Comparative analysis of genetic diversity among species of Chrysanthemum and its related genera using inter-simple sequence repeat and sequence-related amplified polymorphism markers

In this study, inter-simple sequence repeats (ISSRs) and sequence-related amplified polymorphism (SRAP) were applied to assess the genetic diversity in 38 species of Chrysanthemum and related genera. A total of 204 and 567 bands were amplified by 24 ISSR and 25 SRAP primers, of which 196 (97%) and 557 (99%) were polymorphic, respectively. The ISSR-based genetic similarity ranged from 0.016 to 0.886 and averaged 0.201, while the SRAP-based genetic similarity varied from 0.010 to 0.811 and averaged 0.122. Both the ISSR and SRAP techniques revealed similar clustering patterns and grouped species of Chrysanthemum and Ajania together. The results of principal coordinate analysis corroborated the unweighted pair group method with arithmetic average clustering. Additionally, results from ISSR and SRAP data were significantly correlated (r = 0.89, P < 0.001). Knowledge about genetic diversity among species can aid the transfer of traits of interest from the wild into cultivated chrysanthemum in future distant interspecific breeding.

Genetic diversity and expression profiles of cysteine phytases in the sheep rumen during a feeding cycle

Cysteine phytase is the main phytate-degrading enzyme of ruminant animals. To explore the genetic diversity and dynamic expression profile of cysteine phytase in sheep rumen during a feeding cycle, four transcript (0, 4, 9 and 16 h after feeding) and one DNA (9 h after feeding) clone libraries were constructed, respectively. A total of 46 distinct gene fragments were identified, and most of these sequences had low identities (<60%) with known phytases. Great divergence was found in the constitution and abundance of genes at the genome and transcriptional levels, and the transcript data are more reliable to reflect the information of functional genes. Phylogenetic analysis indicated that the genes from uncultured bacteria instead of Firmicutes played the major phytate-degrading role. Further comparative analysis revealed the dynamic constitution of cysteine phytase genes in rumen at different time points.

SIGNIFICANCE AND IMPACT OF THE STUDY

Ruminal phytases, that are cysteine phytases, are novel in sequences and functions. Great divergence in the constitution and abundance of cysteine phytase genes at the genome and transcriptional levels suggested that transcript data are more reliable to reflect the information of functional genes. Phylogenetic and rarefaction analyses indicated that the cysteine phytase genes from uncultured bacteria instead of Firmicutes play the major phytate-degrading role in rumen, and their constitution is dynamic at different time points. This study provides a new insight into ruminal cysteine phytase genes and undermines their expression profiles over a whole feeding cycle.

Abstract 4276: T200: a high depth targeted exome sequencing platform to identify actionable alterations in FFPE solid tumor samples

Background: We developed and established a high depth targeted sequencing platform of 202 genes (all exons) to identify actionable DNA alterations in tumor samples. We aimed a minimum of 500x depth and defined actionable if the aberration had a direct link to an available clinical treatment or clinical trial. Our platform was optimized for FFPE specimens and low input DNA while the data analysis pipeline was designed to detect low frequency mutations and copy number alterations. Over 500 tumor samples and matched normal were analyzed using this platform.

Methods: Libraries were made from a minimum of 170 ng of FFPE DNA (tumors) or blood DNA (matched normal). Capture of 202 genes (over 5,000 exons) was performed using Nimblegen probes to a minimum of 50x fold enrichment. Captured libraries were sequenced using Illumina HiSeq2000. Duplicate reads were removed from the raw data and the reads were mapped hg19 reference genome. We used VarScan2 for calling somatic, germline and loss of heterozygosity SNVs and short indels. Copy number variation was also reported when significant gain/loss on an exon was detected. Additionally, we used other tolls to annotate the functional consequence of the SNVs, such as CanDrA to predict if an SNV is driver or passenger event.

