Genomic organization of <i>CYP19A1</i> showing the 10 SNPs used in the haplotype analysis.

<p>Presented is the <i>CYP19A1</i> gene and locations of the 10 <i>CYP19A1</i> SNPs on chromosome 15 coordinates 51, 536,349–51,338,598 estimated using UCSC Genome Browser February 2009 (GRCh37/hg19). SNPs are indicated by the rs number highlighted in red. Illustrated below the <i>CYP19A1</i> gene are the LD blocks and common haplotypes (≥ 2%) estimated using all SNPs across AA and EA groups separately. The red dotted lines denote the SNPs defined within the corresponding LD block. The lines between blocks link haplotypes that are transmitted with ≥ 2% frequency across blocks. LD blocks constructed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117347#pone.0117347.g001" target="_blank">Fig. 1</a> match haplotype blocks generated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117347#pone.0117347.g002" target="_blank">Fig. 2</a>.</p

Characteristics of <i>CYP19A1</i> SNPs and predicted binding sites and associated regulatory proteins.

<p>Characteristics of <i>CYP19A1</i> SNPs and predicted binding sites and associated regulatory proteins.</p

Clinical implications of <i>CYP19A1</i> SNPs analyzed.

<p>Clinical implications of <i>CYP19A1</i> SNPs analyzed.</p

Ethnic differences in <i>CYP19A1</i> minor allele frequency distribution across populations of European (EA) and African (AA) ancestry.

<p>*p<0.05;</p><p>**p<0.01;</p><p>***p<0.001</p><p>Ethnic differences in <i>CYP19A1</i> minor allele frequency distribution across populations of European (EA) and African (AA) ancestry.</p

Haplotype block structures for genotyped <i>CYP19A1</i> SNPs on chromosome 15q for EA and AA subjects from Arkansas.

<p>Shown above are the approximate locations of each of the ten <i>CYP19A1</i> SNPs (identified by their dbSNP rs number) among EA and AA populations. The values within the figure refer to the D’ values for each pairwise comparison. The color gradient from red to white indicates higher to lower LD with the darker color indicating higher LD between the SNP pairs.</p

Allele and genotype frequencies of the <i>CYP19A1</i> SNPs in various populations.

<p>African Americans; EA: European Americans; CEU: Utah residents with Northern and European ancestry; YRI: Yoruba in Ibadan, Nigeria; HCB: Hans Chinese in Beijing, China; JPT: Japanese in Tokyo, Japan; and GIH Gujarat Indians in Houston, TX</p><p>^a African Americans and European Americans in present study</p><p>^b HapMap data according to NCBI Entrez database</p><p>^c Umamaheswaran et al. (9)</p><p>^d Lee et al. (10)</p><p>^e 1000 Genomes ASW: Population of African ancestry from southwest USA</p><p>Minor allele frequency (in bold)</p><p>Allele and genotype frequencies of the <i>CYP19A1</i> SNPs in various populations.</p

Data_Sheet_1_PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin.pdf

<p>Non-small cell lung cancer (NSCLC) is the major form of lung cancer, with adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being its major subtypes. Smoking alone cannot completely explain the lung cancer etiology. We hypothesize that altered lung microbiome and chronic inflammatory insults in lung tissues contribute to carcinogenesis. Here we explore the microbiome composition of LUAD samples, compared to LUSC and normal samples. Extraction of microbiome DNA in formalin-fixed, paraffin-embedded (FFPE) lung tumor and normal adjacent tissues was meticulously performed. The 16S rRNA product from extracted microbiota was subjected to microbiome amplicon sequencing. To assess the contribution of the host genome, CD36 expression levels were analyzed then integrated with altered NSCLC subtype-specific microbe sequence data. Surprisingly phylum Cyanobacteria was consistently observed in LUAD samples. Across the NSCLC subtypes, differential abundance across four phyla (Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes) was identified based on the univariate analysis (p-value < 6.4e-4 to 3.2e-2). In silico metagenomic and pathway analyses show that presence of microcystin correlates with reduced CD36 and increased PARP1 levels. This was confirmed in microcystin challenged NSCLC (A427) cell lines and Cyanobacteria positive LUAD tissues. Controlling the influx of Cyanobacteria-like particles or microcystin and the inhibition of PARP1 can provide a potential targeted therapy and prevention of inflammation-associated lung carcinogenesis.</p