K-Cl cotransport function and its potential contribution to cardiovascular disease

Hierarchical structural component model for pathway analysis of common variants

BACKGROUND

Genome-wide association studies (GWAS) have been widely used to identify phenotype-related genetic variants using many statistical methods, such as logistic and linear regression. However, GWAS-identified SNPs, as identified with stringent statistical significance, explain just a small portion of the overall estimated genetic heritability. To address this 'missing heritability' issue, gene- and pathway-based analysis, and biological mechanisms, have been used for many GWAS studies. However, many of these methods often neglect the correlation between genes and between pathways.

METHODS

We constructed a hierarchical component model that considers correlations both between genes and between pathways. Based on this model, we propose a novel pathway analysis method for GWAS datasets, Hierarchical structural Component Model for Pathway analysis of Common vAriants (HisCoM-PCA). HisCoM-PCA first summarizes the common variants of each gene, first at the gene-level, and then analyzes all pathways simultaneously by ridge-type penalization of both the gene and pathway effects on the phenotype. Statistical significance of the gene and pathway coefficients can be examined by permutation tests.

RESULTS

Using the simulation data set of Genetic Analysis Workshop 17 (GAW17), for both binary and continuous phenotypes, we showed that HisCoM-PCA well-controlled type I error, and had a higher empirical power compared to several other methods. In addition, we applied our method to a SNP chip dataset of KARE for four human physiologic traits: (1) type 2 diabetes; (2) hypertension; (3) systolic blood pressure; and (4) diastolic blood pressure. Those results showed that HisCoM-PCA could successfully identify signal pathways with superior statistical and biological significance.

CONCLUSIONS

Our approach has the advantage of providing an intuitive biological interpretation for associations between common variants and phenotypes, via pathway information, potentially addressing the missing heritability conundrum.

Kinetic studies of K-Cl cotransport in cultured rat vascular smooth muscle cells

During aging, and development of atherosclerosis and cardiovascular disease (CVD), aortic vascular smooth muscle cells (VSMCs) transition from healthy contractile to diseased synthetic phenotypes. K-Cl cotransport (KCC) maintains cell volume and ion homeostasis in growth and differentiation, and hence is important for VSMC proliferation and migration. Therefore, KCC activity may play a role in the contractile-to-synthetic VSMC phenotypic transition. Early, medium, and late synthetic passage VSMCs were tested for specific cytoskeletal protein expression. KCC-mediated ouabain- and bumetanide-insensitive Rb+ (a K+ congener) influx was determined as Cl--dependent Rb+ influx at different external Rb+ and Cl- ion concentrations, [Rb+]o and [Cl-]o. Expressions of the cytoskeletal proteins α-actin, vimentin, and desmin fell from early through late synthetic VSMCs. KCC kinetic parameters, such as maximum velocity ( Vm), and apparent Cl- and Rb+ affinities ( Km), were calculated with Lineweaver-Burk, Hanes-Woolf, and Hill approximations. Vm values of both Rb+- and Cl--dependent influxes were of equal magnitude, commensurate with a KCC stoichiometry of unity, and rose threefold from early to late synthetic VSMCs. Hill coefficients for Rb+ and Cl- correlated with cell passage number, suggesting increased KCC ligand cooperativity. However, Km values for [Cl-]o were strikingly bimodal with 60-80 mM in early, ~20-30 mM in medium, and 60 mM in late passage cells. In contrast, Km values for [Rb+]o remained steady at ~17 mM. Since total KCC isoform expression was similar with cell passage, structure/function changes of the KCC signalosome may accompany the transition of aortic VSMCs from a healthy to a diseased phenotype.

Regulated phosphorylation of the K-Cl cotransporter KCC3 is a molecular switch of intracellular potassium content and cell volume homeostasis

The defense of cell volume against excessive shrinkage or swelling is a requirement for cell function and organismal survival. Cell swelling triggers a coordinated homeostatic response termed regulatory volume decrease (RVD), resulting in K⁺ and Cl⁻ efflux via activation of K⁺ channels, volume-regulated anion channels (VRACs), and the K⁺-Cl⁻ cotransporters, including KCC3. Here, we show genetic alanine (Ala) substitution at threonines (Thr) 991 and 1048 in the KCC3a isoform carboxyl-terminus, preventing inhibitory phosphorylation at these sites, not only significantly up-regulates KCC3a activity up to 25-fold in normally inhibitory isotonic conditions, but is also accompanied by reversal of activity of the related bumetanide-sensitive Na⁺-K⁺-2Cl⁻ cotransporter isoform 1 (NKCC1). This results in a rapid (<10 min) and significant (>90%) reduction in intracellular K⁺ content (K_i) via both Cl-dependent (KCC3a + NKCC1) and Cl-independent [DCPIB (VRAC inhibitor)-sensitive] pathways, which collectively renders cells less prone to acute swelling in hypotonic osmotic stress. Together, these data demonstrate the phosphorylation state of Thr991/Thr1048 in KCC3a encodes a potent switch of transporter activity, K_i homeostasis, and cell volume regulation, and reveal novel observations into the functional interaction among ion transport molecules involved in RVD.

The SLC12 family of electroneutral cation-coupled chloride cotransporters

The SLC12 family encodes electroneutral cation-coupled chloride cotransporters that are critical for several physiological processes including cell volume regulation, modulation of intraneuronal chloride concentration, transepithelial ion movement, and blood pressure regulation. Members of this family are the targets of the most commonly used diuretic drugs, have been shown to be the causative genes for inherited disease such as Gitelman, Bartter and Andermann syndromes, and potentially play a role in polygenic complex diseases like arterial hypertension, epilepsy, osteoporosis, and cancer.

