Association of ACE and NOS3 Gene Polymorphisms with Blood Pressure in a Case Control Study of Coronary Artery Disease in Punjab, Pakistan

Single nucleotide polymorphisms (SNPs), ACE rs4341 and NOS3 rs1799983 have been reported to be associated with coronary artery disease (CAD) and blood pressure (BP)in many but not all studies. We aimed to investigate the effect of these SNPs on BP and CAD in people from Punjab, Pakistan. A total of 650 subjects (430 CAD cases and 220 controls) were genotyped by TaqMan/KASPar allelic discrimination technique. Two BP measurements were reordered and their mean was calculated. The results showed that the risk allele frequencies (RAFs) of both SNPs were higher in cases than controls but the difference was not statistically significant. For rs4341, RAF in cases and controls was 0.577 vs. 0.525, p = 0.08 and for rs1799983, the RAF was 0.202 vs. 0.178, p = 0.31. The SNPs were not associated with CAD. The CAD odds ratio of rs4341 (1.22,0.97-1.53, p = 0.09) and that of rs1799983 (1.15, 0.86-1.54, p=0.33) was not statistically significant. Mean systolic blood pressure (SBP) and diastolic blood pressure (DBP) were significantly higher in cases than controls (p<0.05) and the SNPs showed a significant association with BP. Each risk allele of rs4341 (G) increased SBP by 10.04±0.8 mmHg and DBP by 2.5±0.6mmHg, while risk allele of rs1799983 (T), increased SBP and DBP by 16.4±0.9mmHg and 8.8±0.6mmHg respectively, all were statistically significant (p<0.05). When a combined effect of genotypes of both SNPs was examined, a significant effect on CAD outcome (p=0.01) was observed when GG of rs4341 and GT of rs1799983 co-existed. Similarly, maximum elevation in BP was observed when risk alleles of both SNPs in homozygous form (GG and TT) appeared together. In conclusion, the SNPs were not independently associated with CAD but were associated with BP in Pakistani subjects under study and may be causing CAD by modulating BP

Common variants in the genes of triglyceride and HDL-C metabolism lack association with coronary artery disease in the Pakistani subjects.

BACKGROUND: Serum Triglyceride (TG) and High Density Lipoprotein (HDL-C) levels are modifiable coronary artery disease (CAD) risk factors. Polymorphisms in the genes regulating TG and HDL-C levels contribute to the development of CAD. The objective of the current study was to investigate the effect of four such single nucleotide polymorphism (SNPs) in the genes for Lipoprotein Lipase (LPL) (rs328, rs1801177), Apolipoprotein A5 (APOA5) (rs66279) and Cholesteryl ester transfer protein (CETP) (rs708272) on HDL-C and TG levels and to examine the association of these SNPs with CAD risk. METHODS: A total of 640 subjects (415 cases, 225 controls) were enrolled in the study. The SNPs were genotyped by KASPar allelic discrimination technique. Serum HDL-C and TG were determined by spectrophotometric methods. RESULTS: The population under study was in Hardy Weinberg equilibrium and minor allele of SNP rs1801177 was completely absent in the studied subjects. The SNPs were association with TG and HDL-C levels was checked through regression analysis. For rs328, the effect size of each risk allele on TG and HDL-C (mmol/l) was 0.16(0.08) and -0.11(0.05) respectively. Similarly, the effect size of rs662799 for TG and HDL-C was 0.12(0.06) and -0.13(0.0.3) and that of rs708272 was 0.08(0.04) and 0.1(0.03) respectively. The risk allele frequencies of the SNPs were higher in cases than controls, but the difference was not significant (p > 0.05) and SNPs were not associated with CAD risk (p > 0.05). The combined gene score of four SNPs significantly raised TG and lowered HDL-C but did not increase CAD risk. CONCLUSION: The studied SNPs were associated with TG and HDL-C levels, but not with CAD in Pakistani population under study

A multigroup diffusion solver using pseudo transient continuation for a radiation-hydrodynamic code with patch-based AMR

