NAP1L1-MLLT10 is a rare recurrent translocation that is associated with HOXA activation and poor treatment response in T-cell acute lymphoblastic leukaemia

International audienceno abstrac

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers

Chromosomal translocations are important drivers of hematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers, often called enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (IGH) and proto-oncogene CCND1 that are common in B cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterised the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with super-enhancer hijacking of other common oncogenes in B cell (MAF, MYC and FGFR3/NSD2) and in T-cell malignancies (LMO2, TLX3 and TAL1). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of epigenomic translocation, where the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers

RUNX1-dependent RAG1 deposition instigates human TCR-δ locus rearrangement

V(D)J recombination of TCR loci is regulated by chromatin accessibility to RAG1/2 proteins, rendering RAG1/2 targeting a potentially important regulator of lymphoid differentiation. We show that within the human TCR-α/δ locus

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Improved risk stratification of patients with atrial fibrillation: an integrated GARFIELD-AF tool for the prediction of mortality, stroke and bleed in patients with and without anticoagulation.

OBJECTIVES: To provide an accurate, web-based tool for stratifying patients with atrial fibrillation to facilitate decisions on the potential benefits/risks of anticoagulation, based on mortality, stroke and bleeding risks. DESIGN: The new tool was developed, using stepwise regression, for all and then applied to lower risk patients. C-statistics were compared with CHA2DS2-VASc using 30-fold cross-validation to control for overfitting. External validation was undertaken in an independent dataset, Outcome Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT-AF). PARTICIPANTS: Data from 39 898 patients enrolled in the prospective GARFIELD-AF registry provided the basis for deriving and validating an integrated risk tool to predict stroke risk, mortality and bleeding risk. RESULTS: The discriminatory value of the GARFIELD-AF risk model was superior to CHA2DS2-VASc for patients with or without anticoagulation. C-statistics (95% CI) for all-cause mortality, ischaemic stroke/systemic embolism and haemorrhagic stroke/major bleeding (treated patients) were: 0.77 (0.76 to 0.78), 0.69 (0.67 to 0.71) and 0.66 (0.62 to 0.69), respectively, for the GARFIELD-AF risk models, and 0.66 (0.64-0.67), 0.64 (0.61-0.66) and 0.64 (0.61-0.68), respectively, for CHA2DS2-VASc (or HAS-BLED for bleeding). In very low to low risk patients (CHA2DS2-VASc 0 or 1 (men) and 1 or 2 (women)), the CHA2DS2-VASc and HAS-BLED (for bleeding) scores offered weak discriminatory value for mortality, stroke/systemic embolism and major bleeding. C-statistics for the GARFIELD-AF risk tool were 0.69 (0.64 to 0.75), 0.65 (0.56 to 0.73) and 0.60 (0.47 to 0.73) for each end point, respectively, versus 0.50 (0.45 to 0.55), 0.59 (0.50 to 0.67) and 0.55 (0.53 to 0.56) for CHA2DS2-VASc (or HAS-BLED for bleeding). Upon validation in the ORBIT-AF population, C-statistics showed that the GARFIELD-AF risk tool was effective for predicting 1-year all-cause mortality using the full and simplified model for all-cause mortality: C-statistics 0.75 (0.73 to 0.77) and 0.75 (0.73 to 0.77), respectively, and for predicting for any stroke or systemic embolism over 1 year, C-statistics 0.68 (0.62 to 0.74). CONCLUSIONS: Performance of the GARFIELD-AF risk tool was superior to CHA2DS2-VASc in predicting stroke and mortality and superior to HAS-BLED for bleeding, overall and in lower risk patients. The GARFIELD-AF tool has the potential for incorporation in routine electronic systems, and for the first time, permits simultaneous evaluation of ischaemic stroke, mortality and bleeding risks. CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier for GARFIELD-AF (NCT01090362) and for ORBIT-AF (NCT01165710)

Two-year outcomes of patients with newly diagnosed atrial fibrillation: results from GARFIELD-AF.

AIMS: The relationship between outcomes and time after diagnosis for patients with non-valvular atrial fibrillation (NVAF) is poorly defined, especially beyond the first year. METHODS AND RESULTS: GARFIELD-AF is an ongoing, global observational study of adults with newly diagnosed NVAF. Two-year outcomes of 17 162 patients prospectively enrolled in GARFIELD-AF were analysed in light of baseline characteristics, risk profiles for stroke/systemic embolism (SE), and antithrombotic therapy. The mean (standard deviation) age was 69.8 (11.4) years, 43.8% were women, and the mean CHA2DS2-VASc score was 3.3 (1.6); 60.8% of patients were prescribed anticoagulant therapy with/without antiplatelet (AP) therapy, 27.4% AP monotherapy, and 11.8% no antithrombotic therapy. At 2-year follow-up, all-cause mortality, stroke/SE, and major bleeding had occurred at a rate (95% confidence interval) of 3.83 (3.62; 4.05), 1.25 (1.13; 1.38), and 0.70 (0.62; 0.81) per 100 person-years, respectively. Rates for all three major events were highest during the first 4 months. Congestive heart failure, acute coronary syndromes, sudden/unwitnessed death, malignancy, respiratory failure, and infection/sepsis accounted for 65% of all known causes of death and strokes for <10%. Anticoagulant treatment was associated with a 35% lower risk of death. CONCLUSION: The most frequent of the three major outcome measures was death, whose most common causes are not known to be significantly influenced by anticoagulation. This suggests that a more comprehensive approach to the management of NVAF may be needed to improve outcome. This could include, in addition to anticoagulation, interventions targeting modifiable, cause-specific risk factors for death. CLINICAL TRIAL REGISTRATION: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Mécanismes de régulation normale et pathologique des remaniements du locus TCRα/δ dans la lymphopoïèse thymique

