Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

Impact of rs2046045 SNP in PDE8B on TSH Levels: Insights into Genetic Susceptibility to Hypothyroidism

Hypothyroidism is the most prevalent thyroid disorder and leads to adverse effects on the human body. Serum thyroid stimulating hormone (TSH) values have been related to polymorphisms in multiple genes that may be involved in the regulation of thyroid function. The single nucleotide polymorphism (SNP) rs2046045 is situated in the intron region of the phosphodiesterase 8B (PDE8B) gene, which encodes a high-affinity cyclic adenosine monophosphate (cAMP)-specific phosphodiesterase widely expressed in thyroid tissue. The principal goal of the present study was to investigate the association between the SNP rs2046045 of the PDE8B gene and hypothyroidism. The study was designed as a case-control study, and a total of 160 hypothyroid and 160 healthy controls were involved. Blood samples were drawn from each individual, and deoxyribonuleic acid (DNA) was separated with a suitable DNA isolation kit. For genotyping, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was employed. The IBM Statistical Package for Social Sciences (SPSS) 25.0 was utilized to analyze the statistical data. Age differences between the patients and controls were not observed in the present study. The genotype frequency of homozygous wild type (TT), homozygous mutate type (GG), and heterozygous (GT) was 45%, 2.5%, and 52.5%, respectively, in control subjects and 27.5%, 11.25%, and 61.25%, respectively, in cases, and showed a significant difference (p = 0.0002). The minor G allele frequency is elevated in hypothyroid patients as compared to healthy control subjects (41.87% vs. 28.75%), p = 0.0005. The presence of the mutant allele G of rs2046045 in the PDE8B gene correlates with elevated serum TSH levels in hypothyroid patients.

Investigating the shared genetic basis and causal relationships between mucosa-associated lymphoid tissue inflammation and psychiatric disorders

Background

Chronic and acute inflammation of the mucosa-associated lymphoid tissue have been positively linked to the development of psychiatric disorders in observational studies. However, it remains unclear whether this association is causal. In the present study, we investigated this association, using as proxies genetically predicted tonsillectomy, appendectomy and appendicitis on psychiatric disorders including major depressive disorder (MDD), schizophrenia (SCZ), bipolar depression (BD) and anxiety (ANX) via a two-sample Mendelian randomization (MR) analysis.

Methods

Genetic association summary statistics for tonsillectomy, appendectomy and appendicitis were sourced from FinnGen Consortium, comprising data from 342,000 participants. Genetic correlations between all exposures and outcome were calculated with Linkage Disequilibrium Score (LDSC) Regression analysis. MR estimates were then calculated to assess their impact on the risk of developing psychiatric disorders. Sensitivity analysis was employed to test for any directional pleiotropy.

Results

Our results suggest that there is no direct causal association between tonsillectomy, appendectomy or appendicitis with a heightened risk for development of psychiatric disorders. The robustness of the results of the main MR analysis was further confirmed with additional sensitivity analyses. However, a moderate inverse genetic correlation was observed between tonsillectomy and MDD traits (rg=-0.39, p-value (P)=7.5x10-5).

Conclusion

Our findings provide, for the first time, evidence that there is no causal association between tonsillectomy or appendectomy on subsequent vulnerability of developing psychiatric disorders. Future studies using larger sample size GWAS should focus on unraveling the confounding factors and mediators to investigate this relationship further.

Rhus tripartite methanolic extract alleviates propylparaben-induced reproductive toxicity via anti-inflammatory, antioxidant, 5-α reductase in male rats

