The Inferred Cardiogenic Gene Regulatory Network in the Mammalian Heart

Cardiac development is a complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory networks was applied to time-course microarray data obtained from the developing mouse heart. Approximately 200 genes of interest were input into the algorithm to generate putative network topologies that are capable of explaining the experimental data via model simulation. To cull specious network interactions, thousands of putative networks are merged and filtered to generate scale-free, hierarchical networks that are statistically significant and biologically relevant. The networks are validated with known gene interactions and used to predict regulatory pathways important for the developing mammalian heart. Area under the precision-recall curve and receiver operator characteristic curve are 9% and 58%, respectively. Of the top 10 ranked predicted interactions, 4 have already been validated. The algorithm is further tested using a network enriched with known interactions and another depleted of them. The inferred networks contained more interactions for the enriched network versus the depleted network. In all test cases, maximum performance of the algorithm was achieved when the purely data-driven method of network inference was combined with a data-independent, functional-based association method. Lastly, the network generated from the list of approximately 200 genes of interest was expanded using gene-profile uniqueness metrics to include approximately 900 additional known mouse genes and to form the most likely cardiogenic gene regulatory network. The resultant network supports known regulatory interactions and contains several novel cardiogenic regulatory interactions. The method outlined herein provides an informative approach to network inference and leads to clear testable hypotheses related to gene regulation

Impact of \u3cem\u3eMYH6\u3c/em\u3e Variants in Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is a clinically and anatomically severe form of congenital heart disease (CHD). Although prior studies suggest that HLHS has a complex genetic inheritance, its etiology remains largely unknown. The goal of this study was to characterize a risk gene in HLHS and its effect on HLHS etiology and outcome. We performed next-generation sequencing on a multigenerational family with a high prevalence of CHD/HLHS, identifying a rare variant in the α-myosin heavy chain (MYH6) gene. A case-control study of 190 unrelated HLHS subjects was then performed and compared with the 1000 Genomes Project. Damaging MYH6 variants, including novel, missense, in-frame deletion, premature stop, de novo, and compound heterozygous variants, were significantly enriched in HLHS cases (P \u3c 1 × 10−5). Clinical outcomes analysis showed reduced transplant-free survival in HLHS subjects with damaging MYH6 variants (P \u3c 1 × 10−2). Transcriptome and protein expression analyses with cardiac tissue revealed differential expression of cardiac contractility genes, notably upregulation of the β-myosin heavy chain (MYH7) gene in subjects with MYH6 variants (P \u3c 1 × 10−3). We subsequently used patient-specific induced pluripotent stem cells (iPSCs) to model HLHS in vitro. Early stages of in vitro cardiomyogenesis in iPSCs derived from two unrelated HLHS families mimicked the increased expression of MYH7 observed in vivo (P \u3c 1 × 10−2), while revealing defective cardiomyogenic differentiation. Rare, damaging variants in MYH6 are enriched in HLHS, affect molecular expression of contractility genes, and are predictive of poor outcome. These findings indicate that the etiology of MYH6-associated HLHS can be informed using iPSCs and suggest utility in future clinical applications

Human Genotyping and An Experimental Model Reveal NPR-C as A Possible Contributor to Morbidity In Coarctation Of The Aorta

Coarctation of the aorta (CoA) is a common congenital cardiovascular (CV) defect characterized by a stenosis of the descending thoracic aorta. Treatment exists, but many patients develop hypertension (HTN). Identifying the cause of HTN is challenging because of patient variability (e.g., age, follow-up duration, severity) and concurrent CV abnormalities. Our objective was to conduct RNA sequencing of aortic tissue from humans with CoA to identify a candidate gene for mechanistic studies of arterial dysfunction in a rabbit model of CoA devoid of the variability seen with humans. We present the first known evidence of natriuretic peptide receptor C (NPR-C; aka NPR3) downregulation in human aortic sections subjected to high blood pressure (BP) from CoA versus normal BP regions (validated to PCR). These changes in NPR-C, a gene associated with BP and proliferation, were replicated in the rabbit model of CoA. Artery segments from this model were used with human aortic endothelial cells to reveal the functional relevance of altered NPR-C activity. Results showed decreased intracellular calcium ([Ca2+]i) activity to C-type natriuretic peptide (CNP). Normal relaxation induced by CNP and atrial natriuretic peptide was impaired for aortic segments exposed to elevated BP from CoA. Inhibition of NPR-C (M372049) also impaired aortic relaxation and [Ca2+]i activity. Genotyping of NPR-Cvariants predicted to be damaging revealed that rs146301345 was enriched in our CoA patients, but sample size limited association with HTN. These results may ultimately be used to tailor treatment for CoA based on mechanical stimuli, genotyping, and/or changes in arterial function