Results: We sequenced over 500 tumor samples and their normal match (blood). The mean coverage for most of samples was over 1500x, which allowed us to detect low frequency mutations (5% or higher) with accuracy. The most common disease sites analyzed where we found genetic alterations were: breast, colon, brain, ovary, endometrial, skin, lung, prostate, head and neck, sarcoma, kidney and stomach. About 98% of all tumors analyzed had at least one somatic alteration (SNVs or copy number) and although the vast majority of the samples analyzed were derived from FFPE blocks, the number of samples that failed was less than 5%. Among the most common genes mutated are several “actionable genes” such as BRAF, EGFR and KRAS. The samples tested in this platform were also tested on ion torrent Ampliseq 46 gene panel (46 overlapping genes) in a CLIA certified laboratory at MD Anderson Cancer Center with a very high level of concordance.

Conclusion: With a very low level of failure and high depth provided, our results indicate that this platform can be used for FFPE tumor samples with high level of accuracy and sensitivity, showing that this platform is reliable to be implemented in clinical settings.

Citation Format: Karina Eterovic, Ken Chen, Hao Zhao, Funda Meric-Bernstam, Raja Luthra, Aldape Kenneth, Mark Routbort, Scott Kopetz, Michael Davies, John de Groot, Stacy Moulder, Yong Mao, Chacha Horombe, Lin-ya Tang, Song Ping, Zhang Qingxiu, Ezzeddine Nader, Lan Zhang, Kenna M. Shaw, John Mendelsohn, Gordon B. Mills. T200: a high depth targeted exome sequencing platform to identify actionable alterations in FFPE solid tumor samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4276. doi:10.1158/1538-7445.AM2014-4276

Abstract 1186: Patient-derived breast cancer xenografts demonstrate molecular evolution in the phosphatidylinositol 3-kinase pathway upon engraftment

Introduction: Patients with breast cancer who do not respond to standard systemic therapy have a poor prognosis. There is a pressing need to develop in vivo models of breast cancer to test novel therapeutics. Directly implanting tumors into immunodeficient mice may more accurately recapitulate human tumor characteristics compared to cell line xenografts. We tested the feasibility of generating breast cancer xenografts (BCXs) and the effect of serial passage on tumor characteristics.

Methods: Tumors from 48 patients with breast cancer were implanted. Patient tumors and BCXs were characterized with short tandem repeat DNA fingerprinting, and a series of BCXs were characterized with next generation sequencing, molecular inversion probe arrays and reverse phase protein arrays. Results: BCXs were established in 15 (31%) of 48 patients and 13 have been serially passaged. BCX engraftment was higher in patients with triple negative compared to ER or PR+ breast cancer (11 of 18, 61% vs. 4 of 30, 13%, p=0.001), and in patients who received neoadjuvant chemotherapy (13 of 25, 52% vs. 2 of 23, 9%, p=0.002). 7 patients developed metastases after surgery; in 5, BCXs developed before distant relapse. Compared to patient tumors, BCXs demonstrated genomic instability. Although mutation status, copy numbers and proteomic profiles were often maintained, an activating PIK3CA mutation was acquired in one BCX lineage and loss of PTEN in another. Proteomics demonstrated activation in PI3K/mTOR signaling in BCXs compared with patient tumors. Notably, 2 of 48 models demonstrated a transformation to induce mouse tumors.

Conclusions: BCXs can be established prior to relapse from breast cancer, especially in patients with poor response to neoadjuvant chemotherapy. Although molecular profiles of BCX are mostly similar to the patient tumor that was implanted, differences such as aberrations in PI3K signaling can occur. Future studies will determine whether molecular evolution in BCXs reflect that seen upon progression/relapse and the potential of in vivo models for individualization of treatment.

Citation Format: Priscilla F. McAuliffe, Argun Akcakanat, Kurt Evans, Agda Karina Eterovic, Hao Zhao, Ken Chen, Takafumi Sangai, Huiqin Chen, Kim-Anh Do, Ashley M. Holder, Chandeshwar Sharma, William Fraser Symmans, Mihai Gagea, Katherine A. Naff, Aysegul Sahin, Asha S. Multani, Gordon B. Mills, Ana Maria Gonzalez-Angulo, Funda Meric-Bernstam. Patient-derived breast cancer xenografts demonstrate molecular evolution in the phosphatidylinositol 3-kinase pathway upon engraftment. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1186. doi:10.1158/1538-7445.AM2014-1186

Abstract 4275: Identifying cancer driver mutations in clinical sequencing data

Background

Cancer therapy is challenged by diverse molecular implementations of oncogenic processes and by variations in therapeutic responses. So far, whole genome sequencing (WGS) and whole exome sequencing (WES) has been implemented in both research and clinical settings to identify oncogenic events in cancer genomes. However, a large number of passenger mutations have been identified and true driver mutations have been disguised. Distinguishing “driver” events from “passenger” events will be a key challenge for the realization of targeted therapy. To elucidate driver mutations that are clinically actionable, the Institute for Personalized Cancer Therapy at MD Anderson cancer center has developed a NGS clinical sequencing platform, T200, to sequence 202 cancer-related genes at high depth in thousands of cancer patients at MD Anderson.

Materials and Methods

The T200 mutation data, including single nucleotide variants (SNV, variant allele frequency &gt;=1%) and copy number variations (CNV), of more than 500 cancer patients treated in MD Anderson Cancer Center were utilized in our study.

Results

1. By analyzing the SNV data, we identified several sets of co-occurring genes across all cancers. Some sets such as KRAS/APC/SMAD4 contain driver genes from multiple signaling pathways, which may indicate essential mechanisms for tumor development and nominate targets for combinational therapy.

2. We elucidated mutual-exclusive mutations that were from genes in the same or different pathways. Several sets of well-known mutual-exclusive SNVs were verified in our analysis such as BRAF/NRAS SNVs in melanoma. We also illustrated novel sets of mutual-exclusive mutational events, such as IDH1/PTEN/PPP1R3A SNVs in brain tumors and EGFR/FGFR3/GNAS/NOTCH4 CNVs in all cancers.

3. SNVs of more than 10 genes were enriched in specific cancer types, such as IDH1 and NF1 in brain tumor, BRAF and MITF in melanoma. CNVs of more than 50 genes were found enriched in one cancer type, such as PDGFRA amplifications in brain tumors and IL6R amplifications in breast cancer. We observed not only expected cancer specific mutations such as BRAF SNVs but also novel mutations such as NF1 SNVs and PDGFRA amplifications.

4. We performed mutual-exclusivity and cancer type enrichment analysis on SNV hotspots. More than 20 SNV hotspots were elucidated, such as BRAF(V600E) in melanoma, IDH1(R132H) in brain tumors, KRAS(G12D) in colorectal cancer, and PIK3CA(H1047L) in breast cancer. In addition, multiple SNV hotspots were found to occur mutual-exclusively, such as BRAF(V600E)/IDH1(R132H)/MPL(L532V) in brain tumors.

Conclusion

Deep target sequencing enables us to systematically determine the potential driver mutation events (including low allele frequency SNVs), which not only help us characterize the landscape of cancer genomic alterations, but also provide comprehensive patient molecular profile to facilitate clinical decision-making and novel clinical trial design.

Citation Format: Tenghui Chen, Hao Zhao, Yong Mao, Yuan Qi, Agda Karina Eterovic, Kenna R. Mills Shaw, Stacy L. Moulder, Michael A. Davies, John F. Degroot, Scott E. Kopetz, Funda Meric-Bernstam, Gordon B. Mills, Ken Chen. Identifying cancer driver mutations in clinical sequencing data. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4275. doi:10.1158/1538-7445.AM2014-4275

Screening genes crucial for pediatric pilocytic astrocytoma using weighted gene coexpression network analysis combined with methylation data analysis

To identify novel genes associated with pediatric pilocytic astrocytoma (PA) for better understanding the molecular mechanism underlying the pediatric PA pathogenesis. Gene expression profile data of GSE50161 and GSE44971 and the methylation data of GSE44684 were downloaded from Gene Expression Omnibus. The differentially expressed genes (DEGs) between PA and normal control samples were screened using the limma package in R, and then used to construct weighted gene coexpression network (WGCN) using the WGCN analysis (WGCNA) package in R. Significant modules of DEGs were selected using the clustering analysis. Function enrichment analysis of the DEGs in significant modules were performed using the WGCNA package and clusterprofiler package in R. Correlation between methylation sites of DEGs and PA was analyzed using the CpGassoc package in R. Totally, 3479 DEGs were screened in PA samples. Thereinto, 3424 DEGs were used to construct the WGCN. Several significant modules of DEGs were selected based on the WGCN, in which the turquoise module was positively related to PA, whereas blue module was negatively related to PA. DEGs (for example, DOCK2 (dedicator of cytokinesis 2), DOCK8 and FCGR2A (Fc fragment of IgG, low affinity IIa)) in blue module were mainly involved in Fc gamma R-mediated phagocytosis pathway and natural killer cell-mediated cytotoxicity pathway. Methylations of 14 DEGs among the top 30 genes in blue module were related to PA. Our data suggest that DOCK2, DOCK8 and FCGR2A may represent potential therapeutic targets in PA that merits further investigation.

Sleep duration and cancer risk: a systematic review and meta-analysis of prospective studies

To assess the risk of cancers associated with sleep duration using a meta-analysis of published cohort studies, we performed a comprehensive search using PubMed, Embase and Web of Science through October 2013. We combined hazard ratios (HRs) from individual studies using meta-analysis approaches. A random effect dose-response analysis was used to evaluate the relationship between sleep duration and cancer risk. Subgroup analyses and sensitivity analyses were also performed. Publication bias was evaluated using Funnel plots and Begg's test. A total of 13 cohorts from 12 studies were included in this meta-analysis, which included 723,337 participants with 15,156 reported cancer outcomes during a follow-up period ranging from 7.5 to 22 years. The pooled adjusted HRs were 1.06 (95% CI: 0.92, 1.23; P for heterogeneity=0.003) for short sleep duration, 0.91 (95% CI: 0.78, 1.07; P for heterogeneity <0.0001) for long sleep duration. In subgroup analyses stratified by cancer type, long duration of sleep showed an inverse relation with hormone-related cancer (HR=0.79; 95% CI: 0.65, 0.97; P for heterogeneity=0.009) and a greater risk of colorectal cancer (HR=1.29; 95% CI: 1.09, 1.52; P for heterogeneity=0.346). Further meta-analysis on dose-response relationships showed that the relative risks of cancer were 1.00 (95% CI: 0.99, 1.01; P for linear trend=0.9151) for one hour of sleep increment per day, and 1.00 (95% CI: 0.98, 1.01; P for linear trend=0.7749) for one hour of sleep increment per night. No significant dose-response relationship between sleep duration and cancer was found on non-linearity testing (P=0.5053). Our meta-analysis suggests a positive association between long sleep duration and colorectal cancer, and an inverse association with incidence of hormone related cancers like those in the breast. Studies with larger sample size, longer follow-up times, more cancer types and detailed measure of sleep duration are warranted to confirm these results.

Prevalence and characterization of Salmonella enterica in dried milk-related infant foods in Shaanxi, China

The aim of this study was to investigate the existence and characteristics of Salmonella enterica in dried milk-related infant foods. Twenty-four (3.4%) of 705 samples, including 5 (2.0%) of 246 powdered infant formula, 18 (4.0%) of 445 infant rice cereal, and 1 (7.1%) of 14 other infant foods, were positive for Salmonella. Fifteen serotypes were identified in 40 Salmonella isolates; Salmonella Duesseldorf (15.0%) and Salmonella Indiana (15.0%) were more frequently detected than other serotypes. Resistance to chloramphenicol (82.5%) was most common, followed by tetracycline (57.5%), ceftiofur (52.5%), kanamycin (52.5%), streptomycin (50.0%), gentamycin (45.0%), nalidixic acid (35.0%), ceftriaxone (32.5%), ciprofloxacin (25.0%), amikacin (20.0%), and cefoxitin (15.0%). Twenty-eight (70.0%) isolates were resistant to ≥ 8 antimicrobials, with 5 (12.5%) being resistant to 14 antimicrobials. Amino acid substitutions in gyrase A (GyrA) were most frequently detected as Ser83Arg/Asp87Glu and in p53-associated Parkin-like cytoplasmic protein (ParC), they were all Ser80Arg; the quinolone resistance gene qnrS (47.5%) was commonly detected as well as aminoglycoside acetyltransferase [aac(6')-Ib; 25.0%], qnrA (17.5%), and qnrB (15.0%) genes. Thirty distinct pulsed-field gel electrophoresis patterns were identified among 40 isolates; no identical pulsed-field gel electrophoresis pattern was detected among Salmonella isolates with the same serovar that was recovered in 2010 and 2012. Our results suggest that dried milk-related infant foods could be contaminated with Salmonella and highlight that the dangers to infant health should not be neglected.

WSNs data acquisition by combining hierarchical routing method and compressive sensing

We address the problem of data acquisition in large distributed wireless sensor networks (WSNs). We propose a method for data acquisition using the hierarchical routing method and compressive sensing for WSNs. Only a few samples are needed to recover the original signal with high probability since sparse representation technology is exploited to capture the similarities and differences of the original signal. To collect samples effectively in WSNs, a framework for the use of the hierarchical routing method and compressive sensing is proposed, using a randomized rotation of cluster-heads to evenly distribute the energy load among the sensors in the network. Furthermore, L1-minimization and Bayesian compressed sensing are used to approximate the recovery of the original signal from the smaller number of samples with a lower signal reconstruction error. We also give an extensive validation regarding coherence, compression rate, and lifetime, based on an analysis of the theory and experiments in the environment with real world signals. The results show that our solution is effective in a large distributed network, especially for energy constrained WSNs.

Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer

Men with metastatic prostate cancer who are treated with androgen deprivation therapies (ADT) usually relapse within 2 to 3 years with disease that is termed castration-resistant prostate cancer (CRPC). To identify the mechanism that drives these advanced tumors, paired-end RNA-sequencing (RNA-seq) was performed on a panel of CRPC bone marrow biopsy specimens. From this genome-wide approach, mutations were found in a series of genes with prostate cancer relevance, including AR, NCOR1, KDM3A, KDM4A, CHD1, SETD5, SETD7, INPP4B, RASGRP3, RASA1, TP53BP1, and CDH1, and a novel SND1:BRAF gene fusion. Among the most highly expressed transcripts were 10 noncoding RNAs (ncRNAs), including MALAT1 and PABPC1, which are involved in RNA processing. Notably, a high percentage of sequence reads mapped to introns, which were determined to be the result of incomplete splicing at canonical splice junctions. Using quantitative PCR (qPCR), a series of genes (AR, KLK2, KLK3, STEAP2, CPSF6, and CDK19) were confirmed to have a greater proportion of unspliced RNA in CRPC specimens than in normal prostate epithelium, untreated primary prostate cancer, and cultured prostate cancer cells. This inefficient coupling of transcription and mRNA splicing suggests an overall increase in transcription or defect in splicing.

IMPLICATIONS

Inefficient splicing in advanced prostate cancer provides a selective advantage through effects on microRNA networks but may render tumors vulnerable to agents that suppress rate-limiting steps in splicing.

