An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus

RNA variants that emerge from editing and alternative splicing form important regulatory stages in protein signalling. In this report, we apply an integrated DNA and RNA variant detection workbench to define the range of RNA variants that deviate from the reference genome in a human melanoma cell model. The RNA variants can be grouped into (i) classic ADAR-like or APOBEC-like RNA editing events and (ii) multiple-nucleotide variants (MNVs) including three and six base pair in-frame non-canonical unmapped exons. We focus on validating representative genes of these classes. First, clustered non-synonymous RNA edits (A-I) in the CDK13 gene were validated by Sanger sequencing to confirm the integrity of the RNA variant detection workbench. Second, a highly conserved RNA variant in the MAP4K5 gene was detected that results most likely from the splicing of a non-canonical three-base exon. The two RNA variants produced from the MAP4K5 locus deviate from the genomic reference sequence and produce V569E or V569del isoform variants. Low doses of splicing inhibitors demonstrated that the MAP4K5-V569E variant emerges from an SF3B1-dependent splicing event. Mass spectrometry of the recombinant SBP-tagged MAP4K5^V569E and MAP4K5^V569del proteins pull-downs in transfected cell systems was used to identify the protein-protein interactions of these two MAP4K5 isoforms and propose possible functions. Together these data highlight the utility of this integrated DNA and RNA variant detection platform to detect RNA variants in cancer cells and support future analysis of RNA variant detection in cancer tissue.

Abstract 2227: An automatic pipeline to find and annotate rare subclonal somatic variants in a paired tumor/normal sample

Identifying and characterizing somatic variants in deep genome sequence data from tumor samples remains challenging and time-consuming. Of special interest in cancer research and diagnostics is the detection and annotation of rare subclonal somatic variants found only in a small proportion of primary tumor cells. Such variants can drive tumor spread and recurrence, but are often neglected in choosing treatments.

Currently, few tools reliably distinguish such rare subclonal variants from sequencing errors. And even among real somatic variants, drivers (of tumor growth, spread, or resistance) are hard to distinguish from passengers. Doing so entails integrating diverse information on variants, genes, pathways, cancer-relevant phenotypes, and treatments (including insights on population allele frequencies and broader evolutionary conservation; known/likely effects on gene product structure, function, expression, and interaction; and relations among gene products, phenotypes, and drugs). Software for effectively integrating such data in light of genomic variation in samples, to highlight relevant findings through clear visualization, has been a pressing need.

Here we present an end-to-end analysis workflow for finding and functionally characterizing rare subclonal variants, using the newly developed CLC Cancer Research Workbench to feed the interpretive platform of Ingenuity Variant Analysis, to identify cancer driver mutations in paired tumor/normal samples. We will show new interesting results from this analysis, which were not shown beforehand on this publicly available cancer dataset (Case Reports in Oncological Medicine, Volume 2013 (2013), Article ID 270362) from a patient with massive acinic cell carcinoma.

Citation Format: Anika Joecker, Nathan Pearson, Cecilie Boysen, Naomi Thomson, Anne-Mette Hein, Bodil Oster, Anne Arens, Bjarne Knudsen, Thomas Knudsen, Dan Richards, Roald Forsberg. An automatic pipeline to find and annotate rare subclonal somatic variants in a paired tumor/normal sample. [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 2227. doi:10.1158/1538-7445.AM2014-2227

Abstract 2334: Identification of differentially expressed genes and somatic mutations in esophageal adenocarinoma cancer patients

High throughput sequencing technologies are currently revolutionizing the cancer research area with rapid improvements in sequencing capacity and time consumption. As a result the most time consuming step has moved from being the sequencing process itself to being the bioinformatic data analysis.

RNA sequencing (RNA-Seq) is used in an increasing number of transcriptomic studies. The great advantage of using RNA-Seq is its ability to precisely quantify transcript levels and identify novel transcripts, isoforms, and splice junctions, while further providing information of the mutational landscape down to single base resolution. To ease the hurdles associated with RNA-Seq data analysis there is an increasing demand for tools that are specifically tailored to RNA-Seq data.

