Negative selection on human genes underlying inborn errors depends on disease outcome and both the mode and mechanism of inheritance

Genetic variants underlying life-threatening diseases, being unlikely to be transmitted to the next generation, are gradually and selectively eliminated from the population through negative selection. We study the determinants of this evolutionary process in human genes underlying monogenic diseases by comparing various negative selection scores and an integrative approach, CoNeS, at 366 loci underlying inborn errors of immunity (IEI). We find that genes underlying autosomal dominant (AD) or X-linked IEI have stronger negative selection scores than those underlying autosomal recessive (AR) IEI, whose scores are not different from those of genes not known to be disease causing. Nevertheless, genes underlying AR IEI that are lethal before reproductive maturity with complete penetrance have stronger negative selection scores than other genes underlying AR IEI. We also show that genes underlying AD IEI by loss of function have stronger negative selection scores than genes underlying AD IEI by gain of function, while genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. These results are replicated in 1,140 genes underlying inborn errors of neurodevelopment. Finally, we propose a supervised classifier, SCoNeS, which predicts better than state-of-the-art approaches whether a gene is more likely to underlie an AD or AR disease. The clinical outcomes of monogenic inborn errors, together with their mode and mechanisms of inheritance, determine the levels of negative selection at their corresponding loci. Integrating scores of negative selection may facilitate the prioritization of candidate genes and variants in patients suspected to carry an inborn error.

Negative (or purifying) selection is the natural process by which deleterious alleles are selectively purged from the population (1). In diploid species, the strength of negative selection at a given locus is predicted to increase with decreasing fitness and increasing dominance of the genetic variants controlling traits: Variation causing early death in the heterozygous state are the least likely to be transmitted to the next generation, as their carriers have fewer offspring than noncarriers (2). Human genetic variants that cause severe diseases are, thus, expected to be the primary targets of negative selection, particularly for diseases affecting heterozygous individuals. In humans, several studies have ranked protein-coding genes according to their levels of negative selection (3–5). Nevertheless, the extent to which negative selection affects human disease-causing genes, and the factors determining its strength, remain largely unknown, particularly because our knowledge of the severity, mode, and mechanism of inheritance of the corresponding human diseases remains incomplete (3, 6–8).The strength of negative selection at a given gene has been traditionally approximated by comparing the coding sequence of the gene in a given species with that of one or several closely related species; it depends on the proportion of amino acid changes that have accumulated during evolution (9–11). With the advent of high-throughput sequencing, intraspecies metrics have been developed, based on the comparison of the probability of predicted loss-of-function (pLOF) mutations for a gene under a random model with the frequency of pLOF mutations observed in population databases (5, 12, 13), which capture the species-specific evolution of genes. Using an interspecies-based method and a hand-curated version of the Online Mendelian Inheritance in Man (hOMIM) database, a previous study elegantly showed that most human genes for which mutations cause highly penetrant diseases, including autosomal dominant (AD) diseases in particular, evolve under stronger negative selection than genes associated with complex disorders (6). However, other studies based on OMIM genes have reported conflicting results (3, 14–17), probably due to the incompleteness and heterogeneity of the datasets used. Moreover, no study has yet addressed this problem with intraspecies metrics, even though it has been suggested that the choice of the reference species for interspecies metrics contributes to discrepancies across studies (6).We aimed to improve the identification of the drivers of negative selection acting on human disease-causing genes, by developing a negative selection score combining several informative intraspecies and interspecies statistics, focusing on inborn errors of immunity (IEI). IEI, previously known as primary immunodeficiencies (18), are genetic diseases that disrupt the development or function of human immunity. They form a large and expanding group of genetic diseases that has been widely studied, and they are well characterized physiologically (immunologically) and phenotypically (clinically) (19–21). IEI are often symptomatic in early childhood, and at least until the turn of the 20th century and the introduction of antibiotics, most individuals with IEI probably died before reaching reproductive maturity. Accordingly, IEI genes have probably been under strong negative selection from the dawn of humankind until very recently. In this study, we investigated whether the severity of IEI and their mode and mechanism of inheritance have left signatures of negative selection of various intensities in the corresponding human genes. Furthermore, we validated our model on genes underlying inborn errors of neurodevelopment (IEND), another group of well-characterized severe genetic diseases.     

