An in silico analysis of the impact of POLE mutations on cladribine docking.

OBJECTIVE: Polymerase ε exonuclease (POLE) is an enzyme involved in DNA replication and may be an attractive therapeutic target in various cancers. Here we sought to model the impact of specific POLE mutations on protein function. Due to the lack of a crystal structure, the tertiary structures of the wild type and four common mutants were modeled using I-Tasser server. MATERIALS AND METHODS: Molecular docking and dynamic simulation studies were performed, and the structure and function of the mutants analyzed through residue conservation analysis and protein folding energy changes. RESULTS: All mutants of POLE gene had favorable binding affinities compared with their wild type of counterpart. The P286R variant, but not the other variants, disrupted cladribine binding to the protein. Similarly, dynamics studies revealed instability of the P286R mutant, while V411L, L424V, and L424F appeared to favor cladribine binding. CONCLUSIONS: Since P286R is a hotspot mutation in endometrioid carcinomas, patients with this variant may not respond to cladribine. Population-based pharmacogenomics studies will be required to validate our results.

A novel homozygous TPM1 mutation in familial pediatric hypertrophic cardiomyopathy and in silico screening of potential targeting drugs.

OBJECTIVE: Familial hypertrophic cardiomyopathy (HCM) is the most common genetic cardiac disease. While sarcomeric gene mutations explain many HCM cases, the genetic basis of about half of HCM cases remains elusive. Here we aimed to identify the gene causing HCM in a non-consanguineous Saudi Arabian family with affected family members and a history of sudden death. The impact of the identified mutation on protein structure and potential drug targets were evaluated in silico. MATERIALS AND METHODS: Triplets (two HCM subjects and one patent ductus arteriosus (PDA) case) and unaffected parents were screened by targeted next-generation sequencing (NGS) for 181 candidate cardiomyopathy genes. In silico structural and functional analyses, including protein modeling, structure prediction, drug screening, drug binding, and dynamic simulations were performed to explore the potential pathogenicity of the variant and to identify candidate drugs. RESULTS: A homozygous missense mutation in exon 1 of TMP1 (assembly GRCh37-chr15: 63340781; G>A) was identified in the triplets [two HCM and one patent ductus arteriosus (PDA)] that substituted glycine for arginine at codon 3 (p.Gly3Arg). The parents were heterozygous for the variant. The mutation was predicted to cause a significant and deleterious change in the TPM1 protein structure that slightly affected drug binding, stability, and conformation. In addition, we identified several putative TPM1-targeting drugs through structure-based in silico screening. CONCLUSIONS: TPM1 mutations are a common cause of HCM and other congenital heart defects. To date, TPM1 has not been associated with isolated PDA; to our knowledge, this is the first report of the homozygous missense variation p.Gly3Arg in TPM1 associated with familial autosomal recessive pediatric HCM and PDA. The identified candidate TPM1 inhibitors warrant further prospective investigation.

The Polymorphism at the microRNA-155 Binding Site in the AGTR1 Gene is not Significantly Associated with Rheumatic Heart Disease in Saudi Arabia Population.

BACKGROUND: Rheumatic Heart Disease (RHD) remains a major cause of cardiovascular diseases and the most devastating effects are shown on children and young adults. RHD is caused due to the interaction between microbial, environmental, immunologic, and genetic factors. The Renin- Angiotensin Aldosterone System (RAAS) has been strongly implicated as the susceptibility pathway in the pathogenesis of the cardiovascular disease. OBJECTIVE: The present study investigated the modulating effect of Angiotensin II type 1 receptor (AGTR1) 1166A>C polymorphism on the RHD and its clinical features in Saudi Arabia. METHODS: AGTR1 1166A>C polymorphism was genotyped in 96 echocardiographically confirmed RHD patients and 142 ethnically matched controls by the TaqMan allelic discrimination method. RESULTS: Genotype distribution of the AGTR1 1166A>C polymorphism was not significantly different between RHD and control groups. Furthermore, AGTR1 1166A>C genotypes are not associated with the clinical features of RHD. These data support that there was no evidence for an association between AGTR1 1166A>C polymorphism and RHD in Saudi Arabia. CONCLUSION: To the best of our knowledge, this is the first study that has investigated the possible association between AGTR1 1166A>C polymorphism and susceptibility to RHD and its clinical features. Even though the AGTR1 gene, 1166A>C (rs5186), was reported to be associated with hypertension, left ventricular hypertrophy and coronary heart disease. The present study did not find any association between AGTR1 1166A>C polymorphism and RHD in Saudi Arabia. Further studies are needed to confirm our findings.

