A genomic-systems biology map for cardiovascular function

The application of functional genomics to Alzheimer's disease

Alzheimer's disease (AD) is a polygenic/complex disorder in which more than 50 genetic loci are involved. Primary and secondary loci are potentially responsible for the phenotypic expression of the disease under the influence of both environmental factors and epigenetic phenomena. The construction of haplotypes as genomic clusters integrating the different genotype combinations of AD-related genes is a suitable strategy to investigate functional genomics in AD. It appears that AD patients show about 3-5 times higher genetic variation than the control population. The analysis of genotype-phenotype correlations has revealed that the presence of the APOE-4 allele in AD, in conjunction with other loci distributed across the genome, influence disease onset, brain atrophy, cerebrovascular perfusion, blood pressure, beta-amyloid deposition, ApoE secretion, lipid metabolism, brain bioelectrical activity, cognition, apoptosis and treatment outcome. Pharmacogenomics studies also indicate that the therapeutic response in AD is genotype-specific and that approximately 15% of the cases with efficacy and/or safety problems are associated with a defective CYP2D6 gene. Consequently, the understanding of functional genomics in AD will foster productive pharmacogenomic studies in the search for effective medications and preventive strategies in AD.

Pleiotropy, homeostasis, and functional networks based on assays of cardiovascular traits in genetically randomized populations

A major problem in studying biological traits is understanding how genes work together to provide organismal structures and functions. Conventional reductionist paradigms attribute functions to particular proteins, motifs, and amino acids. An equally important but harder problem involves the synthesis of data at fundamental levels of biological systems to understand functionality at higher levels. We used subtle, naturally occurring, multigenic variation of cardiovascular (CV) properties in a panel of genetically randomized strains that are derived from the A/J and C57BL/6J strains of mice to perturb CV functions in nonpathologic ways. In this proof-of-concept study, computational analysis correctly identified the known relations among CV properties and revealed functionality at higher levels of the CV system. The network was then used to account for pleiotropies and homeostatic responses in single gene mutant mice and in mice treated with a pharmacologic agent (anesthesia). The CV network accounted for functional dependencies in complementary ways to the insights obtained from genetic networks and biochemical pathways. These networks are therefore an important approach for defining and characterizing functional relations in complex biological systems in health and disease.

Genetic susceptibility to carrageenan-induced innate inflammatory response in inbred strains of rats

Rat models are useful for the genetic dissection of the biology of innate immunity. Inbred rat strains were evaluated for carrageenan-induced innate inflammatory responses. Results indicated that the genetic control of innate immune responses is polygenic and influenced by gender, and may not necessarily be consistent with the genetics of experimental arthritis. The newly identified susceptible strains, in order of decreasing susceptibility, include Dahl salt-sensitive (S), Dahl salt-resistant (R), Milan normotensive strain (MNS) and Wistar Kyoto (WKY) rats. Similarly, the newly identified relatively resistant strains, in decreasing order of resistance, include DA rats, spontaneously hypertensive rats (SHRs) and Brown Norway (BN) rats. Linkage analyses using combinations of these susceptible and resistant strains are proposed.

Automated detection of informative combined effects in genetic association studies of complex traits

There is a growing body of evidence suggesting that the relationships between gene variability and common disease are more complex than initially thought and require the exploration of the whole polymorphism of candidate genes as well as several genes belonging to biological pathways. When the number of polymorphisms is relatively large and the structure of the relationships among them complex, the use of data mining tools to extract the relevant information is a necessity. Here, we propose an automated method for the detection of informative combined effects (DICE) among several polymorphisms (and nongenetic covariates) within the framework of association studies. The algorithm combines the advantages of the regressive approaches with those of data exploration tools. Importantly, DICE considers the problem of interaction between polymorphisms as an effect of interest and not as a nuisance effect. We illustrate the method with three applications on the relationship between (1). the P-selectin gene and myocardial infarction, (2). the cholesteryl ester transfer protein gene and plasma high-density-lipoprotein cholesterol concentration, and (3). genes of the renin-angiotensin-aldosterone system and myocardial infarction. The applications demonstrated that the method was able to recover results already found using other approaches, but in addition detected biologically sensible effects not previously described.

Functional genomics and the comparative physiology of hypoxia

Comparative physiology has proven a powerful approach to our understanding of how animals function under hypoxic conditions and to identifying potential adaptations to environmental oxygen levels. This review considers the potential for using a similar comparative approach with functional genomics to understand the genetic basis of such physiological processes and evolutionary adaptations. Comparative functional genomics is currently limited by genome data, which are available for only a few model organisms. However, comparative studies between model organisms of the same species having slightly different genomes (e.g., in-bred strains of laboratory rodents, transgenic mice, and consomic rats) demonstrate the types of results, as well as the analytical challenges, that are possible if comparative functional genomics is applied to more species. Results from wild and domestic animal studies suggest new models to investigate physiological and evolutionary responses to oxygen levels with functional genomics.

Genetic Models in Applied Physiology. Functional genomics in the mouse: powerful techniques for unraveling the basis of human development and disease

Now that near-complete DNA sequences of both the mouse and human genomes are available, the next major challenge will be to determine how each of these genes functions, both alone and in combination with other genes in the genome. The mouse has a long and rich history in biological research, and many consider it a model organism for the study of human development and disease. Over the past few years, exciting progress has been made in developing techniques for chromosome engineering, mutagenesis, mapping and maintenance of mutations, and identification of mutant genes in the mouse. In this mini-review, many of these powerful techniques will be presented along with their application to the study of development, physiology, and disease.

Novel association suggests multiple independent QTLs within chromosome 5q21-33 region control variation in total humans IgE levels

Asthma is a common, heterogeneous, complex disease accompanied by raised total and specific immunoglobulin-E (IgE) antibody levels. Despite numerous previous reports of linkage and association of asthma, atopy and serum IgE levels to genes within the 5q21-33 region, definitive, replicable results are still not available. We used the classical twin design to (i) estimate the relative contributions of genes and environment to variation in total IgE levels, (ii) assess genetic linkage, and (iii) examine allelic association of 11 microsatellite markers spanning the 5q21-33 region to total IgE. Variation in total IgE level was shown to be highly heritable (65%). Although evidence for linkage of the 11 microsatellites to IgE was not observed, the omnibus test of association, not confounded by population substructure, showed positive association of D5S393 and D5S673 to IgE. Genes in the vicinity of D5S673 include hepatitis A virus receptor (HAVCR-1) and IL-12B. Recently, the mouse orthologue of HAVCR-1, the T-cell membrane family of proteins, have been shown to be in strong association with expression of airway hyperactivity in a mouse model of human asthma and atopy. IL-12B subserves many proinflammatory functions and also induces B cells proliferation.

Genome informatics: current status and future prospects

This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape.

S-nitrosylation in health and disease

S-nitrosylation is a ubiquitous redox-related modification of cysteine thiol by nitric oxide (NO), which transduces NO bioactivity. Accumulating evidence suggests that the products of S-nitrosylation, S-nitrosothiols (SNOs), play key roles in human health and disease. In this review, we focus on the reaction mechanisms underlying the biological responses mediated by SNOs. We emphasize reactions that can be identified with complex (patho)physiological responses, and that best rationalize the observed increase or decrease in specific classes of SNOs across a spectrum of disease states. Thus, changes in the levels of various SNOs depend on specific defects in both enzymatic and non-enzymatic mechanisms of nitrosothiol formation, processing and degradation. An understanding of these mechanisms is crucial for the development of an integrated model of NO biology, and for effective treatment of diseases associated with dysregulation of NO homeostasis.

The role of ACE2 in cardiovascular physiology

The renin-angiotensin system (RAS) is critically involved in cardiovascular and renal function and in disease conditions, and has been shown to be a far more complex system than initially thought. A recently discovered homologue of angiotensin-converting enzyme (ACE)--ACE2--appears to negatively regulate the RAS. ACE2 cleaves Ang I and Ang II into the inactive Ang 1-9 and Ang 1-7, respectively. ACE2 is highly expressed in kidney and heart and is especially confined to the endothelium. With quantitative trait locus (QTL) mapping, ACE2 was defined as a QTL on the X chromosome in rat models of hypertension. In these animal models, kidney ACE2 messenger RNA and protein expression were markedly reduced, making ACE2 a candidate gene for this QTL. Targeted disruption of ACE2 in mice failed to elicit hypertension, but resulted in severe impairment in myocardial contractility with increased angiotensin II levels. Genetic ablation of ACE in the ACE2 null mice rescued the cardiac phenotype. These genetic data show that ACE2 is an essential regulator of heart function in vivo. Basal renal morphology and function were not altered by the inactivation of ACE2. The novel role of ACE2 in hydrolyzing several other peptides-such as the apelin peptides, opioids, and kinin metabolites-raises the possibility that peptide systems other than angiotensin and its derivatives also may have an important role in regulating cardiovascular and renal function.