Here we describe how the newly developed CLC Cancer Research Workbench can be used to analyze and visualize RNA-Seq data with ready-to-use workflows that automatically map, quantify, and annotate transcriptomes. We identify differentially expressed genes and transcripts in Illumina HiSeq transcriptomic data from matched tumor and normal samples from four esophageal adenocarinoma cancer patients, and compare the mutational patterns in the samples with the expression values of the corresponding genes.

Results are visualized in a track based genome browser view, which provides the means for quick and easy navigation as well as allowing the user to simultaneously view and annotate multiple samples and different data types (e.g. genes, transcript expression levels, and detected variants).

Citation Format: Bodil Oster, Anika Joecker, Anne-Mette K. Hein, Patrick Dekker, Robert O'Neill, Adam Krejci, Anne Arens, Naomi Thomson, Cecilie Boysen, Søren Mønsted, Roald Forsberg, Bjarne Knudsen, Thomas Knudsen, Richard Lussier, Ted R. Hupp. Identification of differentially expressed genes and somatic mutations in esophageal adenocarinoma cancer patients. [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 2334. doi:10.1158/1538-7445.AM2014-2334

Putative cis-regulatory drivers in colorectal cancer

The cis-regulatory effects responsible for cancer development have not been as extensively studied as the perturbations of the protein coding genome in tumorigenesis. To better characterize colorectal cancer (CRC) development we conducted an RNA-sequencing experiment of 103 matched tumour and normal colon mucosa samples from Danish CRC patients, 90 of which were germline-genotyped. By investigating allele-specific expression (ASE) we show that the germline genotypes remain important determinants of allelic gene expression in tumours. Using the changes in ASE in matched pairs of samples we discover 71 genes with excess of somatic cis-regulatory effects in CRC, suggesting a cancer driver role. We correlate genotypes and gene expression to identify expression quantitative trait loci (eQTLs) and find 1,693 and 948 eQTLs in normal samples and tumours, respectively. We estimate that 36% of the tumour eQTLs are exclusive to CRC and show that this specificity is partially driven by increased expression of specific transcription factors and changes in methylation patterns. We show that tumour-specific eQTLs are more enriched for low CRC genome-wide association study (GWAS) P values than shared eQTLs, which suggests that some of the GWAS variants are tumour specific regulatory variants. Importantly, tumour-specific eQTL genes also accumulate more somatic mutations when compared to the shared eQTL genes, raising the possibility that they constitute germline-derived cancer regulatory drivers. Collectively the integration of genome and the transcriptome reveals a substantial number of putative somatic and germline cis-regulatory cancer changes that may have a role in tumorigenesis.

Human herpesvirus-6B protein U19 contains a p53 BOX I homology motif for HDM2 binding and p53 stabilization

In order to establish a successful infection, it is of crucial importance for invading viruses to alter the activities of the regulatory protein p53. Beta-herpesviruses stabilize p53 and likely direct its activities towards generation of a replication-friendly environment. We here study the mechanisms behind HHV-6B-induced stabilization and inactivation of p53. Stable transgene expression of the HHV-6B protein U19 was sufficient to achieve upregulation of p53. U19 bound directly to the p53-regulating protein HDM2 in vitro, co-precipitated together with HDM2 in lysates, and co-localized with HDM2 in the nucleus when overexpressed. U19 contained a sequence with a putative p53 BOX I-motif for HDM2 binding. Mutation of the two key amino acids within this motif was sufficient to inhibit all the described U19 functions. Our study provides further insight into p53-modulating strategies used by herpesviruses and elucidates a mechanism used by HHV-6B to circumvent the antiviral response.

