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

Abstract

We have used a stepwise approach consisting of initial interrogation, confirmation and fine mapping to analyze STAT3, IL1B and IFNGR1 as modifiers of cystic fibrosis disease building upon the data and sample collection of the European Cystic Fibrosis Twin and Sibling Study. We have observed direct correlation between the length of the intronic microsatellite STAT3Sat to STAT3 expression levels among F508del-CFTR homozygous patients (P¼0.0075), and an association of longer STAT3Sat-alleles with the presence of CFTR-mediated residual chloride secretion (P¼0.0031), measured as the manifestation of the CF basic defect in intestinal tissue. Both, family-based analysis by TDT and case-reference comparison identified consistently the same intragenic IL1B haplotype as a risk variant (P raw ¼0.055 for TDT, P raw o0.3 for case-reference comparison). Using haplotypeguided hierarchical fine mapping, we have identified two single nucleotide exchanges for which concordant and discordant sibling pairs differ at a 7 kb -spanning core haplotype in IFNGR1 (P raw ¼0.0113). Taken together, our findings imply that immunorelevant pathways and ion secretion, dominated by CFTR in intestinal and respiratory epithelium, merge at the level of the epithelial cell to integrate the signaling of cytokines due to innate and acquired immune defense.

The Contribution of the Airway Epithelial Cell to Host Defense

“…While a target of such regulatory networks might be the CFTR gene itself, it is equally plausible that the configuration of the epithelial cell is altered to promote more efficient trafficking of the CFTR ion channel, known for its short half-life [ 41 ] and its prolonged residence in a subapical compartment [ 42 – 44 ], to the apical membrane. So far, an association with the CF basic defect has been described for genes encoding the two transcription factors STAT3 [ 39 ] and the epithelial-specific transcription factor EHF [ 45 ], the latter being a positional candidate that has been selected for replication based on a genome-wide study undertaken to identify modifiers of CF lung disease severity [ 46 ]. However, in order to effectively select therapeutic targets in the future, the central molecular pathways that are used by host defense modifier genes which have an impact on CFTR-mediated residual function or ENaC activity in epithelial cells need to be identified.…”

“…Several researchers have selected genes encoding for cytokines such as TNFA , IL1B, and TGFB1 as candidate genes because of their known role in infection, immunology, and inflammation [ 13 , 34 – 38 ]. Among these immunologically relevant candidate genes, IL1B has been replicated in two truly independent studies [ 35 , 39 ], albeit the molecular variant has not been mapped by the base yet. The cytokine receptors TNFR1 and IFNGR1 have been studied as modifier genes in European CF Twin and Sibling Study [ 13 , 39 , 40 ].…”

“…Among these immunologically relevant candidate genes, IL1B has been replicated in two truly independent studies [ 35 , 39 ], albeit the molecular variant has not been mapped by the base yet. The cytokine receptors TNFR1 and IFNGR1 have been studied as modifier genes in European CF Twin and Sibling Study [ 13 , 39 , 40 ]. Until now, the CF basic defect that can be assessed by nasal potential difference measurement in vivo has only been used by the European CF Twin and Sibling Study for an association study.…”

Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies

“…Construction of an association network (see Figure 7D) shows that all of these genes have been linked by co-expression or co-localization in other studies, or have proven functional relationships with each other and with other genes known to be regulated in CF. The most connected gene in this network is IL1B, an important mediator of the inflammatory response and a known modifier of CF lung disease [57]. …”

Current Concepts and Controversies in Innate Immunity of Cystic Fibrosis Lung Disease

“…A more recent meta-analysis [17] has identified 5 loci: MUC4/MUC20 , SLC9A3 , HLA Class II and AGTR2/SLC6A14 to be associated with the lung function in CF. Labenski et al [18 ]have reported 2 cytokine receptor genes, INFGR1 and IL1B , and a transcription factor, STAT3, which is associated with the basic CFTR defect as candidate modifier genes in a study comparing F508del homozygous CF patient subsets. Some lesser-known genetic variations linked to CF lung disease are EDNRA [19], IL-8 [20] and SERPINA1 [9].…”