| 1. |
- Milani, Lili, et al.
(författare)
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DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia.
- 2010
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 115:6, s. 1214-25
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Tidskriftsartikel (refereegranskat)abstract
- Despite improvements in the prognosis of childhood acute lymphoblastic leukemia (ALL), subgroups of patients would benefit from alternative treatment approaches. Our aim was to identify genes with DNA methylation profiles that could identify such groups. We determined the methylation levels of 1320 CpG sites in regulatory regions of 416 genes in cells from 401 children diagnosed with ALL. Hierarchical clustering of 300 CpG sites distinguished between T-lineage ALL and B-cell precursor (BCP) ALL and between the main cytogenetic subtypes of BCP ALL. It also stratified patients with high hyperdiploidy and t(12;21) ALL into 2 subgroups with different probability of relapse. By using supervised learning, we constructed multivariate classifiers by external cross-validation procedures. We identified 40 genes that consistently contributed to accurate discrimination between the main subtypes of BCP ALL and gene sets that discriminated between subtypes of ALL and between ALL and controls in pairwise classification analyses. We also identified 20 individual genes with DNA methylation levels that predicted relapse of leukemia. Thus, methylation analysis should be explored as a method to improve stratification of ALL patients. The genes highlighted in our study are not enriched to specific pathways, but the gene expression levels are inversely correlated to the methylation levels.
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| 2. |
- Nordlund, Jessica, et al.
(författare)
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DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia
- 2015
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Ingår i: Clinical Epigenetics. - : Springer Science and Business Media LLC. - 1868-7083 .- 1868-7075. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background: 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. Results: We used the methylation status of similar to 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. Conclusions: 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.
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| 3. |
- Nordlund, Jessica, et al.
(författare)
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Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
- 2013
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 14:9, s. r105-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resistance and relapse in ALL is poorly understood.RESULTS:We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status.CONCLUSIONS:Our results suggest an important biological role for DNA methylation in the differences between ALL subtypes and in their clinical outcome after treatment.
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| 4. |
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| 5. |
- Aeppli, Christoph, et al.
(författare)
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Use of Cl and C Isotopic Fractionation to Identify Degradation and Sources of Polychlorinated Phenols : Mechanistic Study and Field Application
- 2013
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 47:2, s. 790-797
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Tidskriftsartikel (refereegranskat)abstract
- The widespread use of chlorinated phenols (CPs) as a wood preservative has led to numerous contaminated sawmill sites. However, it remains challenging to assess the extent of in situ degradation of CPs. We evaluated the use of compound-specific chlorine and carbon isotope analysis (Cl- and C-CSLA) to assess CP biotransformation. In a laboratory system, we measured isotopic fractionation during oxidative 2,4,6-trichlorophenol dechlorination by representative soil enzymes (C. fumago chloroperoxidase, horseradish peroxidase, and laccase from T. versicolor). Using a mathematical model, the validity of the Rayleigh approach to evaluate apparent kinetic isotope effects (AKIE) was confirmed. A small but significant Cl-AKIE of 1.0022 +/- 0.0006 was observed for all three enzymes, consistent with a reaction pathway via a cationic radical species. For carbon, a slight inverse isotope effect was observed (C-AKIE = 0.9945 +/- 0.0019). This fractionation behavior is clearly distinguishable from reported reductive dechlorination mechanisms. Based on these results we then assessed degradation and apportioned different types of technical CP mixtures used at two former sawmill sites. To our knowledge, this is the first study that makes use of two-element CSIA to study sources and transformation of CPs in the environment.
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| 6. |
- Blohm, My, et al.
