Identification of regulatory variants associated with genetic susceptibility to meningococcal disease

Abstract

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes.

Figure 1

Genomic data for rs4823231 and motif disruption. (A) UCSC genome browser view of the RELA and H3K27ac ChIP-seq data generated in two nasopharyngeal epithelial cell lines. (B) Potential disruption of transcription factor motifs induced by rs4823231. The SNP position is indicated by the red boxes. Ref: reference, Alt: alternate.

Figure 2

Genomic data for rs11913168. RELA and H3K27ac ChIP-seq data following LPS stimulation of Detroit 562 and FaDu cells are represented. The SNP of interest is indicated with a black line. The lower panel (B) consists of a magnification of the dashed box in the upper panel (A).

Figure 3

LIF expression and NF-kB regulation. (A) The bar graph consists of the average log2FC between two RNA-seq experiments following 4 stimuli in Detroit 562 cells (green – see legend) or LPS stimulation in FaDu cells (orange) compared to the control condition without any treatment. (B) LIF expression following LPS stimulation in FaDu cells without (DMSO) or with pre-treatment with BAY 11–7082 (BAY inhibitor) compared to the control condition without treatment. Each dot represent the results from one experiment and the black dash is the mean between duplicates. Significance was tested with a 2-sample T-test for which the P-value is reported.