Next-Generation Sequencing (NGS) Methods Show Superior or Equivalent Performance to Non-NGS Methods on BRAF, EGFR, and KRAS Proficiency Testing Samples.

CONTEXT.­: There has been a rapid expansion of next-generation sequencing (NGS)-based assays for the detection of somatic variants in solid tumors. However, limited data are available regarding the comparative performance of NGS and non-NGS assays using standardized samples across a large number of laboratories. OBJECTIVE.­: To compare the performance of NGS and non-NGS assays using well-characterized proficiency testing samples provided by the College of American Pathologists (CAP) Molecular Oncology Committee. A secondary goal was to compare the use of preanalytic and postanalytic practices. DESIGN.­: A total of 17 343 responses were obtained from participants in the BRAF, EGFR, KRAS, and the Multigene Tumor Panel surveys across 84 different proficiency testing samples interrogating 16 variants and 3 wild-type sequences. Performance and preanalytic/postanalytic practices were analyzed by method. RESULTS.­: While both NGS and non-NGS achieved an acceptable response rate of greater than 95%, the overall performance of NGS methods was significantly better than that of non-NGS methods for the identification of variants in BRAF (overall 97.8% versus 95.6% acceptable responses, P = .001) and EGFR (overall 98.5% versus 97.3%, P = .01) and was similar for KRAS (overall 98.8% and 97.6%, P = .10). There were specific variant differences, but in all discrepant cases, NGS methods outperformed non-NGS methods. NGS laboratories also more consistently used preanalytic and postanalytic practices suggested by the CAP checklist requirements than non-NGS laboratories. CONCLUSIONS.­: The overall analytic performance of both methods was excellent. For specific BRAF and EGFR variants, NGS outperformed non-NGS methods and NGS laboratories report superior adherence to suggested laboratory practices.

Proximal tibial extra-axial chordoma masquerading as renal cell carcinoma metastasis.

Chordomas are rare, locally aggressive notochordal tumors, which most frequently occur in the neuraxis. We describe the case of a 74-year-old male with a history of renal cell carcinoma, who presented with a slowly enlarging mass in his left leg. While the clinical history and imaging suggested metastatic renal cell carcinoma, immunohistochemical staining with brachyury ultimately made the diagnosis of extra-axial chordoma. At 74 years of age, our patient is the oldest ever reported with bony extra-axial chordoma objectively confirmed by brachyury staining. A detailed case discussion and a review of the available literature on this rare clinicopathologic entity are provided.

Transfusion reactions in pediatric compared with adult patients: a look at rate, reaction type, and associated products.

BACKGROUND: The majority of reports on transfusion reactions address adult patients. Less is known about the types, incidence, and other clinical details of transfusion reactions in pediatric populations. Furthermore, to our knowledge, there have been no previous reports directly comparing these aspects between adults and pediatric patient populations to assess if there are differences. STUDY DESIGN AND METHODS: Between the period of January 1, 2011, and February 1, 2013, all reported adult and pediatric transfusion reactions at Vanderbilt University Medical Center (VUMC) were evaluated by transfusion medicine clinical service. The information was subsequently shared with the hemovigilance database. Data provided to hemovigilance included age, sex, blood product associated with the reaction, severity of the reaction, and the type of transfusion reactions. These were collated with hospital and blood bank information system-acquired data on overall admission and product transfusion. RESULTS: A total of 133,671 transfusions were performed at VUMC during the study period including 20,179 platelet (PLT) transfusions, 31,605 plasma transfusions, 79,933 red blood cell (RBC) transfusions, and 2154 cryoprecipitate transfusions. Over the same period, 108 pediatric and 277 adult transfusion reactions were recorded. This corresponds to an incidence of 6.2 reactions per 1000 transfusions within the pediatric (age < 21) population and an incidence of 2.4 reactions per 1000 transfusions within the adult population. In both adult and pediatric populations, transfusion reactions were most commonly associated with PLT, followed by RBC, and then plasma transfusions. Within the pediatric population, subset analysis identified multiple differences when compared to the adult population, including an increased incidence of allergic transfusion reactions (2.7/1000 vs. 1.1/1000, p < 0.001), febrile nonhemolytic transfusion reactions (1.9/1000 vs. 0.47/1000, p < 0.001), and hypotensive transfusion reactions (0.29/1000 vs. 0.078/1000, p < 0.05). Interestingly, while the reaction incidence was the same between sexes in adults, in pediatric patients, reactions were more common in male patients (7.9/1000 pediatric males vs. 4.3/1000 pediatric females, p < 0.01). CONCLUSION: To our knowledge this is the first study to provide detailed comparisons of acute transfusion reactions to all blood products between pediatric and adult populations at a single institution and supported by a single transfusion service and culture. Collectively these data provide insight into pediatric transfusion reactions and demonstrate a general increase in the incidence of transfusion reactions within the pediatric compared to adult population.