We present a scheme to solve the nonlinear multigroup radiation diffusion (MGD) equations. The method is incorporated into a massively parallel, multidimensional, Eulerian radiation-hydrodynamic code with adaptive mesh refinement (AMR). The patch-based AMR algorithm refines in both space and time creating a hierarchy of levels, coarsest to finest. The physics modules are time-advanced using operator splitting. On each level, separate level-solve packages advance the modules. Our multigroup level-solve adapts an implicit procedure which leads to a two-step iterative scheme that alternates between elliptic solves for each group with intra-cell group coupling. For robustness, we introduce pseudo transient continuation (PTC). We analyze the magnitude of the PTC parameter to ensure positivity of the resulting linear system, diagonal dominance and convergence of the two-step scheme. For AMR, a level defines a subdomain for refinement. For diffusive processes such as MGD, the refined level uses Dirichet boundary data at the coarse-fine interface and the data is derived from the coarse level solution. After advancing on the fine level, an additional procedure, the sync-solve (SS), is required in order to enforce conservation. The MGD SS reduces to an elliptic solve on a combined grid for a system of G equations, where G is the number of groups. We adapt the partial temperature scheme for the SS; hence, we reuse the infrastructure developed for scalar equations. Results are presented. (Abridged)Comment: 46 pages, 14 figures, accepted to JC

Effect of SORT1, APOB and APOE polymorphisms on LDL-C and coronary heart disease in Pakistani subjects and their comparison with Northwick Park Heart Study II

BACKGROUND: Many SNPs have been identified in genes regulating LDL-C metabolism, but whether their influence is similar in subjects from different ethnicities is unclear. Effect of 4 such SNPs on LDL-C and coronary heart disease (CHD) was examined in Pakistani subjects and was compared with middle aged UK men from Northwick Park Heart Study II (NPHSII). METHODS: One thousand nine hundred sixty-five (1770 non CHD, 195 CHD) UK and 623 (219 non CHD, 404 CHD) Pakistani subjects were enrolled in the study. The SNPs SORT1 rs646776, APOB rs1042031 and APOE rs429358, rs7412 were genotyped by TaqMan/KASPar technique and their gene score was calculated. LDL-C was calculated by Friedewald equation, results were analyzed using SPSS. RESULTS: Allele frequencies were significantly different (p = <0.05) between UK and Pakistani subjects. However, the SNPs were associated with LDL-C in both groups. In UK non CHD, UK CHD, Pakistani non CHD and Pakistani CHD respectively, for rs646776, per risk allele increase in LDL-C(mmol/l) was 0.18(0.04), 0.06(0.11), 0.15(0.04) and 0.27(0.06) respectively. For rs1042031, per risk allele increase in LDL-C in four groups was 0.11(0.04), 0.04(0.14), 0.15(0.06) and 0.25(0.09) respectively. For APOE genotypes, compared to Ɛ3, each Ɛ2 decreased LDL-C by 0.11(0.06), 0.07(0.15), 0.20(0.08) and 0.38(0.09), while each Ɛ4 increased LDL-C by 0.43(0.06), 0.39(0.21), 0.19(0.11) and 0.39(0.14) respectively. Overall gene score explained a considerable proportion of sample variance in four groups (3.8 %, 1.26 % 13.7 % and 12.3 %). Gene score in both non-CHD groups was significantly lower than CHD subjects. CONCLUSIONS: The SNPs show a dose response association with LDL-C levels and risk of CHD in both populations

Surface acoustic waves induced micropatterning of cells in gelatin methacryloyl (GelMA) hydrogels

Acoustic force patterning is an emerging technology that provides a platform to control the spatial location of cells in a rapid, accurate, yet contactless manner. However, very few studies have been reported on the usage of acoustic force patterning for the rapid arrangement of biological objects, such as cells, in a three-dimensional (3D) environment. In this study, we report on a bio-acoustic force patterning technique, which uses surface acoustic waves (SAWs) for the rapid arrangement of cells within an extracellular matrix-based hydrogel such as gelatin methacryloyl (GelMA). A proof-of-principle was achieved through both simulations and experiments based on the in-house fabricated piezoelectric SAW transducers, which enabled us to explore the effects of various parameters on the performance of the built construct. The SAWs were applied in a fashion that generated standing SAWs (SSAWs) on the substrate, the energy of which subsequently was transferred into the gel, creating a rapid, and contactless alignment of the cells (&lt;10 s, based on the experimental conditions). Following ultraviolet radiation induced photo-crosslinking of the cell encapsulated GelMA pre-polymer solution, the patterned cardiac cells readily spread after alignment in the GelMA hydrogel and demonstrated beating activity in 5–7 days. The described acoustic force assembly method can be utilized not only to control the spatial distribution of the cells inside a 3D construct, but can also preserve the viability and functionality of the patterned cells (e.g. beating rates of cardiac cells). This platform can be potentially employed in a diverse range of applications, whether it is for tissue engineering, in vitro cell studies, or creating 3D biomimetic tissue structures

GWAS implicated risk variants in different genes contribute additively to increase the risk of coronary artery disease (CAD) in the Pakistani subjects