Genomics and homeostasis

The Cannon lecture this year illustrates how knowledge of DNA sequences of complex living organisms is beginning to shape the landscape of physiology in the 21st century. Enormous challenges and opportunities now exist for physiologists to relate the galaxy of genes to normal and pathological functions. The first extensive genomic systems biology map for cardiovascular and renal function was completed last year as well as a new hypothesis-generating tool ("physiological profiling") that enables us to hypothesize relationships between specific genes responsible for the regulation of regulatory pathways. Techniques of chromosomal substitution (consomic and congenic rats) are beginning to confirm statistical results from linkage analysis studies, narrow the regions of genetic interest for positional cloning, and provide genetically well-defined control strains for physiological studies. Patterns of gene expression identified by microarray and mapping of expressed genes to chromosomal sites are adding to the understanding of systems physiology. The previously unimaginable goal of connecting approximately 36,000 genes to the complex functions of mammalian systems is indeed well underway.

Advancing drug discovery through systems biology

Pharmaceutical companies are facing an urgent need to both increase their lead compound and clinical candidate portfolios and satisfy market demands for continued innovation and revenue growth. Here, we outline an emerging approach that attempts to facilitate and alleviate many of the current drug discovery issues and problems. This is, in part, achieved through the systematic integration of technologies, which results in a superior output of data and information, thereby enhancing our understanding of biological function, chemico-biological interactions and, ultimately, drug discovery. Systems biology is one new discipline that is positioned to significantly impact this process.

Genome-wide searches for blood pressure quantitative trait loci in the stroke-prone spontaneously hypertensive rat of a Japanese colony

OBJECTIVES

Although several quantitative trait loci for blood pressure have been reported in stroke-prone spontaneously hypertensive rats (SHRSP), the results are not always concordant among different crosses. To evaluate potential confounding factors in linkage analysis, we performed genome-wide screens in F2 populations derived from SHRSP and Wistar-Kyoto rats of a Japanese colony.

METHODS

Two F cohorts were independently produced: F2-1 (110 male and 110 female rats), and F2-2 (174 male and 184 female rats). Blood pressure was measured longitudinally (from 2 to 5 months of age and 1 month after salt-loading) in F2-1, while it was measured at 13 weeks of age in F2-2. Subsequent to an initial screen with 251 markers in F2-1 male progeny, 170 markers were selected and characterized in the remaining populations.

RESULTS

When 578 rats were analyzed together, markers from five chromosomal regions showed significant linkage to blood pressure at 13 weeks of age. The strongest and the most consistent linkage was found on rat chromosome 1 (a maximal log of the odds score reached 8.3). In the other regions, the degree of linkage was more prominent in either of sexes. Some evidence of age-specific and sex-specific linkage was detected in five additional regions in the F2-1 cohort. In the Japanese colony, however, there was no significant linkage to several chromosomal regions previously reported in other SHRSP colonies.

CONCLUSIONS

Our data provide solid evidence of a chromosome-1 linkage and demonstrate the importance of aging, sex, and dietary manipulation in linkage analysis. Also, the combination of parental rat strains seems to be critical when searching for blood pressure quantitative trait loci.

Genetics of obesity and type 2 diabetes: tracking pathogenic traits during the predisease period

The modern generalization of sedentary life and caloric abundance has created new physiological conditions capable of changing the level of expression of a number of genes involved in fuel metabolism and body weight regulation. It is likely that the genetic variants or alleles of these genes have in the past participated in the adaptation of human physiology to its evolutionary constraints. The nature and prevalence of polymorphisms responsible for the quantitative variation of complex metabolic traits may have been different among human populations, depending on their environment and ancestral genetic background. These polymorphisms could likely explain differences in disease susceptibility and prevalence among groups of humans. From complex traits to potentially complex alleles, understanding the molecular genetic basis underlying quantitative variation will continue to be a growing concern among geneticists dealing with obesity and type 2 diabetes, the main fuel disorders of the modern era. Genomics and genetic epidemiology now allow high-level linkage and association studies to be designed. But the pooling of large trans-geographic cohorts may in fact increase the genetic heterogeneity of studied traits and dilute genotype-phenotype associations. In this article, we underscore the importance of selecting the traits to be subjected to quantitative genetic analysis. Although this is not possible for most other multifactorial diseases, obesity and type 2 diabetes can be subjected to a pregenetic dissection of complexity into simpler quantitative traits (QTs). This dissection is based on the pathogenic mechanisms, and the time course of the traits, and the individuals' age, within the predisease period rather than on descriptive parameters after disease diagnosis. We defend that this approach of phenotypes may ease future associations to be established between QTs of intermediate complexity and genetic polymorphisms.