Lipid rafts and caveolin-1 coordinate interleukin-1beta (IL-1beta)-dependent activation of NFkappaB by controlling endocytosis of Nox2 and IL-1beta receptor 1 from the plasma membrane.

Recent evidence suggests that signaling by the proinflammatory cytokine interleukin-1beta (IL-1beta) is dependent on reactive oxygen species derived from NADPH oxidase. Redox signaling in response to IL-1beta is known to require endocytosis of its cognate receptor (IL-1R1) following ligand binding and the formation of redox-active signaling endosomes that contain Nox2 (also called redoxosomes). The consequent generation of reactive oxygen species by redoxosomes is responsible for the downstream recruitment of IL-1R1 effectors (IRAK, TRAF6, and IkappaB kinase kinases) and ultimately for activation of the transcription factor NFkappaB. Despite this knowledge of the signaling events that occur downstream of redoxosome formation, an understanding of the mechanisms that coordinate the genesis of redoxosomes following IL-1beta stimulation has been lacking. Here, we demonstrate that lipid rafts play an important role in this process. We show that Nox2 and IL-1R1 localize to plasma membrane lipid rafts in the unstimulated state and that IL-1beta signals caveolin-1-dependent endocytosis of both proteins into the redoxosome. We also show that inhibiting lipid raft-mediated endocytosis prevents NFkappaB activation. Finally, we demonstrate that Vav1, a Rac1 guanine exchange factor and activator of Nox2, is recruited to lipid rafts following IL-1beta stimulation and that it is required for NFkappaB activation. Our results fill in an important mechanistic gap in the understanding of early IL-1R1 and Nox2 signaling events that control NFkappaB activation, a redox-dependent process important in inflammation.

Signaling components of redox active endosomes: the redoxosomes.

Subcellular compartmentalization of reactive oxygen species (ROS) plays a critical role in transmitting cell signals in response to environmental stimuli. In this regard, signals at the plasma membrane have been shown to trigger NADPH oxidase-dependent ROS production within the endosomal compartment and this step can be required for redox-dependent signal transduction. Unique features of redox-active signaling endosomes can include NADPH oxidase complex components (Nox1, Noxo1, Noxa1, Nox2, p47phox, p67phox, and/or Rac1), ROS processing enzymes (SOD1 and/or peroxiredoxins), chloride channels capable of mediating superoxide transport and/or membrane gradients required for Nox activity, and novel redox-dependent sensors that control Nox activity. This review will discuss the cytokine and growth factor receptors that likely mediate signaling through redox-active endosomes, and the common mechanisms whereby they act. Additionally, the review will cover ligand-independent environmental injuries, such as hypoxia/reoxygenation injury, that also appear to facilitate cell signaling through NADPH oxidase at the level of the endosome. We suggest that redox-active endosomes encompass a subset of signaling endosomes that we have termed redoxosomes. Redoxosomes are uniquely equipped with redox-processing proteins capable of transmitting ROS signals from the endosome interior to redox-sensitive effectors on the endosomal surface. In this manner, redoxosomes can control redox-dependent effector functions through the spatial and temporal regulation of ROS as second messengers.

Endosomal Nox2 facilitates redox-dependent induction of NF-kappaB by TNF-alpha.

Growing evidence suggests that NADPH oxidase (Nox)-derived reactive oxygen species (ROS) play important roles in regulating cytokine signaling. We have explored how TNF-alpha induction of Nox-dependent ROS influences NF-kappaB activation. Cellular stimulation by TNF-alpha induced NADPH-dependent superoxide production in the endosomal compartment, and this ROS was required for IKK-mediated activation of NF-kappaB. Inhibiting endocytosis reduced the ability of TNF-alpha to induce both NADPH-dependent endosomal superoxide and NF-kappaB, supporting the notion that redox-dependent signaling of the receptor occurs in the endosome. Molecular analyses demonstrated that endosomal H(2)O(2) was critical for the recruitment of TRAF2 to the TNFR1/TRADD complex after endocytosis. Studies using both Nox2 siRNA and Nox2-knockout primary fibroblasts indicated that Nox2 was critical for TNF-alpha-mediated induction of endosomal superoxide. Redox-active endosomes that form after TNF-alpha or IL-1 beta induction recruit several common proteins (Rac1, Nox2, p67(phox), SOD1), while also retaining specificity for ligand-activated receptor effectors. Our studies suggest that TNF-alpha and IL-1 beta signaling pathways both can use Nox2 to facilitate redox activation of their respective receptors at the endosomal level by promoting the redox-dependent recruitment of TRAFs. These studies help to explain how cellular compartmentalization of redox signals can be used to direct receptor activation from the plasma membrane.

JunD protects the liver from ischemia/reperfusion injury by dampening AP-1 transcriptional activation.

The AP-1 transcription factor modulates a wide range of cellular processes, including cellular proliferation, programmed cell death, and survival. JunD is a major component of the AP-1 complex following liver ischemia/reperfusion (I/R) injury; however, its precise function in this setting remains unclear. We investigated the functional significance of JunD in regulating AP-1 transcription following partial lobar I/R injury to the liver, as well as the downstream consequences for hepatocellular remodeling. Our findings demonstrate that JunD plays a protective role, reducing I/R injury to the liver by suppressing acute transcriptional activation of AP-1. In the absence of JunD, c-Jun phosphorylation and AP-1 activation in response to I/R injury were elevated, and this correlated with increased caspase activation, injury, and alterations in hepatocyte proliferation. The expression of dominant negative JNK1 inhibited c-Jun phosphorylation, AP-1 activation, and hepatic injury following I/R in JunD-/- mice but, paradoxically, led to an enhancement of AP-1 activation and liver injury in JunD+/- littermates. Enhanced JunD/JNK1-dependent liver injury correlated with the acute induction of diphenylene iodonium-sensitive NADPH-dependent superoxide production by the liver following I/R. In this context, dominant negative JNK1 expression elevated both Nox2 and Nox4 mRNA levels in the liver in a JunD-dependent manner. These findings suggest that JunD counterbalances JNK1 activation and the downstream redox-dependent hepatic injury that results from I/R, and may do so by regulating NADPH oxidases.

Comparative EST analyses in plant systems.

Expressed sequence tag (EST) data are a major contributor to the known plant sequence space. Organization of the data into non-redundant clusters representing tentative unique genes provides snapshots of the gene repertoires of a species. This chapter reviews availability of sequences and sequence analysis results and describes several resources and tools that should facilitate broad-based utilization of EST data for gene structure annotation, gene discovery, and comparative genomics.

Identification of X-linked genes required for migration and programmed cell death of Drosophila melanogaster germ cells.

Drosophila germ cells form at the posterior pole of the embryo and migrate to the somatic gonad. Approximately 50% of the germ cells that form reach their target. The errant cells within the embryo undergo developmentally regulated cell death. Prior studies have identified some autosomal genes that regulate germ cell migration, but the genes that control germ cell death are not known. To identify X-linked genes required for germ cell migration and/or death, we performed a screen for mutations that disrupt these processes. Here we report the identification of scattershot and outsiders, two genes that regulate the programmed death of germ cells. The scattershot gene is defined by a mutation that disrupts both germ cell migration and the death of germ cells ectopic to the gonad. Maternal and zygotic expression of scattershot is required, but the migration and cell death functions can be genetically uncoupled. Zygotic expression of wild-type scattershot rescues germ cell pathfinding, but does not restore the programmed death of errant cells. The outsiders gene is required zygotically. In outsiders mutant embryos, the appropriate number of germ cells is incorporated into the gonad, but germ cells ectopic to the gonad persist.