The zCOSMOS 10k-Bright Spectroscopic Sample

We present spectroscopic redshifts of a large sample of galaxies with I_(AB) < 22.5 in the COSMOS field, measured from spectra of 10,644 objects that have been obtained in the first two years of observations in the zCOSMOS-bright redshift survey. These include a statistically complete subset of 10,109 objects. The average accuracy of individual redshifts is 110 km s^(–1), independent of redshift. The reliability of individual redshifts is described by a Confidence Class that has been empirically calibrated through repeat spectroscopic observations of over 600 galaxies. There is very good agreement between spectroscopic and photometric redshifts for the most secure Confidence Classes. For the less secure Confidence Classes, there is a good correspondence between the fraction of objects with a consistent photometric redshift and the spectroscopic repeatability, suggesting that the photometric redshifts can be used to indicate which of the less secure spectroscopic redshifts are likely right and which are probably wrong, and to give an indication of the nature of objects for which we failed to determine a redshift. Using this approach, we can construct a spectroscopic sample that is 99% reliable and which is 88% complete in the sample as a whole, and 95% complete in the redshift range 0.5 < z < 0.8. The luminosity and mass completeness levels of the zCOSMOS-bright sample of galaxies is also discussed

Mass and environment as drivers of galaxy evolution in SDSS and zCOSMOS and the origin of the Schechter function

We explore the inter-relationships between mass, star-formation rate and environment in the SDSS, zCOSMOS and other surveys. The differential effects of mass and environment are completely separable to z ~ 1, indicating that two distinct processes are operating, "mass-quenching" and "environment-quenching". Environment-quenching, at fixed over-density, evidently does not change with epoch to z ~ 1, suggesting that it occurs as large-scale structure develops in the Universe. The observed constancy of the mass-function shape for star-forming galaxies, demands that the mass-quenching of galaxies around and above M*, must be proportional to their star-formation rates at all z < 2. We postulate that this simple mass-quenching law also holds over a much broader range of stellar mass and epoch. These two simple quenching processes, plus some additional quenching due to merging, then naturally produce (a) a quasi-static Schechter mass function for star-forming galaxies with a value of M* that is set by the proportionality between the star-formation and mass-quenching rates, (b) a double Schechter function for passive galaxies with two components: the dominant one is produced by mass-quenching and has exactly the same M* as the star-forming galaxies but an alpha shallower by +1, while the other is produced by environment effects and has the same M* and alpha as the star-forming galaxies, and is larger in high density environments. Subsequent merging of quenched galaxies modifies these predictions somewhat in the denser environments, slightly increasing M* and making alpha more negative. All of these detailed quantitative relationships between the Schechter parameters are indeed seen in the SDSS, lending strong support to our simple empirically-based model. The model naturally produces for passive galaxies the "anti-hierarchical" run of mean ages and alpha-element abundances with mass.Comment: 66 pages, 19 figures, 1 movie, accepted for publication in ApJ. The movie is also available at http://www.exp-astro.phys.ethz.ch/zCOSMOS/MF_simulation_d1_d4.mo

