Alanna C. Morrison, Ph.D. - US grants

DESCRIPTION (provided by applicant): Increased erythrocyte sodium-lithium countertransport is observed in patients with essential hypertension. Genomic regions influencing inter-individual variation in sodium-lithium countertransport have been identified by linkage analyses. While numerous studies of complex disease traits have carried out genome-wide linkage analyses, few have successfully used this information to identify underlying disease susceptibility genes. We propose a practical research strategy to follow-up a replicated linkage peak on chromosome 10 identified from genome-wide scans for sodium-lithium countertransport. This region contains only 55 genes in the overlap of the 1 LOD confidence intervals from each Phase of the Rochester Family Heart Study. This allows for the examination of the contribution of every gene to the primary and secondary traits of interest (i.e. sodium-lithium countertransport and hypertension, respectively). The goal of the project is the identification of allelic variation influencing sodium-lithium countertransport as well as risk of developing essential hypertension.

DESCRIPTION (provided by applicant): Several studies in the past decade indicate that genetic variation in members of the solute carrier (SLC) gene family is associated with blood pressure phenotypes. However, the coverage of these studies is such that members of the SLC gene family were not systematically assessed. Given the kidney's dominant role in blood pressure regulation by controlling body fluid volume, it is hypothesized that the 126 SLC genes expressed in the kidney are of particular importance. In order to examine the relationship between single nucleotide polymorphisms (SNPs) in kidney-expressed SLC genes and blood pressure, this application takes advantage of genome-wide association study (GWAS) data in adults of European ancestry. As a part of the Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) consortium, a total of 7,126 SNPs in 120 kidney-expressed SLC genes were evaluated for an association with systolic and diastolic blood pressure. Based on replication across cohorts and a meta-analysis of results, the SLC1A1 gene was significantly associated with diastolic blood pressure levels and the SLC6A13 gene was significantly associated with systolic blood pressure levels in adults of European ancestry. Together, these results indicate that two kidney-expressed SLC genes warrant additional investigation into their role in blood pressure. In White participants from the Atherosclerosis Risk in Communities (ARIC) study, SLC1A1 and SLC6A13 will be investigated by resequencing in 300 individuals from the upper tail of the blood pressure distribution and in 300 age- and gender-matched individuals from the lower tail of the blood pressure distribution. SNPs identified by resequencing will be genotyped in all ARIC Whites and evaluated for an association with blood pressure levels. SNPs associated with blood pressure will also be investigated in ARIC African Americans and in White, African American and Hispanic hypertensive sibships from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. Finally, cellular model systems will be used in order to better understand the transport properties of the SLC genes in which they reside and how these mechanisms are affected by genetic variation in the gene. The proposed research has direct relevance to public health by aiding in the discovery of functional variation(s) influencing blood pressure levels and the occurrence of hypertension. This will potentially leading to improved prediction of antihypertensive medication response, the development of simple laboratory tests to more accurately identify young normotensive individuals predisposed to develop hypertension and to a better understanding of the etiology of this disease. PUBLIC HEALTH RELEVANCE: The proposed research has direct relevance to public health by aiding in the discovery of functional variation(s) influencing blood pressure levels and the occurrence of hypertension. Measurement of genetic variation may improve prediction of antihypertensive medication response beyond conventional approaches, resulting in a significant public health impact. Additionally, these proposed studies may lead to the development of simple laboratory tests to more accurately identify young normotensive individuals predisposed to develop hypertension and to a better understanding of the etiology of this disease.

