Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture

This work is licensed under a Creative Commons Attribution 3.0 Unported License.-- et al.Advances in sequencing technologies are giving unprecedented insights into the spectrum of somatic mutations underlying acute myeloid leukaemia with a normal karyotype (AML-NK). It is clear that the prognosis of individual patients is strongly influenced by the combination of mutations in their leukaemia and that many leukaemias are composed of multiple subclones, with differential susceptibilities to treatment. Here, we describe a method, employing targeted capture coupled with next-generation sequencing and tailored bioinformatic analysis, for the simultaneous study of 24 genes recurrently mutated in AML-NK. Mutational analysis was performed using open source software and an in-house script (Mutation Identification and Analysis Software), which identified dominant clone mutations with 100% specificity. In each of seven cases of AML-NK studied, we identified and verified mutations in 2-4 genes in the main leukaemic clone. Additionally, high sequencing depth enabled us to identify putative subclonal mutations and detect leukaemia-specific mutations in DNA from remission marrow. Finally, we used normalised read depths to detect copy number changes and identified and subsequently verified a tandem duplication of exons 2-9 of MLL and at least one deletion involving PTEN. This methodology reliably detects sequence and copy number mutations, and can thus greatly facilitate the classification, clinical research, diagnosis and management of AML-NK.We acknowledge the use of the National Institute of Health Research (NIHR) Biomedical Research Centre, University of Cambridge. We thank Drs J Craig and C Crawley of Cambridge University NHS Hospitals trust for allowing us to approach their patients for samples. GV is funded by a Wellcome Trust Senior Fellowship in Clinical Science. Work in GV’s laboratory is also funded by Leukaemia Lymphoma Research and the Kay Kendal Leukaemia Fund.Peer Reviewe

Dynamic variation of CD5 surface expression levels within individual chronic lymphocytic leukemia clones.

Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of clonally derived mature CD5high B cells; however, the cellular origin of CLL is still unknown. Patients with CLL also harbor variable numbers of CD5low B cells, but the clonal relationship of these cells to the bulk disease is unknown and can have important implications for monitoring, treating, and understanding the biology of CLL. Here, we use B-cell receptors (BCRs) as molecular barcodes to first show by single-cell BCR sequencing that the great majority of CD5low B cells in the blood of CLL patients are clonally related to CD5high CLL B cells. We investigate whether CD5 state switching was likely to occur continuously as a common event or as a rare event in CLL by tracking somatic BCR mutations in bulk CLL B cells and using them to reconstruct the phylogenetic relationships and evolutionary history of the CLL in four patients. Using statistical methods, we show that there is no parsimonious route from a single or low number of CD5low switch events to the CD5high population, but rather, large-scale and/or dynamic switching between these CD5 states is the most likely explanation. The overlapping BCR repertoires between CD5high and CD5low cells from CLL patient peripheral blood reveal that CLL exists in a continuum of CD5 expression. The major proportion of CD5low B cells in patients are leukemic, thus identifying CD5low B cells as an important component of CLL, with implications for CLL pathogenesis, clinical monitoring, and the development of anti-CD5-directed therapies

Evi1 Counteracts Anti-Leukemic and Stem Cell Inhibitory Effects of All-Trans Retinoic Acid on Flt3-ITD/Npm1c-Driven Acute Myeloid Leukemia Cells.

All-trans retinoic acid (atRA) has a dramatic impact on the survival of patients with acute promyelocytic leukemia, but its therapeutic value in other types of acute myeloid leukemia (AML) has so far remained unclear. Given that AML is a stem cell-driven disease, recent studies have addressed the effects of atRA on leukemic stem cells (LSCs). atRA promoted stemness of MLL-AF9-driven AML in an Evi1-dependent manner but had the opposite effect in Flt3-ITD/Nup98-Hoxd13-driven AML. Overexpression of the stem cell-associated transcription factor EVI1 predicts a poor prognosis in AML, and is observed in different genetic subtypes, including cytogenetically normal AML. Here, we therefore investigated the effects of Evi1 in a mouse model for cytogenetically normal AML, which rests on the combined activity of Flt3-ITD and Npm1c mutations. Experimental expression of Evi1 on this background strongly promoted disease aggressiveness. atRA inhibited leukemia cell viability and stem cell-related properties, and these effects were counteracted by overexpression of Evi1. These data further underscore the complexity of the responsiveness of AML LSCs to atRA and point out the need for additional investigations which may lay a foundation for a precision medicine-based use of retinoids in AML

Phosphorus Magnetic Resonance Spectroscopy (31P MRS) and cardiovascular disease: The importance of energy