MiRNA-362-3p induces cell cycle arrest through targeting of E2F1, USF2 and PTPN1 and is associated with recurrence of colorectal cancer

Colorectal cancer (CRC) is one of the leading causes of cancer deaths in Western countries. A significant number of CRC patients undergoing curatively intended surgery subsequently develop recurrence and die from the disease. MicroRNAs (miRNAs) are aberrantly expressed in cancers and appear to have both diagnostic and prognostic significance. In this study, we identified novel miRNAs associated with recurrence of CRC, and their possible mechanism of action. TaqMan(®) Human MicroRNA Array Set v2.0 was used to profile the expression of 667 miRNAs in 14 normal colon mucosas and 46 microsatellite stable CRC tumors. Four miRNAs (miR-362-3p, miR-570, miR-148 a* and miR-944) were expressed at a higher level in tumors from patients with no recurrence (p<0.015), compared with tumors from patients with recurrence. A significant association with increased disease free survival was confirmed for miR-362-3p in a second independent cohort of 43 CRC patients, using single TaqMan(®) microRNA assays. In vitro functional analysis showed that over-expression of miR-362-3p in colon cancer cell lines reduced cell viability, and proliferation mainly due to cell cycle arrest. E2F1, USF2 and PTPN1 were identified as potential miR-362-3p targets by mRNA profiling of HCT116 cells over-expressing miR-362-3p. Subsequently, these genes were confirmed as direct targets by Luciferase reporter assays and their knockdown in vitro phenocopied the effects of miR-362-3p over-expression. We conclude that miR-362-3p may be a novel prognostic marker in CRC, and hypothesize that the positive effects of augmented miR-362-3p expression may in part be mediated through the targets E2F1, USF2 and PTPN1.

A beta-mixture model for dimensionality reduction, sample classification and analysis

Background

Patterns of genome-wide methylation vary between tissue types. For example, cancer tissue shows markedly different patterns from those of normal tissue. In this paper we propose a beta-mixture model to describe genome-wide methylation patterns based on probe data from methylation microarrays. The model takes dependencies between neighbour probe pairs into account and assumes three broad categories of methylation, low, medium and high. The model is described by 37 parameters, which reduces the dimensionality of a typical methylation microarray significantly. We used methylation microarray data from 42 colon cancer samples to assess the model.

Results

Based on data from colon cancer samples we show that our model captures genome-wide characteristics of methylation patterns. We estimate the parameters of the model and show that they vary between different tissue types. Further, for each methylation probe the posterior probability of a methylation state (low, medium or high) is calculated and the probability that the state is correctly predicted is assessed. We demonstrate that the model can be applied to classify cancer tissue types accurately and that the model provides accessible and easily interpretable data summaries.

Conclusions

We have developed a beta-mixture model for methylation microarray data. The model substantially reduces the dimensionality of the data. It can be used for further analysis, such as sample classification or to detect changes in methylation status between different samples and tissues.

Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas

In our study, whole-genome methylation arrays were applied to identify novel genes with tumor specific DNA methylation of promoter CpG islands in pre-malignant and malignant colorectal lesions. Using a combination of Illumina HumanMethylation27 beadchips, Methylation-Sensitive High Resolution Melting (MS-HRM) analysis, and Exon arrays (Affymetrix) the DNA methylation pattern of ∼14,000 genes and their transcript levels were investigated in six normal mucosas, six adenomas and 30 MSI and MSS carcinomas. Sixty eight genes with tumor-specific hypermethylation were identified (p < 0.005). Identified hypermethylated sites were validated in an independent sample set of eight normal mucosas, 12 adenomas, 40 MSS and nine MSI cancer samples. The methylation patterns of 15 selected genes, hypermethylated in adenomas and carcinomas (FLI1, ST6GALNAC5, TWIST1, ADHFE1, JAM2, IRF4, CNRIP1, NRG1 and EYA4), in carcinomas only (ABHD9, AOX1 and RERG), or in MSI but not MSS carcinomas (RAMP2, DSC3 and MLH1) were validated using MS-HRM. Four of these genes (MLH1, AOX1, EYA4 and TWIST1) had previously been reported to be hypermethylated in CRC. Eleven genes, not previously known to be affected by CRC specific hypermethylation, were identified and validated. Inverse correlation to gene expression was observed for six of the 15 genes with Spearman correlation coefficients ranging from -0.39 to -0.60. For six of these genes the altered methylation patterns had a profound transcriptional association, indicating that methylation of these genes may play a direct regulatory role. The hypermethylation changes often occurred already in adenomas, indicating that they may be used as biomarkers for early detection of CRC.

Human herpesvirus 6B induces phenotypic maturation without IL-10 and IL-12p70 production in dendritic cells

Human herpesvirus 6B (HHV-6B) is the causative agent of the common childhood febrile illness, exanthema subitum. The virus is predominantly regarded as a T-cell tropic virus, although in reality it has the ability to infect a wide variety of cell types including monocytes, macrophages and dendritic cells (DC). Although DC are important immune regulators, the modulating effects of HHV-6B on DC are controversial. Here, we examine the phenotypic and functional consequences of HHV-6B infection of DC. The addition of HHV-6B to immature DC led to expression of the nuclear viral p41 protein and cell surface expression of the viral glycoprotein gp60/110 consistent with HHV-6B infection. Nevertheless, HHV-6B did not induce noticeable cytopathogenic effects or cell death in infected DC. Importantly, HHV-6B infection induced a partial phenotypic maturation of immature DC as demonstrated by a substantial increase in the expression of HLA-DR, CD86 and CD40, whereas only a minor increase in CD80 and CD83 was observed. This phenotypic maturation was, however, not followed by functional maturation, because HHV-6B infection did not induce IL-10 and IL-12p70 production in immature DC. However, infected DC were still able to react to bacteria-derived stimuli such as lipopolysaccaharide by an even more pronounced production of IL-10 and IL-12p70 when compared to that of uninfected DC.

[Seroprevalence of Lyme Borreliosis and tick-borne encephalitis in workers at risk, in eastern France]

OBJECTIVE

The aim of this article was to assess the seroprevalence of Lyme Borreliosis and tick-borne encephalitis (TBE) among occupationally exposed forest workers.

METHODS

Workers exposed to tick bites in Eastern France were interviewed by occupational health physicians of the mutualité sociale agricole (MSA) on their sociodemographic features, their occupational activity, their last tick bite, their clinical history, and their means of prevention. Blood sampling was carried out for antibody detection.

RESULTS

Among the 2975 subjects included in the study, the observed seroprevalence was 14.1% for Lyme borreliosis and 3.4% for TBE. Age, occupational activity, and place of residence significantly influenced the serological status of Lyme borreliosis. The seroprevalence was significantly higher among woodcutters (17.5%) than among other occupational categories (p<.001). Seroprevalence in Alsace (26.9%) and Lorraine (16.5%) were significantly higher than in other regions (p<0.001 and p<0.01, respectively). The seroprevalence of TBE was significantly higher in Alsace (5.5%; p<0.001). The rates of seroprevalence for both infections varied according to forest areas. The multifactorial analysis of prevention practices revealed three types of behaviors as far as protection was concerned: "rigorous", "partial", or "insufficient".

CONCLUSION

These results do not change the present French indications for use of TBE vaccine. They highlight the importance of information on these diseases and the need for further studies on microbial ecology and risk-factors identification.