Evidence showed that herbal medicine could be beneficial for protection against diseases that may be exist in consequence of exposure to environmental toxicants. Propylparaben (PrP) is used as preservative in food, pharmaceuticals, and cosmetics. It is classified as one of endocrine disruptive chemicals (EDCs). This study evaluated the protective effect of Rhus tripartita methanolic extract (RTME) against reproductive toxicity induced by PrP in male rats. A total of 60 Wister albino rats were divided into four groups (15 rats for each group). Group I (control): rats received the vehicle (DMSO), group II: normal rats received RTME (10 mg/kg/day), group III: rats received PrP (10 mg/kg/day), and group IV: rats received PrP (10 mg/kg/day) and RTME (10 mg/kg/day) for 4 weeks. At the end of experiment, levels of testosterone, dihydrotestosterone (DHT), and 5α-reductase were analyzed in sera. Data obtained showed a significant reduction in the levels of testosterone, dihydrotestosterone (DHT), and 5α- reductase in rats given PrP versus control (p < 0.001) and RTME treatment improved these parameters but not returned to normal. Data obtained showed a significant elevation in levels of IL-6 and TNF-α in the testis of rats given PrP versus control (p < 0.001), these inflammatory mediators were significant reduced in rats treated with RTME compared with untreated rats (p < 0.001). There was a positive correlation between level of DHT and antioxidant enzymes activities (r = 0.56). A significant elevation in the levels of MDA with reduction in the activities of GST, GSPx, SOD, and catalase (p < 0.001) in rat testicular tissues of PrP group versus control (p < 0.001) was found. Treatment with RTME significantly reduced the levels of MDA and enhanced activities of GST, GSPx, SOD, and catalase (p < 0.001) compared to untreated group (p < 0.001). In conclusion, the active ingredient components of RTME abrogate the toxicity of PrP by exhibiting antioxidative and anti-inflammatory effects, enhancing 5-α reductase with improved hormonal status against PrP- induced testicular damage. Toxicity of propylparaben, and effect of Rhus tripartita methanolic extract.

Evaluation of male infertility treatment following Rhus coriaria extract administration on rats exposed to morphine

Morphine is the most common analgesic drug that is widely used in post-operative interventions. This drug causes free radical accumulation leading to spermatogenesis failure. Antioxidant agents like Sumach (Rhus coriaria) neutralize cellular free radicals. In this study, the properties of antioxidative, modulative of inflammatory cytokines, and apoptotic genes following Sumach extract administration on morphine-induced fertility destruction in male Wistar rats was evaluated. Sixty-four animals were grouped (n = 8) including; 1: control, 2: morphine, 3-5: Sumach (200, 400, 800 mg/kg), and 6-8: morphine + Sumach. Hydroalcoholic extract of Sumach seeds was prepared. Treatments with Sumach extract were applied orally and intraperitoneally daily for 8 weeks. The P53, Bcl2 and caspase-3 genes expression were measured by real-time PCR. Cytokines involved in inflammation were evaluated by ELISA. Sperm parameters, total antioxidant capacity (TAC), testosterone, and germinal layer height (GLH) were assessed. All parameters (investigated in this study) in Morphine group reduced significantly than the control group (P ˂ 0.01) (except P53 and caspase-3 genes expression and inflammatory cytokine which were improved). All factors in Sumach and Sumach + Morphine groups were significantly enhanced compared to the Morphine group (P ˂ 0.01) (except P53 and caspase-3 genes expression and inflammatory cytokine which were declined). Morphine disrupted the physiological function of male fertility system. Besides, all doses of Sumach showed no therapeutic changes compared to the control group. Sumach with anti-infertility features compensates the toxic effect of Morphine administration.

Meta-Analysis of SNP-Environment Interaction With Overlapping Data

Meta-analysis, which combines the results of multiple studies, is an important analytical method in genome-wide association studies. In genome-wide association studies practice, studies employing meta-analysis may have overlapping data, which could yield false positive results. Recent studies have proposed models to handle the issue of overlapping data when testing the genetic main effect of single nucleotide polymorphism. However, there is still no meta-analysis method for testing gene-environment interaction when overlapping data exist. Inspired by the methods of testing the main effect of gene with overlapping data, we proposed an overlapping meta-regulation method to address the issue in testing the gene-environment interaction. We generalized the covariance matrices of the regular meta-regression model by employing Lin’s and Han’s correlation structures to incorporate the correlations introduced by the overlapping data. Based on our proposed models, we further provided statistical significance tests of the gene-environment interaction as well as joint effects of the gene main effect and the interaction. Through simulations, we examined type I errors and statistical powers of our proposed methods at different levels of data overlap among studies. We demonstrated that our method well controls the type I error and simultaneously achieves statistical power comparable with the method that removes overlapping samples a priori before the meta-analysis, i.e., the splitting method. On the other hand, ignoring overlapping data will inflate the type I error. Unlike the splitting method that requires individual-level genotype and phenotype data, our proposed method for testing gene-environment interaction handles the issue of overlapping data effectively and statistically efficiently at the meta-analysis level.

