Genetic architecture of band neutrophil fraction in Iceland

Abstract

The characteristic lobulated nuclear morphology of granulocytes is partially determined by composition of nuclear envelope proteins. Abnormal nuclear morphology is primarily observed as an increased number of hypolobulated immature neutrophils, called band cells, during infection or in rare envelopathies like Pelger-Huët anomaly. To search for sequence variants affecting nuclear morphology of granulocytes, we performed a genome-wide association study using band neutrophil fraction from 88,101 Icelanders. We describe 13 sequence variants affecting band neutrophil fraction at nine loci. Five of the variants are at the Lamin B receptor (LBR) locus, encoding an inner nuclear membrane protein. Mutations in LBR are linked to Pelger-Huët anomaly. In addition, we identify cosegregation of a rare stop-gain sequence variant in LBR and Pelger Huët anomaly in an Icelandic eight generation pedigree, initially reported in 1963. Two of the other loci include genes which, like LBR, play a role in the nuclear membrane function and integrity. These GWAS results highlight the role proteins of the inner nuclear membrane have as important for neutrophil nuclear morphology.

Fig. 1. Manhattan plot for GWAS of band neutrophil fraction in the Icelanders (N = 88,101).

Variants at nine loci reached genome-wide significance and are labeled. All variants with p values below their respective variant-class thresholds, indicated by horizontal dashed lines, are marked as green dots. Red dashed line: adjusted p value significance threshold for variants predicted to lead to loss-of-function (p threshold = 2.4 × 10⁻⁷). Yellow dashed line: adjusted p value significance threshold for variants predicted to have moderate impact on gene function (p threshold = 4.9 × 10⁻⁸). Cyan dashed line: adjusted p value significance threshold for variants predicted to have low impact on gene function (p threshold = 4.4 × 10⁻⁹). Green dashed line: adjusted p value significance threshold for other variants in Dnase I hypersensitivity sites (p threshold = 2.2 × 10⁻⁹). Gray dashed line: adjusted p value significance threshold for all other variants (p threshold = 7.4 × 10⁻¹⁰). Variants are plotted by chromosomal position (x axis) and −log10[p] values (y axis). For clarity, only variants with p < 0.005 are plotted.

Fig. 2. Associations of sequence variants at the LBR locus with band neutrophil fraction in Iceland.

Variants are colored according to correlation (r²) to the most significant variant associated with band neutrophil fraction (legend at top-right). –log10p values along the left y axis and correspond to the variant depicted on the plot. The right y axis shows calculated recombination rates at the chromosomal location, plotted as a solid blue line. The common 3’-UTR variant rs14205[G] is the top marker associated with band neutrophil fraction and is depicted as a purple diamond.

Fig. 3. Pedigree of carriers of p.Arg76Ter in LBR.

All eight carriers (and ten obligate carriers) can be traced back to ancestors in the late eighteenth century. The founding couple have a total number of 9707 descendants. Roman numerals indicate generation, year of birth of the founding couple is noted above the symbols, and standardized band neutrophil fractions are noted below the symbols. Left part half-filled object = affected by Pelger-Huët anomaly according to ref. , question mark on left side = no data for the individual. We note that no genotypic data are available for the listed carriers in the loop formed in generations II, III, and IV. Their carrier status is based on the disease state of carrier IV.1. as presented in ref. .