A genome-wide association study of bronchodilator response in participants of European and African ancestry from six independent cohorts

Introduction Bronchodilator response (BDR) is a measurement of acute bronchodilation in response to short-acting β2-agonists, with a heritability between 10 and 40%. Identifying genetic variants associated with BDR may lead to a better understanding of its complex pathophysiology. Methods We performed a genome-wide association study (GWAS) of BDR in six adult cohorts with participants of European ancestry (EA) and African ancestry (AA) including community cohorts and cohorts ascertained on the basis of obstructive pulmonary disease. Validation analysis was carried out in two paediatric asthma cohorts. Results A total of 10 623 EA and 3597 AA participants were included in the analyses. No single nucleotide polymorphism (SNP) was associated with BDR at the conventional genome-wide significance threshold (p<5×10−8). Performing fine mapping and using a threshold of p<5×10−6 to identify suggestive variants of interest, we identified three SNPs with possible biological relevance: rs35870000 (within FREM1), which may be involved in IgE- and IL5-induced changes in airway smooth muscle cell responsiveness; rs10426116 (within ZNF284), a zinc finger protein, which has been implicated in asthma and BDR previously; and rs4782614 (near ATP2C2), involved in calcium transmembrane transport. Validation in paediatric cohorts yielded no significant SNPs, possibly due to age–genotype interaction effects. Conclusion Ancestry-stratified and ancestry-combined GWAS meta-analyses of over 14 000 participants did not identify genetic variants associated with BDR at the genome-wide significance threshold, although a less stringent threshold identified three variants showing suggestive evidence of association. A common definition and protocol for measuring BDR in research may improve future efforts to identify variants associated with BDR.publishedVersio

Distribution of Hyperpolarized Xenon in the Brain Following Sensory Stimulation: Preliminary MRI Findings

In hyperpolarized xenon magnetic resonance imaging (HP 129Xe MRI), the inhaled spin-1/2 isotope of xenon gas is used to generate the MR signal. Because hyperpolarized xenon is an MR signal source with properties very different from those generated from water-protons, HP 129Xe MRI may yield structural and functional information not detectable by conventional proton-based MRI methods. Here we demonstrate the differential distribution of HP 129Xe in the cerebral cortex of the rat following a pain stimulus evoked in the animal's forepaw. Areas of higher HP 129Xe signal corresponded to those areas previously demonstrated by conventional functional MRI (fMRI) methods as being activated by a forepaw pain stimulus. The percent increase in HP 129Xe signal over baseline was 13–28%, and was detectable with a single set of pre and post stimulus images. Recent innovations in the production of highly polarized 129Xe should make feasible the emergence of HP 129Xe MRI as a viable adjunct method to conventional MRI for the study of brain function and disease

African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

BACKGROUND: Asthma is the most common chronic disease in children, occurring at higher frequencies and with more severe disease in children with African ancestry. METHODS: We tested for association with haplotypes at the most replicated and significant childhood-onset asthma locus at 17q12-q21 and asthma in European American and African American children. Following this, we used whole-genome sequencing data from 1060 African American and 100 European American individuals to identify novel variants on a high-risk African American-specific haplotype. We characterized these variants in silico using gene expression and ATAC-seq data from airway epithelial cells, functional annotations from ENCODE, and promoter capture (pc)Hi-C maps in airway epithelial cells. Candidate causal variants were then assessed for correlation with asthma-associated phenotypes in African American children and adults. RESULTS: Our studies revealed nine novel African-specific common variants, enriched on a high-risk asthma haplotype, which regulated the expression of GSDMA in airway epithelial cells and were associated with features of severe asthma. Using ENCODE annotations, ATAC-seq, and pcHi-C, we narrowed the associations to two candidate causal variants that are associated with features of T2 low severe asthma. CONCLUSIONS: Previously unknown genetic variation at the 17q12-21 childhood-onset asthma locus contributes to asthma severity in individuals with African ancestries. We suggest that many other population-specific variants that have not been discovered in GWAS contribute to the genetic risk for asthma and other common diseases

HP ¹²⁹Xe spectrum obtained from rat brain <i>in vivo</i> after the administration of HP ¹²⁹Xe gas.

