Targeting Chromatin Complexes in Myeloid Malignancies and Beyond: From Basic Mechanisms to Clinical Innovation

The aberrant function of chromatin regulatory networks (epigenetics) is a hallmark of cancer promoting oncogenic gene expression. A growing body of evidence suggests that the disruption of specific chromatin-associated protein complexes has therapeutic potential in malignant conditions, particularly those that are driven by aberrant chromatin modifiers. Of note, a number of enzymatic inhibitors that block the catalytic function of histone modifying enzymes have been established and entered clinical trials. Unfortunately, many of these molecules do not have potent single-agent activity. One potential explanation for this phenomenon is the fact that those drugs do not profoundly disrupt the integrity of the aberrant network of multiprotein complexes on chromatin. Recent advances in drug development have led to the establishment of novel inhibitors of protein–protein interactions as well as targeted protein degraders that may provide inroads to longstanding effort to physically disrupt oncogenic multiprotein complexes on chromatin. In this review, we summarize some of the current concepts on the role epigenetic modifiers in malignant chromatin states with a specific focus on myeloid malignancies and recent advances in early-phase clinical trials

LISA Science Results in the Presence of Data Disturbances

Each spacecraft in the Laser Interferometer Space Antenna houses a proof mass which follows a geodesic through spacetime. Disturbances which change the proof mass position, momentum, and/or acceleration will appear in the LISA data stream as additive quadratic functions. These data disturbances inhibit signal extraction and must be removed. In this paper we discuss the identification and fitting of monochromatic signals in the data set in the presence of data disturbances. We also present a preliminary analysis of the extent of science result limitations with respect to the frequency of data disturbances

eXframe: reusable framework for storage, analysis and visualization of genomics experiments

<p>Abstract</p> <p>Background</p> <p>Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types.</p> <p>Results</p> <p>We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients.</p> <p>Conclusion</p> <p>The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.</p

Prosody, Accessibility, and Sentential Negation in Brazilian Portuguese

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Singular solutions of fully nonlinear elliptic equations and applications

We study the properties of solutions of fully nonlinear, positively homogeneous elliptic equations near boundary points of Lipschitz domains at which the solution may be singular. We show that these equations have two positive solutions in each cone of $\mathbb{R}^n$, and the solutions are unique in an appropriate sense. We introduce a new method for analyzing the behavior of solutions near certain Lipschitz boundary points, which permits us to classify isolated boundary singularities of solutions which are bounded from either above or below. We also obtain a sharp Phragm\'en-Lindel\"of result as well as a principle of positive singularities in certain Lipschitz domains.Comment: 41 pages, 2 figure

A novel mutation in the miR-128b gene reduces miRNA processing and leads to glucocorticoid resistance of MLL-AF4 Acute Lymphocytic Leukemia cells

MLL-AF4 Acute Lymphocytic Leukemia has a poor prognosis, and the mechanisms by which these leukemias develop are not understood despite intensive research based on well-known concepts and methods. MicroRNAs (miRNAs) are a new class of small noncoding RNAs that post-transcriptionally regulate expression of target mRNA transcripts. We recently reported that ectopic expression of miR-128b together with miR-221, two of the miRNAs downregulated in MLL-AF4 ALL, restores glucocorticoid resistance through downregulation of the MLL-AF4 chimeric fusion proteins MLL-AF4 and AF4-MLL that are generated by chromosomal translocation t(4;11). Here we report the identification of new mutations in miR-128b in RS4;11 cells, derived from MLL-AF4 ALL patient. One novel mutation significantly reduces the processing of miR-128b. Finally, this base change occurs in a primary MLL-AF4 ALL sample as an acquired mutation. These results demonstrate that the novel mutation in miR-128b in MLL-AF4 ALL alters the processing of miR-128b and that the resultant downregulation of mature miR-128b contributes to glucocorticoid resistance through the failure to downregulate the fusion oncogenes.National Institutes of Health (U.S.) (NIH Grant R01 DK068348)Netherlands Organization for Scientific ResearchDutch Cancer SocietyJapan Society for the Promotion of Scienc

Pesticide Ground Water Monitoring Project Phase VIII

During Phase VIII monitoring (March 24, 2000 to June 30, 2001 ), 86 samples were collected from 77 new wells and 9 samples were collected from wells with previous detectable herbicide

Epidemiology of Contemporary Seroincident HIV Infection in the Navy and Marine Corps

