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Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.

AimsIn addition to providing external quality assessment (EQA) schemes, United Kingdom National External Quality Assessment service (UK NEQAS) for Molecular Genetics also supports the education of laboratories. As an enhancement to the Molecular Pathology EQA scheme, a human cell-line reference sample, manufactured by Thermo Fisher Scientific (AcroMetrix), was provided for analysis. This contained many variants, present at frequencies between 1% and 17.9%.MethodsOne hundred and one laboratories submitted results, with a total of 2889 test results on 53 genes being reported. Known polymorphisms, 46/2889 (1.59%) results, were excluded. Variants detected in the seven most commonly reported (and clinically relevant) genes, KRAS, NRAS, BRAF, EGFR, PIK3CA, KIT and PDGFRA, are reported here, as these genes fall within the scope of UK NEQAS EQA schemes.ResultsNext generation sequencing (NGS) was the most commonly performed testing platform. There were between 5 and 27 validated variants in the seven genes reported here. Eight laboratories correctly reported all five NRAS variants, and two correctly reported all eight BRAF variants. The validated mean variant frequency was lower than that determined by participating laboratories, with single-gene testing methodologies showing less variation in estimated frequencies than NGS platforms. Laboratories were more likely to correctly identify clinically relevant variants.ConclusionsOver 100 laboratories took the opportunity to test the ‘educational reference sample’, showing a willingness to further validate their testing platforms. While it was encouraging to see that the most widely reported variants were those which should be included in routine testing panels, reporting of variants was potentially open to interpretation, thus clarity is still required on whether laboratories selectively reported variants, by either clinical relevance or variant frequency.

The insulin-induced gene 1 protein (Insig1) inhibits the cholesterol biosynthesis pathway by retaining transcription factor SREBP in the endoplasmic reticulum, and by causing the degradation of HMGCR, the rate-limiting enzyme in cholesterol biosynthesis. Liver-specific microRNA miR-122, on the other hand, enhances cholesterol biosynthesis by an unknown mechanism. We have found that Insig1 mRNAs are generated by alternative cleavage and polyadenylation, resulting in specific isoform mRNA species. During high cholesterol abundance, the short 1.4-kb Insig1 mRNA was found to be preferentially translated to yield Insig1 protein. Precursor molecules of miR-122 down-regulated the translation of the 1.4-kb Insig1 isoform mRNA by interfering with the usage of the promoter-proximal cleavage–polyadenylation site that gives rise to the 1.4-kb Insig1 mRNA. These findings argue that precursor miR-122 molecules modulate polyadenylation site usage in Insig1 mRNAs, resulting in down-regulation of Insig1 protein abundance. Thus, precursor microRNAs may have hitherto undetected novel functions in nuclear gene expression.

While the breakthrough discovery of DNA structure was in 1953, many innovations still needed to occur before labs could generate the sequential order of nucleotides in genetic material. Results began to materialize 15 years later in 1968, when Wu and Kaiser performed “cohesive end” sequencing on phage DNA using radiolabeled nucleotides and Escherichia coli DNA polymerase (1). This method produced reads of 10 to 20 bases, and fragments were separated by two-dimensional chromatography.

All viruses require cellular ribosomes to translate their mRNAs. Viruses producing methyl-7 (m7) GTP-capped mRNAs, like Herpes Simplex Virus-1 (HSV-1), stimulate cap-dependent translation by activating mTORC1 to inhibit the translational repressor 4E-binding protein 1 (4E-BP1). Here, we establish that the HSV-1 kinase Us3 masquerades as Akt to activate mTORC1. Remarkably, Us3 displays no sequence homology with the cellular kinase Akt, yet directly phosphorylates tuberous sclerosis complex 2 (TSC2) on the same sites as Akt. TSC2 depletion rescued Us3-deficient virus replication, establishing that Us3 enhances replication by phosphorylating TSC2 to constitutively activate mTORC1, effectively bypassing S6K-mediated feedback inhibition. Moreover, Us3 stimulated Akt substrate phosphorylation in infected cells, including FOXO1 and GSK3. Thus, HSV-1 encodes an Akt surrogate with overlapping substrate specificity to activate mTORC1, stimulating translation and virus replication. This establishes Us3 as a unique viral kinase with promising drug development potential.