Role of ASXL2 in Normal and Malignant Hematopoiesis

Les gènes ASXL (ASXL1, ASXL2 et ASXL3) sont les homologues mammifères du gène Additional sex combs (Asx) présent chez la Drosophile. En 2009, des mutations somatiques impliquant ASXL1 ont été identifiées chez ~ 10-20% des patients atteints d’hémopathies myéloïdes. Le rôle et l’implication des autres membres de la famille dans l’hématopoïèse normale et pathologique sont encore inconnus.Dans ce travail, nous avons identifié pour la 1ère fois, par séquençage haut débit, des mutations somatiques récurrentes d’ASXL2 (22,7%) chez des adultes et enfants atteints de leucémies aiguës myéloïdes (LAM) avec translocation t(8 ;21) (c.-à-d AML1-ETO (AE) ou RUNX1/RUNX1T1). Ces mutations n’ont pas été retrouvées dans d’autres sous types de LAM et sont mutuellement exclusives des mutations d’ASXL1. Le séquençage de l'ARN (RNAseq) d'échantillons de patients a révélé un profil transcriptionnel spécifique chez les patients mutés pour ASXL2. Bien que la survie globale soit similaire, les patients porteurs de mutations d’ASXL1 ou ASXL2 ont une incidence cumulative de rechute de 54,6% et 36,0% comparativement à 25% pour les patients non mutés (P = 0,226). Ces résultats, évoquant une coopération entre ASXL1/2 et AE lors de la leucémogenèse, sont importants car les t(8 ;21) sont parmi les anomalies cytogénétiques les plus fréquentes en matière de LAM. D’autre part, il est bien établi que AE nécessite la coopération d’altérations géniques supplémentaires pour induire la leucémie.Nous avons ensuite exploré le rôle d’ASXL2 dans l’hématopoïèse normale. Nous avons d’abord démontré in vitro que les mutations d’ASXL2 entrainent une diminution de son expression. Nous avons ensuite généré un modèle de souris invalidées pour Asxl2 (KO conditionnel). Par transplantations compétitive et non compétitive, nous avons montré que le KO pour Asxl2 ou Asxl1 et Asxl2 (double KO) induit une diminution et un défaut d’auto renouvellement des cellules souches hématopoïétiques (CSH) ainsi que des cytopénies, avec un phénotype plus sévère que le KO d’Asxl1 seul. L’analyse du transcriptome (par RNAseq) des CSH a révélé un nombre de gènes dérégulés par la perte d’Asxl2 25 fois plus important qu’avec Asxl1. De plus les gènes dérégulés par la perte d’Asxl2 recoupent les cibles transcriptionnelles d’AML1-ETO. Ces données suggérant qu’Asxl2 pourrait être un médiateur important de la leucémogenèse, nous avons ensuite étudié le rôle d’ASXL2 dans les LAM avec t(8 ;21). In vitro, par CHIP Seq, nous avons mis en évidence, dans des lignées t(8;21), un enrichissement des sites de liaisons à l’ADN d’ASXL2 au niveau de ceux d’AML1-ETO. De plus, en infectant ces lignées avec un shRNA dirigé contre ASXL2, nous avons étudié la marque H3K4me1 qui est augmentée de façon majeure dans le contexte leucémique. Afin de comprendre les effets in vivo d’ASXL2 dans la leucémogenèse, nous avons réalisé des greffes de cellules de moelle osseuse de souris KO infectées avec un rétrovirus pour AE9a. Ces souris développent une LAM plus rapidement que les souris contrôles AE9a lors de greffes secondaires, suggérant à nouveau un rôle spécifique d’Asxl2. Afin d’élucider le mécanisme impliqué, nous avons réalisé de l’ATAC seq sur ces souris et mis en évidence des différences importantes dans l’accessibilité de la chromatine, notamment au niveau des gènes Hoxa et Meis1.Pour la première fois, nous décrivons l’incidence des mutations d’ASXL2 dans les LAM et le rôle d’ASXL2 dans l’hématopoïèse. Nous suggèrerons un rôle spécifique dans les LAM avec t(8;21), qui pourrait être associé à des modifications de la marque d’histone H3K4me1. Ces spécificités pourraient résulter en de nouvelles options thérapeutiques chez les patients.The ASXL family of genes (ASXL1, ASXL2, and ASXL3) are mammalian homologs of the Drosophilia