The peopling of Lakshadweep Archipelago.

The archipelago of Lakshadweep is considered as a stopover to the maritime route since ancient time. It is not very clear when the human first occupied these islands, however in the long history of the islands, the local legends suggest that Lakshadweep has been ruled by different kingdoms. To have a better understanding of peopling of Lakshadweep, we have analysed 557 individuals from eight major islands for mitochondrial DNA and 166 individuals for Y chromosome markers. We found a strong founder effect for both paternal and maternal lineages. Moreover, we report a close genetic link of Lakshadweep islanders with the Maldives, Sri Lanka and India. Most of the Lakshadweep islands share the haplogroups specific to South Asia and West Eurasia, except Minicoy Island that also shares haplogroups of East Eurasia. The paternal and maternal ancestries of the majority of island populations suggest their arrival from distinct sources. We found that the maternal ancestry was closer to South Indian populations, whereas the paternal ancestry was overwhelmed with the haplogroups, more common in the Maldives and North of India. In conclusion, our first genetic data suggest that the majority of human ancestry in Lakshadweep is largely derived from South Asia with minor influences from East and West Eurasia.

Next-generation sequencing identifies a homozygous mutation in ACADVL associated with pediatric familial dilated cardiomyopathy.

OBJECTIVE: Pediatric familial dilated cardiomyopathy (DCM) is a rare and severe heart disease. The genetics of familial DCM are complex and include over 100 known disease-causing genes, but many causative genes are unknown. We aimed to identify the causative gene for DCM in a consanguineous Saudi Arabian family with affected family members and a history of sudden death. PATIENTS AND METHODS: Affected (two children) and unaffected (one sibling and the mother) family members were screened by next-generation sequencing (NGS) for 181 candidate DCM genes and underwent metabolic screening. Fifty-seven clinically annotated controls and 46 DCM cases were then tested for the identified mutation. In silico structural and functional analyses including protein modeling, structure prediction and dynamic simulations were performed. RESULTS: A homozygous missense mutation in exon 15 of the acyl-CoA dehydrogenase very long chain gene (ACADVL; chr17:7127303; G>A) was identified in affected subjects that substituted histidine for arginine at codon 450 (p.R450H). The variant was heterozygous in the mother and unaffected sister. The mutation was absent in 57 clinically annotated controls and 48 pediatric DCM cases. The mutation was predicted to cause a significant and deleterious change in the ACADVL protein structure that affected drug binding, stability, and conformation. Metabolic screening confirmed VLCAD deficiency in affected individuals. CONCLUSIONS: The ACADVL R450H mutation is an uncommon cause of the DCM phenotype that appears to be autosomal recessive. Targeted NGS is useful for identifying the causative mutation(s) in familial DCM of unknown genetic cause.

Digenic Inheritance of LAMA4 and MYH7 Mutations in Patient with Infantile Dilated Cardiomyopathy.

Background and objectives: Dilated cardiomyopathy (DCM) is a rare cardiac disease characterised by left ventricular enlargement, reduced left ventricular contractility, and impaired systolic function. Childhood DCM is clinically and genetically heterogenous and associated with mutations in over 100 genes. The aim of this study was to identify novel variations associated with infantile DCM. Materials and Methods: Targeted next generation sequencing (NGS) of 181 cardiomyopathy-related genes was performed in three unrelated consanguineous families from Saudi Arabia. Variants were confirmed and their frequency established in 50 known DCM cases and 80 clinically annotated healthy controls. Results: The three index cases presented between 7 and 10 months of age with severe DCM. In Family A, there was digenic inheritance of two heterozygous variants: a novel variant in LAMA4 (c.3925G > A, p.Asp1309Asn) and a known DCM mutation in MYH7 (c.2770G > A; p.Glu924Lys). The LAMA4 p.Asp1309Asn variant was predicted to be likely pathogenic according to international guidelines. The other two families had no identifiable potentially deleterious variants. Conclusions: Inheritance of two genetic variants may have a synergistic or dose effect to cause severe DCM. We report of a novel p.Asp1309Asn variation associated with DCM. Targeted NGS is useful in the molecular diagnosis of DCM and to guide whole-family management and counselling.

