Paula Aranaz

Genetic variation at MECOM , TERT , JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms

Clonal proliferation in myeloproliferative neoplasms (MPN) is driven by somatic mutations in JAK2, CALR or MPL, but the contribution of inherited factors is poorly characterized. Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2V617F-negative MPN: rs12339666 (JAK2; meta-analysis P=1.27 × 10−10) and rs2201862 (MECOM; meta-analysis P=1.96 × 10−9). Two additional SNPs, rs2736100 (TERT) and rs9376092 (HBS1L/MYB), achieve genome-wide significance when including JAK2V617F-positive cases. rs9376092 has a stronger effect in JAK2V617F-negative cases with CALR and/or MPL mutations (Breslow–Day P=4.5 × 10−7), whereas in JAK2V617F-positive cases rs9376092 associates with essential thrombocythemia (ET) rather than polycythemia vera (allelic χ2 P=7.3 × 10−7). Reduced MYB expression, previously linked to development of an ET-like disease in model systems, associates with rs9376092 in normal myeloid cells. These findings demonstrate that multiple germline variants predispose to MPN and link constitutional differences in MYB expression to disease phenotype.

Mutations in SETBP1 are recurrent in myelodysplastic syndromes and often coexist with cytogenetic markers associated with disease progression

Whole exome sequencing was performed in a patient with myelodysplastic syndrome before and after progression to acute myeloid leukaemia. Mutations in several genes, including SETBP1, were identified following leukaemic transformation. Screening of 328 patients with myeloid disorders revealed SETBP1 mutations in 14 patients (4·3%), 7 of whom had −7/del(7q) and 3 had i(17)(q10), cytogenetic markers associated with shortened overall survival and increased risk of leukaemic evolution. SETBP1 mutations were frequently acquired at the time of leukaemic evolution, coinciding with increase of leukaemic blasts. These data suggest that SETBP1 mutations may play a role in MDS and chronic myelomonocytic leukaemia disease progression.

LNK can also be mutated outside PH and SH2 domains in myeloproliferative neoplasms with and without V617FJAK2 mutation

LNK (SH2B3) is a member of a family of adaptor proteins that hare a proline-rich N-terminal dimerization domain, a pleckstrin omology (PH) domain, a Src homology 2 (SH2) domain, and a onserved C-terminal tyrosine residue [1]. It has been proposed s a putative tumor suppressor because it is a negative regulator f several cytokine receptors [2]. LNK−/− mice exhibit a MPN-like henotype with anomalies of hematopoiesis and abnormal accuulation of erythroid cells, megakaryocytes and B lymphocytes n different hematopoietic compartments [3]. In addition, some enome-wide association studies have found that one SNP in exon of this gene (rs3184504 and p.R262W) shows a significant assoiation with eosinophil counts (a common feature of some MPNs), everal blood parameters [4] and hypertension [5,6]. Recently, LNK mutations have been described in myeloprolifrative neoplasms, mainly in exon 2 that encodes part of the PH omain (encoded by exons 2–4) [7–9]. We have analysed the whole coding sequence of LNK in a cohort f 44 V617FJAK2 negative MPNs (four with polycythemia vera, 15 ith essential thrombocythemia, four with primary myelofibrosis, ne with chronic eosinophilic leukemia not otherwise specified, ve with MPNs unclassifiable and 15 with chronic myelomonoytic leukemia) [10] as well as 20 V617FJAK2 positive MPNs (8 V, 8 ET and 4 PMF) and 20 non-leukemic samples by dHPLC see Supplementary information), a highly sensitive, low-cost and edium-throughput method. The melting characteristics of exon (even when divided into fragments) made it impossible to scan or mutations by dHPLC analysis, so in this case samples were irectly sequenced. Results (Table 1) showed the presence of a eletion of 24 bp in exon 8 in a PMF V617FJAK2 negative sample c.1795 1818del and p.S480 E487del) and a c.1217T>C (p.F287S) hange in exon 4 of a PV V617FJAK2 positive sample (Fig. 1) also arboring a TET2 p.N1385S mutation. No changes were detected in NK exon 2. Analysis of exons 3, 4 and the coding part of the exon

Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutations

Two megalencephaly (MEG) syndromes, megalencephaly-capillary malformation (MCAP) and megalencephaly-polymicrogyriapolydactyly-hydrocephalus (MPPH), have recently been defined on the basis of physical and neuroimaging features. Subsequently, exome sequencing of ten MEG cases identified de-novo postzygotic mutations in PIK3CA which cause MCAP and de-novo mutations in AKT and PIK3R2 which cause MPPH. Here we present findings from exome sequencing three unrelated megalencephaly patients which identified a causal PIK3CA mutation in two cases and a causal PIK3R2 mutation in the third case. However, our patient with the PIK3R2 mutation which is considered to cause MPPH has a marked bifrontal band heterotopia which is a feature of MCAP. Furthermore, one of our patients with a PIK3CA mutation lacks syndactyly/polydactyly which is a characteristic of MCAP. These findings suggest that the overlap between MCAP and MPPH may be greater than the available studies suggest. In addition, the PIK3CA mutation in one of our patients could not be detected using standard exome analysis because the mutation was observed at a low frequency consistent with somatic mosaicism. We have therefore investigated several alternative methods of exome analysis and demonstrate that alteration of the initial allele frequency spectrum (AFS), used as a prior for variant calling in samtools, had the greatest power to detect variants with low mutant allele frequencies in our 3 MEG exomes and in simulated data. We therefore recommend non-default settings of the AFS in combination with stringent quality control when searching for causal mutation(s) that could have low levels of mutant reads due to post-zygotic mutation.

Bioinformatic analyses of CALR mutations in myeloproliferative neoplasms support a role in signaling

Bioinformatic analyses of CALR mutations in myeloproliferative neoplasms support a role in signaling

CBL mutations in myeloproliferative neoplasms are also found in the gene's proline-rich domain and in patients with the V617FJAK2

Background Despite the discovery of the p.V617F in JAK2, the molecular pathogenesis of some chronic myeloproliferative neoplasms remains unclear. Although very rare, different studies have identified CBL (Cas-Br-Murine ecotropic retroviral transforming sequence) mutations in V617FJAK2-negative patients, mainly located in the RING finger domain. In order to determine the frequency of CBL mutations in these diseases, we studied different regions of all CBL family genes (CBL, CBLB and CBLC) in a selected group of patients with myeloproliferative neoplasms. We also included V617FJAK2-positive patients to check whether mutations in CBL and JAK2 are mutually exclusive events. Design and Methods Using denaturing high performance liquid chromatography, we screened for mutations in CBL, CBLB and CBLC in a group of 172 V617FJAK2-negative and 232 V617FJAK2-positive patients with myeloproliferative neoplasms not selected for loss of heterozygosity. The effect on cell proliferation of the mutations detected was analyzed on a 32D(FLT3) cell model. Results An initial screening of all coding exons of CBL, CBLB and CBLC in 44 V617FJAK2-negative samples revealed two new CBL mutations (p.C416W in the RING finger domain and p.A678V in the proline-rich domain). Analyses performed on 128 additional V617FJAK2-negative and 232 V617FJAK2-positive samples detected three CBL changes (p.T402HfsX29, p.P417R and p.S675C in two cases) in four V617FJAK2-positive patients. None of these mutations was found in 200 control samples. Cell proliferation assays showed that all of the mutations promoted hypersensitivity to interleukin-3 in 32D(FLT3) cells. Conclusions Although mutations described to date have been found in the RING finger domain and in the linker region of CBL, we found a similar frequency of mutations in the proline-rich domain. In addition, we found CBL mutations in both V617FJAK2-positive (4/232; 1.7%) and negative (2/172; 1.2%) patients and all of them promoted hypersensitivity to interleukin-3.

A new potential oncogenic mutation in the FERM domain of JAK2 in BCR/ABL1-negative and V617F-negative chronic myeloproliferative neoplasms revealed by a comprehensive screening of 17 tyrosine kinase coding genes

BCR/ABL1-negative chronic myeloproliferative neoplasms (CMPNs) are a heterogeneous group of clonal hematological malignancies. Over recent years, some genetic events in tyrosine kinase (TK) genes have been described as causal events of these diseases. To identify new genetic aberrations underlying these diseases, we used denaturing high performance liquid chromatography and fluorescence in situ hybridization (FISH) to analyze 17 genes from two receptor-TK families (III and IV) and from three cytoplasmic-TK families (Syk, Abl, and Jak) on samples from 44 BCR/ABL1-negative and JAK2(V617F)-negative CMPN patients with different clinical phenotypes. Although screening by FISH did not reveal novel chromosomal aberrations, several sequence changes were detected. None of them were frequent events, but we identified a new potential activating mutation in the FERM domain of JAK2(R340Q). None of the germline JAK2(V617F) single-nucleotide polymorphisms detected differed in distribution between patients and control subjects. In summary, data presented here show that these genes are not frequently mutated or rearranged in CMPNs, suggesting that molecular events causing these disorders must be located in other genes.