Additional sex combs (Asx) gene. In 2009 somatic mutations involving ASXL1 were originally identified in ~10-20% of patients with myeloid malignancies. Despite this association, alterations in other ASXL family members and their potential function in normal or malignant hematopoiesis were unknown.We identified, by next generation sequencing, the surprising finding of highly recurrent somatic ASXL2 mutations (22.7%) in adult and pediatric acute myeloid leukemia (AML) patients bearing the AML1-ETO (AE) translocation (i.e. RUNX1/RUNX1T1, t(8;21)). Interestingly these mutations were only found in patients with t(8 ;21) and mutually exclusive with ASXL1 mutations. RNA sequencing (RNAseq) of primary AE AML patient samples revealed that ASXL2-mutants form a distinct transcriptional subset of AE AML. Although overall survival was similar between ASXL1 and ASXL2 mutant t(8;21) AML patients and their wild-type counterparts, patients with ASXL1 or ASXL2 mutations had a cumulative incidence of relapse of 54.6% and 36.0%, respectively, compared with 25% in ASXL1/2 wild-type counterparts (P=0.226). These findings are of immediate biological importance as AE translocations are amongst the most common cytogenetic alterations in AML and it is well established that AE requires additional genetic alterations to induce leukemogenesis.Given the above human genetic data, we set out to perform a functional comparison of ASXL1 and ASXL2 on hematopoiesis and determine the functional basis for frequent mutations in AE AML. In vitro analyses of ASXL2 mutations revealed that these mutations resulted in substantial reduction of ASXL2 protein expression. We therefore generated Asxl2 conditional knockout (cKO) mice to delineate the effect of ASXL2 loss on hematopoiesis. Competitive and noncompetitive transplantation revealed that Asxl2 or compound Asxl1/2 loss resulted in cell-autonomous, rapid defects of hematopoietic stem cell (HSC) function, self-renewal, and number with peripheral blood leukopenia and thrombocytopenia. RNA-seq of HSCs revealed twenty-fold greater differentially expressed genes in Asxl2 cKO mice relative to Asxl1 cKO mice. Interestingly, genes differentially expressed with Asxl2 loss significantly overlapped with direct transcriptional targets of AE, findings not seen in Asxl1 cKO mice.Overall, the above data suggest that Asxl2 may be a critical mediator of AE leukemogenesis. To functionally interrogate the role of ASXL2 loss in leukemogenesis we first utilized an in vitro model with RNAi-mediated depletion of ASXL2 in the SKNO1 cell line. Anti-ASXL2 and AE ChIPSeq revealed significant co-occupancy of ASXL2 with AE binding sites. Moreover, analysis of histone modification ChIP-Seq revealed an enrichment in intergenic and enhancer H3K4me1 abundance following ASXL2 loss. Next, to understand the in vivo effects of Asxl2 loss in the context of AE, we performed retroviral bone marrow (BM) transplantation assays using AE9a in Asxl2 cKO mice. In contrast to the failure of HSC function with Asxl2 deletion alone, mice reconstituted with BM cells expressing AE9a in Asxl2-deficient background had a shortened leukemia-free survival compared to Asxl2-wildtype control. Moreover, ATAC Sequencing showed an increase of chromatin occupancy with Asxl2 loss at known leukemogenic loci, including the HoxA and Meis1 loci.Overall, these data reveal that ASXL2 is required for hematopoiesis and has differing biological and transcriptional functions from ASXL1. Moreover, this work identifies ASXL2 as a novel mediator of AE transcriptional function and provides a new model of penetrant AE AML based on genetic events found in a substantial proportion of t(8;21) AML patients. Further interrogation of the enhancer alterations generated by ASXL2 loss in AE AML may highlight new therapeutic approaches for this subset of AM