Targeted Next-Generation Sequencing of 406 Genes Identified Genetic Defects Underlying Congenital Heart Disease in Down Syndrome Patients.

Down syndrome (DS) is the most common autosomal chromosome anomaly. DS is frequently associated with congenital heart disease (CHD). Patients with DS have 40-60% chance of having CHD. It means that CHD in DS is not only due to trisomy 21 and there are some other genetic factors underlying CHD in DS children. In this study, a total of 240 DNA samples from patients were analyzed including 100 patients with CHD only, 110 patients having CHD along with DS and 30 patients with isolated DS. A cardiovascular gene panel consisting of probes for 406 genes was used to screen DNA samples of all 240 patients for mutation identification. All variants were annotated and common variants were obtained. Briefly, 28 common variants (variants common in two or more than two individuals) were obtained in a group of samples containing DNA from DS patients having CHD as well, 63 variants were found to be unique to DS group of samples and 73 variants have been identified in patients with CHD only. In order to identify genomic variations determining the risk for CHD in DS, only those variants present in DS-CHD group and absent in isolated CHD and/or isolated DS group were considered for further analysis. Variants specific to DS-CHD group were further evaluated based on expression and function data and pathogenicity of the variant of interest. We have implicated mutations in GATA3, KCNH2, ENG, FLNA, and GUSB genes as an underlying risk factor for CHD in DS patients.

Transforming Growth Factor-ß1 gene polymorphism and osteoporosis in postmenopausal egyptian women.

Transforming growth factor-ß1 (TGF-ß1) is a wide spread bone matrix protein that affect the function, formation and cell-cell interactions of osteoclasts and osteoblasts to regulate bone remodeling and sustain adequate bone mass. The aim of this study is to evaluate the role of the two polymorphism of transforming growth factor-ß1 T869C and C-509T in developing osteoporosis in postmenopausal Egyptian women. This study was performed on 138 postmenopausal osteoporosis/osteopenic women and 128 postmenopausal female control group. There was a significant statistical difference in the CC, CT and TT (T869C) genotype frequencies between the osteopenia/osteoporosis and control subjects (p value <0.001). There was a non-significant statistical difference in the CC, CT and TT (T-509C) genotype frequencies between the osteopenia/osteoporosis and control subjects (p value <0.082). There was a significant statistical difference between TT,CT and CC of (T869C) and T score, Z score and calcium of osteopenia/osteoporosis group (p value <0.001). There was a non-significant statistical difference between TT, CT and CC of (T-509C) and T score, Z score of osteopenia/osteoporosis group (p value 0.32,0.31),but there was a statistically significant difference between the three genotyping and serum calcium and creatinine (p value 0.04). Multivariate regression analysis showed that T869C polymorphism is a significant risk factor for osteopenia/ osteoporosis (OR 3.57, 95% CI= 1.56-5.67). We concluded that T869C polymorphism of the TGF-ß1 gene has an impact on bone mineral density and enhancement of the susceptibility to osteopenia/osteoporosis in Egyptian women.

Rotationally inelastic collisions of excited NaK and NaCs molecules with noble gas and alkali atom perturbers.