Background: Coronary artery disease (CAD) remains the single most important cause of mortality worldwide. Many candidate and GWAS genetic variants have been identified in the recent years. In the current study, we selected six SNPs from various genes that have originally been identified in GWAS studies and examined the association of SNPs individually and as a genetic risk score (GRS) with CAD and blood lipid levels in the Pakistani subjects. Methods: Six hundred twenty-four (404 cases and 219 controls) subjects were genotyped for variants rs10757274 in CDKN2A gene, rs17465637 in MIA3 gene, rs7025486 in DAB2IP gene, rs17228212 in SMAD3 gene, rs981887 in MRAS gene and rs1746048 in CXCL12 gene, by TaqMan and KASPar allele discrimination techniques. Serum lipid parameters were measured using commercially available kits. Statistical analyses were done using SPSS version 22. Results: Individually, the single SNPs were not associated with CAD (p < 0.05). However, the combined GRS of 6 SNPs was significantly higher in cases than controls (4.89 ± 0.11 vs 4.58 ± 0.08, p = 0.024). Among blood lipids, GRS showed significant positive association with serum triglycerides levels (p = 0.022). Conclusion: The GRS was quantitatively associated with CAD risk and showed association with serum triglycerides levels, suggesting that the mechanism of these variants is likely to be in part at least through creating an atherogenic lipid profile in subjects carrying high numbers of risk alleles

CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement

Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.

BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR.We thank beamline scientists at Diamond Light Source for help during data collection of crystal and SAXS. The crystallization experiments were performed in the Crystallographic X-ray facility at the Department of Biochemistry, University of Cambridge. We are grateful to the Facility Manager, Dr. Dimitri Chirgadze, for his assistance in using these facilities and advice during crystal structure determination. We also thank Dr. Yanfen Hu (University of Texas Health Science Center at San Antonia) for the pFlag-BRCA1 plasmid and Dr. Angela Pacitto (University of Cambridge) for reading the manuscript. We thank Dr. Adriana Paulucci-Holthanuzen (Department of Genetics-MD Anderson Microscopy Core Facility) for assistance with images and analysis. Q.W., T.O. and T.L.B. are funded by the Wellcome Trust (Grant 093167/Z/10/Z). A.P. is an awardee of the Schissler Foundation Fellowship, the Center for Cancer Epigenetics Scholarship and the Andrew Sowell-Wade Huggins Scholarship. This work is supported by the National Institutes of Health grant (CA155025 to B.W) with funds from the University of Texas MD Anderson Cancer Center (IRG, Center for Cancer Epigenetics, Center for Genetics and Genomics Pilot Award). S.M. is funded by the Medical Research Council (grant 98101 to C.V.R.) and C.V.R. is a Royal Society Research Professor. T.K.F and B.X. are supported by National Institutes of Health grant (R01CA138804 to B.X).This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.molcel.2015.12.01

Genetic risk analysis of coronary artery disease in Pakistani subjects using a genetic risk score of 21 variants

BACKGROUND AND AIMS: Conventional coronary artery disease (CAD) risk factors like age, gender, blood lipids, hypertension and smoking have been the basis of CAD risk prediction algorithms, but provide only modest discrimination. Genetic risk score (GRS) may provide improved discrimination over and above conventional risk factors. Here we analyzed the genetic risk of CAD in subjects from Pakistan, using a GRS of 21 variants in 18 genes and examined whether the GRS is associated with blood lipid levels. METHODS: 625 (405 cases and 220 controls) subjects were genotyped for variants, NOS3 rs1799983, SMAD3 rs17228212, APOB rs1042031, LPA rs3798220, LPA rs10455872, SORT1 rs646776, APOE rs429358, GLUL rs10911021, FTO rs9939609, MIA3 rs17465637, CDKN2Ars10757274, DAB2IP rs7025486, CXCL12 rs1746048, ACE rs4341, APOA5 rs662799, CETP rs708272, MRAS rs9818870, LPL rs328, LPL rs1801177, PCSK9 rs11591147 and APOE rs7412 by TaqMan and KASPar allele discrimination techniques. RESULTS: Individually, the single SNPs were not associated with CAD except APOB rs1042031 and FTO rs993969 (p = 0.01 and 0.009 respectively). However, the combined GRS of 21 SNPs was significantly higher in cases than controls (19.37 ± 2.56 vs. 18.47 ± 2.45, p = 2.9 × 10(-5)), and compared to the bottom quintile, CAD risk in the top quintile of the GRS was 2.96 (95% CI 1.71-5.13). Atherogenic blood lipids showed significant positive association with GRS. CONCLUSIONS: The GRS was quantitatively associated with CAD risk and showed association with blood lipid levels, suggesting that the mechanism of these variants is likely to be, in part at least, through creating an atherogenic lipid profile in subjects carrying high numbers of risk alleles