Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans

Extensive folding variability between homologous chromosomes in mammalian cells

Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.

Genomic heterozygosity is associated with a lower risk of osteoarthritis

BACKGROUND

Genomic heterozygosity has been shown to confer a health advantage in humans and play a protective role in complex diseases. Given osteoarthritis (OA) is a highly polygenic disease, we set out to determine if an association exists between OA and genomic heterozygosity.

RESULTS

End-stage knee and hip OA patients and healthy controls were recruited from the Newfoundland and Labrador (NL) population. The Arthritis Research UK Osteoarthritis Genetics (arcOGEN) consortium database was utilized as a replication cohort. DNA was extracted from blood samples and genotyped. Individual rates of observed heterozygosity (HetRate) and heterozygosity excess (HetExcess) relative to the expected were mathematically derived, and standardized to a z-score. Logistic regression modeling was used to examine the association between OA and HetRate or HetExcess. A total of 559 knee and hip OA patients (mean age 66.5 years, body mass index (BMI) 33.7 kg/m2, and 55% females) and 118 healthy controls (mean age 56.4 years, BMI 29.5 kg/m2, and 59% female) were included in the NL cohort analysis. We found that OA had an inverse relationship with HetRate and HetExcess with odds ratios of 0.64 (95% CI: 0.45-0.91) and 0.65 (95% CI: 0.45-0.93) per standard deviation (SD), respectively. The arcOGEN data included 2,019 end-stage knee and hip OA patients and 2,029 healthy controls, validating our findings with HetRate and HetExcess odds ratios of 0.60 (95% CI: 0.56-0.64) and 0.44 (95% CI: 0.40-0.47) per SD, respectively.

CONCLUSIONS

Our results are the first to clearly show evidence, from two separate cohorts, that reduced genomic heterozygosity confers a risk for the future development of OA.

Next Generation Sequencing of Genotype Variants and Genetic Association between Heat Shock Proteins HSPA1B Single Nucleotide Polymorphism at the g.31829044 Locus and Heat Tolerance: A Pilot Quasi-Experimental Study

Heat tolerance and exertional heat stroke (EHS) are rare health conditions that have been described and characterised but have never been genetically solved. Knowledge of the role of single nucleotide polymorphisms (SNPs) in heat shock proteins (HSPs) genes and their associations with heat tolerance and EHS is limited. This pilot study aimed to identify SNP in HSPA1B, HSP90AA2 and DNAJA1 genes and their associations with heat tolerance and EHS history in a quasi-experimental design. Participants comprised Australian Defence Force members (ADF) who had a history of EHS and the general population. Genomic DNA samples were extracted from the venous blood samples of 48 participants, sequenced and analysed for SNP. Forty-four per cent (44%) of the participants were heat intolerant, and 29% had a history of EHS. Among participants with a history of EHS, there was an association between heat tolerance and HSPA1B SNP at the g.31829044 locus. However, there were no associations between HSPA1B and HSP90AA2 SNP and heat tolerance. All participants had the same distribution for the DNAJA1 SNP. In conclusion, the findings indicate an association between the HSPA1B genetic variant at the g.31829044 locus and heat tolerance among ADF participants with a history of EHS. Further research with a larger number of military participants will shed more light on the associations between HSP genes and heat tolerance.

Glutathione S-Transferase Omega-2 and Transforming Growth Factor-β1 Polymorphisms in Iranian Glaucoma Patients

Background

To investigate the association of glutathione s-transferase omega 2 (GSTO2) (142N > D) and transforming growth factor-β1 (TGF-β1) (869T > C) gene polymorphisms on the pathogenesis of two common types of glaucoma (including primary open-angle glaucoma (POAG) and chronic angle-closure glaucoma (CACG)) in the Iranian population.

Methods

A total of 100 glaucoma patients (60% males and 40% females with an age mean ± SD of 34.66 ± 14.25 years; 56 cases of POAG and 44 cases of CACG) were enrolled in this study. GSTO2 (142N > D) and TGF-β1 (869T > C) polymorphisms were evaluated by PCR-based methods in patients and controls.

Results

At locus GSTO2 (142N > D), the odds of ND genotype with respect to DD and NN genotypes were 1.55 and 2.08 times higher in POAG and CACG patients compared to those of patients in the control group (95% CI₁: 0.80–2.98; 95% CI₂: 1.00–4.33) which was statistically significant in CACG patients. However, the odds of DD and NN genotypes against the reference genotype in two patients group were not statistically significant as compared to those of patients in the control group. There was a significant association between the ND genotype and male patients (OR = 2.28, 95% CI: 1.06–4.92). The analysis of TGF-β1 (869T > C) polymorphisms showed no significant difference between the genotypes of TGF-β1 (869T > C) polymorphisms in patients and control groups; however, the CT genotype of TGF-β1 significantly differed between female controls and patients (OR = 0.42, 95% CI: 0.18–0.96).

