CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.

We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short-read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/ .

Análisis de GATA1 en los trastornos mieloproliferativos asociados a la trisomía 21 / GATA1 analysis in myeloproliferative disorders associated to trisomy 21

Introducción: La enfermedad mieloproliferativa transitoria neonatal y la leucemia aguda megacarioblástica del síndrome de Down se consideran manifestaciones distintas de la misma enfermedad. La mayoría de casos de enfermedad mieloproliferativa transitoria no requiere tratamiento mientras que la leucemia aguda megacarioblástica del síndrome de Down se caracteriza por una elevada sensibilidad a la quimioterapia, lo que ha llevado a la reducción en la intensidad de dosis de tratamiento administrada. Ambas entidades comparten mutaciones específicas en los exones 2 y 3,1 del factor de transcripción GATA1. Pacientes y métodos: Hemos analizado los hallazgos biológicos incluyendo la presencia de mutaciones de GATA1 en cuatro pacientes con enfermedad mieloproliferativa transitoria neonatal (2) y leucemia aguda megacarioblástica (2) incluyendo un paciente fenotípicamente normal portador de un mosaicismo para la trisomía 21. Resultados: En los cuatro casos hemos encontrado la presencia de una clona GATA1 mutante y en tres de ellos se describe una mutación puntual en el exón 2 de dicho gen. Dada la heterogeneidad fenotípica de los blastos megacariocíticos y el bajo porcentaje de estos elementos, la detección de mutaciones en GATA1 resultó de gran utilidad para establecer el diagnóstico. Además, sucesivos resultados normales del análisis mutacional de GATA1 permitieron establecer la remisión molecular en 2 pacientes. Conclusiones: Concluimos que el análisis mutacional de GATA1 es una herramienta útil para el diagnóstico y manejo de los trastornos mieloproliferativos asociados a la trisomía 21 (AU)

Introduction: Neonatal transient myeloproliferative disorder and acute megakaryoblastic leukaemia of Down syndrome are considered different manifestations of the same disease. In most cases, transient myeloproliferative disorders require no treatment, while acute megakaryoblastic leukaemia of Down's syndrome is characterised by an increased sensitivity to chemotherapy and its treatment should be adapted with a reduction in dose intensity. Both entities share specific mutations at exón 2 of the transcription factor GATA1. Patients and methods: We analysed biological features and GATA1 mutations in 4 patients with transient abnormal myelopoiesis (2) and acute megakaryoblastic leukaemia (2) including one phenotypically normal trisomy 21 mosaicism. We found abnormal GATA1 mutated clones in each case, and a specific point mutation at exón 2 was detected in three cases. Given the heterogeneous phenotype of megakaryoblastic blasts and the low percentage of blasts at presentation, the recognition of GATA1 mutations was helpful for diagnosis. In addition, molecular remission was established in 2 patients after subsequent normal mutational GATA1 analysis. Conclusions: We conclude that GATA1 mutational study is a useful tool for the diagnosis and management of trisomy 21 associated myeloproliferative disorders (AU)

Clinical significance of Gata-1, Gata-2, EKLF, and c-MPL expression in acute myeloid leukemia.

The aim of this study was to evaluate the biological correlation and prognostic impact of Gata-1, Gata-2, EKLF, and c-MPL transcript level in a group of 41 acute myeloid leukemia (AML) patients. Gata-1 overexpression was related to advanced age and a low percentage of bone marrow blasts and was associated with the expression of CD34 antigen and lymphoid T markers. The negative impact of Gata-1 expression on the probability of achieving complete remission has been confirmed. Gata-2 overexpression was associated with a low percentage of blasts in BM and males. Expression of c-MPL was associated with CD34+ AML and M2 FAB AML subtype. A higher expression of EKLF was found in secondary AML versus primary AML. Nevertheless, patients expressing EKLF had a longer overall survival and event free survival than those patients that did not express EKLF. Our study has identified expression of EKLF as a factor with a favorable impact on prognosis in AML.

Antioxidant N-acetyl-L-cysteine inhibits erythropoietin-induced differentiation of erythroid progenitors derived from mouse fetal liver.

To determine the role of reactive oxygen species in erythroid differentiation, we investigated the effects of an antioxidant, N-acetyl-L-cysteine (NAC), on the differentiation of erythroid progenitors derived from mouse fetal liver. In response to erythropoietin (Epo), erythroid progenitors undergo differentiation in vitro and express erythroid-specific genes such as betamajor-globin, Alas2, MafK, p45, Eklf, and Gata1. Expression of these genes was decreased in the presence of NAC, whereas the expression of c-myb, which is downregulated during erythroid differentiation, remained constant. Moreover, NAC treatment inhibited an increase in the number of cells expressing high levels of erythroid-specific antigen TER119. Treatment with another antioxidant, pyrrolidine dithiocarbamate, also caused the attenuation of TER119 expression. These results suggest that reactive oxygen species are involved in Epo-mediated erythroid differentiation.

The effect of VEGF on blood vessels and blood cells during Xenopus development.

Vascular endothelial growth factor (VEGF) is known to play an essential role in vascular development. We have overexpressed VEGF122 or VEGF170, which are equivalent to mouse VEGF120 and VEGF164, in developing Xenopus embryos. Overexpression of VEGF170 but not VEGF122 demonstrated an absence of expression of hematopoietic markers alpha-globin and GATA-1 but only in the posterior portion of the blood island. Interestingly, strong signals of endothelial markers, msr, fli-1, and tie-2, were detectable in those regions, instead of hematopoietic markers. These results suggested both that injection of VEGF170 resulted in disturbance of vasculogenesis in the posterior portion of the blood island, with excessive production of endothelial cells at the expense of blood cells, and that the anterior and posterior portions of the VBI may have distinct characteristics.

Ethanol disrupts the formation of hypochord and dorsal aorta during the development of embryonic zebrafish.

Exposure to ethanol during human embryonic period has severe teratogenic effects on the cardiovascular system. In our study, we demonstrated that ethanol of gradient concentrations can interfere with the establishment of circulatory system in embryonic zebrafish. The effective concentration to cause 50% malformations (EC50) was 182.5 mmol/L. The ethanol pulse exposure experiment displayed that dome stage during embryogenesis is the sensitive time window to ethanol. It is found that 400 mmol/L ethanol pulse exposure can induce circulatory defects in 43% treated embryos. We ruled out the possibility that ethanol can interfere with the process of hematopoiesis in zebrafish. By employing in situ hybridization with endothelial biomarker (Flk-1), we revealed that ethanol disrupts the establishment of trunk axial vasculature, but has no effect on cranial vessels. Combined with the results of semi-thin histological sections, the in situ hybridization experiments with arterial and venous biomarkers (ephrinB2, ephB4) suggested that ethanol mainly interrupts the development of dorsal aorta while has little effect on axial vein. Further study indicated the negative influence of ethanol on the development of hypochord in zebrafish. The consequent lack of vasculogenic factors including Radar and Ang-1 partly explains the defects in formation and integrity of dorsal aorta. These results provide important clues to the study of adverse effects of ethanol on the cardiovascular development in human fetus.