Application of passive sampling in assessing the occurrence and risk of antibiotics and endocrine disrupting chemicals in the Yangtze Estuary, China

Polar organic chemical integrative sampler (POCIS) was used in assessing the occurrence and risk of 12 widely used antibiotics and 5 most potent endocrine disrupting chemicals (EDCs) in the Yangtze Estuary, China. During laboratory validation, the kinetics of pollutant uptake by POCIS were linear, and the sampling rates of most compounds were raised by flow rate and salinity, reaching the highest values at salinity 14‰. The sampling rates varied with the target compounds with the EDCs showing the highest values (overall average=0.123Ld(-1)), followed by chloramphenicols (0.100Ld(-1)), macrolides (0.089Ld(-1)), and finally sulfonamides (0.056Ld(-1)). Validation in the Yangtze Estuary in 2013 showed that the field sampling rates were significantly greater for all compounds except bisphenol A, in comparison to laboratory results, and high-frequency spot sampling is critical for fully validating the passive sampler. The field studies show that antibiotics were widely detected in the Yangtze Estuary, with concentrations varying from below quantification to 1613ngL(-1), suggesting their widespread use and persistence in estuarine waters. The dominating pollutants in July were sulfonamides with a total concentration of 258ngL(-1) and in October were macrolides with a total concentration of 350ngL(-1). The calculation of risk quotient suggested that sulfapyridine, sulfaquinoxaline and erythromycin-H2O may have caused medium damage to sensitive organisms such as fish.

Subharmonic aided pressure estimation for monitoring interstitial fluid pressure in tumours--in vitro and in vivo proof of concept

The feasibility of using subharmonic aided pressure estimation (SHAPE) to noninvasively estimate interstitial fluid pressure (IFP) was studied. In vitro, radiofrequency signals, from 0.2 ml/l of Definity (Lantheus Medical Imaging, N Billerica, MA) were acquired within a water-tank with a Sonix RP ultrasound scanner (Analogic Ultrasound, Richmond, BC, Canada; fT/R=6.7/3.35 MHz and fT/R=10/5 MHz) and the subharmonic amplitudes of the signals were compared over 0-50 mmHg. In vivo, five swine with naturally occurring melanomas were studied. Subharmonic signals were acquired from tumours and surrounding tissue during infusion of Definity and compared to needle-based pressure measurements. Both in vitro and in vivo, an inverse linear relationship between hydrostatic pressure and subharmonic amplitude was observed with r(2)=0.63-0.95; p<0.05, maximum amplitude drop 11.36 dB at 10 MHz and -8 dB, and r(2) as high as 0.97; p<0.02 (10 MHz and -4/-8 dB most promising), respectively, indicating that SHAPE may be useful in monitoring IFP.

Activation of glucagon-like peptide-1 receptor inhibits tumourigenicity and metastasis of human pancreatic cancer cells via PI3K/Akt pathway

AIMS

It has been reported that glucagon-like peptide-1 (GLP-1) agents are associated with an increased risk of pancreatic cancer in patients with type 2 diabetes. Reports have indicated that GLP-1 promotes pancreatic metaplasia and premalignant lesions. The aims of this study were to determine the effects of GLP-1-based therapy on pancreatic cancer cells.

METHODS

Immunohistochemistry was used to investigate GLP-1 receptor (GLP-1R) expression in 30 human pancreatic cancer tissues. We also analysed associated clinicopathological data and each patient's prognosis. Two human pancreatic cancer cell lines were used to evaluate the in vitro effects of the GLP-1R agonist liraglutide on cell growth, migration and invasion. Mouse xenograft models of human pancreatic cancer were established to evaluate the effects of liraglutide in vivo.

RESULTS

Human pancreatic cancer tissues showed lower levels or a lack of GLP-1R expression when compared with levels in the tumour-adjacent pancreatic tissues. Negative GLP-1R expression occurred more frequently in advanced tumours with larger diameters and lymphatic metastasis, and was associated with a poor prognosis. GLP-1R activation with liraglutide inhibited tumourigenicity and metastasis of human pancreatic cancer cells in vitro and in vivo. Akt activation was dose-dependently inhibited by liraglutide, and the PI3K inhibitors, LY294002 and wortmannin, displayed similar suppressive effects to liraglutide in human pancreatic cancer cells.

CONCLUSIONS

GLP-1R activation has an antitumour effect on human pancreatic cancers via inhibition of the PI3K/Akt pathway. This finding suggests that GLP-1-based therapies may be beneficial, rather than harmful, in treating type 2 diabetic patients with pancreatic cancer.