Kallmann Syndrome Due to Heterozygous Mutation in SOX10 Coexisting With Waardenburg Syndrome Type II: Case Report and Review of Literature

INTRODUCTION

Kallmann syndrome (KS) is idiopathic hypogonadotropic hypogonadism with olfactory loss or decline. Waardenburg syndrome type II (WS2) is a clinically and genetically heterogeneous disease, characterized by congenital sensorineural deafness and abnormal pigmentation of the iris, hair, and skin. Recently, mutations in the well-known WS pathogenic gene SOX10 have been found in some KS patients with deafness, but whether SOX10 is a co-pathogenic gene of KS and WS remains uncertain. Here, we report a rare case of KS and WS2 co-occurrence due to SOX10 mutations.

METHODS

Detailed histories were collected through questionnaires and physical examination. Blood samples of the patient and his family members were collected after obtaining informed consents. Suspected mutations were amplified and verified by Sanger sequencing after the next generation sequencing of related genes. The raw sequence data were compared to the known gene sequence data in publicly available sequence data bases using Burrows-Wheeler Aligner software (BWA, 0.7.12-r1039).

RESULTS

A 28-year-old male patient sought treatment for hypogonadism and the absence of secondary sexual characteristics. In addition, he showed signs of obesity, hyposmia, sensorineural hearing loss, and blue iris. Magnetic resonance imaging (MRI) of the olfactory bulb showed small bilateral olfactory bulbs and tracts and diaphragma cerebri. MRI of the pituitary gland revealed a flat pituitary gland in the sella. Laboratory examination demonstrated hypogonadotropic hypogonadism, pituitary hypothyroidism, subclinical hypothyroidism, and the presence of insulin resistance with normal blood glucose levels. Sequencing of the SOX10 gene showed a 20 bp insertion in between coding bases 1,179 and 1,180 (c.1179_1180insACTATGGCTCAGCCTTCCCC). This results in a frame-shifting mutation of the 394th amino acid serine in exon4 with the resulting the amino acid sequence of the protein predicted to be TMAQPSP PSPAPSLTTL TISPQDPIMA TRARPLASTR PSPIWGPRSG PSTRPSLTPA PQGPSPTAPH TGSSQYIRHC PGPKGGPVAT TPRPAPAPSL CALFLAHLRP GGGSGGG*.

CONCLUSION

SOX10 plays an important role in some critical stages of neural crest cell development and SOX10 mutation may be a common pathogenic factor for both KS and WS. Therefore, SOX10 mutation analysis should be considered for KS patients with combined WS clinical manifestations, especially deafness.

Meta-Analysis of SNP-Environment Interaction with Heterogeneity

Meta-analyses are widely used in genome-wide association studies to combine the results obtained from multiple studies. Classical random-effects methods treat genetic heterogeneity as a random effect and consider it as a portion of the variance associated with a fixed effect of the variant. Recent work suggests performing hypothesis testing with the null hypothesis under which neither fixed nor random effects exist for a variant. This method has been shown to perform better than classical random-effects methods. In this work, we propose a meta-analysis of testing single nucleotide polymorphism (SNP)-environment interaction in the presence of genetic heterogeneity. We introduced the random effects of the SNP and SNP-environment interaction under test into a meta-regression model to account for heterogeneity. A test for the SNP-environment interaction was formulated to test for fixed and random effects of the interaction simultaneously. Similarly, a test for total genetic effects was formulated to test for fixed effects of the SNP and the SNP-environment interaction together with their random effects. We performed simulations to study the null distribution and statistical power of the proposed tests. We show that the new methods have higher power than classical random-effects and fixed-effects meta-regression methods when heterogeneity effects are large.