Background and Objectives: The heart is the organ with the highest metabolic demand in the body, and it relies on high ATP turnover and efficient energy substrate utilisation in order to function normally. The derangement of myocardial energetics may lead to abnormalities in cardiac metabolism, which herald the symptoms of heart failure (HF). In addition, phosphorus magnetic resonance spectroscopy (31P MRS) is the only available non-invasive method that allows clinicians and researchers to evaluate the myocardial metabolic state in vivo. This review summarises the importance of myocardial energetics and provides a systematic review of all the available research studies utilising 31P MRS to evaluate patients with a range of cardiac pathologies. Materials and Methods: We have performed a systematic review of all available studies that used 31P MRS for the investigation of myocardial energetics in cardiovascular disease. Results: A systematic search of the Medline database, the Cochrane library, and Web of Science yielded 1092 results, out of which 62 studies were included in the systematic review. The 31P MRS has been used in numerous studies and has demonstrated that impaired myocardial energetics is often the beginning of pathological processes in several cardiac pathologies. Conclusions: The 31P MRS has become a valuable tool in the understanding of myocardial metabolic changes and their impact on the diagnosis, risk stratification, and prognosis of patients with cardiovascular diseases

Contemporary role of cardiac magnetic resonance in the management of patients with suspected or known coronary artery disease

Cardiac magnetic resonance imaging (CMR) is a useful non-invasive radiation-free imaging modality for the management of patients with coronary artery disease (CAD). CMR cine imaging provides the “gold standard” assessment of ventricular function, late gadolinium enhancement (LGE) provides useful data for the diagnosis and extent of myocardial scar and viability, while stress imaging is an established technique for the detection of myocardial perfusion defects indicating ischemia. Beyond its role in the diagnosis of CAD, CMR allows accurate risk stratification of patients with established CAD. This review aims to summarize the data regarding the role of CMR in the contemporary management of patients with suspected or known coronary artery disease

Recurrent histone mutations in T-cell acute lymphoblastic leukaemia.

Mutations affecting key modifiable histone type 3 (H3; Supplementary Table 1) residues are frequent oncogenic events in certain solid tumours (Feinberg, et al 2016), and have also recently been implicated in a subset of acute myeloid leukaemia (AML)(Lehnertz, et al 2017). Here, we systematically reviewed the somatic mutations in >20,000 cancer specimens to identify tumours harbouring H3 mutations. In a subset of T-cell acute lymphoblastic leukaemia (T-ALL) we identified non-methionine mutations of the key modifiable H3 residues, lysine (K) 27 and 36

Identification Of A Germline F692L Drug Resistance Variant In Cis With Flt3-ITD In Knock-In Mice

Letter to the Editor.-- Dovey, Oliver M. et al.Internal tandem duplication (ITD) mutations in the juxtamembrane domain of the fms-like tyrosine kinase 3 (FLT3) gene occur in approximately one quarter of cases of acute myeloid leukemia (AML), are associated with constitutive activation of the kinase and confer a poor prognosis.BC is funded by the >China Scholarship Council> for his visiting studies in UK. AM is funded by the Kay Kendall Leukaemia Fund project grant. CG was funded by a Bloodwise Clinical Research Training Fellowship. IV is funded by Spanish Ministerio de Economía y Competitividad subprograma Ramón y Cajal. We thank Servicio Santander Supercomputación for their support. OMD, JLC and GSV are funded by a Wellcome Trust Senior Fellowship in Clinical Science (WT095663MA) and this work was also funded by the Wellcome Trust Sanger InstitutePeer Reviewe

Identification Of A Germline F692L Drug Resistance Variant In Cis With Flt3-ITD In Knock-In Mice

Letter to the Editor.-- Dovey, Oliver M. et al.Internal tandem duplication (ITD) mutations in the juxtamembrane domain of the fms-like tyrosine kinase 3 (FLT3) gene occur in approximately one quarter of cases of acute myeloid leukemia (AML), are associated with constitutive activation of the kinase and confer a poor prognosis.BC is funded by the >China Scholarship Council> for his visiting studies in UK. AM is funded by the Kay Kendall Leukaemia Fund project grant. CG was funded by a Bloodwise Clinical Research Training Fellowship. IV is funded by Spanish Ministerio de Economía y Competitividad subprograma Ramón y Cajal. We thank Servicio Santander Supercomputación for their support. OMD, JLC and GSV are funded by a Wellcome Trust Senior Fellowship in Clinical Science (WT095663MA) and this work was also funded by the Wellcome Trust Sanger InstitutePeer Reviewe

SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness.

Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically