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Exploring pleiotropy using principal components.

A standard multivariate principal components (PCs) method was utilized to identify clusters of variables that may be controlled by a common gene or genes (pleiotropy). Heritability estimates were obtained and linkage analyses performed on six individual traits (total cholesterol (Chol), high and low density lipoproteins, triglycerides (TG), body mass index (BMI), and systolic blood pressure (SBP)) and on each PC to compare our ability to identify major gene effects. Using the simulated data from Genetic Analysis Workshop 13 (Cohort 1 and 2 data for year 11), the quantitative traits were first adjusted for age, sex, and smoking (cigarettes per day). Adjusted variables were standardized and PCs calculated followed by orthogonal transformation (varimax rotation). Rotated PCs were then subjected to heritability and quantitative multipoint linkage analysis. The first three PCs explained 73% of the total phenotypic variance. Heritability estimates were above 0.60 for all three PCs. We performed linkage analyses on the PCs as well as the individual traits. The majority of pleiotropic and trait-specific genes were not identified. Standard PCs analysis methods did not facilitate the identification of pleiotropic genes affecting the six traits examined in the simulated data set. In addition, genes contributing 20% of the variance in traits with over 0.60 heritability estimates could not be identified in this simulated data set using traditional quantitative trait linkage analyses. Lack of identification of pleiotropic and trait-specific genes in some cases may reflect their low contribution to the traits/PCs examined or more importantly, characteristics of the sample group analyzed, and not simply a failure of the PC approach itself.

Blood Pressure↗

[Mechanism of cytokine pleiotropy and mutual regulation].

Cytokines manifest overlapping effects on many cell types and their production is regulated by a cytokine network. This minireview summarizes the current understanding of how affinity converter molecules, shared by several cytokines, is related to cytokine pleiotropy, and how Th1/Th2 are differentially developed and regulated through a cytokine network, especially, negative loop. Finally, the importance of the temporal expression of cytokines, in relation to the physiological relevance of the network, is pointed out.

Animals↗

[Alzheimer's disease and brain evolution: is Alzheimer's disease an example of antagonistic pleiotropy?].

INTRODUCTION: Alzheimer's disease (AD) appears to be exclusive to our species. This suggests a relationship between the disease and genetic, functional and structural changes that have taken place throughout the evolution of the human brain. DEVELOPMENT: The expression of genes linked to neurotransmission, neuroplasticity, axonal transport, aerobic metabolism and neuroprotection seems to have increased within the human cerebral cortex and such phenomena represent adaptations that induce greater neuronal activity throughout a long lifespan. High levels of neuroplasticity increase neuronal vulnerability to factors capable of triggering the lesions that are typically found in AD. Several genes related to increased neuronal activity are extremely vulnerable to factors related to old age, such as oxidative stress. Some kind of dysfunction in such genes can disrupt proper regulation of a number of pathways (neuroplasticity, axonal transport) and promote the abnormal accumulation of peptides that is characteristic of AD. Possessing certain polymorphisms of neuroprotective genes or of the electron transport chain could afford protection against AD. Increased intake of animal fats could alter the balance of polyunsaturated fatty acids in the neuronal membrane and favour a higher susceptibility to oxidative stress. CONCLUSIONS: AD could constitute an example of antagonistic pleiotropy: the increased expression of advantageous genes at an early age could turn out to be harmful at an advanced age.

Aging↗

[Non-classic effects of luliberin confirming the pleiotropy of neuropeptides].

The effects of synthetic neuropeptide LH-RH and its analogues were studied in experiments on 174 white male rats. The influence of the substances was shown on instrumental avoidance learning in Y-shaped maze. Convulsive and anticonvulsive effects of the preparations were studied on experimental model of corasol seizures. The analgetic effect of the substances was evaluated by behavioural pain reaction to electrical stimulation of the tail root. Analgetic, anticonvulsive, and psychostimulating LH-RH properties confirm polyfunctionality and "pleiotropy" of neuropeptides as a class of new endogenous informational compounds.

Analgesics↗

The contribution of pleiotropy to blood pressure and body-mass index variation: the Gubbio Study.

Blood pressure (BP), body-mass index (BMI), and quantitative phenotypes thought to influence BP (e.g., lithium-sodium countertransport activity) were studied in 2,184 households comprising 5,376 people in Gubbio, Italy. Variance-components models were used to partition the variation of these phenotypes into components characterizing the effects of age-related, measured environmental, additive genetic, pleiotropic, unmeasured shared-household, and individual-specific (or random) factors. The goal of the investigation was to estimate the contribution of pleiotropy to variation in BP and BMI in population-based samples. Although our results suggest that numerous significant bivariate genetic correlations exist between BP and some of the traits investigated, they ultimately lead us to reject a prominent role for any individual bivariate pleiotropic system influencing the natural variation of BP. However, because we found evidence that many traits enter into small-impact pleiotropic relationships with BP, we cannot rule out the possibility that pleiotropic genes, when considered collectively, may contribute to BP variation at the population level. Similar results were obtained when BMI was taken as the primary variable of interest. We argue that the small but significant portion of BP variation explained by individual genes displaying bivariate pleiotropic effects is intuitive, in light of the relatively low heritabilities associated with quantitative cardiovascular phenotypes and the low phenotypic correlations between BP, BMI, and many other physiologically linked measures of cardiovascular function. Our results not only bear directly on both the nature of the multifactorial determinants of BP and the maintenance of BP variation in the population at large, but also emphasize the utility of variance-components models in epidemiologic and population genetics research. We discuss the implications of our results for genetic epidemiologists and medical researchers studying hypertension, as well as the limitations of our study and areas for future research.

Blood Pressure↗

Seven types of pleiotropy.

Pleiotropy, a situation in which a single gene influences multiple phenotypic traits, can arise in a variety of ways. This paper discusses possible underlying mechanisms and proposes a classification of the various phenomena involved.

Animals↗

Genetic pleiotropy underlying obesity and autoimmune disorders: a large-scale cross-trait gwas analysis in European ancestry populations.

BACKGROUND: Obesity and autoimmune disorders represent a significant comorbidity burden, yet their shared genetic architecture is not fully understood. Elucidating the pleiotropic genetic basis underlying both conditions is crucial for unraveling the mechanisms driving their co-occurrence and advancing therapeutic strategies. METHODS: We conducted a large-scale cross-trait analysis integrating genome-wide association study (GWAS) summary data for obesity and 17 autoimmune diseases. Genetic correlations were assessed using LD score regression and high-definition likelihood. Cross-trait pleiotropic analysis was performed using Stratified Pleiotropic Locus Mapping (PLACO) to identify shared loci, followed by Bayesian colocalization to confirm shared causal variants. Gene-level and tissue-specific heritability analyses were conducted, and drug targets were prioritized via summary-based Mendelian randomization (SMR). Finally, immune co-localization and bidirectional Mendelian randomization were employed to elucidate immunological mechanisms and causal relationships. RESULTS: Our analysis identified eight autoimmune diseases with significant genetic correlations to obesity. We discovered 10,324 pleiotropic SNPs, which mapped to 52 independent risk loci, with nine loci confirmed as shared causal variants by colocalization. Gene-level analysis revealed 133 unique pleiotropic genes, including CLN3, SH2B1, and MMEL1, enriched in pathways of hematopoietic cell differentiation and immune homeostasis. Tissue-specific heritability was most prominent in the spleen, whole blood, and EBV-transformed lymphocytes. Immuno-co-localization implicated six IgD+ CD38- %B cell-related traits as key pathological conduits. Bidirectional Mendelian randomization established a causal role of obesity in hypothyroidism, psoriasis, and multiple sclerosis, while revealing an inverse causal association of type 1 diabetes with obesity risk. CONCLUSIONS: This study demonstrates a robust shared genetic foundation between obesity and multiple autoimmune diseases, pinpointing specific pleiotropic loci, genes, and immune cell subsets. Our findings provide a mechanistic framework for their comorbidity and highlight potential targets for therapeutic intervention.

Humans↗

Phenotypic pleiotropy of missense variants in human B cell confinement receptor P2RY8.

Missense variants can have pleiotropic effects on protein function, and predicting these effects can be difficult. We performed near-saturation deep mutational scanning of P2RY8, a G protein-coupled receptor that promotes germinal center B cell confinement. We assayed the effect of each variant on surface expression, migration, and proliferation. We delineated variants that affected both expression and function, affected function independently of expression, and discrepantly affected migration and proliferation. We also used cryo-electron microscopy to determine the structure of activated, ligand-bound P2RY8, providing structural insights into the effects of variants on ligand binding and signal transmission. We applied the deep mutational scanning results to both improve computational variant effect predictions and to characterize the phenotype of germline variants and lymphoma-associated variants. Together, our results demonstrate the power of integrating deep mutational scanning, structure determination, and in silico prediction to advance the understanding of a receptor important in human health.

Humans↗

Exploiting pleiotropy to enhance variant discovery with functional false discovery rates.

The cost of recruiting participants for genome-wide association studies (GWASs) can limit sample sizes and hinder the discovery of genetic variants. Here we introduce the surrogate functional false discovery rate (sfFDR) framework that integrates summary statistics of related traits to increase power. The sfFDR framework provides estimates of FDR quantities such as the functional local FDR and q value, and uses these estimates to derive a functional P value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses. Compared with a standard analysis, sfFDR substantially increased power (equivalent to a 52% increase in sample size) in a study of obesity-related traits from the UK Biobank and discovered eight additional lead SNPs near genes linked to immune-related responses in a rare disease GWAS of eosinophilic granulomatosis with polyangiitis. Collectively, these results highlight the utility of exploiting related traits in both small and large studies.

Humans↗

Life expectancy, antagonistic pleiotropy, and the testis of dogs and men.

BACKGROUND: Prostate cancer and benign prostatic hyperplasia are important age-related prostatic diseases that are under the influence of testicular hormones. However, the disparity between male and female life expectancy within the human population cannot be explained solely by the prevalence of prostatic disease-related mortality. The purpose of this paper is to explore the possibility that the testis exerts a detrimental effect on life span. METHODS: First, we review previously published and unpublished data on the influence of the testis on the life span of dogs and men. Aging in pet dogs and men is then discussed in terms of evolutionary theory, emphasizing the significance of a prolonged postreproductive life span and possible consequences of late-acting deleterious genes in these two species. Finally, we present preliminary data that orchiectomy can reduce DNA damage within the brain of elderly male dogs. RESULTS AND CONCLUSIONS Taken together, these observations raise the intriguing possibility that interventions to antagonize the testis might have much broader therapeutic applications that will extend well beyond the treatment of prostate cancer.

Adolescent↗

Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network.

The vast majority (>95%) of single-gene mutations in yeast affect not only the expression of the mutant gene, but also the expression of many other genes. These data suggest the presence of a previously uncharacterized "gene expression network"--a set of interactions between genes which dictate gene expression in the native cell environment. Here, we quantitatively analyze the gene expression network revealed by microarray expression data from 273 different yeast gene deletion mutants.(1) We find that gene expression interactions form a robust, error-tolerant "scale-free" network, similar to metabolic pathways(2) and artificial networks such as power grids and the internet.(3-5) Because the connectivity between genes in the gene expression network is unevenly distributed, a scale-free organization helps make organisms resistant to the deleterious effects of mutation, and is thus highly adaptive. The existence of a gene expression network poses practical considerations for the study of gene function, since most mutant phenotypes are the result of changes in the expression of many genes. Using principles of scale-free network topology, we propose that fragmenting the gene expression network via "genome-engineering" may be a viable and practical approach to isolating gene function.

Animals↗

Group 6: Pleiotropy and multivariate analysis.