DESCRIPTION (provided by applicant): Moderate alcohol consumption has been associated with a reduction in the risk of CHD. These beneficial effects are most commonly attributed to alcohol-induced changes in lipids, although the mechanisms underlying the cardioprotective effects of low to moderate alcohol consumption are unknown. Lipid levels are influenced by multiple factors, including environmental (e.g. alcohol) and genetic factors, and while the independent effects of each of these factors on lipids have been widely studied, their combined effects have been less studied and are less understood. Previous studies have primarily utilized a candidate gene approach to investigate pre-selected genetic variation within lipid metabolism genes; however, advances in polymorphism discovery, population genetics and genotyping technologies have yielded a genome-wide collection of SNPs that span the human genome. Therefore, it is now possible (and more plausible) to utilize a genome-wide association approach to identify gene-alcohol interactions influencing lipids. The ARIC study [N~16,000] has been genotyped for >1,000,000 SNPs spanning the human genome, and the proposed research will leverage the full scope of this resource to identify gene-alcohol interactions influencing lipd levels, with replication facilitated through pre-arranged collaborations with the CARDIA Study [N~3,750] and the Dallas Heart Study [N~3,550]. Further genotyping of functional variants and/or TagSNPs within the genes/regions of the top replicated hits will aid in our identification o putative functional variants that specifically interact with alcohol consumption to influence lipid levels.

DESCRIPTION (provided by applicant): This proposal is in response to PAR-13-382, supporting secondary data analyses of existing large genomic datasets for the purpose of identifying gene-by-environment (GxE) interactions. Lung function and its decline in older adulthood is likely the result of genetic and environmental influences. Cigarette smoking is a key environmental context for loss of lung function over time. Genome-wide association studies (GWAS) identified 26 genetic loci associated with cross-sectional spirometric measures of lung function. Recent GWAS of the longitudinal change in lung function have identified additional novel loci. To date, there is only one published genome-wide study of GxE interaction on lung function that considers smoking as the environment of interest. This genome-wide GxE study used common variation and cross-sectional information on lung function and smoking to identify three novel loci not previously associated with lung function. In aggregate, these published studies made important contributions to understanding the etiology of lung function, and were facilitated by the organizational structure and support of the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium and the CHARGE Pulmonary Working Group. Additional investigation is warranted to further understand how smoking interacts with genetic factors to influence lung function. The objective of this proposal is to elucidate the complex interplay of genes and environment underlying lung function using state-of-the-art statistical methods and analysis strategies that leverage available data resources. Ongoing work within the CHARGE Pulmonary Working Group includes analysis of data from the Illumina HumanExome BeadChip (the exome chip) for ~33,800 individuals of European ancestry with spirometric measures of lung function, all of whom also have longitudinal measures of smoking history and lung function. An additional ~6,000 individuals of African ancestry have measures of lung function, smoking history, and exome chip data, and ~3,800 also have longitudinal measures. Spirometric measures include forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and their ratio (FEV1/FVC). These measures of lung function are important clinical tools for diagnosing pulmonary disease, classifying its severity, and evaluating its progression over time. The large volume of phenotype and exome chip data available within the CHARGE consortium provides a unique, cost-effective opportunity to apply new analytical approaches and methods. This application has two novel aspects: 1) investigation of rare variation and environmental interactions, and 2) investigation of longitudinal measures of environmental factors. The proposed research represents the next step in the efforts to investigate the interplay of genetic variation and environmental factors influencing lung function. Results from this study may disclose novel genetic susceptibilities to smoking exposure or a greater understanding of the role of smoking in the development, progression, and severity of declining lung function.

