Novel polymorphisms in the myosin light chain kinase gene confer risk for acute lung injury

Abstract

The genetic basis of acute lung injury (ALI) is poorly understood. The myosin light chain kinase (MYLK) gene encodes the nonmuscle myosin light chain kinase isoform, a multifunctional protein involved in the inflammatory response (apoptosis, vascular permeability, leukocyte diapedesis). To examine MYLK as a novel candidate gene in sepsis-associated ALI, we sequenced exons, exon-intron boundaries, and 2 kb of 5' UTR of the MYLK, which revealed 51 single-nucleotide polymorphisms (SNPs). Potential association of 28 MYLK SNPs with sepsis-associated ALI were evaluated in a case-control sample of 288 European American subjects (EAs) with sepsis alone, subjects with sepsis-associated ALI, or healthy control subjects, and a sample population of 158 African American subjects (AAs) with sepsis and ALI. Significant single locus associations in EAs were observed between four MYLK SNPs and the sepsis phenotype (P<0.001), with an additional SNP associated with the ALI phenotype (P=0.03). A significant association of a single SNP (identical to the SNP identified in EAs) was observed in AAs with sepsis (P=0.002) and with ALI (P=0.01). Three sepsis risk-conferring haplotypes in EAs were defined downstream of start codon of smooth muscle MYLK isoform, a region containing putative regulatory elements (P<0.001). In contrast, multiple haplotypic analyses revealed an ALI-specific, risk-conferring haplotype at 5' of the MYLK gene in both European and African Americans and an additional 3' region haplotype only in African Americans. These data strongly implicate MYLK genetic variants to confer increased risk of sepsis and sepsis-associated ALI.

Figure 1.

Genomic organization of MYLK and position of selected common SNPs on chromosome 3 with minor allele frequencies and pairwise linkage disequilibrium from European American control subjects. A shows the MYLK gene structure based on the representative mRNA sequence (GenBank Accession no. U48959) on chromosome 3 (hg16; UCSC Genome Browser on Human July 2003 Assembly). Exons are represented by blue boxes connected by gray bars representing introns, and the black bars at both sides indicate 5′ and 3′ flanking regions (5′ to 3′ direction). The horizontal dashed lines below the gene structure represented the MAF cutoff lines of 25%, 50%, and 75%, respectively. Positions and MAFs of the 17 common SNPs analyzed are represented by vertical lines below the gene structure with green color stands for MAF in EAs and the pink color for AAs measured from the bottom edge of the gray bar. B shows the LD between 17 common SNPs in EAs (estimated from 170 chromosomes) and AAs (estimated from 120 chromosomes), respectively. The strength of LD between respective pairs of SNPs is depicted by progression of color: for all D′ with LOD of > 2, the color moves from red to light blue as D′ runs from 1 (represent perfect LD) to 0; for D′ with LOD of < 2, it is represented by white.

Figure 2.

Chromosome 3 distributions of −log₁₀ (P value) for single MYLK SNP or haplotypes from SNP windowing across the MYLK gene in EAs. Results from the ALI versus control comparison (A), the sepsis versus control comparison (B), and the ALI versus sepsis comparison (C) are displayed. The y axis indicates the value of −log₁₀ (P), the x axis indicates the relative position for each SNP marker locus at the MYLK gene region on human chromosome 3 in the 5′ to 3′ direction. The vertical line in black represents the position of each SNP marker on the x axis and its height on y axis, indicating the value of −log₁₀ (P). The horizontal lines in red represent the 2-SNP windowing, and the lines in blue represent the 3-SNP windowing.