Matrix analysis for the dissection of interactions of G-protein beta3 subunit C825T genotype, allograft function, and posttransplant hypertension in kidney transplantation

BACKGROUND

Complex relationships between genes and environment and the resulting biological impact have been dissected predominantly by conventional association studies. A major limitation of such studies results from the fact that only bidirectional investigations of genes and clinical end-points are commonly performed. The authors, therefore, applied matrix analyses to account for interactions between genetic and environmental factors influencing kidney allograft function.

METHODS

By using matrices of correlation coefficients we tested the genetic effect of a variant within the gene encoding the beta3-subunit of heterotrimeric G-proteins (Gbeta3-C825T polymorphism) on posttransplant hypertension and kidney allograft function. This strategy allowed the authors to account for the influence of additional well-established genetic, clinical, and environmental confounders. The authors studied 281 consecutive white kidney recipients recruited between 1988 and 1993. Correlation coefficients of indices of relative change (percent) of systolic blood pressure (BP) and creatinine clearance (CrCl) were used in correlation coefficient matrices to elucidate interactions of parametrical biological parameters with environmental and genetic risk factors.

RESULTS

A significant relationship was found between decreasing CrCl and increasing systolic BP in only those recipients who carried the Gbeta3-825TT genotype and did not lose graft during the first 3 years (R2 = 0.25; P = 0.021).

CONCLUSIONS

In transplant recipients who did not lose their graft during the first 3 years after transplantation, the Gbeta3-TT genotype contributed to accelerated loss of allograft function by exaggeration of posttransplant hypertension. This relationship could only be elucidated by means of matrix analyses that allow the detection of complex relations between clinical, genetic, and environmental factors.

Identification of hypertension-related QTLs in African American sib pairs

To link hypertension-related phenotypes with chromosomal loci, genome scans were performed in 150 African American sib pairs concordant for essential hypertension. Phenotypes included blood pressure, anthropomorphic measurements, and estimates of body fluid compartments as determined by impedance plethysmography. These phenotypes were also measured in 335 normotensive African Americans. Phenotypes with LOD scores >3.3 were further evaluated for significance by use of permutation procedures. Significant linkage was detected for body mass index (BMI) on chromosomes 1 and 8 and for the ratio of extracellular water to total body water (ECF/TBW) on chromosomes 3, 5, 6, and 7. Both BMI and ECF/TBW were greater in hypertensive sibs than in normotensive subjects (P<0.001). In a subset of hypertensive sibs and normotensive subjects, average 24-hour blood pressures were correlated with ECF/TBW (P<0.01). A region linked to BMI in the hypertensive sibs corresponds to a region of conserved synteny containing blood pressure-related QTLs in an F2 cross of Brown NorwayxDahl salt-sensitive rats. Focusing on hypertension-related phenotypes is a promising approach for identifying the genetic determinants of hypertension.

Genetic approaches to the molecular understanding of type 2 diabetes

The appreciation that individual susceptibility to type 2 diabetes (T2D) and related components of the dysmetabolic syndrome has a strong inherited component provides a coherent framework within which to develop a molecular understanding of the pathogenesis of T2D. This review focuses on the main approaches currently adopted by researchers seeking to identify the inherited basis of T2D and the present state of our knowledge. One central theme that emerges is that progress in defining the genetic basis of the common, multifactorial forms of T2D is hindered by etiological heterogeneity: T2D is likely to represent the final common pathway of diverse interacting primary disturbances. Such heterogeneity equally compromises efforts to understand the basis for T2D by use of other approaches, such as cellular biochemistry and classical physiology. Analyses that seek to ally sophisticated physiological characterization with measures of genomic variation are likely to provide powerful tools for redressing the loss of power associated with such heterogeneity.

Renal medullary nitric oxide deficit of Dahl S rats enhances hypertensive actions of angiotensin II