(författare)
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Learning by doing : an observational study of the learning curve for ultrasonic fundus-first dissection in elective cholecystectomy
- 2022
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Ingår i: Surgical Endoscopy. - : Springer. - 0930-2794 .- 1432-2218. ; 36, s. 4602-4613
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Surgical safety and patient-related outcomes are important considerations when introducing new surgical techniques. Studies about the learning curves for different surgical procedures are sparse. The aim of this observational study was to evaluate the learning curve for ultrasonic fundus-first (FF) dissection in elective laparoscopic cholecystectomy (LC).METHODS: The study was conducted at eight hospitals in Sweden between 2017 and 2019. The primary endpoint was dissection time, with secondary endpoints being intra- and postoperative complication rates and the surgeon's self-assessed performance level. Participating surgeons (n = 16) were residents or specialists who performed LC individually but who had no previous experience in ultrasonic FF dissection. Each surgeon performed fifteen procedures. Video recordings from five of the procedures were analysed by two external surgeons. Patient characteristics and data on complications were retrieved from the Swedish Registry of Gallstone Surgery and Endoscopic Retrograde Cholangiopancreatography (GallRiks).RESULTS: Dissection time decreased as experience increased (p = 0.001). Surgeons with limited experience showed more rapid progress. The overall complication rate was 14 (5.8%), including 3 (1.3%) potentially technique-related complications. Video assessment scores showed no correlation with the number of procedures performed. The self-assessed performance level was rated lower when the operation was more complicated (p < 0.001).CONCLUSIONS: Our results show that dissection time decreased with increasing experience. Most surgeons identified both favourable and unfavourable aspects of the ultrasonic FF technique. The ultrasonic device is considered well suited for gallbladder surgery, but most participating surgeons preferred to dissect the gallbladder the traditional way, beginning in the triangle of Calot. Nevertheless, LC with ultrasonic FF dissection can be considered easy to learn with a low complication rate during the initial learning curve, for both residents and specialists.
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| 7. |
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| 8. |
- Brattsand, Göran, et al.
(författare)
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Equalis/SFKK rekommenderar harmonisering av enheter vid hormonbestämningar -Något också för Norden?
- 2012
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Ingår i: Klinisk Biokemi i Norden. - 1101-2013. ; 24:4, s. 20-27
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Tidskriftsartikel (refereegranskat)abstract
- Equalis och Svensk Förening för Klinisk Kemi (SFKK) rekommenderar att de kliniska laboratorierna i Sverige använder enhetliga måttenheter vid hormonbestämningar för ökad jämförbarhet och patientsäkerhet. Vid analys i serum eller plasma med nuvarande metoder rekommenderas följande enheter:• Adrenokortikotropt hormon (ACTH): pmol/L• Insulin: mIE/L• Parathormon (PTH): pmol/L• Prolaktin: mIE/L• Tillväxthormon (GH): μg/L• Östradiol: pmol/L• Aldosteron: pmol/L• Reninkoncentration: mIE/L
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| 9. |
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| 10. |
- Campbell, D, et al.
(författare)
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The cyanobacterium Synechococcus resists UV-B by exchanging photosystem II reaction-center D1 proteins
- 1998
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 95:1, s. 364-369
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Tidskriftsartikel (refereegranskat)abstract
- Current ambient UV-B levels can significantly depress productivity in aquatic habitats, largely because UV-B inhibits several steps of photosynthesis, including the photooxidation of water catalyzed by photosystem II, We show that upon UV-B exposure the cyanobacterium Synechococcus sp, PCC 7942 rapidly changes the expression of a family of three psbA genes encoding photosystem II D1 proteins, In wild-type cells the psbAI gene is expressed constitutively, but strong accumulations of psbAII and psbAIII transcripts are induced within 15 min of moderate UV-B exposure (0.4 W/m(2)), This transcriptional response causes an exchange of two distinct photosystem II D1 proteins, D1:1 is encoded by psbAI, but on UV-B exposure, it is largely replaced by the alternate D1:2 form, encoded by both psbAII and psbAIII, The total content of D1 and other photosystem II reaction center protein, D2, remained unchanged throughout the UV exposure, as did the content and composition of the phycobilisome, Wild-type cells suffered only slight transient inhibition of photosystem II function under UV-B exposure, In marked contrast, under the same UV-B treatment, a mutant strain expressing only psbAI suffered severe (40%) and sustained inhibition of photosystem II function, Another mutant strain with constitutive expression of psbAII and psbAIII was almost completely resistant to the UV-B treatment, showing no inhibition of photosystem II function and only a slight drop in electron transport, In Synechococcus the rapid exchange of alternate D1 forms, therefore, accounts for much of the cellular resistance to UV-B inhibition of photosystem II activity and photosynthetic electron transport, This molecular plasticity may be an important element in community-level responses to UV-B, where susceptibility to UV-B inhibition of photosynthesis changes diurnally.
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