Citations

Genetic College Many genomic elements in humans are associated with behavior, including educational attainment. In a genome-wide association study including more than 100,000 samples, Rietveld et al. (p. 1467 , published online 30 May; see the Perspective by Flint and Munafò ) looked for genes related to educational attainment in Caucasians. Small genetic effects at three loci appeared to impact educational attainment.

Abstract Barrett's esophagus is the precursor lesion of esophageal adenocarcinoma, whose progression follows sequential stages. However, the low progression rate and the inadequacy and subjective interpretation of histologic grading in predicting Barrett's esophagus progression call for more objective biomarkers that can improve risk prediction. We conducted a genome-wide profiling of 754 human microRNAs (miRNA) in 35 normal epithelium, 34 Barrett's esophagus, and 36 esophageal adenocarcinoma tissues using TaqMan real-time PCR-based profiling. Unsupervised hierarchical clustering using 294 modestly to highly expressed miRNAs showed clear clustering of two groups: normal epithelium versus Barrett's esophagus/esophageal adenocarcinoma tissues. Moreover, there was an excellent clustering of Barrett's metaplasia (without dysplasia) tissues from normal epithelium tissues. However, Barrett's esophagus tissues of different stages and esophageal adenocarcinoma tissues were interspersed. There were differentially expressed miRNAs at different stages. The majority of miRNA aberrations involved upregulation of expression in Barrett's esophagus and esophageal adenocarcinoma tissues, with the most dramatic alterations occurring at the Barrett's metaplasia stage. Known oncomiRs, such as miR-21, miR-25, and miR-223, and tumor suppressor miRNAs, including miR-205, miR-203, let-7c, and miR-133a, showed progressively altered expression from Barrett's esophagus to esophageal adenocarcinoma. We also identified a number of novel miRNAs that showed progressively altered expression, including miR-301b, miR-618, and miR-23b. The significant miRNA alterations that were exclusive to esophageal adenocarcinoma but not Barrett's esophagus included miR-375 downregulation and upregulation of five members of the miR-17-92 and its homologue clusters, which may become promising biomarkers for esophageal adenocarcinoma development. Cancer Prev Res; 6(3); 196–205. ©2013 AACR.

Limited diffraction beams, such as Durnin's J 0 Bessel beam, are a class of nonspreading solutions to the isotropic/homogeneous scalar wave equation. These beams can be approximately produced with finite aperture and energy over a deep depth of field. In this paper, we report the application of a broadband J 0 Bessel beam to nondestructive evaluation (NDE) of materials. Pulse-echo images of a stainless steel block phantom were obtained with both the Jo Bessel beam and a conventional focused Gaussian beam. Results show that uniformly high resolutions were obtained with the J 0 Bessel beam over a large distance. In addition, the lateral resolution of the J 0 Bessel beam is almost independent of the speed of sound of the materials inspected. In contrast, the lateral resolution of images obtained with the conventional focused Gaussian beam changes dramatically with the distance and the focal length of the beam in water is greatly reduced by the steel block. Therefore, limited diffraction beams could be useful for nondestructive evaluation of materials of different speeds of sound. Restoration of pulse-echo images obtained with these beams could be simplified.