Estradiol modulation of phenylephrine-induced excitatory responses in ventromedial hypothalamic neurons of female rats

Estrogens act within the ventromedial nucleus of the hypothalamus (VMN) to facilitate lordosis behavior. Estradiol treatment in vivo induces alpha(1b)-adrenoreceptor mRNA and increases the density of alpha(1B)-adrenoreceptor binding in the hypothalamus. Activation of hypothalamic alpha(1)-adrenoceptors also facilitates estrogen-dependent lordosis. To investigate the cellular mechanisms of adrenergic effects on VMN neurons, whole-cell patch-clamp recordings were carried out on hypothalamic slices from control and estradiol-treated female rats. In control slices, bath application of the alpha(1)-agonist phenylephrine (PHE; 10 microM) depolarized 10 of 25 neurons (40%), hyperpolarized three neurons (12%), and had no effect on 12 neurons (48%). The depolarization was associated with decreased membrane conductance, and this current had a reversal potential close to the K(+) equilibrium potential. The alpha(1b)-receptor antagonist chloroethylclonidine (10 microM) blocked the depolarization produced by PHE in all cells. From estradiol-treated rats, significantly more neurons in slices depolarized (71%) and fewer neurons showed no response (17%) to PHE. PHE-induced depolarizations were significantly attenuated with 4-aminopyridine (5 mM) but unaffected by tetraethylammonium chloride (20 mM) or blockers of Na(+) and Ca(2+) channels. These data indicate that alpha(1)-adrenoceptors depolarize VMN neurons by reducing membrane conductance for K(+). Estradiol amplifies alpha(1b)-adrenergic signaling by increasing the proportion of VMN neurons that respond to stimulation of alpha(1b)-adrenergic receptors, which is expected in turn to promote lordosis.     

Procoagulant platelets: Laboratory detection and clinical significance

Platelets play a critical role in both haemostasis and thrombosis, and it is now evident that not all platelets behave the same when they are called to action. A functionally distinct subpopulation of platelets forms in response to maximal agonist stimulation: the procoagulant platelet. This platelet subpopulation is defined by its ability to expose phosphatidylserine on its surface, allowing for coagulation factor complexes to form and generate bursts of thrombin and fibrin to stabilize platelet clots. Reduced levels of procoagulant platelets have been linked to bleeding in Scott's syndrome and haemophilia A patients, and elevated levels have been demonstrated in many thrombotic disorders, including identifying patients at higher risk for stroke recurrence. One obstacle for incorporating an assay for measuring procoagulant platelets into clinical management algorithms is the lack of consensus on the exact definition and markers for this subpopulation. This review will outline the biological characteristics of procoagulant platelets and the laboratory assays currently used to identify them in research settings. It will summarize the findings of clinical research demonstrating the relevance of measuring the procoagulant platelet levels in patients and will discuss how an appropriate assay can be used to elucidate the mechanism behind the formation of this subpopulation, facilitating novel drug discovery to improve upon current outcomes in cardiovascular and other thrombotic disorders.     

Application of evidence-based dentistry: from research to clinical periodontal practice

Dentists need to make daily decisions regarding patient care, and these decisions should essentially be scientifically sound. Evidence-based dentistry is meant to empower clinicians to provide the most contemporary treatment. The benefits of applying the evidence-based method in clinical practice include application of the most updated treatment and stronger reasoning to justify the treatment. A vast amount of information is readily accessible with today's digital technology, and a standardized search protocol can be developed to ensure that a literature search is valid, specific and repeatable. It involves developing a preset question (population, intervention, comparison and outcome; PICO) and search protocol. It is usually used academically to perform commissioned reviews, but it can also be applied to answer simple clinical queries. The scientific evidence thus obtained can then be considered along with patient preferences and values, clinical patient circumstances and the practitioner's experience and judgment in order to make the treatment decision. This paper describes how clinicians can incorporate evidence-based methods into patient care and presents a clinical example to illustrate the process.     

Small steps: barriers and facilitators to physical health self-management by people living with mental illness

It has been established that people with mental illness experience mortality and morbidity from all the major health conditions at 2–3 times the rate of those without mental illness. One way to overcome this problem is to encourage consumers of mental health services to self-manage their physical health. The purpose of the study was to investigate the facilitators and barriers to physical health self-management by people living with a mental illness. The study was underpinned by a hermeneutic phenomenological framework and utilised focus groups for data collection. A total of 27 participants, who lived in the community, had a diagnosed mental illness and who also had a co-morbid chronic physical health condition were included in one of three focus groups. The collected data were thematically analysed to identify common experiences and difficulties. It was found that participants were well aware of the need to attend to physical health issues. However, a number of factors at the individual, social and system levels impeded their ability to do so. Barriers to self-management included the debilitating nature of mental illness, poor physical health literacy, stigma from medical staff and social isolation, which resulted in a lack of support. Whereas informal peer networks, group participation and where it was offered, the support and encouragement from healthcare professionals facilitated health self-management.