<p>The spectrum was acquired from 50 averages using an RF pulse with a flip angle of 90°, and a frequency of 55.477 MHz. At least four separate peaks are discernable, the largest of which occurs at 194.7 ppm downfield from the HP ¹²⁹Xe gas peak at 0 ppm. The SNR of the largest peak is 476.</p

Superimposition of a rat brain atlas [<b>18</b>] showing four regions of interest (ROIs) analyzed for changes in HP ¹²⁹Xe signal following forepaw stimulation, including cingulate cortex (Cg), primary somatosensory cortex and SS1 forelimb region (SS1 and SS1 fl), and secondary samatosensory cortex (SS2).

<p>Superimposition of a rat brain atlas <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021607#pone.0021607-Paxinos1" target="_blank">[<b>18</b>]</a> showing four regions of interest (ROIs) analyzed for changes in HP ¹²⁹Xe signal following forepaw stimulation, including cingulate cortex (Cg), primary somatosensory cortex and SS1 forelimb region (SS1 and SS1 fl), and secondary samatosensory cortex (SS2).</p

Vital Signs Data (N = 3).

<p>Vital Signs Data (N = 3).</p

HP ¹²⁹Xe distribution in the rat brain.

<p>(<b>3a</b>) HP ¹²⁹Xe CSI image acquired with a 2D CSI pulse sequence from rat head under normal breathing conditions (slice thickness 10 mm). (<b>3b</b>) same image with false color applied. Warmer colors indicate increased HP ¹²⁹Xe signal intensity. (<b>3c</b>) Proton MRI of a rat head showing a 1 mm coronal slice through the brain acquired with a RARE pulse sequence. (<b>3d</b>) Proton image shown with overlay of HP ¹²⁹Xe MRI, in which only HP ¹²⁹Xe signal with an SNR above 2 are shown. FOV was 25 mm.</p

Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma.

BACKGROUND: Identifying novel epigenetic signatures associated with serum immunoglobulin E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE-mediated diseases. METHODS: We performed an epigenome-wide association study using whole blood from Framingham Heart Study (FHS; n&nbsp;=&nbsp;3,471, 46% females) participants and validated results using the Childhood Asthma Management Program (CAMP; n&nbsp;=&nbsp;674, 39% females) and the Genetic Epidemiology of Asthma in Costa Rica Study (CRA; n&nbsp;=&nbsp;787, 41% females). Using the closest gene to each IgE-associated CpG, we highlighted biologically plausible pathways underlying IgE regulation and analyzed the transcription patterns linked to IgE-associated CpGs (expression quantitative trait methylation loci; eQTMs). Using prior UK Biobank summary data from genome-wide association studies of asthma and allergy, we performed Mendelian randomization (MR) for causal inference testing using the IgE-associated CpGs from FHS with methylation quantitative trait loci (mQTLs) as instrumental variables. FINDINGS: We identified 490 statistically significant differentially methylated CpGs associated with IgE in FHS, of which 193 (39.3%) replicated in CAMP and CRA (FDR &lt; 0.05). Gene ontology analysis revealed enrichment in pathways related to transcription factor binding, asthma, and other immunological processes. eQTM analysis identified 124 cis-eQTMs for 106 expressed genes (FDR &lt; 0.05). MR in combination with drug-target analysis revealed CTSB and USP20 as putatively causal regulators of IgE levels (Bonferroni adjusted P&nbsp;&lt;&nbsp;7.94E-04) that can be explored as potential therapeutic targets. INTERPRETATION: By integrating eQTM and MR analyses in general and clinical asthma populations, our findings provide a deeper understanding of the multidimensional inter-relations of DNA methylation, gene expression, and IgE levels. FUNDING: US NIH/NHLBI grants: P01HL132825, K99HL159234. N01-HC-25195 and HHSN268201500001I

HP ¹²⁹Xe fMRI data from three animals.

<p>The HP ¹²⁹Xe signal is shown as a false colour overlay on the corresponding 1 mm thick coronal proton reference image taken from the same animal. The left panel shows HP ¹²⁹Xe signal intensity during baseline and the right panel shows HP ¹²⁹Xe signal intensity after injection of capsaicin 20 ul (3 mg/ml) into the right forepaw. Colour scale represents SNR and only signal with SNR above 2 are shown. Superimposition of a rat brain atlas (18) demarcates specific areas of the brain: cingulate cortex (Cg), motor cortex (M), primary somatosensory cortex and SS1 forelimb region (SS1 and SS1 fl), secondary samatosensory cortex (SS2), and striatum (CPu).</p

Percent HP ¹²⁹Xe signal change in four brain regions^*.

<p>*Measured from regions of interest (ROIs) in hemisphere contralateral to pain stimulus.</p