Human Immunodeficiency Virus (HIV) infection continues at a steady rate among U.S. Sailors and Marines. This study provides the first service-specific description of HIV infection demographics. All Sailors and Marines identified as HIV infected between January 2005 and August 2010 were included. The project compared personnel and epidemiologic data, and tested reposed sera in the Department of Defense Serum Repository. This group comprised 410 Sailors and 86 Marines, predominantly men. HIV infected Marines were more likely to be foreign born than their Navy counterparts, 42% versus 10%, p \u3c 0.001. Approximately half of the patients had deployed including to the wars in Iraq or Afghanistan. Nearly half of each group was infected by the age of 25. Similar to the U.S. epidemic, Black race was over-represented. Unlike national rates, Hispanic Sailors and Marines were not over-represented. Demographics were distinct for those of specific occupational specialties. Certain ship classes carried lower incidences. Clustering of HIV infection risk occurred around deployment. The Navy and Marine Corps have different patterns of HIV infection, which may merit distinct approaches to prevention. The Navy may have unique targets for prevention efforts to include pipeline training and first assignment as well as particular occupational environments

The relative importance of graft surveillance and warfarin therapy in infrainguinal prosthetic bypass failure

BackgroundWe sought to describe modes of failure and associated limb loss after infrainguinal polytetrafluoroethylene bypass grafting in patients lacking a saphenous venous conduit and to define specific clinical or hemodynamic factors prognostic for bypass failure.MethodsWe identified 121 patients (mean age, 67 years; 90 men and 31 women) with determinable outcomes (minimum follow-up, 2 months; mean, 17 months) after 130 prosthetic infrainguinal bypasses between 1997 and 2005. Ischemic presentation was rest pain in 52%, tissue loss in 34%, and disabling claudication and/or popliteal aneurysm in 14%, with 24% of patients requiring a redo bypass. Distal targets were the above-knee (n = 44), distal popliteal (n = 27), or tibial/pedal (n = 59) arteries. Sixty-six (77%) of the below-knee (BK) target (distal popliteal or tibial) bypasses had distal anastomotic adjuncts (vein cuff or patch). Duplex graft surveillance was performed at 1, 4, and 7 months after surgery and twice yearly thereafter, with recording of midgraft velocities and imaging encompassing inflow and outflow vessels. Arteriography and open/endovascular intervention was performed for stenoses identified by duplex scanning (peak systolic velocity >300 cm/s; velocity ratio >3.5). An attempt was made to salvage occluded grafts by using catheter-directed thrombolysis or open techniques. Eighty-six patients (74% of BK bypasses) were placed on chronic warfarin therapy with a target international normalized ratio range between 2 and 3. Prognostic factors were identified by using univariate statistics and multivariate logistic regression analysis.ResultsThree-year primary, assisted, and secondary patency rates were 39%, 43%, and 59%, respectively, for all bypasses, with no difference noted between above-knee and BK grafts (P = .5). At 3 years, freedom from limb loss was 75%, and patient survival was only 70%, with no adverse effect on survival imparted by amputation. Sixty-nine total adverse events occurred as a result of thrombotic occlusion (n = 51), duplex scan–detected stenosis (n = 13), or graft infection (n = 5). Forty-nine percent of all initial graft occlusions eventually led to amputation. Twenty-three grafts (27% of 86 patients) in patients maintained on chronic warfarin were subtherapeutic at the time of occlusion. Use of a distal anastomotic adjunct with BK bypasses reduced graft thrombosis (35% with vs 60% without) but did not impart a significant patency advantage (P = .07). Multivariate analysis revealed low graft flow (midgraft velocity ≤45 cm/s; odds ratio [OR], 6.1; 95% confidence interval [CI], 1.9-19.2), use of warfarin (OR, 8.4; 95% CI, 2.1-34.5), and therapeutic warfarin (OR, 24.6; 95% CI, 5.7-106) to be independently predictive for bypass patency. Graft patency was maintained in 89% of grafts remaining therapeutic on warfarin compared with only 55% of subtherapeutic or nonanticoagulated grafts (P < .001). Low-flow grafts (n = 61) occluded more frequently than higher-flow grafts (46% vs 13%; P < .001). Therapeutic warfarin augmented the patency of low-flow (P < .001) but not high-flow (P = .15) grafts.ConclusionsLow graft flow was a more common mode of prosthetic bypass failure than development of duplex scan–detected stenotic lesions during follow-up. Early duplex scanning may be more important for characterizing midgraft velocity and related thrombotic potential and selecting patients for chronic anticoagulation. Maintenance of therapeutic warfarin is paramount in optimizing prosthetic bypass patency and limb preservation