ABSTRACT IDX184 is a liver-targeted prodrug of 2′-methylguanosine (2′-MeG) monophosphate. This study investigated the safety, tolerability, antiviral activity, and pharmacokinetics of IDX184 as a single agent in treatment-naïve patients with genotype-1 chronic hepatitis C virus (HCV) infection. Forty-one patients with baseline HCV RNA ≥ 5 log 10 IU/ml, alanine aminotransferase (ALT) ≤ 2.5× the upper limit of normal, and compensated liver disease were dosed. Sequential cohorts of 10 patients, randomized 8:2 (active:placebo), received 25, 50, 75, and 100 mg of IDX184 once daily for 3 days, with a 14-day follow-up. There were no safety-related treatment discontinuations or serious adverse events. The adverse events and laboratory abnormalities observed for IDX184- and placebo-treated patients were similar. At the end of the 3-day treatment period, changes from baseline in HCV RNA levels (means ± standard deviations) were −0.5 ± 0.6, −0.7 ± 0.2, −0.6 ± 0.3, and −0.7 ± 0.5 log 10 for the 25-, 50-, 75-, and 100-mg doses, respectively, while viral load remained unchanged for the pooled placebo patients (−0.05 ± 0.3 log 10 ). Patients with genotype-1a and patients with genotype-1b responded similarly. Serum ALT levels decreased, especially at daily doses ≥ 75 mg. During the posttreatment period, plasma viremia and serum aminotransferase levels returned to near pretreatment levels. No resistance mutations associated with IDX184 were detected. Plasma exposure of IDX184 and its nucleoside metabolite 2′-MeG was dose related and low. Changes in plasma viral load correlated with plasma exposure of 2′-MeG. In conclusion, the results from this proof-of-concept study show that small doses of the liver-targeted prodrug IDX184 were able to deliver significant antiviral activity and support further clinical evaluation of the drug candidate.

Abstract Purpose: Lung cancer in never-smokers (LCINS) is increasingly recognized as a distinct disease from that in ever-smokers owing to substantial differences in etiology, clinical characteristics, and prognosis. Therefore, we aimed to identify prognostic markers specific for LCINS. Experimental Design: First, 11,930 single-nucleotide polymorphisms (SNP) in 904 inflammation-related genes were genotyped, and their associations with overall survival in 411 patients with LCINS at MD Anderson Cancer Center were analyzed. Next, validation of the top 27 SNPs in 311 patients with LCINS at Mayo Clinic was conducted. Results: Three SNPs (IL17RA:rs879576, BMP8A:rs698141, and STY:rs290229) were validated (P < 0.05), and two SNPs (CD74:rs1056400 and CD38:rs10805347) reached borderline significance (P = 0.08) in the Mayo Clinic population. We validated a survival-tree created in the MD Anderson population exploring gene–gene interactions in the Mayo Clinic population. This survival-tree stratified patients into subsets with significantly different risks of death: patients with the rs1056400_GG/rs698141_GA + AA genotype had significantly higher risk of death in both MD Anderson (HR:2.32, 95%CI: 1.58–3.41) and Mayo (HR:1.97, 95%CI: 1.11–3.50) populations compared with those with the rs1056400_GG/rs698141_GG or rs1056400_GA + AA genotype. We evaluated these five SNPs in 996 ever-smokers from MD Anderson and found no significant associations. Conclusions: Our study provides strong evidence that inflammation-related genetic variations can affect clinical outcomes in LCINS, which may lead to significant biologic insight into these outcomes. Clin Cancer Res; 18(21); 5983–91. ©2012 AACR.

Abstract High throughput sequencing technologies open up a new dimension in cancer genomics by enabling the characterization of cancer genomes at base-pair resolution. To date, the majority of large-scale genomics projects rely on fresh-frozen biospecimens in their studies, which are difficult to obtain and often lack long-term clinical data. Unlike fresh-frozen samples, archived formalin-fixed paraffin-embedded (FFPE) tissues are more readily accessible, and are often associated with known clinical outcomes and more complete clinical annotations. However, sequencing library preparation methods need to be further optimized with regard to applicability to FFPE samples. To test whether next-generation sequencing technologies could overcome previously reported artifacts associated with formalin fixation and report accurate sequencing results, we compared whole-genome and targeted enrichment DNA sequencing data obtained from five FFPE tumor samples for which matching frozen tissues were available. We successfully generated sequencing libraries using 1 µg of genomic DNA as input material and a modified TruSeq™ sample preparation protocol. We designed a custom enrichment pool targeting exons from 215 cancer-related genes and utilized this pool to pull-down and sequence approximately 1.3 Mb region of the genome with an average 400x coverage depth to test if deep sequencing would improve validation of tumor-specific somatic mutations. We used the Illumina sequence analysis pipeline and the Windows-based second generation DNA sequencing software NextGENe® to analyze the data and identify sequence variations that are different from the human reference genome. CNV detection was overall higher among FFPE samples compared with fresh-frozen samples, demonstrating that tissue processing impacts sequencing data quality. We obtained good concordance in variant calls between matched FFPE and fresh-frozen samples. Discordant variant calls were mainly due to low depth of coverage in the regions where variant calls were made. Improvements to DNA sequencing methods for archived samples will significantly enhance cancer research and will result in more reliable prediction of individual cancer therapies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3179. doi:1538-7445.AM2012-3179

