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Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genome-wide association study

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Summary

Background

Idiopathic pulmonary fibrosis (IPF) is a devastating disease that probably involves several genetic loci. Several rare genetic variants and one common single nucleotide polymorphism (SNP) of MUC5B have been associated with the disease. Our aim was to identify additional common variants associated with susceptibility and ultimately mortality in IPF.

Methods

First, we did a three-stage genome-wide association study (GWAS): stage one was a discovery GWAS; and stages two and three were independent case-control studies. DNA samples from European-American patients with IPF meeting standard criteria were obtained from several US centres for each stage. Data for European-American control individuals for stage one were gathered from the database of genotypes and phenotypes; additional control individuals were recruited at the University of Pittsburgh to increase the number. For controls in stages two and three, we gathered data for additional sex-matched European-American control individuals who had been recruited in another study. DNA samples from patients and from control individuals were genotyped to identify SNPs associated with IPF. SNPs identified in stage one were carried forward to stage two, and those that achieved genome-wide significance (p<5 × 10−8) in a meta-analysis were carried forward to stage three. Three case series with follow-up data were selected from stages one and two of the GWAS using samples with follow-up data. Mortality analyses were done in these case series to assess the SNPs associated with IPF that had achieved genome-wide significance in the meta-analysis of stages one and two. Finally, we obtained gene-expression profiling data for lungs of patients with IPF from the Lung Genomics Research Consortium and analysed correlation with SNP genotypes.

Findings

In stage one of the GWAS (542 patients with IPF, 542 control individuals matched one-by-one to cases by genetic ancestry estimates), we identified 20 loci. Six SNPs reached genome-wide significance in stage two (544 patients, 687 control individuals): three TOLLIP SNPs (rs111521887, rs5743894, rs5743890) and one MUC5B SNP (rs35705950) at 11p15.5; one MDGA2 SNP (rs7144383) at 14q21.3; and one SPPL2C SNP (rs17690703) at 17q21.31. Stage three (324 patients, 702 control individuals) confirmed the associations for all these SNPs, except for rs7144383. Linkage disequilibrium between the MUC5B SNP (rs35705950) and TOLLIP SNPs (rs111521887 [r2=0·07], rs5743894 [r2=0·16], and rs5743890 [r2=0·01]) was low. 683 patients from the GWAS were included in the mortality analysis. Individuals who developed IPF despite having the protective TOLLIP minor allele of rs5743890 carried an increased mortality risk (meta-analysis with fixed-effect model: hazard ratio 1·72 [95% CI 1·24–2·38]; p=0·0012). TOLLIP expression was decreased by 20% in individuals carrying the minor allele of rs5743890 (p=0·097), 40% in those with the minor allele of rs111521887 (p=3·0 × 10−4), and 50% in those with the minor allele of rs5743894 (p=2·93 × 10−5) compared with homozygous carriers of common alleles for these SNPs.

Interpretation

Novel variants in TOLLIP and SPPL2C are associated with IPF susceptibility. One novel variant of TOLLIP, rs5743890, is also associated with mortality. These associations and the reduced expression of TOLLIP in patients with IPF who carry TOLLIP SNPs emphasise the importance of this gene in the disease.

Funding

National Institutes of Health; National Heart, Lung, and Blood Institute; Pulmonary Fibrosis Foundation; Coalition for Pulmonary Fibrosis; and Instituto de Salud Carlos III.

Introduction

Idiopathic pulmonary fibrosis (IPF) has a low incidence (4·6–16·3 cases per 100 000 person-years),1, 2 but is a devastating disease of unknown aetiology that is characterised by an interstitial fibrotic process and high mortality.3 Lung transplantation is the only treatment option that successfully improves survival; immunosuppression regimens have been shown to be harmful.4 Several rare genetic variants mostly associated with familial IPF and a common single nucleotide polymorphism (SNP) of MUC5B in sporadic IPF have been identified, suggesting that genetic factors contribute to disease.5, 6 As yet, no genetic variant has been associated with IPF outcomes. Therefore, identification of genetic variants associated with susceptibility to IPF and alleles involved in the heterogeneity of disease course and mortality is an important research focus.

Mutations in TERT or TERC result in telomere shortening and are associated with both familial and non-familial IPF.7 A previous genome-wide association study (GWAS) examining about 250 000 SNPs in only 159 IPF cases8 supported this association. Rare heterozygous variants in SFTPA2 and SFTPC have also been implicated in familial IPF.9 These findings suggest that the aetiology of IPF might involve several genetic loci.

GWAS continues to be the method of choice for identification of common genetic variants associated with complex diseases.10 In view of the power of GWAS to detect expected effects for common variants with realistic sample sizes,8 we postulated that an independent GWAS of IPF would identify novel polymorphisms associated with disease susceptibility and allow assessment of whether these loci were also associated with mortality. Although new knowledge of IPF susceptibility could provide targets for novel treatment strategies, identification of genes associated with mortality in patients with IPF might draw attention to potential therapeutic targets and enable prognostication.

Section snippets

Study design and samples

First, we did a three-stage GWAS (figure 1). Stage one was a discovery GWAS in European Americans for susceptibility to IPF. Identified susceptibility loci were followed up for replication in two independent case-control association studies (stages two and three). Second, we assessed the association between susceptibility loci and mortality in three case series with follow-up data selected from stages one and two (figure 1). Finally, we assessed the correlation between SNP genotypes and gene

Results

Table 1 shows the sample sizes for each stage of the GWAS. As expected, similar to a large single-centre experience for first presentation of IPF,19 the cases included in stage one had a wide range of disease severity and age (table 2). Patients in stage two had similar overall severity to those in stage one. Patients in stage three had more severe disease than did those in stages one and two, as assessed by forced vital capacity (FVC) and diffusing capacity for carbon monoxide (DLCO). However

Discussion

We have identified novel genetic variants residing in two genetic loci—in TOLLIP at 11p15.5 and in SPPL2C at 17q21.31—that are associated with IPF susceptibility in European Americans, and have replicated the previously identified association with an SNP in MUC5B. As far as we are aware, we have shown for the first time that one of the novel genetic variants for susceptibility—rs5743890 in TOLLIP—is also associated with IPF mortality (panel).

MUC5B and TOLLIP reside at the same genetic locus.

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