Conclusion

The presented results revealed that there was a significant association between the ND genotype of GSTO2 and the pathogenesis of glaucoma. Furthermore, this genotype can be considered as a sex-dependent genetic risk factor for the development of glaucoma. In contrast, the CT genotype of TGF-β1 is suggested to be a protective genetic factor against the pathogenesis of glaucoma.

Haematological Indicators of Response to Erythropoietin Therapy in Chronic Renal Failure Patients on Haemodialysis: Impact of Angiotensin-Converting Enzyme rs4343 Gene Polymorphism

PURPOSE

This is the first cross-sectional study studying the changes in haematological indicators of the response to recombinant human erythropoietin (rHuEPO) therapy in chronic renal failure (CRF) patients on haemodialysis (HD) stratified according to ACE G2350A (rs4343) gene polymorphism.

DESIGN

An observational cross-sectional study.

SETTING

Nephrology department and Biochemistry and molecular biology department, faculty of medicine, Cairo University.

PATIENTS

A total of 256 CRF patients on HD for at least six months (162 male and 103 female) and 160 healthy subjects (122 male and 38 female) were recruited in the current study after signing a consent form. ACE G2350A (rs4343) Insertion/Deletion (I/D) was tested, the association between ACE G2350A (RS4343) gene polymorphisms and patients response to rHuEpo was evaluated.

RESULTS

ACE G2350A (rs4343) I/D was the most prevalent genotype, while I/I genotype was the lowest prevalent among patient or control subjects included in the study. D allele is the most prevalent allele, either among patients or the control group. Hemoglobin (Hb) level in patients with I/I and Deletion/Deletion (D/D) genotype was significantly higher compared to those with I/D genotype (P = 0.012 and P = 0.005, respectively). Serum iron in the I/D genotype was significantly higher than those with either I/I or D/D genotype (P = 0.045 and P = 0.018, respectively). Angiotensin-converting enzyme (ACE) content, total leukocytic count (TLC), and soluble erythropoietin receptor (sEpoR) were independent predictors of Hb level. The ACE gene, TLC, and serum iron were the independent factors that may affect the Haematocrit (Hct) level. ACE G2350A (rs4343) gene polymorphisms may affect the HD patient's responses to rHuEPOs.

CONCLUSION

In HD patients, screening for ACE G2350A (rs4343) gene polymorphisms before rHuEpo administration may help predict patient response.

Association between Three Variants in the PRKAA2 gene, rs2796498, rs9803799, and rs2746342, with 10-year ASCVD Risk on Newly Diagnosed T2DM in Yogyakarta, Indonesia

BACKGROUND: AMPK has pivotal roles in glucose and lipid metabolism, including  AMPKa2, which PRKAA2 encodes. Metformin as an anti-hyperglycemia agent acts through AMPK. Poor glycemia control among patients with type 2 diabetes mellitus (T2DM) could increase atherosclerosis cardiovascular disease (ASCVD) risk. Therefore, PRKAA2 genetic variation might contribute to 10-year ASCVD risk in patients with newly diagnosed T2DM receiving monotherapy metformin. AIM: The study aimed to detect an association between PRKAA2 genetic variation with 10 year-ASCVD risk among newly diagnosed T2DM patients prescribed monotherapy metformin. METHODS: This present study was a case-control study involving 107 participants. Analysis of PRKAA2 genetic variation was performed using the TaqMan assay. RESULTS: A total of 91 participants who fulfilled our criteria enrolled in this study. Most of the participants were female, with mean age 54.40±7.75 years old, mean HbA1c level of 8.35±1.31%, and the lipid profile indicated normal conditions. There was a significant difference in age (p<0.01), HbA1c level (p=0.04), sex (p<0.01), and smoking status (p<0.01) between low-risk and high-risk groups. The GT genotype of rs9803799 had 187.86 times higher possibility for high-risk of 10-year ASCVD risk than TT genotype (OR=187.86, 95%CI:2.98–11863.51). The dominant model of rs9803799 showed that GT+GG had 94.33 times higher possibility for high-risk of 10-year ASCVD risk than TT genotype (OR=94.33; 95%CI:2.32–3841.21). Other results showed that G allele of rs980377 had 20.48 times higher possibility for high-risk of 10-year ASCVD risk than T allele (OR = 20.48; 95%CI:1.48–283.30). These associations were found after multivariate analysis. CONCLUSION: Our findings indicated that rs9803799 as one of PRKAA2 genetic variations might impact the 10-year ASCVD risk among newly diagnosed T2DM patients receiving monotherapy metformin. After considering non-genetic factors, patient assessment should include potential genetic factors in cases with hyperglycemia involving treatment affecting glucose and lipid metabolism such as monotherapy metformin.   Keywords: PRKAA2, genetic variation, atherosclerosis cardiovascular disease, type 2 diabetes mellitus, metformin, Indonesia

Factors affecting attitudes toward migrants-An evolutionary approach

OBJECTIVE

To understand migration from an evolutionary perspective, this phenomenon has so far been mainly investigated in animal species. We therefore aim to investigate the potential evolutionary roots of attitudes toward migrants in humans.