A central role for CK1 in catalyzing phosphorylation of the p53 transactivation domain at serine 20 after HHV-6B viral infection

The tumor suppressor protein p53 is activated by distinct cellular stresses including radiation, hypoxia, type I interferon, and DNA/RNA virus infection. The transactivation domain of p53 contains a phosphorylation site at Ser20 whose modification stabilizes the binding of the transcriptional co-activator p300 and whose mutation in murine transgenics induces B-cell lymphoma. Although the checkpoint kinase CHK2 is implicated in promoting Ser20 site phosphorylation after irradiation, the enzyme that triggers this phosphorylation after DNA viral infection is undefined. Using human herpesvirus 6B (HHV-6B) as a virus that induces Ser20 site phosphorylation of p53 in T-cells, we sought to identify the kinase responsible for this virus-induced p53 modification. The p53 Ser20 kinase was fractionated and purified using cation, anion, and dye-ligand exchange chromatography. Mass spectrometry identified casein kinase 1 (CK1) and vaccinia-related kinase 1 (VRK1) as enzymes that coeluted with virus-induced Ser20 site kinase activity. Immunodepletion of CK1 but not VRK1 removed the kinase activity from the peak fraction, and bacterially expressed CK1 exhibited Ser20 site kinase activity equivalent to that of the virus-induced native CK1. CK1 modified p53 in a docking-dependent manner, which is similar to other known Ser20 site p53 kinases. Low levels of the CK1 inhibitor D4476 selectively inhibited HHV-6B-induced Ser20 site phosphorylation of p53. However, x-ray-induced Ser20 site phosphorylation of p53 was not blocked by D4476. These data highlight a central role for CK1 as the Ser20 site kinase for p53 in DNA virus-infected cells but also suggest that distinct stresses may selectively trigger different protein kinases to modify the transactivation domain of p53 at Ser20.

Induction of cell-cell fusion from without by human herpesvirus 6B

Human herpesvirus (HHV) 6A induce fusion from without (FFWO), whereas HHV-6B is believed to be ineffective in this process. Here, we demonstrate that HHV-6B induces rapid fusion in both epithelial cells and lymphocytes. The fusion was identified 1 h postinfection, could be inhibited by antibodies to HHV-6B gH and to the cellular receptor CD46, and was dependent on virus titer but independent of de novo protein synthesis and UV inactivation of the virus. Comparisons indicate that HHV-6A is only 10-fold more effective in inducing FFWO than HHV-6B. These data demonstrate that HHV-6B can induce FFWO in epithelial cells and lymphocytes.

Aluminum concentration in deciduous teeth is dependent on tooth type and dental status

Aluminum (Al) concentration was assessed in deciduous teeth in relation to sex, year of birth, tooth type, and the presence of caries and roots. Three hundred and twenty-three deciduous teeth from children born during the period 1952 93 in a county in southeast Sweden were sampled, and the Al content determined by graphite furnace atomic absorption spectrophotometry. The arithmetic mean of the Al concentration was 0.58 +/- 0.64 ppm dry weight (mean +/- standard deviation) and differed significantly between incisors (1.05 +/- 1.04 ppm) and canines (0.48 +/- 0.50 ppm) and between incisors and molars (0.53 +/- 0.55 ppm). A significant difference was found between teeth with and without caries. No significant differences were found between sexes. The Al concentration correlated significantly with tooth weight for incisors (r = -0.47) and canines (r = -0.45) but not for molars (r = 0.03). No significant change in Al concentration was found over time. Caries-free deciduous molars are suggested as the most useful teeth for biological monitoring of aluminum.

Evaluation of cause-related periodontal therapy and compliance with maintenance care recommendations

An evaluation of the long-term clinical effects of an intense period of cause-related periodontal therapy provided by dental hygiene students, was made in patients with moderately advanced periodontitis. By the evaluation, we also intended to gain information about compliance with given recommendations for periodontal health maintenance. The results after 3 years without supervision by the specialist team showed that achieved beneficial effects on the gingival conditions were maintained despite a significant increase in plaque prevalence. Recommendations as to the daily use of a variety of additional oral hygienic measures besides toothbrushing met with a considerable lack of compliance. Maintenance visits to the referring general practitioner were mostly made once a year and included regular dental care. Despite this, no further deterioration of periodontal status was observed. The results indicate that it may be possible to maintain successful effects of periodontal therapy in this patient category with less personal and professional effort than traditionally recommended.