Abstract Chromosome rearrangements that result in gene fusions have important roles in the initial steps of tumorigenesis especially in leukemias and lymphomas, but the biological and clinical impact of gene fusions in the common solid tumor has been less appreciated. We previously generated RNAseq data from 12 oropharyngeal tumors along with matched normal tissue from the same patients. We utilized and compared two bioinformatic pipelines, SnowShoes-FTD and FusionHunter to identify two novel fusion events involving of MGST3-ZMAT5 and MS4A7-DKFZp586P0123. These fusions were validated utilizing. Reverse transcriptase polymerase chain reaction (RT-PCR) and Sanger sequencing validated. In the first translocation the 5′ UTR of MGST3 was fused with exon 1 of ZMAT5, and in the second translocation the exon 2 of MS4A7 was fused with 3′ UTR of DKFZp586P0123. These precise fusions were not present in the matched normal tissue, however, they were only found in the single tumor in which they were identified. Given a growing and powerful set of high-throughput massively parallel sequencing technologies, the future for genome-wide analysis of chromosome rearrangement appears open in many directions. Ultimately, we hope that this integrative methodology will elucidate key aspects of tumor biology as well as generate novel targets for cancer diagnostics and therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3100. doi:1538-7445.AM2012-3100

Abstract Lung cancer in never-smokers is increasingly recognized as distinct from that in ever-smokers owing to substantial differences in etiology, clinical characteristics, and prognosis. Therefore, we aimed to identify prognostic markers specific for lung cancer in never-smokers in a two-stage study. First, 11,930 single-nucleotide polymorphisms (SNPs) in 904 inflammation-related genes were genotyped, and their associations with overall survival in 411 never-smokers with lung cancer at The University of Texas MD Anderson Cancer Center were analyzed. Next, fast-track validation of the top 37 SNPs in 311 never-smokers with lung cancer at Mayo Clinic was performed. Three SNPs (interleukin 17 receptor A:rs879576, bone morphogenetic protein 8A:rs698141, and spleen tyrosine kinase:rs290229) were validated (p<0.05), and two more SNPs (CD74:rs1056400 and CD38:rs10805347) were borderline significant (p=0.08) in the Mayo Clinic population. In combined analysis of the MD Anderson and Mayo Clinic patients, IL17RA:rs879576 resulted in a 40% reduction in the risk of death (p=4.1 × 10−5 [p=0.61, heterogeneity test]). We successfully validated a survival tree created in MD Anderson population based on gene-gene interactions in the Mayo Clinic population. This survival tree stratified patients into subsets with significantly different risks of death: patients at MD Anderson with the rs1056400_GG/rs698141_GA+AA genotype had a 2.32-fold higher risk of death (p=1.72 × 10−5) and 9-month shorter median survival time (MST) (p=4.5 × 10−4, log-rank test) than did those with the rs1056400_GG/rs698141_GG or rs1056400_GA+AA genotype in the discovery phase. Also, the patients at Mayo Clinic with the former genotype had an approximately twofold higher risk of death (p=0.02) and a strikingly shorter (by 26 months) MST (p=0.029, log-rank test) than did those with the latter genotype in the validation phase. We evaluated these five SNPs in 996 ever-smokers and found no significant associations. To our knowledge, this is the first study to systematically evaluate the associations of genetic variations in major inflammation-related genes with outcome of lung cancer in never-smokers. It provides strong evidence that inflammation-related genetic variations can affect clinical outcomes in these patients, which may lead to significant biological insight into these outcomes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2929. doi:1538-7445.AM2012-2929

Neural cells derived from induced pluripotent stem cells from patients with genetic forms of Parkinson’s disease provide insights into disease pathogenesis.