MicroRNAs (miRNAs), which can be expressed in a cell-type and tissue-specific manner, can influence the activities of genes that control cell growth and differentiation. Viruses often have clear tissue tropisms, raising the possibility that cellular miRNAs might modulate their pathogenesis. In this Review, we discuss recent findings that some vertebrate viruses either encode miRNAs or subvert cellular miRNAs, and that these miRNAs participate in both the infectious and the latent phase of the viral life cycle.

microRNAs (miRNAs) are small RNAs that in general down-regulate the intracellular abundance and translation of target mRNAs. We noted that sequestration of liver-specific miR-122 by modified antisense oligonucleotides resulted in a dramatic loss of hepatitis C virus (HCV) RNA in cultured human liver cells. A binding site for miR-122 was predicted to reside close to the 5' end of the viral genome, and its functionality was tested by mutational analyses of the miRNA-binding site in viral RNA, resulting in reduced intracellular viral RNA abundance. Importantly, ectopic expression of miR-122 molecules that contained compensatory mutations restored viral RNA abundance, revealing a genetic interaction between miR-122 and the viral RNA genome. Studies with replication-defective viral RNAs demonstrated that miR-122 affected mRNA abundance by positively modulating RNA replication. In contrast, interaction of miR-122 with the 3'-noncoding region (3'NCR) of the cellular mRNA encoding the cationic amino acid transporter CAT-1 resulted in the down-regulation of CAT-1 protein abundance. These findings provide evidence that a specific miRNA can regulate distinct target mRNAs in both a positive and negative fashion. The positive role of miR-122 in viral replication suggests that this miRNA could be targeted for antiviral therapy.

Efforts to improve on cancer therapy have begun to capitalize on recent advances in our understanding of tumorigenesis. Tumor-specific characteristics are being exploited to develop selective antibodies and pharmacological inhibitors that specifically target cancer cells, and these agents are already showing clinical promise. None of these approaches, however, has captured our imagination as much as the use of replication-competent viruses to kill cancer cells. Whereas normal cells resist replication, tumor cells have an impaired antiviral response that sensitizes them to oncolytic viruses. One such virus is reovirus, a benign, naturally occurring virus that can effect tumor regression in animal models. Reovirus is demonstrating much promise in pre-clinical studies of cancer therapy and in clinical trials, where a lack of toxicity and signs of efficacy are generating excitement for this novel potential cancer therapeutic.

Brain and leptomeningeal metastases are common in breast cancer patients and our current treatments are ineffective. Reovirus type 3 is a replication competent, naturally occurring virus that usurps the activated Ras-signaling pathway (or an element thereof) of tumor cells and lyses them but leaves normal cells relatively unaffected. In this study we evaluated reovirus as an experimental therapeutic in models of central nervous system (CNS) metastasis from breast cancer. We found all breast cancer cell lines tested were susceptible to reovirus, with > 50% of these cells lysed within 72 h of infection. In vivo neurotoxicity studies showed only mild local inflammation at the injection site and mild communicating hydrocephalus with neither diffuse encephalitis nor behavioral abnormalities at the therapeutically effective dose of reovirus (intracranial) (ie 10(7) plaque-forming units) or one dose level higher. In vivo, a single intratumoral administration of reovirus significantly reduced the size of tumors established from two human breast cancer cell lines and significantly prolonged survival. Intrathecal administration of reovirus also remarkably prolonged survival in an immunocompetent racine model of leptomeningeal metastases. These data suggest that the evaluation of reovirus as an experimental therapeutic for CNS metastases from breast cancer is warranted.

