From the Cover: Whole-genome association study identifies STK39 as a hypertension susceptibility gene

Abstract

Hypertension places a major burden on individual and public health, but the genetic basis of this complex disorder is poorly understood. We conducted a genome-wide association study of systolic and diastolic blood pressure (SBP and DBP) in Amish subjects and found strong association signals with common variants in a serine/threonine kinase gene, STK39. We confirmed this association in an independent Amish and 4 non-Amish Caucasian samples including the Diabetes Genetics Initiative, Framingham Heart Study, GenNet, and Hutterites (meta-analysis combining all studies: n = 7,125, P < 10(-6)). The higher BP-associated alleles have frequencies > 0.09 and were associated with increases of 3.3/1.3 mm Hg in SBP/DBP, respectively, in the Amish subjects and with smaller but consistent effects across the non-Amish studies. Cell-based functional studies showed that STK39 interacts with WNK kinases and cation-chloride cotransporters, mutations in which cause monogenic forms of BP dysregulation. We demonstrate that in vivo, STK39 is expressed in the distal nephron, where it may interact with these proteins. Although none of the associated SNPs alter protein structure, we identified and experimentally confirmed a highly conserved intronic element with allele-specific in vitro transcription activity as a functional candidate for this association. Thus, variants in STK39 may influence BP by increasing STK39 expression and consequently altering renal Na(+) excretion, thus unifying rare and common BP-regulating alleles in the same physiological pathway.

Fig. 1.

Whole genome association scan results for SBP in 542 AFDS subjects. SNPs from each chromosome are represented by a different color and ordered by physical location.

Fig. 2.

(A) Exonic structure, association between STK39 SNPs and SBP/DBP. (B) LD relationship among SNPs. The locations of associated SNPs in LD bins 1 and 2 are denoted by black and gray bars, respectively. Pairwise LD relationships (r²) among SNPs are indicated by color (black = 1; white = 0; shades of gray = 0 < r² < 1).

Fig. 3.

rs6749447 genotype-specific mean SBP among AFDS subjects in the initial GWA scan (A), replication AFDS set (B), and HAPI subjects (C). The number of subjects, mean, and SEM are shown for each genotype group. Genotype-specific means were calculated using SBP adjusted for age, sex, and diabetes status. Significance levels of association to SBP are shown along with genetic models.

Fig. 4.

(A) Pairwise alignment of human-mouse (Top) and human-opossum (Bottom) genomic sequence of the BP-associated region in STK39. Percent sequence identity is shown on the right. Exons are in blue; intronic CEs are in red. The locations of 7 CEs are indicated by bars above the graph. (B) Luciferase activity of CE3 and CE5 bearing different alleles. The 2 alleles associated with higher BP are indicated by an asterisk (*).

Fig. 5.

Immunolocalization of SPAK in kidney. (A) SPAK strongly localizes to the TAL of the loop of Henle and the CCDs. (B) Immunolocalization of aquaporin 2 in the same section as in (A) as a segment-specific marker for CCDs. (C) Immunolocalization of SPAK in the DCTs. (D) Immunolocalization of NCC as a segment-specific marker for DCTs. Bar = 4.3 μm.