Genetics of hypertension and cardiovascular disease and their interconnected pathways: lessons from large studies

Blood pressure (BP), hypertension (HT) and cardiovascular disease (CVD) are common complex phenotypes, which are affected by multiple genetic and environmental factors. This article describes recent genome-wide association studies (GWAS) that have reported causative variants for BP/HT and CVD/heart traits and analyzes the overlapping associated gene polymorphisms. It also examines potential replication of findings from the HyperGEN data on African Americans and whites. Several genes involved in BP/HT regulation also appear to be involved in CVD. A better picture is emerging, with overlapping hot-spot regions and with interconnected pathways between BP/HT and CVD. A systemic approach to full understanding of BP/HT and CVD development and their progression to disease may lead to the identification of gene targets and pathways for the development of novel therapeutic interventions.

ROS activate KCl cotransport in nonadherent Ehrlich ascites cells but K+ and Cl- channels in adherent Ehrlich Lettré and NIH3T3 cells

Addition of H(2)O(2) (0.5 mM) to Ehrlich ascites tumor cells under isotonic conditions results in a substantial (22 +/- 1%) reduction in cell volume within 25 min. The cell shrinkage is paralleled by net loss of K(+), which was significant within 8 min, whereas no concomitant increase in the K(+) or Cl(-) conductances could be observed. The H(2)O(2)-induced cell shrinkage was unaffected by the presence of clofilium and clotrimazole, which blocks volume-sensitive and Ca(2+)-activated K(+) channels, respectively, and is unaffected by a raise in extracellular K(+) concentration to a value that eliminates the electrochemical driving force for K(+). On the other hand, the H(2)O(2)-induced cell shrinkage was impaired in the presence of the KCl cotransport inhibitor (dihydro-indenyl)oxyalkanoic acid (DIOA), following substitution of NO(3)(-) for Cl(-), and when the driving force for KCl cotransport was omitted. It is suggested that H(2)O(2) activates electroneutral KCl cotransport in Ehrlich ascites tumor cells and not K(+) and Cl(-) channels. Addition of H(2)O(2) to hypotonically exposed cells accelerates the regulatory volume decrease and the concomitant net loss of K(+), whereas no additional increase in the K(+) and Cl(-) conductance was observed. The effect of H(2)O(2) on cell volume was blocked by the serine-threonine phosphatase inhibitor calyculin A, indicating an important role of serine-threonine phosphorylation in the H(2)O(2)-mediated activation of KCl cotransport in Ehrlich cells. In contrast, addition of H(2)O(2) to adherent cells, e.g., Ehrlich Lettré ascites cells, a subtype of the Ehrlich ascites tumor cells, and NIH3T3 mouse fibroblasts increased the K(+) and Cl(-) conductances after hypotonic cell swelling. Hence, H(2)O(2) induces KCl cotransport or K(+) and Cl(-) channels in nonadherent and adherent cells, respectively.

Physiology of cell volume regulation in vertebrates

The ability to control cell volume is pivotal for cell function. Cell volume perturbation elicits a wide array of signaling events, leading to protective (e.g., cytoskeletal rearrangement) and adaptive (e.g., altered expression of osmolyte transporters and heat shock proteins) measures and, in most cases, activation of volume regulatory osmolyte transport. After acute swelling, cell volume is regulated by the process of regulatory volume decrease (RVD), which involves the activation of KCl cotransport and of channels mediating K(+), Cl(-), and taurine efflux. Conversely, after acute shrinkage, cell volume is regulated by the process of regulatory volume increase (RVI), which is mediated primarily by Na(+)/H(+) exchange, Na(+)-K(+)-2Cl(-) cotransport, and Na(+) channels. Here, we review in detail the current knowledge regarding the molecular identity of these transport pathways and their regulation by, e.g., membrane deformation, ionic strength, Ca(2+), protein kinases and phosphatases, cytoskeletal elements, GTP binding proteins, lipid mediators, and reactive oxygen species, upon changes in cell volume. We also discuss the nature of the upstream elements in volume sensing in vertebrate organisms. Importantly, cell volume impacts on a wide array of physiological processes, including transepithelial transport; cell migration, proliferation, and death; and changes in cell volume function as specific signals regulating these processes. A discussion of this issue concludes the review.

Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes

MOTIVATION

Gene set analysis allows formal testing of subtle but coordinated changes in a group of genes, such as those defined by Gene Ontology (GO) or KEGG Pathway databases. We propose a new method for gene set analysis that is based on principal component analysis (PCA) of genes expression values in the gene set. PCA is an effective method for reducing high dimensionality and capture variations in gene expression values. However, one limitation with PCA is that the latent variable identified by the first PC may be unrelated to outcome.

RESULTS

In the proposed supervised PCA (SPCA) model for gene set analysis, the PCs are estimated from a selected subset of genes that are associated with outcome. As outcome information is used in the gene selection step, this method is supervised, thus called the Supervised PCA model. Because of the gene selection step, test statistic in SPCA model can no longer be approximated well using t-distribution. We propose a two-component mixture distribution based on Gumbel exteme value distributions to account for the gene selection step. We show the proposed method compares favorably to currently available gene set analysis methods using simulated and real microarray data.

SOFTWARE

The R code for the analysis used in this article are available upon request, we are currently working on implementing the proposed method in an R package.