We report measurements of rate coefficients at T ≈ 600 K for rotationally inelastic collisions of NaK molecules in the 2(A)1Σ+ electronic state with helium, argon, and potassium atom perturbers. Several initial rotational levels J between 14 and 44 were investigated. Collisions involving molecules in low-lying vibrational levels (v = 0, 1, and 2) of the 2(A)1Σ+ state were studied using Fourier-transform spectroscopy. Collisions involving molecules in a higher vibrational level, v = 16, were studied using pump/probe, optical-optical double resonance spectroscopy. In addition, polarization spectroscopy measurements were carried out to study the transfer of orientation in these collisions. Many, but not all, of the measurements were carried out in the "single-collision regime" where more than one collision is unlikely to occur within the lifetime of the excited molecule. The analysis of the experimental data, which is described in detail, includes an estimate of effects of multiple collisions on the reported rate coefficients. The most significant result of these experiments is the observation of a strong propensity for ΔJ = even transitions in collisions involving either helium or argon atoms; the propensity is much stronger for helium than for argon. For the initial rotational levels studied experimentally, almost all initial orientation is preserved in collisions of NaK 2(A)1Σ+ molecules with helium. Roughly between 1/3 and 2/3 of the orientation is preserved in collisions with argon, and almost all orientation is destroyed in collisions with potassium atoms. Complementary measurements on rotationally inelastic collisions of NaCs 2(A)1Σ+ with argon do not show a ΔJ = even propensity. The experimental results are compared with new theoretical calculations of collisions of NaK 2(A)1Σ+ with helium and argon. The calculations are in good agreement with the absolute magnitudes of the experimentally determined rate coefficients and accurately reproduce the very strong propensity for ΔJ = even transitions in helium collisions and the less strong propensity for ΔJ = even transitions in argon collisions. The calculations also show that collisions with helium are less likely to destroy orientation than collisions with argon, in agreement with the experimental results.

Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation.

Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.

Is MTHFR 677 C>T Polymorphism Clinically Important in Polycystic Ovarian Syndrome (PCOS)? A Case-Control Study, Meta-Analysis and Trial Sequential Analysis.

BACKGROUND: Optimum efficiency of the folate pathway is considered essential for adequate ovarian function. 677 C>T substitution in the 5, 10-methylene tertrahydrofolatereductase (MTHFR) gene compromises activity of the MTHFR enzyme by about 50%. The significance of correlation between 677C>T substitution and PCOS remains dubious due to the low power of published studies. METHODS AND RESULTS: We analyzed MTHFR 677 C>T site in ethnically two different PCOS case-control groups (total 261 cases and 256 controls) from India. The data analysis revealed a lack of association between this polymorphism and PCOS [OR = 1.11 (95%CI = 0.71-1.72), P = 0.66]. Group-wise analysis on the basis of ethnicity also revealed no association in any of the ethnic groups [Indo-Europeans, P = 1; Dravidians, P = 0.70]. Homocysteine levels did not differ significantly between cases (15.51 µmol/L, SD = 2.89) and controls (15.89 µmol/L, SD = 2.23). We also undertook a meta-analysis on 960 cases and 1028 controls, which suggested a significant association of the substitution with PCOS in the dominant model of analysis (OR = 1.47 (95%CI = 1.04-2.09), P = 0.032]. Trial sequential analysis corroborated findings of the traditional meta-analysis. However, we found that the conclusions of meta-analysis were strongly influenced by studies that deviated from the Hardy Weinberg equilibrium. A careful investigation of each study and a trial sequential analysis suggested that 677 C>T substitution holds no clinical significance in PCOS in most of the populations. CONCLUSION: In conclusion, MTHFR 677 C>T polymorphism does not affect PCOS risk in India. The association seen in the meta-analysis is due to an outlier study and studies showing deviation from the Hardy Weinberg equilibrium.

The MTHFR C677T polymorphism is associated with mitral valve rheumatic heart disease.

