Dynamic evolution of clonal epialleles revealed by methclone.

We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone.

An optimized algorithm for detecting and annotating regional differential methylation.

BACKGROUND: DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional analysis of enriched or whole-genome bisulfate conversion sequencing data, even though such data are increasingly common. Here, we describe an open-source, optimized method for determining empirically based DMRs (eDMR) from high-throughput sequence data that is applicable to enriched whole-genome methylation profiling datasets, as well as other globally enriched epigenetic modification data. RESULTS: Here we show that our bimodal distribution model and weighted cost function for optimized regional methylation analysis provides accurate boundaries of regions harboring significant epigenetic modifications. Our algorithm takes the spatial distribution of CpGs into account for the enrichment assay, allowing for optimization of the definition of empirical regions for differential methylation. Combined with the dependent adjustment for regional p-value combination and DMR annotation, we provide a method that may be applied to a variety of datasets for rapid DMR analysis. Our method classifies both the directionality of DMRs and their genome-wide distribution, and we have observed that shows clinical relevance through correct stratification of two Acute Myeloid Leukemia (AML) tumor sub-types. CONCLUSIONS: Our weighted optimization algorithm eDMR for calling DMRs extends an established DMR R pipeline (methylKit) and provides a needed resource in epigenomics. Our method enables an accurate and scalable way of finding DMRs in high-throughput methylation sequencing experiments. eDMR is available for download at http://code.google.com/p/edmr/.

Rituximab purging and/or maintenance in patients undergoing autologous transplantation for relapsed follicular lymphoma: a prospective randomized trial from the lymphoma working party of the European group for blood and marrow transplantation.

PURPOSE: The objective of this randomized trial was to assess the efficacy and safety of rituximab as in vivo purging before transplantation and as maintenance treatment immediately after high-dose chemotherapy and autologous stem-cell transplantation (HDC-ASCT) in patients with relapsed follicular lymphoma (FL). PATIENTS AND METHODS: Patients with relapsed FL who achieved either complete or very good partial remission with salvage chemotherapy were randomly assigned using a factorial design to rituximab purging (P+; 375 mg/m(2) once per week for 4 weeks) or observation (NP) before HDC-ASCT and to maintenance rituximab (M+; 375 mg/m(2) once every 2 months for four infusions) or observation (NM). RESULTS: From October 1999 to April 2006, 280 patients were enrolled. The median age was 51 years (range, 26 to 70 years), and baseline characteristics were well balanced between groups. On average, patients were 44 months (range, 3 to 464 months) from diagnosis, with 79% having received two lines and 15% three lines of prior therapy. Median follow-up was 8.3 years. In contrast to purging, 10-year progression-free survival (PFS) was 48% for P+ and 42% for NP groups (hazard ratio [HR], 0.80; 95% CI, 0.58 to 1.11; P = .18); maintenance had a significant effect on PFS (10-year PFS, 54% for M+ and 37% for NM; HR, 0.66; 95% CI, 0.47 to 0.91; P = .012). Overall survival (OS) was not improved by either rituximab purging or maintenance. CONCLUSION: Rituximab maintenance after HDC-ASCT is safe and significantly prolongs PFS but not OS in patients undergoing transplantation for relapsed FL. Pretransplantation rituximab in vivo purging, even in rituximab-naive patients, failed to improve PFS or OS.

Myeloid leukaemia treatment and survival--the South Australian experience, 1977 to 2002.

OBJECTIVE: To evaluate trends in survival and treatment for myeloid leukaemia in South Australia during 1977-2002, using population-based survival data plus data on survival and treatment of patients at three teaching hospitals. METHODS: Population data were analysed using relative survival methods and hospital registry data using disease-specific survival. Univariate and multivariable analyses were undertaken. Multiple logistic regression analysis was used to investigate factors associated with first-line chemotherapy. RESULTS: South Australia recorded 1,572 new cases of acute myeloid leukaemia (AML) in 1977-2002, together with 536 cases of chronic myeloid leukaemia (CML). Of these cases, 42.6% were recorded in teaching hospital registries. The five-year survival for AML at the teaching hospitals of 14.5% was similar to the corresponding 12.0% for South Australia as a whole. The five-year survival for CML at these hospitals was higher, however, at 48.1% compared with 37.5% for all South Australian cases. Younger patients had higher survivals, both for AML and CML. An increase in survival was evident for more recently diagnosed cases for both leukaemia types, after adjusting for age. This increase in survival was accompanied by an increase over time in the proportion of patients at teaching hospitals having a primary course of chemotherapy. Cytarabine in combination with other agents was the most common induction therapy for AML. While hydroxyurea was the most common first-line treatment of CML, there were changes in clinical policies towards higher-dose treatments, plus trials of new agents and combination therapies. CONCLUSIONS: Secular gains in survival have occurred from AML and CML in association with an increased use of chemotherapy.