Impact de l'Imatinib sur la prévalence de la leucémie myéloïde chronique dans la région Nord-Pas-de-Calais

LILLE2-BU Santé-Recherche (593502101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

INRAtion 2.6, Programa informatico de calculo, analisis y gestion de raciones en rumiantes

International audienc

INRAtion 2.6, Programa informatico de calculo, analisis y gestion de raciones en rumiantes

International audienc

Distinct DNA Methylation and Expression Profiles Underlie CMML Responsiveness to Decitabine and Uncover Novel Mechanism of Resistance

Abstract Myelodysplastic syndromes (MDS) and the related disorder chronic myelomonocytic leukemia (CMML) are characterized by abnormal DNA hypermethylation and the DNA methyltransferase inhibitors (DMTis) azacytidine and decitabine (DAC) are frequently used as frontline therapy in these patients. However, DMTis are ineffective for ~50% of the patients who must still undergo treatment for at least 6 months before they can be deemed resistant. Therefore, it is of critical importance to identify baseline molecular differences associated with DMTi sensitivity that can help (i) to improve patient risk-stratification at diagnosis and (ii) identify the underlying mechanisms of resistance to these agents. Previous efforts to identify baseline DNA methylation differences at promoter regions between DMTi responders and non-responders have not been successful, so we hypothesized that any potential differences would be located distally from promoter regions. For this purpose we studied 40 CMML patients at diagnosis, all of whom had been uniformly treated with DAC 20 mg/m2/day x 5 days as frontline therapy. After 6 cycles of therapy patients were classified as responders (n=19, hematological improvement or better), or non-responders (n=21, stable or progressive disease). Mutational analysis showed no significant differences in the frequency of mutations in TET2, ASXL1, DNMT3A, RUNX1, TP53, JAK2, KIT, KRAS, EZH2, IDH1/2 and spliceosome genes. Using Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) we analyzed the baseline methylation status at ~3M CpG sites across the genome of 39/40 CMML patients. We identified 158 statistically significant differentially methylated regions (DMRs) (FDR<0.1 and methylation difference ≥25%) between the two groups. DAC-sensitive patients displayed both regions of higher methylation as well as regions with lower methylation compared to DAC-resistant patients. As predicted, DMRs were depleted at promoters (DMRs 9% vs. Background [BG] 21%, p-value: 3.4×10-5) and CpG islands (DMRs 8% vs. BG 25%, p-value: 1.5×10-8). Further analysis showed that hypermethylated DMRs were enriched at intronic regions (Hyper DMRs 58% vs. BG 33%, p-value: 3.7×10-6) while hypomethylated DMRs were enriched at intergenic regions (Hypo DMRs 49% vs. BG 38%, p-value: 2.6×10-2). Moreover, hypermethylated DMRs were significantly enriched for enhancer regions, and in particular, enhancers located within gene bodies (hyper DMRs 38% vs. BG 18%, p-value: 2.3×10-5). KEGG pathway analysis showed a significant enrichment of DMRs in the MAPK signaling pathway (FDR<0.01). Next, using a support vector machine algorithm with 10-fold cross validation we were able to develop a classifier capable of predicting response to DAC with high level of accuracy (ROC AUC: 0.99) based solely on the DNA methylation status at diagnosis of 17 genomic regions. Three different random splits of the cohort into training and test sets achieved correct predictions for 85.7%, 89.47%, and 100% of cases, respectively, demonstrating the accuracy and potential utility of such a classifier. Finally, RNA-seq analysis identified 53 differentially expressed genes between responders (n=8) and non-responders (n=6) at diagnosis. Genes implicated in cell cycle and DNA replication were overexpressed in responders. By contrast, very few genes were overexpressed at the time of diagnosis in primary resistant patients. Among these were CXCL4 and CXCL7 which, given their reported contributions to cell cycle arrest and chemoresistance, were tested for their functional roles in DAC resistance. Pre-treatment of normal CD34+ cells for 72 h with 10nM DAC significantly reduced colony formation (p<0.05) but the addition of 50ng/mL of CXCL4 and CXCL7 restored colony formation to that of untreated cells. Moreover, treatment of primary CMML cells with 10 nM DAC for 72h significantly reduced viability of these cells, while concomitant treatment with 50ng/mL of CXCL4 and CXCL7 was sufficient to abrogate this effect. Taken together, our findings demonstrate that (i) specific DNA methylation profiles targeting non-promoter regulatory regions are associated with DAC sensitivity, (ii) these differences can be harnessed for the development of clinical biomarkers predictive of response and (iii) we identified a novel mechanism of resistance to DAC mediated through two chemokines that are exclusively overexpressed in non-responders. Disclosures No relevant conflicts of interest to declare

JAK2 and MPL protein levels determine TPO-induced megakaryocyte proliferation vs differentiation.

Megakaryopoiesis is a 2-step differentiation process, regulated by thrombopoietin (TPO), on binding to its cognate receptor myeloproliferative leukemia (MPL). This receptor associates with intracytoplasmic tyrosine kinases, essentially janus kinase 2 (JAK2), which regulates MPL stability and cell-surface expression, and mediates TPO-induced signal transduction. We demonstrate that JAK2 and MPL mediate TPO-induced proliferation arrest and megakaryocytic differentiation of the human megakaryoblastic leukemia cell line UT7-MPL. A decrease in JAK2 or MPL protein expression, and JAK2 chemical inhibition, suppress this antiproliferative action of TPO. The expression of JAK2 and MPL, which progressively increases along normal human megakaryopoiesis, is decreased in platelets of patients diagnosed with JAK2- or MPL-mutated essential thrombocytemia and primary myelofibrosis, 2 myeloproliferative neoplasms in which megakaryocytes (MKs) proliferate excessively. Finally, low doses of JAK2 chemical inhibitors are shown to induce a paradoxical increase in MK production, both in vitro and in vivo. We propose that JAK2 and MPL expression levels regulate megakaryocytic proliferation vs differentiation in both normal and pathological conditions, and that JAK2 chemical inhibitors could promote a paradoxical thrombocytosis when used at suboptimal doses