NFAT5 and SLC4A10 Loci Associate with Plasma Osmolality

Abstract

Disorders of water balance, an excess or deficit of total body water relative to body electrolyte content, are common and ascertained by plasma hypo- or hypernatremia, respectively. We performed a two-stage genome-wide association study meta-analysis on plasma sodium concentration in 45,889 individuals of European descent (stage 1 discovery) and 17,637 additional individuals of European descent (stage 2 replication), and a transethnic meta-analysis of replicated single-nucleotide polymorphisms in 79,506 individuals (63,526 individuals of European descent, 8765 individuals of Asian Indian descent, and 7215 individuals of African descent). In stage 1, we identified eight loci associated with plasma sodium concentration at P<5.0 × 10^-6 Of these, rs9980 at NFAT5 replicated in stage 2 meta-analysis (P=3.1 × 10^-5), with combined stages 1 and 2 genome-wide significance of P=5.6 × 10^-10 Transethnic meta-analysis further supported the association at rs9980 (P=5.9 × 10^-12). Additionally, rs16846053 at SLC4A10 showed nominally, but not genome-wide, significant association in combined stages 1 and 2 meta-analysis (P=6.7 × 10^-8). NFAT5 encodes a ubiquitously expressed transcription factor that coordinates the intracellular response to hypertonic stress but was not previously implicated in the regulation of systemic water balance. SLC4A10 encodes a sodium bicarbonate transporter with a brain-restricted expression pattern, and variant rs16846053 affects a putative intronic NFAT5 DNA binding motif. The lead variants for NFAT5 and SLC4A10 are cis expression quantitative trait loci in tissues of the central nervous system and relevant to transcriptional regulation. Thus, genetic variation in NFAT5 and SLC4A10 expression and function in the central nervous system may affect the regulation of systemic water balance.

Keywords: human genetics; hypernatremia; hyponatremia; water-electrolyte balance.

Figure 1.

Stage 1 genome-wide association −log10 P value (Manhattan) plot identifies candidate loci. The green dotted line indicates the P value threshold for following SNPs in stage 2 meta-analysis (P<5 × 10⁻⁶). The blue dotted line indicates the genome-wide significance threshold (P<5 × 10⁻⁸).

Figure 2.

Sequence context of rs9980 and rs7193778 in the NFAT5 region coincides with functional genomic annotation. Depicted are ENCODE data displayed in the UCSC Genome Browser. (A) shows NFAT5 (exons connected by a blue line) and H3K27ac histone acetylation in the seven ENCODE cell lines (chromosome 16: 68087500–68307500 of human reference genome build NCBI build 36/hg18 and ENCODE histone modification track). Each color represents one of seven cell lines; peak height is the sum of activity in all cell types and proportional to the levels of enrichment of the H3K27ac histone mark across the genome as determined by ChIP-Seq assays. H3K27ac peaks coincide with the NFAT5 promoter region and the vicinity of rs7193778. SNP rs9980 resides in the 3′ untranslated region. (B) illustrates an expanded view of approximately 40 kb upstream of the NFAT5 TSS and depicts the H3K27ac triple peak of the NFAT5 superenhancer as well as the locations of ENCODE/Epigenome Roadmap experimentally confirmed DNaseI-hypersensitive sites above the H3K27ac peaks. The darkness of each site is proportional to the maximum signal strength observed in any cell line, and the adjacent numbers indicate numbers of tissues and cell lines in which hypersensitivity was detected (of a total of 125 tested tissues/cells). C illustrates the approximately 3-kb H3K27ac triple peak of the NFAT5 superenhancer region, depicting rs7193778 relative to H3K27ac marks, DNaseI-hypersensitive sites, and a partial list of the 115 ChIP-Seq–confirmed transcription factor binding sites (of 161 tested) as gray boxes. The darkness of the boxes is proportional to the maximum signal strength observed in any cell line contributing to the cluster. The small DNaseI-hypersensitive region immediately 5′ of rs7193778 (marked 2) was detected in only astrocytes of the CNS (spinal cord; HA-sp cell line) and pancreatic islets (not shown: expression of SLC4A10 is restricted to CNS and pancreatic islets). A DNaseI-sensitive region (DHS1020946) identified through the Regulatory Elements Database (http://dnase.genome.duke.edu/index.php; in the text) crosses the variant (orange bar) and maps to a cluster of motifs operative to astrocytes.