Growth factor pleiotropy is controlled by a receptor Tyr/Ser motif that acts as a binary switch.

Pleiotropism is a hallmark of cytokines and growth factors; yet, the underlying mechanisms are not clearly understood. We have identified a motif in the granulocyte macrophage-colony-stimulating factor receptor composed of a tyrosine and a serine residue that functions as a binary switch for the independent regulation of multiple biological activities. Signalling occurs either through Ser585 at lower cytokine concentrations, leading to cell survival only, or through Tyr577 at higher cytokine concentrations, leading to cell survival as well as proliferation, differentiation or functional activation. The phosphorylation of Ser585 and Tyr577 is mutually exclusive and occurs via a unidirectional mechanism that involves protein kinase A and tyrosine kinases, respectively, and is deregulated in at least some leukemias. We have identified similar Tyr/Ser motifs in other cell surface receptors, suggesting that such signalling switches may play important roles in generating specificity and pleiotropy in other biological systems.

Non-HLA immunogenetic polymorphisms and the risk of complications after allogeneic hemopoietic stem-cell transplantation.

BACKGROUND: Existing data indicate that non-human leukocyte antigen (HLA) immunogenetic polymorphisms influence the risk of complications after allogeneic hemopoietic stem-cell transplantation. However, prior studies have been limited by small sample size and limited genotyping. METHODS: We examined 22 polymorphisms in 11 immunoregulatory genes including cytokines, mediators of apoptosis, and host-defense molecules by polymerase chain reaction using sequence-specific primers in 160 related myeloablative transplants. Associations were confirmed in two independent cohorts. RESULTS: An intronic polymorphism in the tumor necrosis factor gene (TNF 488A) was associated with the risk of acute graft-versus-host disease (GVHD) (odds ratio [OR] 16.9), grades II to IV acute GVHD (OR 3.3), chronic GVHD (OR 12.5), and early death posttransplant (OR 3.4). Recipient Fas -670G and donor interleukin (IL)-6 -174G were independent risk factors for acute GVHD. Recipient IL-10 ATA and Fas -670 genotype were independent risk factors for chronic GVHD. Recipient IL-1beta +3953T was associated with hepatic acute GVHD, and Fas -670G was associated with major infection. CONCLUSIONS: These results highlight the potential importance of cytokine and apoptosis gene polymorphisms in stem-cell transplantation, and indicate that non-HLA genotyping may be useful to identify individuals at the highest risk of complications and new targets for therapeutic intervention.

More than a sore mouth: patients' experience of oral mucositis.

PURPOSE/OBJECTIVES: To explore patients' experience of chemotherapy-induced oral mucositis. DESIGN: Interpretive descriptive, phenomenologic. SETTING: The cancer center of a metropolitan teaching hospital in South Australia. SAMPLE: A purposive sample of six participants undergoing intensive cytotoxic therapy associated with autologous hematopoietic stem cell transplantation. METHODS: Patients were interviewed at different stages of their treatment trajectory and asked to relate their experience of oral mucositis as it developed and resolved. FINDINGS: Participants' reports indicated three distinct phases representing linear time in the course of their mucositis: the preparatory phase, the peak phase, and the persisting phase. Five themes further abstracted were the presence of nurses, therapeutic interventions, manifestations of mucositis, the distress of eating (and not eating), and whether the treatment was worthwhile. CONCLUSIONS: Oral mucositis is much more than a sore mouth. The effects of mucositis are widespread and can have a marked effect on patients' psychological well-being. IMPLICATIONS FOR NURSING: Care centers often focus on pain control through pharmacologic intervention and overlook the effects of other sequelae. Nurses' role in helping patients to cope with mucositis should encompass more than providing pharmacologic pain relief.