Analysis techniques using data on several traits simultaneously allow researchers to dissect the genetic architecture affecting correlated traits, and can increase the power to detect pleiotropic genes, i.e., genes that influence two or more traits. Several of the papers in this group from Genetic Analysis Workshop 13 presented promising univariate summaries of multiple traits that detected linkage signals that standard single-trait univariate methods did not. Other papers found linkage signals using multivariate techniques that univariate techniques missed, although this was not uniformly the case. Some papers also considered the correlation among measurements of a single trait taken at different ages to assess whether the genetic architecture of the trait changed over age. Applications of the Framingham Heart Study data identified major loci jointly influencing body mass index and high-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides, total cholesterol and triglycerides, and various combinations of four traits involved in metabolic syndrome.

Cardiovascular Diseases↗

Multivariate genetic analysis of apo AI concentration and HDL subfractions: evidence for major locus pleiotropy.

A major locus influencing apolipoprotein AI (apo AI) serum levels was detected using data from the Donner Laboratory Family Study. This locus accounts for 46% of the phenotypic variability in apo AI levels. Multivariate segregation analysis revealed that this major locus also has significant pleiotropic effects on the relative distribution of high density lipoproteins.

Apolipoprotein A-I↗

Genetic pleiotropy for resting metabolic rate with fat-free mass and fat mass: the Québec Family Study.

Shared genetic and familial environmental causes for the associations among resting metabolic rate (RMR), fat-free mass (FFM), and fat mass (FM) were investigated in families participating in phase 2 of the Québec Family Study. A multivariate familial correlation model assessing the pattern of significant cross-trait correlations between family members (e.g., RMR in parents with FFM in offspring) was used to infer the etiology of the associations. For each of FM and FFM with RMR, significant sibling, parent-offspring, and intraindividual cross-trait correlations suggests the associations are familial. Furthermore, the lack of significant spouse cross-trait correlations suggests that the familial aggregation is primarily genetic. Bivariate heritability estimates suggest that as much as 45% to 50% of the shared variance between FFM and RMR may be genetic, and as much as 28% to 34% for FM and RMR. This study supports the notion that the gene(s) affecting each of FFM and FM also influence the RMR. Moreover, the lack of any familial associations between FFM and FM suggests that the effects of each body size component on RMR are independent, i.e., more than one genetic source on the RMR-body size association. The possibility that RMR is an oligogenic trait (i.e., more than one underlying genetic etiology) should be further investigated using more complex multivariate segregation methods until specific genes can be tested.

Adipose Tissue↗

Functional pleiotropy of the neurohormone melatonin: antioxidant protection and neuroendocrine regulation.

