributional specification. The Bayesian Information Criterion (BIC) is more robust to distributional misspecification than Akaike's Information Criterion (AIC) under certain conditions, and outperforms AIC in larger samples and when comparing more complex models. An approximation to the Minimum Description Length (MDL; Rissanen, J. (1996). IEEE Transactions on Information Theory 42:40-47, Rissanen, J. (2001). IEEE Transactions on Information Theory 47:1712-1717) criterion, involving the empirical Fisher information matrix, exhibits variable patterns of performance due to the complexity of estimating Fisher information matrices. Results indicate that a relatively new information-theoretic criterion, Draper's Information Criterion (DIC; Draper, 1995), which shares features of the Bayesian and MDL criteria, performs similarly to or better than BIC. Results emphasize the importance of further research into theory and computation of information-theoretic criteria.

Bayes Theorem↗

Lineage dependency and lineage-survival oncogenes in human cancer.

Although cell-lineage and differentiation models dominate tumour classification and treatment, the recognition that cancer is also a genomic disease has prompted a reconfiguration of cancer taxonomies according to molecular criteria. Recent evidence indicates that a synthesis of lineage-based and genetic paradigms might offer new insights into crucial and therapeutically pliable tumour dependencies. For example, MITF (microphthalmia-associated transcription factor), which is a master regulator of the melanocyte lineage, might become a melanoma oncogene when deregulated in certain genetic contexts. MITF and other lineage-survival genes therefore implicate lineage dependency (or lineage addiction) as a newly recognized mechanism that is affected by tumour genetic alterations.

Cell Lineage↗

Evolution through genetically controlled allometry space.

Understanding evolutionary change requires phenotypic differences between organisms to be placed in a genetic context. However, there are few cases where it has been possible to define an appropriate genotypic space for a range of species. Here we address this problem by defining a genetically controlled space that captures variation in shape and size between closely related species of Antirrhinum. The axes of the space are based on an allometric model of leaves from an F2 of an interspecific cross between Antirrhinum majus and Antirrhinum charidemi. Three principal components were found to capture most of the genetic variation in shape and size, allowing a three-dimensional allometric space to be defined. The contribution of individual genetic loci was determined from QTL analysis, allowing each locus to be represented as a vector in the allometric space. Leaf shapes and sizes of 18 different Antirrhinum taxa, encompassing a broad range of leaf morphologies, could be accurately represented as clouds within the space. Most taxa overlapped with, or were near to, at least one other species in the space, so that together they defined a largely interconnected domain of viable forms. It is likely that the pattern of evolution within this domain reflects a combination of directional selection and evolutionary tradeoffs within a high dimensional space.

Antirrhinum↗

The context of human genetic evolution.

The debate on modern human origins has often focused on the relationship between genes and fossils. Although more and more genetic evidence has been accumulating in favor of a recent African origin for modern humans, it has been assumed by many that the fossil evidence remains ambiguous. On the contrary, it has been clear for some time that the fossil evidence does not support the multiregional model: Fossils and archeology indicate a pattern of multiple dispersals from and beyond Africa, against which the genetic data can be compared. The continuing value of paleobiology is in complementing genetic information by revealing the context of human evolution: locating the dispersals and extinctions of populations in time and space, correlating these events with the environmental forces that shaped them, and providing an increasingly detailed understanding of the morphology and technology of early humans.

Animals↗

Steroid hormone receptors: an update.

Steroid hormones (SHs) are lipophilic molecules derived from cholesterol and synthesized in the adrenal cortex (glucocorticoids, mineralocorticoids, and adrenal androgens), the testes (testicular androgens, oestrogen), and the ovary and placenta (oestrogens and progestagens or progestins). SHs reach their target cells via the blood, where they are bound to carrier proteins, and because of their lipophilic nature pass the cell membrane by simple diffusion. Within the target cells SHs bind to steroid hormone receptors (SHRs), the key mediators of SH action, which are complexed to chaperones, e.g. heat shock protein 90 (Hsp90), that help other proteins to fold and prevent aggregation. SHRs are intracellular transcription factors that can be activated, among other possibilities, by the specific and high affinity binding of ligand to exert positive or negative effects on the expression of target genes. Binding of agonistic or antagonistic ligands leads to different allosteric changes of SHRs making them competent to exert positive or negative effects on the expression of target genes by different mechanisms. (i) After dissociation of chaperones the liganded SHR-complexes can bind to chromatin organized DNA sequences in the vicinity of target genes, termed hormone response elements (HREs). The HRE-recruited hormone-receptor-complexes are then able to initiate chromatin remodelling and to relay activating or repressing signals to the target genes transcription machinery; (ii) through protein-protein interactions with other sequence-specific transcription factors, SHRs can also regulate the activity of many genes that are switched on, for instance, during stress or an inflammatory response; (iii) the SH response can also be integrated in the intracellular signalling network via cross-talk of SHRs with signal transduction pathways that transmit extracellular signals via membrane receptors and activation of protein kinase cascades to nuclear transcription factors that activate various target genes. By all these different mechanisms SHRs modulate numerous and specific responses in a large variety of cells, whereby their particular effect depends on the physiological, cellular and genetic context.

Binding Sites↗

Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in barley.

We present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eighty-three SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.

Expressed Sequence Tags↗

Effect of nef alleles on replication of human immunodeficiency virus type 1.

The effect of multiple alleles of nef of the human immunodeficiency virus type 1 (HIV-1) on virus replication was examined. Nef alleles used include some derived from isolates of virus passaged in tissue culture as well as others obtained by direct cloning of viral DNA from tissues of infected patients. The effect of nef on virus replication was evaluated in the context of a derivative of the HXB2 provirus shown previously to require nef for rapid growth in CD4+ human T cell lines and in primary peripheral blood mononuclear cells. The results of the experiments show that in this genetic context all of the studied viruses carrying nef alleles that express stable Nef proteins replicate more rapidly than do their, otherwise isogenic, nef-defective counterparts. Two of the nef alleles derived from primary tissues produce unstable proteins. These studies demonstrate that naturally occurring nef alleles can increase the rate of virus replication in both primary peripheral blood mononuclear cells and in a CD4+ T cell line. The results also demonstrate that functional variation exists among naturally occurring nef alleles.

Acquired Immunodeficiency Syndrome↗

Allelic variation in the effects of the nef gene on replication of human immunodeficiency virus type 1.

The effects of the viral gene nef on human immunodeficiency virus type 1 (HIV-1) replication in culture were investigated using nef alleles of the HIV-1 IIIB and ELI strains. The results demonstrate significant allelic variation in the effect of nef on virus replication in both an established human CD4+ T-cell line and primary human lymphocytes. In the context of the HXB2 virus, the ELI nef allele but not the IIIB nef allele permits initiation of efficient low-multiplicity infection in primary peripheral blood mononuclear cells, including unfractionated peripheral blood lymphocytes, T cells, and monocyte/macrophages. Within the same genetic context, the IIIB nef allele slightly retards replication of the virus in a T-cell line, whereas the ELI nef allele accelerates replication of the virus. Sequences in the IIIB and ELI genomes outside of nef also moderate the effects of nef on HIV-1 replication. nef did not appear to determine the host-cell preference of the virus. These studies may help to reconcile apparently conflicting reports on the role of nef in HIV-1 replication and suggest that HIV-1 nef may play an important role in viral pathogenesis.

Alleles↗