Specific viral oncolysis of cancer cells has aroused great interest as a potential anti-cancer therapy. Reovirus was proposed as an anti-cancer biotherapeutic several years ago, as it elicits virus-mediated death of human cancer cells both in vitro and in mouse model systems. A common model system for reovirus oncolysis is the NOD/ LtSz-scid/scid (SCID/NOD) immunocomprimised mouse. While human tumour xenografts are effectively killed by intra-tumour injections of reovirus, the mice often exhibit discoloration and necrosis of extremities including feet, distal leg, tail and ears several weeks after injection. This phenomenon never occurs in sham-injected mice, nor is it observed in wild type or nude mice. The pathogenesis of this "Black Foot" lesion has not yet been described, but may be of relevance for future human studies of biotherapeutics. Examination of SCID/NOD mice was performed at various time points following intratumoral injection of reovirus. Immunohistological evaluation of tissues reveals infection of cardiac myocytes and venous endothelial cells at approximately 2 days post infection. Over time, venules and veins showed a mixed inflammatory vasculitis and thrombus formation. Synchronously, the heart showed diffuse myocyte death, with dystrophic calcification. The results indicate that the "Black Foot" syndrome is likely due to venous vasculitis secondary to reovirus infection, on a background of reovirus myocarditis and heart failure. The rationale for the selective susceptibility of venous over arterial endothelium to reovirus infection is currently unknown. The results of this study may be relevant to the use of oncolytic viruses, particularly reovirus, in the anti-cancer therapy of immunosuppressed patients.

In the hopes that a better understanding of cancer biology would allow for the development of novel, more effective therapeutics, a concerted effort over the past 20 years has focussed on the molecular mechanisms of cell growth control and tumorigenesis. Recently, there has been a renewal of interest and optimism in the field, on account of a confluence of ideas from molecular oncology and virology, leading to the development of novel virus-based therapeutics for the treatment of cancer. Viruses have been used in the past as potential cancer therapeutics; a large variety of agents have been tested, including rabies, adenovirus, paramyxovirus, Newcastle disease virus and mumps virus [1]. Although ‘responses’ have been documented, little has emerged from such trials in terms of a longstanding, oncolytic virus therapeutic mainstay. Fortunately, new technologies and insight have allowed for a re-examination of oncolytic viruses; an understanding of cancer biology and signalling, for example, has permitted the characterisation of the selectivity of viruses such as reovirus for cells with an activated Ras signalling pathway [2,3]. Discovery of the ability of adenovirus E1B protein to interact with the tumor suppressor, p53, not only helped to delineate p53’s role in cell cycle control, but also provided the foundation for the development of E1B-deleted mutants as potential cancer therapeutics [4,5]. Similarly, an awareness of herpes virus biology has permitted the engineering of non-neurovirulent mutants lacking genes necessary for * Corresponding author. Tel.: +1-403-2207548; fax: +1-4032708520. E-mail address: plee@ucalgary.ca (P.W.K. Lee).

Hepatitis C virus (HCV) is an important human liver pathogen that has infected over 170 million people worldwide, often leading to liver cirrhosis and hepatocellular carcinoma 1. While the efficacies of novel inhibitors of the viral polymerase and protease enzymes are being explored in numerous clinical trials, current therapies against HCV infections are limited to a combined administration of pegylated interferon-α and ribavirin. However, this combination therapy has considerable side effects, which include influenza-like symptoms, depression and anemia 2. Moreover, even after 48 weeks of therapy, sustained virologic response rates are observed in only half of the patients infected with the prevalent genotype 1 HCV 2. Thus, there is a need for exploring novel therapeutic approaches that target both viral and host factors that are essential for viral growth.

MicroRNA 122 (miR-122) promotes hepatitis C virus (HCV) RNA abundance through a direct interaction with the viral RNA and stimulates the mevalonate pathway in the animal liver. We found that overexpression of miR-122 enhanced viral RNA accumulation without affecting genes in the mevalonate pathway, such as the 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) gene. However, inhibition of miR-122 decreased both HCV RNA and HMGCR RNA with little effects on the rates of HCV and HMGCR RNA synthesis. Loss of HCV RNA could not be restored by isoprenoid intermediate metabolites. Overall, these findings suggest that miR-122 modulates viral RNA abundance independently of its effect on isoprenoid metabolism.

As the incidence of cancer continues to escalate, the demand for alternative anticancer therapeutics increases. The use of viruses in cancer treatment is well documented (1); however, as knowledge in the fields of virology, cell biology, and oncology expands, refined techniques and novel viral-based therapeutics emerge. The oncolytic potential of a wide spectrum of viruses has been explored, such as adenovirus (2,3), herpes simplex virus (HSV) (4,5), vesicular stomatitis virus (6), vaccinia virus (7), poliovirus (8), and mammalian reovirus (9).

Introduction: Application of targeted NGS assays to comprehensively screen cancer genes has highlighted the need for a well-characterized control to ensure consistency in variant calls. CLIA and CAP guidelines mandate that labs utilize positive run controls which are currently limited to known patient samples or cell lines containing 10's of mutations. These materials do not cover the breadth of potential mutations that could be observed in current highly mutliplexed NGS tests. Materials and Methods: AcroMetrix® Oncology Hotspot Control is a DNA control containing more than 500 COSMIC (Catalogue of Somatic Mutations in Cancer) variants in 53 genes. Covering SNP and indels, the control is designed to function on many platforms and technologies. Formulated as a mixture of synthetic and genomic DNA, the control mimics the complexity of patient samples. Variants were confirmed by Sanger sequencing and quantified by digital PCR. To benchmark product performance, two lots of the controЀ were tested in 19 labs worldwide. Testing was performed using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHPv2) on the Ion Torrent Personal Genome Machine® as well as with the Illumina® TruSeq® Amplicon Cancer Panel (TruSeq) and TruSight® Tumor Panel (TruSight) on the MiSeq® instrument. Each lab utilized an established assay and their in house bioinformatics pipeline. Results: In internal tests, good concordance was observed between expected and detected SNP's with greater than 90% being detected on the CHPv2 (382/385), TruSeq® Amplicon Cancer Panel (TSCAP) (319/351) and TruSight® Tumor Panel (TSTP) (209/230). For deletions, detection varied from 66.7%(12/18) for CHPv2 and TruSight® to 76%(16/21) for TruSeq® tests. For insertions, detection was 70%(7/10) for TruSight® and 54% each for CHPv2(6/11) and TruSeq® (7/13). Labs varied in their ability to detect variants; while some labs, running the TSTP, detected over 87% (241/277) of total variants, others detected less than half of expected variants (122/277). Similar variations in detections rates were observed in TSCAP (38%-86%) and CHPv2 (40%-90%). Refining the bioinformatics in variant calling allowed one lab to improve their variant detection by 130% (157 variants detected prior and 410 variants after improvement). Conclusions: AcroMetrix® Oncology Hotspot Control provides a wide variety of variants, including many that are difficult to source. This control will enable laboratories to monitor variation between assay lots and operators, and will facilitate result comparison across laboratories. The control also ensures that bioinformatics pipelines are performing acceptably over time and through updates to ensure reliable variant calling. The availability of controls that target clinically-relevant mutations will significantly improve NGS adoption rates and confidence in NGS results. AcroMetrix® Oncology Hotspot Control is For In Vitro Diagnostic Use. Citation Format: Nakul Nataraj, Mona D. Shahbazian, Aron Lau, Mahjabeen Yucekul, Patty Chiang, Suzy Van Le, Kara Norman. A highly multiplexed control material to satisfy the complex needs of targeted next generation sequencing (NGS) oncology assays. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4900. doi:10.1158/1538-7445.AM2015-4900

Reovirus is a benign human virus that was recently found to have oncolytic properties and is currently in clinical trials as a potential cancer therapy. We have previously demonstrated that activation of Ras signaling, a common event in cancer, renders cells susceptible to reovirus oncolysis. In this study, we investigate which elements downstream of Ras are important in reovirus infection. By using a panel of NIH 3T3 cells transformed with activated Ras mutated in the effector-binding domain, we found that only the RasV12G37 mutant, which was unable to signal to Raf or phosphatidylinositol 3-kinase but retained signaling capability to guanine nucleotide-exchange factors (GEFs) for the small G protein, Ral (known as RalGEFs), was permissive to reovirus. Expression of the activated mutant of the RalGEF, Rlf, also allowed reovirus replication. Specific inhibition of the Ral pathway by using dominant-negative RalA rendered normally permissive H-Ras cells (cells expressing activated Ras) resistant to reovirus. To further identify elements downstream of RalGEF that promote reovirus infection, we used chemical inhibitors of the downstream signaling elements p38 and JNK. We found that reovirus infection was blocked in the presence of the p38 inhibitor but not the JNK inhibitor. Together, these results implicate a Ras/RalGEF/p38 pathway in the regulation of reovirus replication and oncolysis.

The human reovirus is an oncolytic virus that specifically targets cancer cells with an activated Ras pathway. Because it is replication competent and highly specific for cancer cells, this virus has the potential to be an effective antimetastatic cancer agent through remote site delivery. In this study, we exploited the ability of reovirus to replicate in murine cells to test the efficacy of this virus in eliminating distal and/or metastatic tumors in immune-competent mice. We found that i.v. therapy with reovirus not only inhibited metastatic tumor growth but also led to a significant improvement in animal survival. Combining i.v. reovirus treatment with immune suppression (cyclosporine A or anti-CD4/anti-CD8 antibodies) resulted in further reduction in tumor size and a considerable prolongation in survival, compared with viral therapy alone. Combined therapy was also effective in overcoming a preexisting immunity to reovirus (a common occurrence in humans and thus a potential impediment to oncolytic effectiveness) to induce metastatic tumor regression. This is the first study to use systemic delivery of an oncolytic agent in conjunction with immune-suppressive drugs to effectively prolong animal survival. Altogether, our results suggest that i.v. reovirus therapy may present a feasible, novel alternative in the treatment of metastatic cancer in humans.

We have previously shown that human reovirus replication is restricted to cells with an activated Ras pathway, and that reovirus could be used as an effective oncolytic agent against human glioblastoma xenografts. This study examines in more detail the feasibility of reovirus as a therapeutic for breast cancer, a subset of cancer in which direct activating mutations in the ras proto-oncogene are rare, and yet where unregulated stimulation of Ras signaling pathways is important in the pathogenesis of the disease. We demonstrate herein the efficient lysis of breast tumor-derived cell lines by the virus, whereas normal breast cells resist infection in vitro. In vivo studies of reovirus breast cancer therapy reveal that viral administration could cause tumor regression in an MDA-MB-435S mammary fat pad model in severe combined immunodeficient mice. Reovirus could also effect regression of tumors remote from the injection site in an MDA-MB-468 bilateral tumor model, raising the possibility of systemic therapy of breast cancer by the oncolytic agent. Finally, the ability of reovirus to act against primary breast tumor samples not propagated as cell lines was evaluated; we found that reovirus could indeed replicate in ex vivo surgical specimens. Overall, reovirus shows promise as a potential breast cancer therapeutic.