OBJECTIVE: Rheumatic heart disease (RHD) is a serious complication of rheumatic fever (RF). Plasma homocysteine (Hcy) levels are increased in RHD patients. MTHFR catalyzes the irreversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate and plays a vital role in Hcy metabolism. We hypothesize that the MTHFR C677T polymorphism is associated with a risk of RHD. PATIENTS AND METHODS: Eighty-six patients with RHD and 130 matched controls without a history of RHD were eligible for the study. The diagnosis of RHD was made according to modified Jones' criteria and echocardiography. Using echocardiography, RHD patients were further divided into mitral valve lesion (MVL) and combined valve lesion (CVL) groups. MTHFR C677T polymorphisms were genotyped by DNA sequencing. The chi-squared test was used to evaluate differences in genotypes. RESULTS: Control genotypes were in Hardy-Weinberg equilibrium. The C677T homozygous genotype (OR = 4.09; 95% CIs 1.16-14.44; p = 0.020) and recessive model (TT vs. CC+CT; OR = 4.05; 95% CIs 1.17-14.04; p = 0.019) were significantly associated with MVL RHD. CONCLUSIONS: This is the first study to investigate the association between the MTHFR C677T polymorphism and risk of RHD. The MTHFR C677T polymorphism is associated with RHD in patients with MVLs, perhaps via an Hcy-mediated cytokine effect.

SRD5A2 gene polymorphisms and the risk of benign prostatic hyperplasia but not prostate cancer.

BACKGROUND: Testosterone, a primary androgen in males, is converted into its most active form, dihydrotestosterone (DHT), by 5α-reductase type 2 (encoded by the SRD5A2 gene) in the prostate. DHT is necessary for prostatic growth and has five times higher binding affinity than testosterone for androgen receptors. We hypothesized that polymorphic variations in the SRD5A2 gene may affect the risk of benign prostatic hyperplasia and prostate cancer. MATERIALS AND METHODS: We analyzed SRD5A2 gene polymorphisms in 217 BPH patients, 192 PCa cases, and 171 controls. Genotyping was undertaken using direct DNA sequencing. Genotype data were compared between cases and controls using a Chi square statistical tool. RESULTS: We found that the A49T locus was monomorphic with 'AA' genotype in all subjects. At V89L locus, the presence of 'VV' showed a marginally significant correlation with increased BPH risk (p=0.047). At the (TA)n locus, longer TA repeats were found to be protective against BPH (p=0.003). However, neither of these polymoprhisms correlated with the risk of PCa. CONCLUSIONS: We conclude that A49T is monomorphic in the study population, VV marginally correlates with BPH risk, and longer (TA)n repeats are protective against BPH. None of these polymorphisms affect the risk of PCa.

Mitochondrial DNA variations associated with recurrent pregnancy loss among Indian women.

Several genetic factors have been found to be associated with recurrent pregnancy loss (RPL). However, not many attempts have been made to associate the mitochondrial DNA (mtDNA) variations with RPL. Therefore, we have analyzed the complete mtDNA of 100 women with RPL and 12 aborted fetal tissues. Our analysis revealed a total of 681 variations, most of which were in NADH Dehydrogenase (ND) genes that encode mitochondrial enzyme Complex I. Presence of T4216C variation (ND1 gene) in 9% of the RPL women and several pathogenic, and novel mutations suggest the role of mtDNA variations in RPL.

CAG repeat variation in the mtDNA polymerase gamma is not associated with oligoasthenozoospermia.

Variations in the trinucleotide-CAG repeat number of the catalytic subunit of the mitochondrial DNA polymerase gamma (POLG) have been speculated to be associated with male infertility. The ten CAG repeats (10/10) were found to be the most common allele (88%), absence of which was found to be associated with male infertility. As no study on Indian population was conducted so far to support this view, we investigated the distribution of the POLG-CAG repeats in 509 oligoasthenozoospermic and 241 normozoospermic control Indian men from the same ethnic background. Our study suggested that the distribution of common allele (10/10) was almost similar in both infertile (75%) and normozoospermic (75.5%) men. Further, we had analysed the CAG repeat number in as many as 1306 Indian men belonging to different ethnic, geographical and linguistic backgrounds and found the common allele 10/10 at a frequency of 78.4%. Our study, therefore, suggests that the 10-CAG repeat is the most common allele present in Indian populations, but its absence and the occurrence of the other mutant homozygous (non 10/non 10) genotype should not be understood as being specific to infertility. It, thus, suggests that the POLG-CAG repeat variation is not associated with male infertility in Indian populations, and hence is not a useful marker for screening infertile men.