Abstract Chromosomal aberrations occur frequently during malignant progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC). In this study, we applied Illumina's 317K high-density SNP arrays to profile chromosomal aberrations at each of the four sequential stages of progression - Barrett's metaplasia (BM), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and EAC. We observed significant trends of increasing LOH/deletion associated with the degree of progression. The average numbers of chromosome arms with LOH/deletion per sample were 0.30, 3.21, 7.70, and 11.90 for BM, LGD, HGD, and EAC, respectively (p-for trend=4.82×10−7). The mean percentages of SNPs with LOH/deletion events were 0.1%, 1.8%, 6.6%, and 17.2% for BM, LGD, HGD, and EAC, respectively (p-for trend=2.64×10−6). In BM, there were scattered chromosome deletions at 3p14.2 (10%), 16q23.1 (5%), and 9p21 (5%), which became predominant aberrations in LGD. More importantly, the 3p14.2 (68.4%) and 16q23.1 (50%) LOH/deletion in LGD was exclusively limited to narrow regions within the FHIT (3p14.2) and WWOX (16q23.1) genes, the two most frequent common fragile sites in the human genome. In contrast, the 9p21 deletion (68.4%) occurred in larger regions (encompassing p16 gene), often involving the whole 9p arm. A significant increase in LOH/deletion of other chromosomes was seen in HGD and there was widespread LOH/deletion across the whole genome in EAC. 17p (47.6%) LOH was the most frequent event in EAC, which mostly spanned the entire 17p arm with only one focal site of LOH at 17p13.1. There were many recurrent small regions of LOH/deletion that disrupted a single gene, most of which are common fragile sites in the human genome. RUNX1 is a potential tumor suppressor gene in EAC. Amplifications were rarer than LOH/deletions. The average numbers of chromosome arms with amplification per sample were 0.30, 0.42, 1.90, and 8.50 for BM, LGD, HGD, and EAC, respectively (p-for trend=1.35×10−9). The mean percentages of SNPs with amplification were 0.5%, 0.4%, 1.5%, and 8.0% for BM, LGD, HGD, and EAC, respectively (p-for trend=1.26×10−8). The most frequent chromosome amplifications in EAC were 8q24.21 (36.6%, MYC), 8p23.1 (31.7%, CTSB), 7q21 (30.8%, CDK6), 20q13.2 (28.6%, ZNF217), and 7p11.2 (25.6%, EGFR). We then analyzed the associations of chromosomal aberrations with clinical features and pathological response in EAC patients treated with neoadjuvant chemoradiation. The number and size of LOH/deletion were significantly associated with pathological response. Non-responders had a greater number (16.4 vs. 8.5, p=0.060) and larger size (662.2 Mb vs. 290.7 Mb, p=0.034) of LOH/deletions, and higher percentage of aberrant SNPs (25.2% vs. 11.2%, p=0.030) than responders. This study provides a genome-wide catalogue of chromosome aberrations occurring during the malignant progression from BE to EAC with the highest resolution to date. Our data support genetic instability and p16 loss as drivers of early neoplastic progression from metaplasia to dysplasia, and p53 aberrations as late events critical for progression to adenocarcinoma. Chromosomal aberrations can predict malignant progression and treatment response in EAC, which may have important clinical implications for cancer prevention and personalized treatment of EAC. Citation Information: Cancer Prev Res 2010;3(1 Suppl):A14.