Numerical Confirmation of Late-time t^{1/2} Growth in Three-dimensional Phase Ordering

Results for the late-time regime of phase ordering in three dimensions are reported, based on numerical integration of the time-dependent Ginzburg-Landau equation with nonconserved order parameter at zero temperature. For very large systems ($700^3$) at late times, $t \ge 150,$ the characteristic length grows as a power law, $R(t) \sim t^n$, with the measured $n$ in agreement with the theoretically expected result $n=1/2$ to within statistical errors. In this time regime $R(t)$ is found to be in excellent agreement with the analytical result of Ohta, Jasnow, and Kawasaki [Phys. Rev. Lett. {\bf 49}, 1223 (1982)]. At early times, good agreement is found between the simulations and the linearized theory with corrections due to the lattice anisotropy.Comment: Substantially revised and enlarged, submitted to PR

Dynamic Phase Transition, Universality, and Finite-size Scaling in the Two-dimensional Kinetic Ising Model in an Oscillating Field

We study the two-dimensional kinetic Ising model below its equilibrium critical temperature, subject to a square-wave oscillating external field. We focus on the multi-droplet regime where the metastable phase decays through nucleation and growth of many droplets of the stable phase. At a critical frequency, the system undergoes a genuine non-equilibrium phase transition, in which the symmetry-broken phase corresponds to an asymmetric stationary limit cycle for the time-dependent magnetization. We investigate the universal aspects of this dynamic phase transition at various temperatures and field amplitudes via large-scale Monte Carlo simulations, employing finite-size scaling techniques adopted from equilibrium critical phenomena. The critical exponents, the fixed-point value of the fourth-order cumulant, and the critical order-parameter distribution all are consistent with the universality class of the two-dimensional equilibrium Ising model. We also study the cross-over from the multi-droplet to the strong-field regime, where the transition disappears

Molecular biology of histidine decarboxylase and prostaglandin receptors

Histamine and prostaglandins (PGs) play a variety of physiological roles as autacoids, which function in the vicinity of their sources and maintain local homeostasis in the body. They stimulate target cells by acting on their specific receptors, which are coupled to trimeric G proteins. For the precise understanding of the physiological roles of histamine and PGs, it is necessary to clarify the molecular mechanisms involved in their synthesis as well as their receptor-mediated responses. We cloned the cDNAs for mouse l-histidine decarboxylase (HDC) and 6 mouse prostanoid receptors (4 PGE2 receptors, PGF receptor, and PGI receptor). We then characterized the expression patterns and functions of these genes. Furthermore, we established gene-targeted mouse strains for HDC and PG receptors to explore the novel pathophysiological roles of histamine and PGs. We have here summarized our research, which should contribute to progress in the molecular biology of HDC and PG receptors

Cross sections and double-helicity asymmetries of midrapidity inclusive charged hadrons in p+p collisions at sqrt(s)=62.4 GeV

Unpolarized cross sections and double-helicity asymmetries of single-inclusive positive and negative charged hadrons at midrapidity from p+p collisions at sqrt(s)=62.4 GeV are presented. The PHENIX measurements for 1.0 < p_T < 4.5 GeV/c are consistent with perturbative QCD calculations at next-to-leading order in the strong coupling constant, alpha_s. Resummed pQCD calculations including terms with next-to-leading-log accuracy, yielding reduced theoretical uncertainties, also agree with the data. The double-helicity asymmetry, sensitive at leading order to the gluon polarization in a momentum-fraction range of 0.05 ~< x_gluon ~< 0.2, is consistent with recent global parameterizations disfavoring large gluon polarization.Comment: PHENIX Collaboration. 447 authors, 12 pages, 5 figures, 5 tables. Submitted to Physical Review

Inclusive cross section and double helicity asymmetry for pi^0 production in p+p collisions at sqrt(s) = 62.4 GeV

The PHENIX experiment presents results from the RHIC 2006 run with polarized proton collisions at sqrt(s) = 62.4 GeV for inclusive pi^0 production at mid-rapidity. Unpolarized cross section results are measured for transverse momenta p_T = 0.5 to 7 GeV/c. Next-to-leading order perturbative quantum chromodynamics calculations are compared with the data, and while the calculations are consistent with the measurements, next-to-leading logarithmic corrections improve the agreement. Double helicity asymmetries A_LL are presented for p_T = 1 to 4 GeV/c and probe the higher range of Bjorken_x of the gluon (x_g) with better statistical precision than our previous measurements at sqrt(s)=200 GeV. These measurements are sensitive to the gluon polarization in the proton for 0.06 < x_g < 0.4.Comment: 387 authors from 63 institutions, 10 pages, 6 figures, 1 table. Submitted to Physical Review D. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm