DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML)

Pediatric acute myeloid leukemia (AML) is a heterogeneous disease composed of clinically relevant subtypes defined by recurrent cytogenetic aberrations. The majority of the aberrations used in risk grouping for treatment decisions are extensively studied, but still a large proportion of pediatric AML patients remain cytogenetically undefined and would therefore benefit from additional molecular investigation. As aberrant epigenetic regulation has been widely observed during leukemogenesis, we hypothesized that DNA methylation signatures could be used to predict molecular subtypes and identify signatures with prognostic impact in AML. To study genome-wide DNA methylation, we analyzed 123 diagnostic and 19 relapse AML samples on Illumina 450k DNA methylation arrays. We designed and validated DNA methylation-based classifiers for AML cytogenetic subtype, resulting in an overall test accuracy of 91%. Furthermore, we identified methylation signatures associated with outcome in t(8;21)/RUNX1-RUNX1T1, normal karyotype, and MLL/KMT2A-rearranged subgroups (p < 0.01). Overall, these results further underscore the clinical value of DNA methylation analysis in AML

DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML)

Pediatric acute myeloid leukemia (AML) is a heterogeneous disease composed of clinically relevant subtypes defined by recurrent cytogenetic aberrations. The majority of the aberrations used in risk grouping for treatment decisions are extensively studied, but still a large proportion of pediatric AML patients remain cytogenetically undefined and would therefore benefit from additional molecular investigation. As aberrant epigenetic regulation has been widely observed during leukemogenesis, we hypothesized that DNA methylation signatures could be used to predict molecular subtypes and identify signatures with prognostic impact in AML. To study genome-wide DNA methylation, we analyzed 123 diagnostic and 19 relapse AML samples on Illumina 450k DNA methylation arrays. We designed and validated DNA methylation-based classifiers for AML cytogenetic subtype, resulting in an overall test accuracy of 91%. Furthermore, we identified methylation signatures associated with outcome in t(8;21)/RUNX1-RUNX1T1, normal karyotype, and MLL/KMT2A-rearranged subgroups (p < 0.01). Overall, these results further underscore the clinical value of DNA methylation analysis in AML

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL.We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5.Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.Swedish Foundation for Strategic Research RBc08-008 Swedish Cancer Society CAN2010/592 Swedish Childhood Cancer Foundation 11098 Swedish Research Council for Science and Technology 90559401 Swedish Research Council FORTE Swedish Research Council FORMAS Swedish Research Council VINNOVA Swedish Research Council VR 259-2012-2

ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing

Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use

The Arctic Summer Cloud Ocean Study (ASCOS): overview and experimental design

The climate in the Arctic is changing faster than anywhere else on earth. Poorly understood feedback processes relating to Arctic clouds and aerosol-cloud interactions contribute to a poor understanding of the present changes in the Arctic climate system, and also to a large spread in projections of future climate in the Arctic. The problem is exacerbated by the paucity of research-quality observations in the central Arctic. Improved formulations in climate models require such observations, which can only come from measurements in situ in this difficult-to-reach region with logistically demanding environmental conditions. The Arctic Summer Cloud Ocean Study (ASCOS) was the most extensive central Arctic Ocean expedition with an atmospheric focus during the International Polar Year (IPY) 2007-2008. ASCOS focused on the study of the formation and life cycle of low-level Arctic clouds. ASCOS departed from Longyearbyen on Svalbard on 2 August and returned on 9 September 2008. In transit into and out of the pack ice, four short research stations were undertaken in the Fram Strait: two in open water and two in the marginal ice zone. After traversing the pack ice northward, an ice camp was set up on 12 August at 87°21′ N, 01°29′ W and remained in operation through 1 September, drifting with the ice. During this time, extensive measurements were taken of atmospheric gas and particle chemistry and physics, mesoscale and boundary-layer meteorology, marine biology and chemistry, and upper ocean physics. ASCOS provides a unique interdisciplinary data set for development and testing of new hypotheses on cloud processes, their interactions with the sea ice and ocean and associated physical, chemical, and biological processes and interactions. For example, the first-ever quantitative observation of bubbles in Arctic leads, combined with the unique discovery of marine organic material, polymer gels with an origin in the ocean, inside cloud droplets suggests the possibility of primary marine organically derived cloud condensation nuclei in Arctic stratocumulus clouds. Direct observations of surface fluxes of aerosols could, however, not explain observed variability in aerosol concentrations, and the balance between local and remote aerosols sources remains open. Lack of cloud condensation nuclei (CCN) was at times a controlling factor in low-level cloud formation, and hence for the impact of clouds on the surface energy budget. ASCOS provided detailed measurements of the surface energy balance from late summer melt into the initial autumn freeze-up, and documented the effects of clouds and storms on the surface energy balance during this transition. In addition to such process-level studies, the unique, independent ASCOS data set can and is being used for validation of satellite retrievals, operational models, and reanalysis data sets

Heat stress at preschool yards. A mixed-method geographical study in Gothenburg, Sweden.

As climate change is predicted to generate higher temperature and more frequent heat waves and extreme temperature events in Sweden, issues related to heat will be more accentuated in the future. Children are both vulnerable to heat and spend much of their time outdoors at preschool yards. This thesis has a broad approach to the issue of heat stress at preschool yards, where modelling of Tmrt as well as interviews with preschool teachers and planners has been conducted in order to explore how heat is affecting preschool yards in Gothenburg. Previous research has shown that shading and vegetation are key factors in lowering Tmrt, and that the urban environment has a great impact in regulating thermal conditions in urban environment. Furthermore, most studies conducted on heat and school environment has been focusing on harmful UV-radiation mitigation or indoor thermal environments. The study has been modelling Tmrt, shading and Sky view factor on 438 preschool yards in SOLWEIG and conducted interviews with 9 preschool teachers and 2 municipal actors involved with planning and preschool yards. The study results indicate that even though heat stress is present at preschool yards in Gothenburg, the issue of heat is mainly seen as an inconvenience rather than a problem and are thus underprioritized to measures of UV-radiation or other problems present at preschools and preschool yards. The study also conclude that shading is the most important factor for keeping low temperature at preschool yards, and that the most important factor of shading is found from trees. Trees and vegetation are also found to hold other desirable factors for preschool yards apart from heat mitigation

Heat stress at preschool yards. A mixed-method geographical study in Gothenburg, Sweden.

As climate change is predicted to generate higher temperature and more frequent heat waves and extreme temperature events in Sweden, issues related to heat will be more accentuated in the future. Children are both vulnerable to heat and spend much of their time outdoors at preschool yards. This thesis has a broad approach to the issue of heat stress at preschool yards, where modelling of Tmrt as well as interviews with preschool teachers and planners has been conducted in order to explore how heat is affecting preschool yards in Gothenburg. Previous research has shown that shading and vegetation are key factors in lowering Tmrt, and that the urban environment has a great impact in regulating thermal conditions in urban environment. Furthermore, most studies conducted on heat and school environment has been focusing on harmful UV-radiation mitigation or indoor thermal environments. The study has been modelling Tmrt, shading and Sky view factor on 438 preschool yards in SOLWEIG and conducted interviews with 9 preschool teachers and 2 municipal actors involved with planning and preschool yards. The study results indicate that even though heat stress is present at preschool yards in Gothenburg, the issue of heat is mainly seen as an inconvenience rather than a problem and are thus underprioritized to measures of UV-radiation or other problems present at preschools and preschool yards. The study also conclude that shading is the most important factor for keeping low temperature at preschool yards, and that the most important factor of shading is found from trees. Trees and vegetation are also found to hold other desirable factors for preschool yards apart from heat mitigation