Schools as Moderators of Genetic Associations with Life Course Attainments: Evidence from the WLS and Add Health

Genetic variants identified in genome-wide association studies of educational attainment have been linked with a range of positive life course development outcomes. However, it remains unclear whether school environments may moderate these genetic associations. We analyze data from two biosocial surveys that contain both genetic data and follow students from secondary school through mid- to late life. We test if the magnitudes of the associations with educational and occupational attainments varied across the secondary schools that participants attended or with characteristics of those schools. Although we find little evidence that genetic associations with educational and occupational attainment varied across schools or with school characteristics, genetic associations with any postsecondary education and college completion were moderated by school-level socioeconomic status. Along similar lines, we observe substantial between-school variation in the average level of educational attainment students achieved for a fixed genotype. These findings emphasize the importance of social context in the interpretation of genetic associations. Specifically, our results suggest that though existing measures of individual genetic endowment have a linear relationship with years of schooling that is relatively consistent across school environments, school context is crucial in connecting an individual's genotype to his or her likelihood of crossing meaningful educational thresholds.

Mutation affecting the proximal promoter of Endoglin as the origin of hereditary hemorrhagic telangiectasia type 1

Background

Hereditary hemorrhagic telangiectasia (HHT) is a vascular multi-organ system disorder. Its diagnostic criteria include epistaxis, telangiectases in mucocutaneous sites, arteriovenous malformations (AVMs), and familial inheritance. HHT is transmitted as an autosomal dominant condition, caused in 85% of cases by mutations in either Endoglin (ENG) or Activin receptor-like kinase (ACVRL1/ACVRL1/ALK1) genes. Pathogenic mutations have been described in exons, splice junctions and, in a few cases with ENG mutations, in the proximal promoter, which creates a new ATG start site. However, no mutations affecting transcription regulation have been described to date in HHT, and this type of mutation is rarely identified in the literature on rare diseases.

Methods

Sequencing data from a family with HHT lead to single nucleotide change, c.-58G > A. The functionality and pathogenicity of this change was analyzed by in vitro mutagenesis, quantitative PCR and Gel shift assay. Student t test was used for statistical significance.

Results

A single nucleotide change, c.-58G > A, in the proximal ENG promoter co-segregated with HHT clinical features in an HHT family. This mutation was present in the proband and in 2 other symptomatic members, whereas 2 asymptomatic relatives did not harbor the mutation. Analysis of RNA from activated monocytes from the probands and the healthy brother revealed reduced ENG mRNA expression in the HHT patient (p = 0.005). Site-directed mutagenesis of the ENG promoter resulted in a three-fold decrease in luciferase activity of the mutant c.-58A allele compared to wild type (p = 0.005). Finally, gel shift assay identified a DNA-protein specific complex.

Conclusions

The novel ENG c.-58G > A substitution in the ENG promoter co-segregates with HHT symptoms in a family and appears to affect the transcriptional regulation of the gene, resulting in reduced ENG expression. ENG c.-58G > A may therefore be a pathogenic HHT mutation leading to haploinsufficiency of Endoglin and HHT symptoms. To the best of our knowledge, this is the first report of a pathogenic mutation in HHT involving the binding site for a transcription factor in the promoter of ENG.

Fragility of epidermis in newborns, children and adolescents

Within their first days of life, newborns' skin undergoes various adaptation processes needed to accommodate the transition from the wet uterine environment to the dry atmosphere. The skin of newborns and infants is considered as a physiological fragile skin, a skin with lower resistance to aggressions. Fragile skin is divided into four categories up to its origin: physiological fragile skin (age, location), pathological fragile skin (acute and chronic), circumstantial fragile skin (due to environmental extrinsic factors or intrinsic factors such as stress) and iatrogenic fragile skin. Extensive research of the past 10 years have proven evidence that at birth albeit showing a nearly perfect appearance, newborn skin is structurally and functionally immature compared to adult skin undergoing a physiological maturation process after birth at least throughout the first year of life. This article is an overview of all known data about fragility of epidermis in 'fragile populations': newborns, children and adolescents. It includes the recent pathological, pathophysiological and clinical data about fragility of epidermis in various dermatological diseases, such as atopic dermatitis, acne, rosacea, contact dermatitis, irritative dermatitis and focus on UV protection.

[A monogenic model of schizophrenia: a shift in paradigms]

Advanced genome technologies, including genome-wide association studies, next generation sequencing analysis, whole exome sequencing, encourage the development of theoretical insights on the role of genetic factors in schizophrenia. In this context, the author considers a monogenic model of schizophrenia and its evolution.