The pineal hormone melatonin exhibits remarkable functional versatility. Shortly after its discovery, melatonin was functionally linked to the regulation of the neuroendocrine axis, particularly to the reproductive system. However, judging from the wide variety of cellular changes that occurred following either pinealectomy, to remove the primary source of melatonin, or the exogenous administration of the indole, it was obvious that the activity of melatonin far transcended its actions on the hypothalamo-pituitary-gonadal system. Roughly 30 months ago it was discovered that melatonin is a highly efficient free radical scavenger and general antioxidant. This implied that melatonin, which is both lipophilic and hydrophilic, has effects not only in every cell but also within every subcellular compartment. These intracellular actions of melatonin, some of which are independent of any receptor interaction and some of which are mediated by nuclear receptors, have become the focus of much of the current investigation. As an antioxidant, melatonin has been shown in vitro to be a highly efficient scavenger of the very reactive and toxic hydroxyl radical. Indeed, on an equimolar basis melatonin proved significantly more efficient in neutralizing the hydroxyl radical than did the two well-known scavengers, glutathione and mannitol. Likewise, melatonin was found to also scavenge the peroxyl radical which is generated during lipid peroxidation; in this regard it was roughly twice as effective as vitamin E (alpha-tocopherol). The antioxidant activities of melatonin have been well documented in tissue homogenates and organisms as well. When rats are treated with the chemical carcinogen safrole, this agent induces the generation of free radicals which in turn extensively damage nuclear DNA; this damage is almost totally eliminated if the animals are cotreated with melatonin. Also, damage to DNA in human lymphocytes due to ionizing radiation, another treatment which is known to induce free radical formation, is greatly reduced if the cells are treated with melatonin prior to radiation. Cytosolic protein seems also to be protected from free radical damage when melatonin is present. When newborn rats are treated with a glutathione-depleting drug at birth, by 2 weeks of age the animals have cataracts. Cataracts form because oxidants damage protein in the presence of low intracellular levels of glutathione. Cataracts induced by this means are essentially prevented if the glutathione-depleted rats are supplemented with melatonin. Finally, membrane lipid peroxidation, induced either in vivo or in vitro by any of several means, all of which involve free radicals, is drastically attenuated in the presence of melatonin. Considering melatonin's ability to cross all morphophysiological barriers and to enter every cell, and all subcellular compartments, the implication is that this indole may play a very important role in the antioxidative defense system of the organism. These findings potentially have important implications for a wide variety of age-related diseases and to aging itself. Melatonin's control of reproductive physiology in photoperiodic mammals is well documented. However, the site of interaction of melatonin with the neuroendocrine axis has been especially difficult to determine. The discovery and cloning of a membrane melatonin receptor on neurosecretory cells in the hypothalamus and on hormone secreting cells of the anterior pituitary gland stimulated a great deal of investigation which has failed to prove the involvement of these receptors in the processes by which melatonin influences reproductive physiology. The recent identification of nuclear melatonin receptors as well as the nonreceptor-mediated actions of the indole are currently being examined as to their association with reproductive function.

Animals↗

A population genetics model for multiple quantitative traits exhibiting pleiotropy and epistasis.

We study a population genetics model of an organism with a genome of L(tot)loci that determine the values of T quantitative traits. Each trait is controlled by a subset of L loci assigned randomly from the genome. There is an optimum value for each trait, and stabilizing selection acts on the phenotype as a whole to maintain actual trait values close to their optima. The model contains pleiotropic effects (loci can affect more than one trait) and epistasis in fitness. We use adaptive walk simulations to find high-fitness genotypes and to study the way these genotypes are distributed in sequence space. We then simulate the evolution of haploid and diploid populations on these fitness landscapes and show that the genotypes of populations are able to drift through sequence space despite stabilizing selection on the phenotype. We study the way the rate of drift and the extent of the accessible region of sequence space is affected by mutation rate, selection strength, population size, recombination rate, and the parameters L and T that control the landscape shape. There are three regimes of the model. If LT< >L(tot), there are many small peaks that can be spread over a wide region of sequence space. Compensatory neutral mutations are important in the population dynamics in this case.

Animals↗

Epistasis and pleiotropy as natural properties of transcriptional regulation.

A statistical thermodynamic model of transcriptional regulation is employed to investigate the likely effects of genetic variation on the stabilization of gene expression. The model is tailored to empirical data on the control of transcription of the hunchback gene by the morphogen Bicoid during Drosophila embryogenesis. Variable parameters include the number of binding sites for activator protein and the DNA-protein and protein-protein cooperative binding energies. Recursions are performed to derive transcriptional response curves over a range of concentrations of activator. Sigmoidal responses are indicative of threshold-dependent activation of gene expression, and the effects of variation of the parameters on the width and location of the threshold are considered. It is shown that there is a minimum threshold width (maximum switch sensitivity) that is a function of the number of binding sites and the level of response desired, but independent of the binding energies. This places a constraint on the evolution of sensitive genetic switches that generate discrete cell types. Inevitable trade-offs between threshold widths and locations for multiple target genes of most transcriptional activators are found to occur. These naturally lead to epistatic and pleiotropic effects, and may favor the generation of networks of compensatory mutations that together produce homeostatic developmental pathways.

Animals↗