Summary of the copy number variation (CNV) analysis by lymphoma subtype.

<p>Summary of the copy number variation (CNV) analysis by lymphoma subtype.</p

Copy Number Variation Analysis on a Non-Hodgkin Lymphoma Case-Control Study Identifies an 11q25 Duplication Associated with Diffuse Large B-Cell Lymphoma

<div><p>Recent GWAS have identified several susceptibility loci for NHL. Despite these successes, much of the heritable variation in NHL risk remains to be explained. Common copy-number variants are important genomic sources of variability, and hence a potential source to explain part of this missing heritability. In this study, we carried out a CNV analysis using GWAS data from 681 NHL cases and 749 controls to explore the relationship between common structural variation and lymphoma susceptibility. Here we found a novel association with diffuse large B-cell lymphoma (DLBCL) risk involving a partial duplication of the C-terminus region of the <i>LOC283177</i> long non-coding RNA that was further confirmed by quantitative PCR. For chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), known somatic deletions were identified on chromosomes 13q14, 11q22-23, 14q32 and 22q11.22. Our study shows that GWAS data can be used to identify germline CNVs associated with disease risk for DLBCL and somatic CNVs for CLL/SLL.</p></div

The figure shows, on the top, the aberrations (deletions in red, duplications in green) found in the 11q25 region in controls and DLBCL cases after CNV analysis using a genotyping array.

<p>On the bottom, the figure shows the locations of the 9 PCR primers designed to cover the LOC283177 gene. qPCR confirmed the partial duplication of LOC283177 (P = 0.004), and the region of breakpoint was determined to be located between primers P4 and P5. Coordinates are shown with respect to the NCBI36/hg18 assembly.</p

Additional file 1: Table S1. of A Fucus vesiculosus extract inhibits estrogen receptor activation and induces cell death in female cancer cell lines

248 genes analyzed for expression profiling (Nanostring™ nCounter®) and 6 housekeeping reference genes. Figure S1. Assays of toxicity. (A) FVE effects on membrane permeability and mitochondrial ATP. (B) Digitonin used as positive control for primary necrosis. (C) CCCP used as positive control for mitochondrial toxicity. Figure S2. Morphological alterations. (A) FVE-untreated and (B) -treated cells with 1.0 % FVE, 48 hr. Figure S3. Heatmap of differential mRNA expression following FVE treatment at 0.25 % and 1.0 % (4 hr) in MCF-7, T47D, MDA-MB-231, HEC-1-B, RL95-2 and OVCAR-3 cell lines; significance level, p <0.05. Figure S4. Treatment of MCF-7, MDA-MB-231, HEC-1-B, MES-SA, AN3-CA, OVCAR-3 and Caov-3 cells with apoptosis (VAD) and autophagy (3MA) inhibitors; *indicates significant difference with FVE without inhibitor (p <0.05). Figure S5. FVE-induced apoptosis via caspase3/7-mediated PARP cleavage in MDA-MB-231 cells; *p <0.05, **p <0.01 compared to controls. Figure S6. FVE down-regulates PI3K/Akt/mTOR signaling in MCF-7 cells. (A) FVE reduced Akt phosphorylation at Ser473 and Thr308, (B) decreased PI3K, 4-EB-P1 and p70S6K phosphorylation, and (C) promoted accumulation of phospho-Beclin-1 and LC3B II. Data are from >3 independent Western blots normalized by β-actin levels; *p <0.05, **p <0.01 compared to controls. Figure S7. FVE down-regulates PI3K/Akt/mTOR signaling in MDA-MB-231 cells. (A) FVE reduced Akt phosphorylation at Ser473 and Thr308, (B) decreased PI3K, 4-EB-P1 and p70S6K phosphorylation, and (C) promoted phospho-Beclin-1 and LC3B II accumulation. Data are from >3 independent Western blots normalized by β-actin levels; *p <0.05, **p < 0.01 compared to controls. Figure S8. Fucoidan up-regulates phosphor-Akt. (A) Fucoidan increased Akt phosphorylation at Ser473 in MCF-7 cells in a concentration-dependent manner; no change in Akt phosphorylation at Thr308. (B) Fucoidan increased Akt phosphorylation at Ser473 in MDA-MB-231 cells in a concentration- and time-dependent manner; no changes observed in Akt phosphorylation at Thr308. (PDF 11350 kb

CLL/SLL-associated SNPs that alter gene expression through <i>cis</i>-acting mechanisms.

<p><i>Notes:</i> Depicted are CLL/SLL-associated SNPs and SNPs in LD that are significantly linked to differential gene expression (BH<0.20). Highlighted in bold are the original GWAS SNPs and the risk allele, or the minor allele when the risk allele is not known.</p>a,b<p>Same SNP influencing expression of two distinct genes.</p>c<p>The synonymous rs28445040 variation (TCC→TCT) does not lead to a substitution for the serine ([Ser]→[Ser]) at amino acid position 223.</p><p><i>Abbreviations:</i> BH, Benjamini-Hochberg; ChrPos, chromosome position; CLL/SLL, chronic lymphocytic leukemia/small lymphocytic lymphoma.</p

CLL/SLL susceptibility loci identified through genome-wide association studies.

<p>Karyotype depicts CLL/SLL-associated SNPs and SNPs in LD with those SNPs that were identified through previous genome-wide association studies (GWAS) and follow-up studies. Independent loci are color-coded with the primary GWAS SNP in dark and SNPs in LD in a lighter shade. Chromosome locations are based on chromosome build 37.1 GRCh37.</p

CLL/SLL susceptibility loci identified through genome-wide association studies and follow-up studies.

<p><i>Notes:</i> In regular font are original independent SNPs identified through GWAS. In italics font are SNPs in LD with the original GWAS SNPs. In bold font are independently validated SNPs used for eQTL analysis and risk alleles as called by the primary study. Nearest gene(s) map within ∼200 kb of each SNP.</p>a<p>OR, CI and <i>P</i>-trend quoted are per copy of risk allele (bold in column 5) from all data combined in the primary study. <i>P-</i>trend, significance of the association between each SNP and risk of CLL/SLL.</p>b<p>Conditional analysis reportedly provided no evidence for an independent role compared to original SNP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029632#pone.0029632-DiBernardo1" target="_blank">[4]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029632#pone.0029632-CrowtherSwanepoel1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029632#pone.0029632-CrowtherSwanepoel4" target="_blank">[12]</a>.</p>c<p>Acquired after fine-scale mapping.</p>d<p>Significance obtained from combined analysis from refs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029632#pone.0029632-CrowtherSwanepoel4" target="_blank">[12]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029632#pone.0029632-CrowtherSwanepoel2" target="_blank">[8]</a>.</p><p><i>Abbreviations:</i> LD, Linkage disequilibrium; OR, odds ratio; CLL/SLL, chronic lymphocytic leukemia/small lymphocytic lymphoma; CI, confidence interval.</p

CLL/SLL-associated SNPs that significantly alter gene expression.

<p>Expression quantitative trait loci (eQTL) analysis identified 19 significant CLL/SLL-associated SNPs linked to differential expression of <i>SP140</i> on chromosome 2 (A), and <i>DACT3</i> and <i>GNG8</i> on chromosome 19 (BH<0.20) (B). eQTL SNPs are depicted on a partial chromosome map that includes the differentially expressed gene(s). Chromosome locations are based on chromosome build 37.1 GRCh37.</p

Logistic regression analysis results for SNPs with <i>p_G</i><0.05.

*<p>Coordinates obtained from Ensembl 64.</p

Genes and categories.

<p>Genes and categories.</p