A meta-analysis of TET2 mutations shows a distinct distribution pattern in de novo acute myeloid leukemia and chronic myelomonocytic leukemia

Recurrent loss of heterozygosity (LOH) in 4q24 in patients with myeloid malignancies has led to the identifi cation of mutations in TET2 in diff erent myeloid neoplasms including myeloproliferative neoplasm (MPN), myelodysplastic syndrome (MDS), mixed myelodysplastic/myeloproliferative neoplasm (MDS/MPN) and acute myeloid leukemia (AML) [1 – 13]. Th eir impact on prognosis remains unresolved, and the mechanisms by which TET2 leads to transformation remain unclear. Based on its homology to TET1, it is possible that TET2 may play a role in epigenetic regulation [14] via the presence of catalytic domains in the two highly conserved regions of the gene. Mutations in these two regions could, by this mechanism, lead to inactivation of a specifi c tumor suppressor gene and/or activation of pro-proliferative pathways, although mutations in other areas of the gene could also result in a modifi cation of the protein. Studies using murine models of Tet2 inactivation show that inactivation of this gene establishes important roles for Tet2 in hematopoiesis and the development of myeloproliferative disease. Beacuse TET2 alterations in patients are commonly heterozygous, TET2 haploinsuffi ciency could be enough to promote defects in a hematopoietic progenitor and myeloproliferation [15]. We have collected data on all TET2 mutations published to date [1 – 13] (a total of 725 mutations in 3274 patients) (Table I) in order to analyze whether: (a) they are evenly distributed throughout the gene, (b) diff erent mutation types (missense, nonsense or frameshift) are more prevalent in diff erent regions of the gene and (c) distinct mutational patterns are found in diff erent types of myeloid neoplasms. To this end, we divided the sequence of the TET2 gene into four regions. Region B1 ( Box 1 ) and region B2 ( Box 2 ) are highly conserved in several species and in all three proteins of the TET family. Th e other two regions, which we denominated F1 and F2, are non-conserved regions (Figure 1). We calculated the frequency of mutations per amino acid in each of these regions (number of mutations divided by the number of amino acids

Low frequency of JAK2 exon 12 mutations in classic and atypical CMPDs.

The BCR-ABL negative chronic myeloproliferative disorders (CMPDs) are a group of stem cell clonal haematological malignancies characterised by abnormal proliferation and survival of one or more myeloid lineage cells. It has been proposed that they are caused by abnormalities in some signal transduction pathways mainly due to acquired somatic mutations, some of them in tyrosine kinase genes. One of the most prevalent mutations is V617F in the pseudokinase domain (JH2) coded by JAK2 exon 14. This mutation, reported in 2005, has been associated with nearly 95% of patients diagnosed of polycythaemia vera (PV) and near a half of the patients with essential thrombocythaemia (ET) and primary myelofibrosis (MF). However, the frequency of this mutation is below 20% for the remaining chronic myeloproliferative disorders and is absent in lymphoid neoplasms. JAK2V617F has been an important milestone in the knowledge of the molecular mechanisms leading to classic myeloproliferative disorders. However, there are still some patients with PV, ET and MF lacking V617F whose molecular defect is unknown. The disease in these cases could be due to other abnormalities in JAK2 or other related genes. In fact, in a few cases new point mutations have been reported, affecting also the JH2 domain, and one mutation affecting the JH1 domain [1] and reviewed in [2], some of them in other haematological malignancies. In addition, 10% of patients diagnosed of MF and some with ET show somatic activating mutations in the thrombopoietin receptor gene (MPL) inducing constitutive cytokine-independent activation of the JAK-STAT pathway.

Optimization and evaluation of zein nanoparticles to improve the oral delivery of glibenclamide. In vivo study using C. elegans.

Graphical abstract Figure. No Caption available. ABSTRACT The aim of this work was to evaluate the capability of zein nanoparticles as oral carriers for glibenclamide (GB). Nanoparticles were prepared by a desolvation procedure in the presence of lysine as stabilizer. A central composite design was used to optimize this preparative process. Under the selected conditions, nanoparticles displayed a size of about 190 nm, a surface charge of −37 mV and a payload of 45 &mgr;g GB/mg. Small‐angle neutron scattering and X‐ray diffraction techniques suggested an internal fractal‐like structure, based on the repetition of spherical blocks of zein units (about 20 nm) grouped to form the nanoparticles. This structure, stabilized by lysine molecules located at the surface, would determine the release of GB (molecularly trapped into the nanoparticles) by a pure diffusion mechanism. Moreover, GB‐loaded nanoparticles induced a significant hypolipidemic effect with a reduction of about 15% in the fat content of C. elegans worms. In addition, did not induce any significant modification in the lifespan of worms. In summary, the employment of zein nanoparticles as delivery systems of glibenclamide may be an interesting approach to develop new oral formulations of this antidiabetic drug.