Studies were designed to examine the hypothesis that the renal medulla of Dahl salt-sensitive (Dahl S) rats has a reduced capacity to generate nitric oxide (NO), which diminishes the ability to buffer against the chronic hypertensive effects of small elevations of circulating ANG II. NO synthase (NOS) activity in the outer medulla of Dahl S rats (arginine-citrulline conversion assay) was significantly reduced. This decrease in NOS activity was associated with the downregulation of protein expression of NOS I, NOS II, and NOS III isoforms in this region as determined by Western blot analysis. In anesthetized Dahl S rats, we observed that a low subpressor intravenous infusion of ANG II (5 ng. kg(-1). min(-1)) did not increase the concentration of NO in the renal medulla as measured by a microdialysis with oxyhemoglobin trapping technique. In contrast, ANG II produced a 38% increase in the concentration of NO (87 +/- 8 to 117 +/- 8 nmol/l) in the outer medulla of Brown-Norway (BN) rats. The same intravenous dose of ANG II reduced renal medullary blood flow as determined by laser-Doppler flowmetry in Dahl S, but not in BN rats. A 7-day intravenous ANG II infusion at a dose of 3 ng. kg(-1). min(-1) did not change mean arterial pressure (MAP) in the BN rats but increased MAP in Dahl S rats from 120 +/- 2 to 138 +/- 2 mmHg (P < 0.05). ANG II failed to increase MAP after NO substrate was provided by infusion of L-arginine (300 microg. kg(-1). min(-1)) into the renal medulla of Dahl S rats. Intravenous infusion of L-arginine at the same dose had no effect on the ANG II-induced hypertension. These results indicate that an impaired NO counterregulatory system in the outer medulla of Dahl S rats makes them more susceptible to the hypertensive actions of small elevations of ANG II.

Angiotensin-converting enzyme 2 is an essential regulator of heart function

Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. Here we show that angiotensin-converting enzyme 2 (ace2) maps to a defined quantitative trait locus (QTL) on the X chromosome in three different rat models of hypertension. In all hypertensive rat strains, ACE2 messenger RNA and protein expression were markedly reduced, suggesting that ace2 is a candidate gene for this QTL. Targeted disruption of ACE2 in mice results in a severe cardiac contractility defect, increased angiotensin II levels, and upregulation of hypoxia-induced genes in the heart. Genetic ablation of ACE on an ACE2 mutant background completely rescues the cardiac phenotype. But disruption of ACER, a Drosophila ACE2 homologue, results in a severe defect of heart morphogenesis. These genetic data for ACE2 show that it is an essential regulator of heart function in vivo.

Dopamine receptor-coupling defect in hypertension

Dopamine synthesized in non-neural tissues, eg, renal proximal tubule, functions in an autocrine or paracrine manner. The effects of dopamine are transduced by two classes of receptors (D1- and D2-like) that belong to the superfamily of G protein-coupled receptors. In genetic hypertension, the D1 receptor, a member of the D1-like receptor family, is uncoupled from its G protein complex, resulting in a decreased ability to regulate renal sodium transport. The impaired D1 receptor/G protein coupling in renal proximal tubules in genetic hypertension is secondary to abnormal phosphorylation and desensitization of the D1 receptor caused by activating single nucleotide polymorphisms of a G protein-coupled receptor kinase, GRK type 4.

A gene expression analysis in rat kidney following high and low salt intake

BACKGROUND

The effects of salt intake on renal regulation have been investigated for decades. To find new pathways and to demonstrate the utility of oligonucleotide expression arrays, we studied whole kidneys.

METHODS

Eight Sprague-Dawley rats were divided into two groups. One group received a 6% salt (by weight) diet, while the other group received a 0.3%, otherwise identical, salt diet for 7 days. The rats were sacrificed after 7 days and the left kidney was subjected to RNA extraction. Oligonucleotide expression arrays (Affymetrix) were used to determine downregulation and upregulation, comparing high with low salt intake. Four rats from each group were studied separately.

RESULTS

The experiments were reproducible. Thirty genes were downregulated with the high-salt diet, while 35 genes were upregulated. The renin gene, beta-2 glycoprotein-1, retinol binding protein, annexin VI, and the PTP2C protein tyrosine phosphatase were among the downregulated genes. The angiotensin II receptor type 1B receptor, HMG-CoA reductase, B7 antigen, and the rat calcium channel beta subunit III were among the upregulated genes. Differentially regulated were the p55 subunit (upregulated) and the p50 subunit (downregulated) of the phosphatidyl inositol 3-kinase enzyme complex. We verified our results by selecting a high-salt downregulated gene (renin) and an upregulated gene (B7 antigen) and subjecting these genes to real-time polymerase chain reaction. The results were consistent.

CONCLUSION

Oligonucleotide expression arrays can detect novel genes encoding for proteins not generally associated with responses to varied salt intake. Experiments of this nature have substantial limitations and require detailed verification. However, overall, the utility is promising.

Rat genetics: attaching physiology and pharmacology to the genome

During the past five years, the Rat Genome Project has been rapidly gaining momentum, especially since the announcement in August 2000 of plans to sequence the rat genome. Combined with the wealth of physiological and pharmacological data for the rat, the genome sequence should facilitate the discovery of mammalian genes that underlie the physiological pathways that are involved in disease. Most importantly, this combined physiological and genomic information should also lead to the development of better pre-clinical models of human disease, which will aid in the development of new therapeutics.