Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets

Chronic obstructive pulmonary disease (COPD) is characterized by reduced lung function and is the third leading cause of death globally. Through genome-wide association discovery in 48,943 individuals, selected from extremes of the lung function distribution in UK Biobank, and follow-up in 95,375 individuals, we increased the yield of independent signals for lung function from 54 to 97. A genetic risk score was associated with COPD susceptibility (odds ratio per 1 s.d. of the risk score (∼6 alleles) (95% confidence interval) = 1.24 (1.20-1.27), P = 5.05 × 10‾⁴⁹), and we observed a 3.7-fold difference in COPD risk between individuals in the highest and lowest genetic risk score deciles in UK Biobank. The 97 signals show enrichment in genes for development, elastic fibers and epigenetic regulation pathways. We highlight targets for drugs and compounds in development for COPD and asthma (genes in the inositol phosphate metabolism pathway and CHRM3) and describe targets for potential drug repositioning from other clinical indications.This work was funded by a Medical Research Council (MRC) strategic award to M.D.T., I.P.H., D.S. and L.V.W. (MC_PC_12010). This research has been conducted using the UK Biobank Resource under application 648. This article presents independent research funded partially by the National Institute for Health Research (NIHR). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the UK Department of Health. This research used the ALICE and SPECTRE High-Performance Computing Facilities at the University of Leicester. Additional acknowledgments and funding details can be found in the Supplementary Note

Candidate gene and microRNA expression studies of schizophrenia

Schizophrenia is a debilitating psychiatric disorder affecting 0.5-1% of the world's population. Schizophrenia has a significant genetic component, but the early search for specific genes has been slowed by a number of factors, including a lack of inexpensive genotyping methods suitable for targeted genetic studies. This work describes the development of an inexpensive multiplexed genotyping assay ideal for candidate gene studies. Furthermore, we describe application of this technology to the study of three schizophrenia candidate genes - SNAP-25, ZDHHC8, and DGCR8. Both SNAP-25 and ZDHHC8 are involved in glutamate signaling at the NMDA receptor, and dysfunction in glutamate signaling at the NMDA receptor is one of the leading theories of the etiology of schizophrenia. DGCR8 is an RNA-binding protein necessary for the processing of microRNAs, a class of small RNAs important in the development and maintenance of the mammalian central nervous system. Though we failed to find evidence of genetic association with ZDHHC8, we did identify a genetic association between schizophrenia and variants within both the SNAP-25 and DGCR8 genes. Our results with DGCR8 provide the first genetic link between the microRNA biogenesis pathway and a major neuropsychiatric disorder. Additionally, we performed quantitative microRNA expression profiling in post-mortem brain samples from patients with schizophrenia, bipolar disorder, and psychiatrically normal controls. We began with a pilot study comparing the expression of 158 microRNAs in the dorsolateral prefrontal cortex (BA9) of post-mortem brain tissue. Based on initial results, we assessed the expression of a number of specific microRNAs in a large, well characterized sample set from patients with schizophrenia (n=35), bipolar disorder (n=35), and psychiatrically normal controls (n=35). In the larger sample set, we observed overexpression of one microRNA, hsa-mir-372. This overexpression was observed in two separate brain regions from patients with both schizophrenia and bipolar disorder, though no differential expression of any microRNA tested was deemed statistically significant.Ph.D.Includes bibliographical references (p. 102-110)

Improvements to bead-based oligonucleotide ligation SNP genotyping assays

We describe a bead-based, multiplexed, oligonucleotide ligation assay (OLA) performed on the Luminex flow cytometer. Differences between this method and those previously reported include the use of far fewer beads and the use of a universal oligonucleotide for signal detection. These innovations serve to significantly reduce the cost of the assay, while maintaining robustness and accuracy. Comparisons are made between the Luminex OLA and both pyrosequencing and direct sequencing. Experiments to assess conversion rates, call rates, and concordance across technical replicates are also presented

Chronological Changes in MicroRNA Expression in the Developing Human Brain

<div><p>Objective</p><p>MicroRNAs (miRNAs) are endogenously expressed noncoding RNA molecules that are believed to regulate multiple neurobiological processes. Expression studies have revealed distinct temporal expression patterns in the developing rodent and porcine brain, but comprehensive profiling in the developing human brain has not been previously reported.</p><p>Methods</p><p>We performed microarray and TaqMan-based expression analysis of all annotated mature miRNAs (miRBase 10.0) as well as 373 novel, predicted miRNAs. Expression levels were measured in 48 post-mortem brain tissue samples, representing gestational ages 14–24 weeks, as well as early postnatal and adult time points.</p><p>Results</p><p>Expression levels of 312 miRNAs changed significantly between at least two of the broad age categories, defined as fetal, young, and adult.</p><p>Conclusions</p><p>We have constructed a miRNA expression atlas of the developing human brain, and we propose a classification scheme to guide future studies of neurobiological function.</p></div

Demographic information of brain tissue donors.

<p>samples excluded from expression analysis.</p><p>UMB# – Sample identifier, NICHD Brain and Tissues Bank for Developmental Disorders.</p><p>GA – gestational age.</p><p>Pool – indicates sample pooling for TaqMan arrays.</p><p>PMI – post-mortem interval (hours).</p

Temporal expression analysis using real-time quantitative PCR.

<p>The number of miRNAs that exceed the indicated fold difference are tabulated for each pair-wise sample type comparison.</p

Support for the Homeobox Transcription Factor Gene ENGRAILED 2 as an Autism Spectrum Disorder Susceptibility Locus

Our previous research involving 167 nuclear families from the Autism Genetic Resource Exchange (AGRE) demonstrated that two intronic SNPs, rs1861972 and rs1861973, in the homeodomain transcription factor gene ENGRAILED 2 (EN2) are significantly associated with autism spectrum disorder (ASD). In this study, significant replication of association for rs1861972 and rs1861973 is reported for two additional data sets: an independent set of 222 AGRE families (rs1861972–rs1861973 haplotype, P=.0016) and a separate sample of 129 National Institutes of Mental Health families (rs1861972–rs1861973 haplotype, P=.0431). Association analysis of the haplotype in the combined sample of both AGRE data sets (389 families) produced a P value of .0000033, whereas combining all three data sets (518 families) produced a P value of .00000035. Population-attributable risk calculations for the associated haplotype, performed using the entire sample of 518 families, determined that the risk allele contributes to as many as 40% of ASD cases in the general population. Linkage disequilibrium (LD) mapping with the use of polymorphisms distributed throughout the gene has shown that only intronic SNPs are in strong LD with rs1861972 and rs1861973. Resequencing and association analysis of all intronic SNPs have identified alleles associated with ASD, which makes them candidates for future functional analysis. Finally, to begin defining the function of EN2 during development, mouse En2 was ectopically expressed in cortical precursors. Fewer En2-transfected cells than controls displayed a differentiated phenotype. Together, these data provide further genetic evidence that EN2 might act as an ASD susceptibility locus, and they suggest that a risk allele that perturbs the spatial/temporal expression of EN2 could significantly alter normal brain development