Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.

BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. RESULTS: We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. CONCLUSION: Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.

Snapshot of cobalt, chromium and nickel exposure in dental technicians.

BACKGROUND: It is not fully understood where and how people are exposed to sensitizing metals. Much can be learnt from studying occupational settings where metals are handled. OBJECTIVES: To quantify cobalt (Co), chromium (Cr) and nickel (Ni) exposure on the skin and in the air, and urine levels, in dental technicians working with tools and alloys that may result in skin and respiratory exposure. METHODS: The metal skin dose was quantified with acid wipe sampling in dental technicians (n = 13). Air exposure was monitored by personal air sampling. Spot urine samples were collected for 24 h. Metals were analysed with inductively coupled plasma mass spectrometry. RESULTS: Before work, Co was detected on the skin of 10 participants (0.00025-0.0039 µg/cm2 ), and Cr (0.00051-0.011 µg/cm2 ) and Ni (0.0062-0.15 µg/cm2 ) on the skin of all participants. After a 2-h period without hand washing, CoCr-exposed participants had more Co on the skin (p = 0.004) than non-CoCr-exposed participants. Co was found in 10 air samples (0.22-155 µg/m3 ), Cr in nine (0.43-71 µg/m3 ), and Ni in four (0.48-3.7 µg/m3 ). Metal urine concentrations were considered to be normal. CONCLUSIONS: Dental technicians were exposed to Co, Cr and Ni on the skin and through the air, which was not reflected in the urine concentrations in this study. Cobalt skin doses may potentially elicit allergic contact dermatitis and cause sensitization.

C4b-binding Protein Protects ß-Cells from Islet Amyloid Polypeptide-induced Cytotoxicity.

C4BP (C4b-binding protein) is a polymer of seven identical α chains and one unique ß chain synthesized in liver and pancreas. We showed previously that C4BP enhances islet amyloid polypeptide (IAPP) fibril formation in vitro Now we report that polymeric C4BP strongly inhibited lysis of human erythrocytes incubated with monomeric IAPP, whereas no lysis was observed after incubation with preformed IAPP fibrils. In contrast, incubation with the monomeric α-chain of C4BP was less effective. These data indicate that polymeric C4BP with multiple binding sites for IAPP neutralizes lytic activity of IAPP. Furthermore, addition of monomeric IAPP to a rat insulinoma cell line (INS-1) resulted in decreased cell viability, which was restored in the presence of physiological concentrations of C4BP. Treatment of INS-1 cells and primary rat islets with IAPP also diminished their ability to secrete insulin upon stimulation with glucose, which was reversed in the presence of C4BP. Further, C4BP was internalized together with IAPP into INS-1 cells. Pathway analyses of mRNA expression microarray data indicated that cells exposed to C4BP and IAPP in comparison with IAPP alone increased expression of genes involved in cholesterol synthesis. Depletion of cholesterol through methyl-ß-cyclodextrin or cholesterol oxidase abolished the protective effect of C4BP on IAPP cytotoxicity of INS-1 cells. Also, inhibition of phosphoinositide 3-kinase but not NF-κB had a similar effect. Taken together, C4BP protects ß-cells from IAPP cytotoxicity by modulating IAPP fibril formation extracellularly and also, after uptake by the cells, by enhancing cholesterol synthesis.

Does size matter for hypoxia tolerance in fish?

Fish cover a large size range, from milligrams to tonnes, and many of them are regularly exposed to large variations in ambient oxygen levels. For more than half a century, there have been various, often divergent, claims regarding the effect of body size on hypoxia tolerance in fish. Here, we attempt to link old and new empirical data with the current understanding of the physiological mechanisms behind hypoxia tolerance. Three main conclusions are drawn: (1) body size per se has little or no impact on the ability to take up oxygen during hypoxic conditions, primarily because the respiratory surface area matches metabolic rate over a wide size range. If size-related differences are seen in the ability for oxygen uptake in a species, these are likely to reflect adaptation to different life-styles or habitat choice. (2) During severe hypoxia and anoxia, where fish have to rely on anaerobic ATP production (glycolysis) for survival, large individuals have a clear advantage over smaller ones, because small fish will run out of glycogen or reach lethal levels of anaerobic end-products (lactate and H(+)) much faster due to their higher mass-specific metabolic rate. (3) Those fish species that have evolved extreme adaptations to hypoxia, including haemoglobins with exceptionally high oxygen affinities and an alternative anaerobic end-product (ethanol), reveal that natural selection can be a much more powerful determinant of hypoxia tolerance than scaling of physiological functions.

Radiation induced spent nuclear fuel dissolution under deep repository conditions.

The dynamics of spent nuclear fuel dissolution in groundwater is an important part of the safety assessment of a deep geological repository for high level nuclear waste. In this paperwe discussthe most important elementary processes and parameters involved in radiation induced oxidative dissolution of spent nuclear fuel. Based on these processes, we also present a new approach for simulation of spent nuclear fuel dissolution under deep repository conditions. This approach accounts for the effects of fuel age, burn up, noble metal nanoparticle contents, aqueous H2 and HCO3- concentration, water chemistry, and combinations thereof. The results clearly indicate that solutes consuming H202 and combined effects of noble metal nanoparticles and H2 have significant impact on the rate of spent nuclear fuel dissolution. Using data from the two possible repository sites in Sweden, we have employed the new approach to estimate the maximum rate of spent nuclear fuel dissolution. This estimate indicates that H2 produced from radiolysis of groundwater alone will be sufficient to inhibit the dissolution completely for spent nuclear fuel older than 100 years.

A mutation in factor I that is associated with atypical hemolytic uremic syndrome does not affect the function of factor I in complement regulation.

Factor I (FI) is the major complement inhibitor that degrades C3b and C4b in the presence of cofactors such as factor H (FH) and membrane cofactor protein (MCP). Recently, mutations and polymorphisms in complement regulator molecules FH and MCP but also in FI have been associated with atypical hemolytic uremic syndrome (aHUS). HUS is a disorder characterized by hemolytic anemia, thrombocytopenia and acute renal failure. In this study, we report three unrelated patients with an identical heterozygous mutation, G261D, in the FI heavy chain who developed severe aHUS at different time points in their lives. Two of the patients also have polymorphisms in FH previously associated with risk of developing aHUS. Testing in particular one patient and control serum samples we did not observe major differences in complement hemolytic activity, FI plasma levels or the capability to degrade C4b or C3b. A recombinant protein was produced in order to analyze the functional consequences of the mutation. Mutant FI had a slightly different migration pattern during electrophoresis under reducing conditions. An alteration due to alternative splicing or glycosylation was ruled out, thus the altered migration may be due to proximity of the mutation to a cysteine residue. The recombinant mutant FI degraded C3b and C4b in a manner comparable to wild-type protein. In conclusion, despite the association between the heterozygous mutation in FI and aHUS we did not observe any abnormalities in the function of FI regarding complement regulation.

C4b-binding protein binds to necrotic cells and DNA, limiting DNA release and inhibiting complement activation.

After cell death, via apoptosis or necrosis, the uptake of dead cells by neighboring cells or phagocytes prevents the release of intracellular content. An array of molecules, including initiation molecules of the complement system, are involved in marking dead cells for uptake. After binding of these molecules, complement activation takes place, which when uncontrolled might result in a proinflammatory state. In the current study we demonstrate that complement inhibitor, C4b-binding protein (C4BP), binds strongly to necrotic cells, irrespective of the cell type used or the method of induction. After binding of the C4BP-protein S (PS) complex to necrotic cells via PS-phosphatidylserine and C4BP-DNA interactions, C4BP-PS inhibits complement activation on these cells. C4BP binds DNA via a patch of positively charged amino acids, mainly on the second complement control domain of the C4BP alpha-chain (affinity constant: 190 nM). Furthermore, C4BP limits DNA release from necrotic cells and inhibits DNA-mediated complement activation in solution. The C4BP-necrotic cell interaction also occurs in vivo as necrotic areas of arteriosclerotic plaques and of various cancers stain strongly positive for C4BP. This study describes a novel mechanism in which C4BP limits the inflammatory potential of necrotic cells.

A chemometric study of active parameters and their interaction effects in a nebulized sheath-liquid electrospray interface for capillary electrophoresis-mass spectrometry.

A chemometrics approach has been used for evaluating the effect of four experimental parameters when coupling capillary electrophoresis (CE) to electrospray ionization-mass spectrometry (ESI-MS). Electrospray voltage, sheath-liquid flow rate, nebulizing gas flow rate, and spray needle position in respect to the MS orifice were varied according to a full factorial design. In addition to main effects, two interaction effects could be identified as significant when measuring the peak intensity of the analytes, from a sample mixture containing peptides and pharmaceuticals. The first interaction effects, between the nebulizing gas flow rate and the sheath-liquid flow rate, and the second interaction effect, between the nebulizing gas flow rate and the spray position, could further explain the impact that these variables have on the spray performance. The number of theoretical plates and the baseline noise were also measured. The sheath-liquid flow was found to significantly affect the separation efficiency, while the noise level mainly was controlled by the nebulizing gas flow. The same factorial design was also used for a CE capillary with lower internal diameter (ID) and the effects of the same variables were compared on those capillaries using equal injection volume for both capillaries. Similar trends were obtained in both capillaries but capillary ID was shown to be a significant variable when evaluating both capillaries in a single model. It was found that a capillary with 25 microm ID provided improved CE-MS performance over than corresponding 50 microm ID capillary. Enhanced sensitivity was obtained using the narrow-bore capillary, and at lower sheath-liquid flow rate the 25 microm ID capillary also gave rise to more efficient peaks.