Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data to identify 10 risk loci for fIIP. Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequencing studies of lung tissue to identify and characterize new fIIP risk loci.We performed genome-wide genotype imputation association analyses in 1616 non-Hispanic white (NHW) cases and 4683 NHW controls followed by validation and replication (878 cases, 2017 controls) genotyping and targeted gene expression in lung tissue. Following meta-analysis of the discovery and replication populations, we identified a novel fIIP locus in the HLA region of chromosome 6 (rs7887 P meta  = 3.7 × 10(-09)). Imputation of classic HLA alleles identified two in high linkage disequilibrium that are associated with fIIP (DRB1*15:01 P = 1.3 × 10(-7) and DQB1*06:02 P = 6.1 × 10(-8)). Targeted RNA-sequencing of the HLA locus identified 21 genes differentially expressed between fibrotic and control lung tissue (Q < 0.001), many of which are involved in immune and inflammatory response regulation. In addition, the putative risk alleles, DRB1*15:01 and DQB1*06:02, are associated with expression of the DQB1 gene among fIIP cases (Q < 1 × 10(-16)).We have identified a genome-wide significant association between the HLA region and fIIP. Two HLA alleles are associated with fIIP and affect expression of HLA genes in lung tissue, indicating that the potential genetic risk due to HLA alleles may involve gene regulation in addition to altered protein structure. These studies reveal the importance of the HLA region for risk of fIIP and a basis for the potential etiologic role of auto-immunity in fIIP.National Heart, Lung and Blood Institute R01-HL095393 R01-HL097163 P01-HL092870 RC2-HL101715 U01-HL089897 U01-HL089856 U01-HL108642 P50-HL089493

Genetic and environmental predictors of serum 25-hydroxyvitamin D concentrations among middle-aged and elderly Chinese in Singapore

10.1017/S0007114512001675British Journal of Nutrition1093493-502BJNU

Predicted binding site of miR15/16/195/497/103/107 in 3′UTR of VPS4a.

<p>Binding site of miR15/16/195/497/103/107 and the SNP, rs16958754[C/T] in the 3′UTR of human VPS4a.</p

Number of samples with multiple alleles from the two HF cohorts.

<p>The complete list of sample ID, SNPs, miRNAs, and gene targets with more than one SNP is given in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101509#pone.0101509.s003" target="_blank">Table S3</a>. *The expected numbers were calculated using 1000 permutations.</p

Overexpression of VPS4a decreases cell number.

<p>(<b>A</b>) Number of HEK 293T cells decreased following transfection with WT VPS4a compared to cells transfected with a control plasmid (Control). Values are mean ± SE, n = 4. (<b>B</b>) Western blot showing increased VPS4a protein following VPS4a transfection in HEK 293T cells <i>vs.</i> cells transfected with a control plasmid at 24 and 48 hours. Bands were normalized to β-actin. Densitometry values are mean ± SE, n = 3.</p

MiR-15a, -16, -195, and -103 expression in peripheral blood and heart tissue in patients with end-stage HF.

<p>(<b>A</b>) miR-15a, -16, -195, and -103 in peripheral blood were decreased in patients with end-stage HF prior to LVAD implant (pre-LVAD) (n = 9) compared to age, gender, and ethnicity matched healthy controls (n = 6). MiR-16 expression increased from end-stage HF prior to LVAD (HF pre-LVAD, n = 9) compared to patients with end-stage HF 7 days post LVAD (HF 7 days post-LVAD) (n = 9). MiR-15a, -16, -195, and -103 were decreased in patients with HF compared to controls. (<b>B</b>) Expression of miR-15/107 family in heart samples was not significantly different between non-failing controls (Controls) (n = 9) and end-stage HF samples (HF pre-LVAD) (n = 10). Samples were in duplicate and target expression normalized to SnU6 for A and B (mean ±SE).</p

Characteristics of patients with end-stage HF. Blood samples were obtained prior to LVAD implantation (n = 9) and 7 days post implant (n = 9).

<p>M-male, F-female, C-Caucasian, AA-African-American, BP-Blood Pressure, HF-Heart Failure, NI-non Ischemic, I- Ischemic, EF- Ejection fraction, BNP- β-Natriuretic Peptide.</p

MiR-16, -103 and -107 interact with the 3′UTR of VPS4a.

<p>Binding of miR-16, -103 or -107 to WT 3′UTR of VPS4a decreases luciferase activity (n = 10) in HEK 293T cells. The SNP rs16958754[C/T] abolishes the interaction of miR-16, -103 or -107 to the mutated 3′UTR of VPS4a resulting in no change in luciferase activity (n = 10) (mean ± SE).</p

MiR-16, -103 and -107 decrease VPS4a mRNA expression.

<p>(<b>A</b>) Expression of VPS4a mRNA in HEK 293T cells decreases following overexpression of miR-16, or -103, or -107 (n = 3). Overexpression of a scrambled control mimic (control) had no effect (n = 3). Samples were run in duplicate and VPS4a expression normalized to 18S. (<b>B</b>) Overexpression of miR-16, -103 and -107 transcript <i>vs.</i> a scrambled control mimic (control) 48 h post transfection in HEK 293T cells (n = 3). Samples were run in duplicate and expression normalized to RNU38B (mean ± SE).</p

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.

We performed a genome-wide association study of non-Hispanic, white individuals with fibrotic idiopathic interstitial pneumonias (IIPs; n = 1,616) and controls (n = 4,683), with follow-up replication analyses in 876 cases and 1,890 controls. We confirmed association with TERT at 5p15, MUC5B at 11p15 and the 3q26 region near TERC, and we identified seven newly associated loci (Pmeta = 2.4 × 10(-8) to 1.1 × 10(-19)), including FAM13A (4q22), DSP (6p24), OBFC1 (10q24), ATP11A (13q34), DPP9 (19p13) and chromosomal regions 7q22 and 15q14-15. Our results suggest that genes involved in host defense, cell-cell adhesion and DNA repair contribute to risk of fibrotic IIPs