La maturation des cellules lymphoïdes T est un processus thymique hautement régulé au cours duquel les réarrangements ordonnés des loci du TCRδ, y, β et enfin α déterminent le développement des lignées yδ et αβ. Les remaniements somatiques des segments géniques V, (D) et J du TCR font intervenir les protéines RAG1/2, les séquences RSS jouxtant ces segments et des éléments régulateurs (enhancers) assurant une cis-régulation de ce processus. Le contrôle de la recombinaison V(D)J se fait grâce à divers mécanismes incluant des mécanismes épigénétiques, l’intervention de facteurs de transcription et la conformation/séquence des RSS. Dans ce travail, nous montrons que les réarrangements du locus TCRδ sont strictement ordonnés chez l’Homme. Le premier réarrangement Dδ2-Dδ3 se produit à un stade ETP (Early T-cell Precursor) CD34+/CD1a-/CD7+dim, et précède systématiquement le réarrangement Dδ2-Jδ1. L’analyse in silico du locus a permis d’identifier un site de fixation clé pour le facteur de transcription RUNX1 à proximité immédiate de l’heptamètre Dδ2-23RSS chez l’Homme mais absent chez la souris. Le recrutement de RUNX1 sur ce site dans les thymocytes très immatures CD34+/CD3- permet d’augmenter l’affinité de fixation des protéines RAG1/2 sur le Dδ2-23RSS de manière spécifique. Ce travail identifie un rôle original de cofacteur de RUNX1 au cours de la recombinaison V(D)J dans la thymopoïèse humaine. Une série d’analyses épigénétiques exhaustives, menées dans le cadre du projet Européen Blueprint, sur les sous-populations thymiques humaines, nous a permis d’établir que l’enhanceosome du TCRα est constitué, comme chez la souris, dès les étapes les plus précoces de la thymopoïèse sans pour autant pouvoir s’activer avant la fin de la β-sélection. Nos résultats préliminaires suggèrent que les protéines homéotiques HOXA (notamment HOXA9) répriment l’activité de l’enhancer alpha (et donc les réarrangements du TCRα en interagissant avec le facteur de transcription ETS1 via leurs homéodomaines. Leur répression, induite par le passage de la β-sélection, aboutit à l’ouverture chromatinienne des segments Vα/Jα via l’activation du TCRα. Ces résultats apportent un éclairage nouveau sur le découplage jusqu’ici inexpliqué entre la formation de l’enhanceosome du TCRα à un stade très immature et son activation, permettant les réarrangements du locus, à un stade thymique bien plus tardif.Maturation of T lymphoid cells is a highly regulated process where ordered thymic rearrangements at the TCRδ, TCRy, TCRβ and finally TCRα loci determine the development into either yδ or αβ T-cell lineages. Somatic rearrangements of V, (D), and J gene segments of TCR loci involve RAG1/2 proteins, RSS sequences juxtaposing V, D, and J genes segments and regulatory elements (enhancers) providing a cis-regulation of this process. The control of the V(D)J recombination is achieved through various mechanisms including epigenetic modifications, involvement of transcription factors and RSS conformation/sequence. In this work, we show that TCRδ rearrangements are strictly ordered in Humans. The first Dδ2-Dδ3 rearrangement occurs at ETP (Early T-Cell Precursor) stage CD34+/CD1a-/CD7+dim, and always precedes Dδ2-Jδ1 rearrangement. In-silico analysis of the locus identified a key binding site for a transcription factor RUNX1 in close proximity to the Dδ2-23RSS heptamer in human, but not in mice. The RUNX1 recruitment at this site in immature CD34+/CD3- thymocytes increases binding affinity of RAG1/2 proteins. This work identifies an original cofactor of human VDJ recombination. A set of comprehensive epigenetic analysis conducted within the Europeen Blueprint project on human thymic subpopulations allowed as to establish that the TCRα enhanceosome (Eα), as in mice, is already formed from the earliest stages of thymopoiesis without being able to be activated before the end of β-selection. Our preliminary results suggest that HOXA homeobox proteins (including HOXA9) suppress the activity of the Eα (thus TCRα rearrangements) by interacting with the transcription factor ETS1 via their homeodomains. Induced by β-selection HOXA repression results in the chromatin opening of the Vα/Jα gene segments through TCRα activation. These finding shed new light on the so far unexplained shift observed between the formation of Eα enhanceosome at a very immature stages and its activation at a much later developmental stages

Silver and Copper Nanoparticles Inhibit Biofilm Formation by Mastitis Pathogens

Bovine mastitis is a common bovine disease, frequently affecting whole herds of cattle. It is often caused by resistant microbes that can create a biofilm structure. The rapidly developing scientific discipline known as nanobiotechnology may help treat this illness, thanks to the extraordinary properties of nanoparticles. The aim of the study was to investigate the inhibition of biofilms created by mastitis pathogens after treatment with silver and copper nanoparticles, both individually and in combination. We defined the physicochemical properties and minimal inhibitory concentration of the nanoparticles and observed their interaction with the cell membrane, as well as the extent of biofilm reduction. The results show that the silver–copper complex was the most active of all nanomaterials tested (biofilm was reduced by nearly 100% at a concentration of 200 ppm for each microorganism species tested). However, silver nanoparticles were also effective individually (biofilm was also reduced by nearly 100% at a concentration of 200 ppm, but at concentrations of 50 and 100 ppm, the extent of reduction was lower than for the complex). Nanoparticles can be used in new alternative therapies to treat bovine mastitis