Citations

Abstract Several platforms for genome sequencing and methods for exon enrichment are now available and continue to evolve quickly. In this study, we compared the performance of whole exome sequencing using two instruments, Illumina's GAIIx and HiSeq 2000, comparing single versus duplicate runs. Eight runs of eight samples each were performed with genomic DNA derived from whole blood and sample libraries prepared with the Agilent SureSelect capture array. One run was conducted in duplicate on the GAIIx, and, for some analyses, the combined data were used. We used TREAT (Targeted RE-sequencing and Annotation Tool), developed in-house for data analysis, including sequence alignment (MAQ, BWA), local re-alignment (GATK), variant calling (utilizing MAQ), annotation (SIFT and Seattle Seq), and visualization. Overall, duplicate runs on the GAIIx platform (compared to a single run) increased the number of total reads by approximately two-fold: from ∼66 M to ∼130 M. For both single and duplicate runs, ∼90% of reads mapped to the reference sequence, and ∼55% of reads mapped on-target. Of importance, the percent coverage of the target region increased substantially with duplicate runs; ∼72% of the target region was covered at 40-fold or more when run in duplicate compared to only ∼52% when run once. At 30x, 20x, and 10x, there was a 1.3- (62% v. 78%), 1.2- (72% v. 84%), and 1.1-fold (84% v. 91%) increase respectively, in the percent coverage of the target region for samples run twice. A similar number of filtered, on-target SNPs per sample (∼24 K) was found for both single and duplicate run analyses. However, a 1.3-fold increase in the number of on-target indels was seen in the duplicate run (∼1,200) compared to the single run (∼900). When the combined data for samples run twice on a GAIIx were compared to the samples run using a HiSeq, the total number of reads were similar (∼130 M), although several of the samples had substantially more reads on the HiSeq platform. Samples run on a HiSeq had an increase in the percent coverage of the target region at 40x (72% v. 81%), 30x (78% v. 86%), 20x (84% v. 91%) and 10x (91% v. 95%) compared to the two-run approach on a GAIIx. A similar number of filtered on-target SNPs (∼24 K/sample) and indels (∼1200) was found with the HiSeq compared to two runs on a GAIIx. In summary, our results demonstrate increases in the total number of reads and in overall coverage with the HiSeq 2000 instrument. The total number of SNPs and indel that mapped on target for the version 1 Agilent SureSelect capture array is ∼25 K and 1,200 per sample, respectively. As capture is of variable efficiency for individual runs, higher average coverage of the target region is necessary for sufficient coverage of poorly captured regions. Additional analyses comparing Agilent SureSelect versions 1 and 2 arrays are underway. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2742. doi:10.1158/1538-7445.AM2011-2742

Abstract Background. The hepatocyte growth factor (HGF) signaling pathway regulates key cellular functions related to tumor invasion and metastasis including cell motility, cell proliferation, and morphogenesis. We previously found that minor alleles at a single-nucleotide polymorphism (SNP; rs5745709) in the gene encoding the cytokine HGF was associated with poorer overall survival in women with invasive epithelial ovarian cancer (EOC) enrolled at Mayo Clinic (MAY) and The Cancer Genome Atlas (TCGA) (HR 1.6, 95% CI 1.3-1.9, p=8.9×10−5). In addition, we found that that genotype correlated with HGF expression in ovarian cancer tissue from TCGA women, suggesting that genetically-regulated expression of HGF may play a role in post-diagnosis survival. To further examine this possibility, we evaluated intensity of antibody immunostaining for HGF, MET (HGF's transmembrane tyrosine kinase receptor), and phospho-MET (pMET; MET's activated form) in tumor cells using tissue microarrays (TMAs) created from genotyped primary peritoneal and EOC cases, and correlated these expression levels with overall survival and HGF SNP genotypes. Methods. Participants were 326 white non-Hispanic women over 20 years of age with histologically-confirmed invasive EOC diagnosed between 1998 and 2009. All cases were enrolled at MAY within one year of diagnosis. Five μm sections of TMAs including three 0.6 mm cores per case were immunostained with HGF, MET, and pMET primary antibodies. Staining levels were classified according to combinations of staining extent and intensity as negative (< 10% cells stained), weak, moderate, or strong. The maximal expression value recorded over the multiple cores for each case was used. Cox proportional hazards regression was used to examine associations of overall survival with HGF, MET and pMET expression levels, adjusted for relevant clinical variables. Associations between expression levels and HGF SNP rs5745709 genotypes were examined using linear regression models. Results. HGF and MET expression were not associated with overall survival in our series of EOC cases (p=0.48 and 0.90, respectively). pMET expression was associated with survival, but in the opposite direction of that hypothesized (HR 0.77, 95% CI 0.39-1.52 for moderate expression; HR 0.55, 95% CI 0.27-1.10 for strong expression; each referent to negative/weak, p=0.01). Expression levels were not significantly associated with HGF rs5745709 genotypes (p=0.80 for HGF expression, p=0.89 for MET, p=0.41 for pMET). Conclusion. HGF expression levels were not associated with overall survival or with HGF SNP genotypes that correlated with survival in a previous study. Functional studies such as this one are crucial as a follow-up to discovery-based studies in order to assess biologic plausibility of observed results. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 893. doi:10.1158/1538-7445.AM2011-893

