Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population.

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (P interaction  = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Microhomology-based choice of Cas9 nuclease target sites

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Digital Infrared Thermal Imaging of Crape Myrtle Leaves Infested with Sooty Mold

The spatial patterns for temperature distribution on crape myrtle leaves infested with sooty mold were investigated using a digital infrared thermal imaging camera. The mean temperatures of the control and sooty regions were 26.98°C and 28.44°C, respectively. In the thermal images, the sooty regions appeared as distinct spots, indicating that the temperatures in these areas were higher than those in the control regions on the same leaves. This suggests that the sooty regions became warmer than their control regions on the adaxial leaf surface. Neither epidermal penetration nor cell wall dissolution by the fungus was observed on the adaxial leaf surface. It is likely that the high temperature of black leaves have an increased cooling load. To our knowledge, this is the first report on elevated temperatures in sooty regions, and the results show spatial heterogeneity in temperature distribution across the leaf surface

Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases

Despite the recent discoveries of and interest in numerous structural variations (SVs)—which include duplications and inversions—in the human and other higher eukaryotic genomes, little is known about the etiology and biology of these SVs, partly due to the lack of molecular tools with which to create individual SVs in cultured cells and model organisms. Here, we present a novel method of inducing duplications and inversions in a targeted manner without pre-manipulation of the genome. We found that zinc finger nucleases (ZFNs) designed to target two different sites in a human chromosome could introduce two concurrent double-strand breaks, whose repair via non-homologous end-joining (NHEJ) gives rise to targeted duplications and inversions of the genomic segments of up to a mega base pair (bp) in length between the two sites. Furthermore, we demonstrated that a ZFN pair could induce the inversion of a 140-kbp chromosomal segment that contains a portion of the blood coagulation factor VIII gene to mimic the inversion genotype that is associated with some cases of severe hemophilia A. This same ZFN pair could be used, in theory, to revert the inverted region to restore genomic integrity in these hemophilia A patients. We propose that ZFNs can be employed as molecular tools to study mechanisms of chromosomal rearrangements and to create SVs in a predetermined manner so as to study their biological roles. In addition, our method raises the possibility of correcting genetic defects caused by chromosomal rearrangements and holds new promise in gene and cell therapy

Schematic outline of customization of pooled CRISPR library.

<p>The gRNA-encoding plasmid DNA in the pooled CRISPR library contained the nucleotide sequence 5’-CGG-3’, which could be used as the PAM sequence for Cas9 proteins. Cas9 RNPs, which are complexes of Cas9 proteins and rc-gRNAs, could selectively cleave plasmid DNA possessing complementary sequences with rc-gRNA. Based on this principle, only the desired gRNAs could be depleted from the pooled CRISPR library.</p

Cas9 RNPs treatment for the <i>HPRT1</i>-depleted CRISPR library generation.

<p>(A) Schematic outline of PCR to assess the quality of the gRNA-depleted library. The forward primer annealed to the U6 promoter and the reverse primers could selectively anneal to the target sequences. While using the primer pairs, amplification occurred in the wild-type library, although not in the gRNA-depleted library. (B) The PCR amplicons of the <i>HPRT1</i>-depleted GeCKOv2 library were analyzed by agarose gel electrophoresis. Each of the GeCKOv2 A and B libraries had three <i>HPRT1</i> gRNAs, all of which were depleted from each library. For all six reverse primers annealed to the <i>HPRT1</i> gRNA-encoding plasmid DNA, amplification occurred with the wild-type libraries as templates, although not with the <i>HPRT1</i>-depleted libraries. A pair of primers annealing to puromycin-encoding sequences in the plasmid DNA was used for internal control amplification. The primer sequences are listed in Table B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199473#pone.0199473.s001" target="_blank">S1 File</a> (C) Targeted deep sequencing analysis of the <i>HPRT1</i>-depleted libraries as described previously[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199473#pone.0199473.ref011" target="_blank">11</a>]. Scatter plots of the <i>HPRT1</i>-depleted GeCKOv2 A (left) and the <i>HPRT1</i>-depleted GeCKOv2 B (right) libraries showed that only <i>HPRT1</i> gRNAs were depleted from the wild-type GeCKOv2 libraries. (D) Relative <i>HPRT1</i> gRNA quantities were calculated from the targeted deep sequencing data. Numerical data are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199473#pone.0199473.s002" target="_blank">S1 Table</a>.</p