Dietary sugars stimulate fatty acid synthesis in adults.

The goal of this study was to determine the magnitude by which acute consumption of fructose in a morning bolus would stimulate lipogenesis (measured by infusion of 13C1-acetate and analysis by GC-MS) immediately and after a subsequent meal. Six healthy subjects [4 men and 2 women; aged (mean +/- SD) 28 +/- 8 y; BMI, 24.3 +/- 2.8 kg/m(2); and serum triacylglycerols (TG), 1.03 +/- 0.32 mmol/L] consumed carbohydrate boluses of sugars (85 g each) in a random and blinded order, followed by a standardized lunch 4 h later. Subjects completed a control test of glucose (100:0) and a mixture of 50:50 glucose:fructose and one of 25:75 (wt:wt). Following the morning boluses, serum glucose and insulin after 100:0 were greater than both other treatments (P < 0.05) and this pattern occurred again after lunch. In the morning, fractional lipogenesis was stimulated when subjects ingested fructose and peaked at 15.9 +/- 5.4% after the 50:50 treatment and at 16.9 +/- 5.2% after the 25:75 treatment, values that were greater than after the 100:0 treatment (7.8 +/- 5.7%; P < 0.02). When fructose was consumed, absolute lipogenesis was 2-fold greater than when it was absent (100:0). Postlunch, serum TG were 11-29% greater than 100:0 and TG-rich lipoprotein-TG concentrations were 76-200% greater after 50:50 and 25:75 were consumed (P < 0.05). The data demonstrate that an early stimulation of lipogenesis after fructose, consumed in a mixture of sugars, augments subsequent postprandial lipemia. The postlunch blood TG elevation was only partially due to carry-over from the morning. Acute intake of fructose stimulates lipogenesis and may create a metabolic milieu that enhances subsequent esterification of fatty acids flowing to the liver to elevate TG synthesis postprandially.

Investigation of in vivo fatty acid metabolism in AFABP/aP2(-/-) mice.

The metabolic impact of the murine adipocyte fatty acid-binding protein (AFABP/aP2) on lipid metabolism was investigated in the AFABP/aP2(-/-) mouse and compared with wild-type C57BL/6J littermates. Mice were weaned on a high-fat diet (59% of energy from fat) and acclimated to meal feeding. Stable isotopes were administered, and indirect calorimetry was performed to quantitate fatty acid flux, dietary fatty acid utilization, and substrate oxidation. Consistent with previous in situ and in vitro studies, fasting serum nonesterified fatty acid (NEFA) release was significantly reduced in AFABP/aP2(-/-) (17.1 +/- 9.0 vs. 51.9 +/- 22.9 mg.kg(-1).min(-1)). AFABP/aP2(-/-) exhibited higher serum NEFA (1.4 +/- 0.6 vs. 0.8 +/- 0.4 mmol/l, AFABP/aP2(-/-) vs. C57BL/6J, respectively) and triacylglycerol (TAG; 0.23 +/- 0.09 vs. 0.13 +/- 0.10 mmol/l) and accumulated more TAG in liver tissue (2.9 +/- 2.3 vs. 1.1 +/- 0.8% wet wt) in the fasted state. For the liver-TAG pool, 16.4 +/- 7.3% of TAG-fatty acids were derived from serum NEFA in AFABP/aP2(-/-). In contrast, a significantly greater portion of C57BL/6J liver-TAG was derived from serum NEFA (42.3 +/- 25.5%) during tracer infusion. For adipose-TAG stores, only 0.29 +/- 0.04% was derived from serum NEFA in AFABP/aP2(-/-), and, in C57BL/6J, 1.85 +/- 0.97% of adipose-TAG was derived from NEFA. In addition, AFABP/aP2(-/-) preferentially oxidized glucose relative to fatty acids in the fed state. These data demonstrate that in vivo disruption of AFABP/aP2(-/-) leads to changes in the following two major metabolic processes: 1) decreased adipose NEFA efflux and 2) preferential utilization of glucose relative to fatty acids.