AbstractThe biological role of vitamin D receptors (VDR), which are abundantly expressed in developing zebrafish (Danio rerio) as early as 48 h after fertilization, and before the development of a mineralized skeleton and mature intestine and kidney, is unknown. We probed the role of VDR in developing zebrafish biology by examining changes in expression of RNA by whole transcriptome shotgun sequencing (RNA-seq) in fish treated with picomolar concentrations of the VDR ligand and hormonal form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3)].We observed significant changes in RNAs of transcription factors, leptin, peptide hormones, and RNAs encoding proteins of fatty acid, amino acid, xenobiotic metabolism, receptor-activator of NFκB ligand (RANKL), and calcitonin-like ligand receptor pathways. Early highly restricted, and subsequent massive changes in more than 10% of expressed cellular RNA were observed. At days post fertilization (dpf) 2 [24 h 1α,25(OH)2D3-treatment], only four RNAs were differentially expressed (hormone vs. vehicle). On dpf 4 (72 h treatment), 77 RNAs; on dpf 6 (120 h treatment) 1039 RNAs; and on dpf 7 (144 h treatment), 2407 RNAs were differentially expressed in response to 1α,25(OH)2D3. Fewer RNAs (n = 481) were altered in dpf 7 larvae treated for 24 h with 1α,25(OH)2D3vs. those treated with hormone for 144 h. At dpf 7, in 1α,25(OH)2D3-treated larvae, pharyngeal cartilage was larger and mineralization was greater. Changes in expression of RNAs for transcription factors, peptide hormones, and RNAs encoding proteins integral to fatty acid, amino acid, leptin, calcitonin-like ligand receptor, RANKL, and xenobiotic metabolism pathways, demonstrate heretofore unrecognized mechanisms by which 1α,25(OH)2D3 functions in vivo in developing eukaryotes.

Abstract — — Chronically infusing a subpressor dose of angiotensin (Ang) II increases blood pressure via poorly defined mechanisms. We found that this hypertensive response is accompanied by increased oxidant stress and is prevented by blocking endothelin (ET) receptors. Thus, we now tested whether blocking oxidant stress decreases both blood pressure and ET levels. We infused Sprague-Dawley rats (via osmotic pumps) with either vehicle (group 1) or Ang II (5 ng · kg −1 · min −1 ; groups 2 to 4) for 15 days. Groups 3 and 4 also received either tempol in the drinking water (1 mmol/L) or vitamin E (5000 IU/kg diet), respectively, for 15 days. We measured systolic blood pressure (SBP) and urinary nitrite excretion every 3 days, and on day 15 we measured systemic and renal venous plasma levels of ET, isoprostanes, and thiobarbituric acid reactive substances (TBARS). SBP in Group 1 did not change throughout the study, whereas Ang II increased SBP (from 132±5 to 151±7 mm Hg). In addition, Ang II increased the systemic and renal venous levels of isoprostanes, TBARS, and ET and caused a transient decrease in urinary nitrites (that returned to control levels by day 9). Both tempol and vitamin E prevented Ang II-induced hypertension and either prevented or tended to blunt the increase in systemic and renal isoprostanes, TBARS, and ET. Finally, both antioxidants abolished the transient decrease in urinary nitrites. These results together with our previous study suggest that subpressor-dose Ang II increases oxidant stress (and isoprostanes). This in turn increases ET levels, which participate in the hypertensive response to Ang II.

We tested the hypothesis that angiotensin II (Ang II)–induced stimulations of endothelin (ET) and isoprostanes are implicated in the slow pressor responses to Ang II. We infused either vehicle (group 1) or Ang II (groups 2 to 4) intravenously at 5 ng/kg per minute via osmotic pumps for 15 days into Sprague-Dawley rats. Groups 3 and 4 received 30 mg/kg per day of either losartan (Ang II type 1 receptor blocker) or bosentan (ETAand ETBreceptor blocker) in their drinking water. We measured systolic blood pressure (SBP) every 3 days during the infusion. Plasma levels of Ang II, ET, isoprostanes, and urinary nitrites were determined at 15 days. Vehicle infusion did not change SBP (from 138±13 to 136±2 mm Hg at day 15). Circulating Ang II, ET, and isoprostane levels were 35±9, 39±3, and 111±10 pg/mL, respectively, whereas urinary nitrites were 2.3±0.4 μg/d. Ang II increased SBP (from 133±10 to 158±8 mm Hg), plasma Ang II (179±77 pg/mL), and isoprostanes (156±19 pg/mL) without altering ET levels (38±5 pg/mL) or urinary nitrites (1.8±0.5 μg/d). Losartan prevented Ang II–induced increases in SBP and isoprostanes (SBP went from 137±5 to 120±4 mm Hg; isoprostanes were 115±15 pg/mL) while increasing urinary nitrite levels (5.2±1.1 μg/d). Losartan did not alter Ang II (141±57 pg/mL) or ET (40±4 pg/mL) levels. Bosentan also blocked Ang II–induced hypertension (from 135±4 to 139±3 mm Hg) but did not decrease isoprostanes (146±14 pg/mL). Ang II (63±11 pg/mL), ET levels (46±2 pg/mL), and urinary nitrites (2.8±0.4 μg/d) were not altered. In conclusion, our results suggest that low-dose Ang II increases isoprostanes via its Ang II type 1 receptor and causes an ET-dependent hypertension, without altering circulating ET levels.