METHODS

We used data from the European Social Survey (n = 83 734), analyzing attitudes toward migrants by performing ordinal mixed models.

RESULTS

We found that men have a more restrictive attitude toward migration than women, which increases with age and is stronger with a child in the household. Attitude toward migrants is also more skeptical if migrants have a different ethnicity and are from poorer countries. Increasing education and religiousness are associated with a more positive attitude toward migrants, particularly toward migrants of different ethnicity and from poorer countries.

DISCUSSION

Although migration flows are a hallmark of the human species, previous findings suggest that (pre-)historic migration flows were at times accompanied by conflict and violence, while at the same time, they insured survival by allowing cultural exchange and the avoidance of inbreeding. Accordingly, we assume that contemporary attitudes toward migration are rooted in our evolutionary past. We discuss the respective behavioral patterns from an evolutionary perspective, arguing that both-a negative attitude as well as openness-make sense.

Germline Genetic Variants of the Renin-Angiotensin System, Hypoxia and Angiogenesis in Non-Small Cell Lung Cancer Progression: Discovery and Validation Studies

Simple Summary

The presence of polymorphic gene variants in the human genome provides extensive genetic (and eventually phenotypic) variation affecting both normal physiological mechanisms and cancer pathogenesis. Functional genetic polymorphisms might have predictive and/or prognostic value in lung cancer, opening novel opportunities to improve prediction and guide clinical reasoning and therapeutics in lung cancer patients. Recent knowledge pinpoints a pleiotropic role for renin-angiotensin system, particularly in the lung and mainly through locally regulated alternative molecules and secondary pathways. Dysregulation of this system play a role in cell proliferation, hypoxia and angiogenesis, which processes are involved in lung cancer progression. Here we suggest that polymorphic variants in genes coding for renin-angiotensin system might play a role in Non-Small Cell Lung Cancer progression.

Abstract

Introduction: The renin–angiotensin system (RAS) is involved in cell proliferation, immunoinflammatory response, hypoxia and angiogenesis, which are critical biological processes in lung cancer. Our aim was to study the association of putatively functional genetic polymorphisms in genes coding for proteins involved in RAS, hypoxia and angiogenesis with non-small cell lung cancer (NSCLC) prognosis. Methods: Genotyping of 52 germline variants from genes of the RAS and hypoxic/angiogenic factors/receptors was performed using MassARRAY iPLEX Gold in a retrospective cohort (n = 167) of advanced NSCLC patients. Validation of the resulting genetic markers was conducted in an independent group (n = 190), matched by clinicopathological characteristics. Results: Multivariate analysis on the discovery set revealed that MME rs701109 C carriers were protected from disease progression in comparison with homozygous T (hazard ratio (HR) = 0.5, 95% confidence interval (CI) = 0.2–0.8, p = 0.010). Homozygous A and T genotypes for KDR rs1870377 were at increased risk for disease progression and death compared to heterozygous (HR = 1.7, 95% CI = 1.2–2.5, p = 0.005 and HR = 2.1, 95% CI = 1.2–3.4, p = 0.006, respectively). Carriers of homozygous genotypes for ACE2 rs908004 presented increased risk for disease progression, only in the subgroup of patients without tumour actionable driver mutations (HR = 2.9, 95% CI = 1.3–6.3, p = 0.010). Importantly, the association of homozygous genotypes in MME rs701109 with risk for disease progression was confirmed after multivariate analysis in the validation set. Conclusion: This study provides evidence that MME polymorphism, which encodes neprilysin, may modulate progression-free survival in advanced NSCLC. Present genetic variation findings will foster basic, translational, and clinical research on their role in NSCLC.

Unbalanced Sample Size Introduces Spurious Correlations to Genome-Wide Heterozygosity Analyses

Excess of heterozygosity (H) is a widely used measure of genetic diversity of a population. As high-throughput sequencing and genotyping data become readily available, it has been applied to investigating the associations of genome-wide genetic diversity with human diseases and traits. However, these studies often report contradictory results. In this paper, we present a meta-analysis of five whole-exome studies to examine the association of H scores with Alzheimer's disease. We show that the mean H score of a group is not associated with the disease status, but ot is associated with the sample size. Across all five studies, the group with more samples has a significantly lower H score than the group with fewer samples. To remove potential confounders in empirical data sets, we perform computer simulations to create artificial genomes controlled for the number of polymorphic loci, the sample size, and the allele frequency. Analyses of these simulated data confirm the negative correlation between the sample size and the H score. Furthermore, we find that genomes with a large number of rare variants also have inflated H scores. These biases altogether can lead to spurious associations between genetic diversity and the phenotype of interest. Based on these findings, we advocate that studies shall balance the sample sizes when using genome-wide H scores to assess genetic diversities of different populations, which helps improve the reproducibility of future research.