PROJECT SUMMARY Fibrinogen, coagulation factor VII (FVII) and factor VIII (FVIII), and its carrier protein von Willebrand factor (vWF) play key roles in modulating the risk of arterial and venous thrombosis. Similarly, D-dimer and tissue plasminogen activator (tPA) reflect ongoing activation of the hemostatic system, and plasminogen activator inhibitor (PAI-1) is the principal inhibitor of tPA. These 7 factors reflect the primary hemostasis phenotypes that have been most commonly measured in population-based studies of healthy adults. Genome-wide association studies (GWAS) successfully identified 70 loci contributing to these clinically relevant phenotypes related to thrombosis and hemostasis. The availability of whole genome sequencing (WGS) data in many of the studies that contributed to these initial efforts will now allow us to expand our knowledge of the genetic variation contributing to plasma levels of these hemostasis traits. The goal of the proposed research is to utilize existing WGS-related resources in multi-ethnic studies to facilitate new genomic discovery in clinically-relevant phenotypes related to thrombosis and hemostasis. We build upon a long-standing history of active collaboration and productivity, and have assembled the largest collection of studies with WGS data (n=37,036 individuals) and measurements for the 7 hemostasis phenotypes (fibrinogen, FVII, FVIII, vWF, D-dimer, tPa, and PAI-1). Generation of WGS data has been supported by NIH initiatives such as the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, the Trans-Omics for Precision Medicine (TOPMed) Program, the Centers for Common Disease Genomics (CCDG), and others. This project provides a coordinated approach for detailed interrogation of genomic data by, (1) utilizing WGS from 10 multi-ethnic studies to assess the contribution of low frequency and rare genetic variation to 7 hemostasis phenotypes; (2) replicating significant findings in >135,000 individuals from an additional 26 studies with imputed genotypes based on TOPMed as a reference panel; and (3) integrating gene expression measurements with summary association statistics from a large- scale common variant GWAS for hemostasis traits involving all 36 studies, then using WGS to interrogate newly discovered genes. These approaches will identify genetic variation contributing to hemostasis traits that will then be evaluated for association with clinical outcomes (e.g., venous thromboembolism, myocardial infarction, and stroke). This proposal brings together extensive WGS resources, hemostasis phenotypes, and capitalizes on advances in genomic technologies and computational analysis in order to contribute to the evidence base that may be used to deliver precision medicine in clinical settings.

PROJECT SUMMARY Fibrinogen is essential for normal blood coagulation and is an integral component of inflammatory pathways. These two processes are deeply intertwined in the development of thrombotic and atherosclerotic diseases. We can better understand the biological and pathophysiological actions of fibrinogen by functionally characterizing the genomic contribution to circulating fibrinogen levels. In the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, we carried out genome-wide association studies (GWAS) in search of genetic determinants of fibrinogen levels. These studies involved tens of thousands of individuals and identified variants within fibrinogen structural genes, as well as 42 other significantly associated loci. However, association studies do not explain which genes at these loci functionally influence fibrinogen levels. It is also important to determine whether genes at these loci act through inflammatory pathways. The goal of this project is to leverage our expertise in genomic studies and functional biology to generate new biological knowledge about the genomic regulation of fibrinogen and to characterize the relationship between fibrinogen and thrombotic and atherosclerotic disease. Our study design enables information exchange between functional biologists with expertise in coagulation biochemistry and thrombosis pathophysiology, and genetic epidemiologists from the CHARGE consortium. The interdisciplinary team will carry out three specific aims. First, we will use siRNA gene silencing to interrogate genes at 42 loci identified by GWAS to be associated with fibrinogen levels, determine their effect on fibrinogen transcription, translation, and secretion, and establish whether these genes modulate fibrinogen levels via an inflammatory (IL6-STAT3) pathway. Second, we will perform an epigenome-wide association study to examine the association between fibrinogen levels and blood methylation levels at CpG sites across the genome. These results are integrated with genetic data to identify genetic variants associated with CpG sites (meQTLs) that are also associated with fibrinogen levels. Candidate genes at fibrinogen-associated meQTLs will also be evaluated using the proposed functional biological methods. Third, we will assess the causal relationship between fibrinogen and thrombotic and atherosclerotic disease using a Mendelian Randomization approach. Knowledge gained from the functional biology experiments will be used to refine the genetic instrument for fibrinogen and additionally create an instrument that is composed only of variants related to the IL6-STAT3 pathway. This team science approach is innovative in its experimental design and in its potential to reveal important, new information impacting human health by translating results of genomic association studies into a clear understanding of fibrinogen's role in thrombotic and atherosclerotic disease.