Reovirus selectively replicates in and destroys cancer cells with an activated Ras signaling pathway. In this study, we evaluated the feasibility of using reovirus (serotype 3, strain Dearing) as an antihuman colon and ovarian cancer agent. In in vitro studies, reovirus infection in human colon and ovarian cell lines was assessed by cytopathic effect as detected by light microscopy, [(35)S]Methionine labeling of infected cells for viral protein synthesis and progeny virus production by plaque assay. We observed that reovirus efficiently infected all five human colon cancer cell lines (Caco-2, DLD-1, HCT-116, HT-29, and SW48) and four human ovarian cancer cell lines (MDAH2774, PA-1, SKOV3, and SW626) which were tested, but not a normal colon cell line (CCD-18Co) or a normal ovarian cell line (NOV-31). We also observed that the Ras activity in the human colon and ovarian cancer cell lines was elevated compared with that in normal colon and ovarian cell lines. In animal models, intraneoplastic as well as i.v. inoculation of reovirus resulted in significant regression of established s.c. human colon and ovarian tumors implanted at the hind flank. Histological studies revealed that reovirus infection in vivo was restricted to tumor cells, whereas the surrounding normal tissue remained uninfected. Additionally, in an i.p. human ovarian cancer xenograft model, inhibition of ascites tumor formation and the survival of animals treated with live reovirus was significantly greater than of control mice treated with UV-inactivated reovirus. Reovirus infection in ex vivo primary human ovarian tumor surgical samples was also confirmed, further demonstrating the potential of reovirus therapy. These results suggest that reovirus holds promise as a novel agent for human colon and ovarian cancer therapy.

e22101 Background: Reproducible control materials that mimic tissue specimens help assess the performance of NGS test procedures. For FFPE samples, controls such as plasmids, genomic DNA, and cell ...

Reovirus is a double-stranded RNA-containing virus that possesses the distinctive ability to replicate in transformed cells while sparing normal cells, both in vitro and in vivo, in rodent models of cancer. The discovery of this property only arose through years of basic research on the biology of reovirus infection. Upon elucidation of the intracellular factors that govern cellular susceptibility, it became clear that reovirus Type 3 Dearing was capable of replicating in cells with an activated Ras signaling pathway, whereas normal, untransformed cells were unable to support reovirus infection (1). Because normal cells are resistant to reovirus, it is not surprising that reovirus infection in humans is usually subclinical (2, 3). Altogether, the potential impact of such findings is impressive when one considers that activating mutations in the ras genes alone contribute to more than 30% of all human cancers and that many other mutations in elements of the Ras pathway can also contribute to oncogenesis (4, 5). Recently, research using murine cancer models has revealed that this genetically unmodified laboratory strain of reovirus can indeed selectively destroy tumor cells, with no manifestations of animal morbidity or mortality (6). This has led the way to investigation into its therapeutic potential in human cancer.

BACKGROUND The apicomplexan parasite Toxoplasma gondii can infect and replicate in virtually any nucleated cell in many species of warm-blooded animals; thus, it has evolved the ability to exploit well-conserved biological processes common to its diverse hosts. Here we have investigated whether Toxoplasma modulates the levels of host microRNAs (miRNAs) during infection. METHODOLOGY/PRINCIPAL FINDINGS Using microarray profiling and a combination of conventional molecular approaches we report that Toxoplasma specifically modulates the expression of important host microRNAs during infection. We show that both the primary transcripts for miR-17 approximately 92 and miR-106b approximately 25 and the pivotal miRNAs that are derived from miR-17 approximately 92 display increased abundance in Toxoplasma-infected primary human cells; a Toxoplasma-dependent up-regulation of the miR-17 approximately 92 promoter is at least partly responsible for this increase. The abundance of mature miR-17 family members, which are derived from these two miRNA clusters, remains unchanged in host cells infected with the closely related apicomplexan Neospora caninum; thus, the Toxoplasma-induced increase in their abundance is a highly directed process rather than a general host response to infection. CONCLUSIONS/SIGNIFICANCE Altered levels of miR-17 approximately 92 and miR-106b approximately 25 are known to play crucial roles in mammalian cell regulation and have been implicated in numerous hyperproliferative diseases although the mechanisms driving their altered expression are unknown. Hence, in addition to the implications of these findings on the host-pathogen interaction, Toxoplasma may represent a powerful probe for understanding the normal mechanisms that regulate the levels of key host miRNAs.