Hierarchical fine mapping of the cystic fibrosis modifier locus on 19q13 identifies an association with two elements near the genes CEACAM3 and CEACAM6

Abstract

On 19q13, TGFB1 and the cystic fibrosis modifier 1 locus (CFM1) have been identified as modifiers of the course of the monogenic disease cystic fibrosis (CF). Recently, we have described a transmission disequilibrium at the microsatellite D19S197, localized between TGFB1 and CFM1. To map the corresponding molecular variants, we have selected informative SNP markers within a 600-kb area and compared two-marker-haplotype-distributions between phenotypically contrasting sib pair groups, intending to type only phylogenetically old markers by aiming for close-to-maximal polymorphism information content of the SNPs. Starting with a seed set of five SNPs that cover intermarker distances of up to 50 kb, we have iteratively added more SNPs to the map, until we could identify two genomic fragments of 3,289 and 2,052 bp for which pairs with contrasting phenotypes showed different haplotype distributions on the final 17-SNP-map (P(raw) = 0.0002, P(corr17SNPs) = 0.0106 and P(raw) = 0.0008, P(corr17SNPs) = 0.0469, respectively). Resequencing of these fragments of four unrelated individuals for each element showed that the mildly and severely affected pairs differ in seven SNPs and concordant pairs differ from discordant pairs in five SNPs. Annotation of these variants indicate that CEACAM6 and a regulatory element near the 3' end of CEACAM3 are associated with CF disease severity and intrapair discordance, respectively. While our approach was only guided by the markers' position, the involvement of genes from the CEACAM family in host defense and innate immunity designates these proteins as likely modifiers of the multi-organ disease cystic fibrosis which is known for its cytokine imbalance and pro-inflammatory phenotype.

Genes that determine immunology and inflammation modify the basic defect of impaired ion conductance in cystic fibrosis epithelia

“…Building on our previous experience,18 22 we developed informative microsatellite markers to interrogate these genes (see supplementary material for details). Results of the association study are displayed in figure 3.…”

Initial interrogation, confirmation and fine mapping of modifying genes: STAT3, IL1B and IFNGR1 determine cystic fibrosis disease manifestation

“…The majority of CF-modifying genes have been investigated by a candidate gene approach as AAT variants have been studied by isoeletric focusing in the early 90 s. 41,42 On the basis of our previous experience, 26,31,33 we have applied a stepwise approach to investigate three candidate genes that have been selected based on transcriptome analysis of intestinal samples for this study. First, we have genotyped at least one highly informative microsatellite in (STAT3 and IFNGR1) or near (IL1B) our gene of interest.…”

“…We have compared cases and reference patient populations to detect an association with CF disease severity, CF intrapair discordance and the CFTR-mediated basic defect using as a first-step informative microsatellite markers to interrogate the candidate genes. 26 Here, we describe previously unreported details of: (1) STAT3 where functional data indicate that the intragenic microsatellite used for initial genotyping determines STAT3 expression levels; (2) IL1B where follow-up analysis with intragenic SNPs confirmed the microsatellite signal; and (3) IFNGR1 where haplotype-guided hierarchical fine mapping 33 allowed us to describe the major modifying variants by the base.…”

“…This approach allows the identification of all SNPs that differ between the case and the reference haplotype, enabling functional annotation to identify the modifier by the base. 33 In this study, we report on STAT3 (first stage of microsatellite genotyping), IL1B (microsatellite genotyping followed up by low-density fine mapping to confirm the allelic association) and IFNGR1 (fine mapping completed including resequencing of contrasting haplotypes).…”

CEACAM6 gene variants in inflammatory bowel disease

“…Interestingly, a recent study indicated that CEACAM6 and a regulatory element near the 39 end of CEACAM3 are associated with disease severity in patients with cystic fibrosis [48]. However, a previous study in IBD patients suggested that heterozygous carriers of the DF508 mutation in the CFTR gene, the main susceptibility gene for patients with cystic fibrosis, might exert a protective effect in CD [49], suggesting opposing effects of genetic risk loci for cystic fibrosis and IBD.…”