Molecular Landscape of Acute Myeloid Leukemia: Prognostic and Therapeutic Implications.

PURPOSE OF REVIEW: The field of acute myeloid leukemia (AML) has been revolutionized in recent years by the advent of high-throughput techniques, such as next-generation sequencing. In this review, we will discuss some of the recently identified mutations that have defined a new molecular landscape in this disease, as well as their prognostic, predictive, and therapeutic implications. RECENT FINDINGS: Recent studies have shown how many cases of AML evolve from a premalignant period of latency characterized by the accumulation of several mutations and the emergence of one or multiple dominant clones. The pattern of co-occurring mutations and cytogenetic abnormalities at diagnosis defines risk and can determine therapeutic approaches to induce remission. Besides the genetic landscape at diagnosis, the continued presence of particular gene mutations during or after treatment carries prognostic information that should further influence strategies to maintain remission in the long term. The recent progress made in AML research is a seminal example of how basic science can translate into improving clinical practice. Our ability to characterize the genomic landscape of individual patients has not only improved our ability to diagnose and prognosticate but is also bringing the promise of precision medicine to fruition in the field

Hematopoietic stem cells made BETter by inhibition.

Bromodomain and extra terminal (BET) proteins comprise the ubiquitously expressed BRD2, BRD3, BRD4 and the testes specific BRDT. These multipurpose proteins contain tandem N-terminal bromodomains that bind acetylated lysine residues of histone (and non-histone) proteins and other protein modules, such as the extra terminal domain, and in some (BRD4, BRDT), a C-terminal domain. They also mediate a number of effects including transcriptional activation via recruitment of other partner proteins. Inhibitors of these proteins are emerging as exciting new therapies for the treatment of hematologic and solid malignancies, offering the possibility of specifically targeting epigenetic readers. We and others have already demonstrated the preclinical efficacy of BET inhibitors in acute myeloid leukemia (AML), while several other papers have documented similar efficacy in myeloma, non-Hodgkin lymphoma, and acute lymphoblastic leukemia. These observations have led to several clinical trials that are currently underway to confirm the efficacy of these drugs in AML and other malignancies. Even though the most mature trials have recently reported limited objective responses of monotherapy in heavily pre-treated AML, lymphoma and myeloma patients, early data suggest that combination therapies with other small molecules or more conventional cytotoxic agents might be particularly promising

Molecular Landscape of Acute Myeloid Leukemia: Prognostic and Therapeutic Implications

Funder: University of CambridgeAbstract: Purpose of Review: The field of acute myeloid leukemia (AML) has been revolutionized in recent years by the advent of high-throughput techniques, such as next-generation sequencing. In this review, we will discuss some of the recently identified mutations that have defined a new molecular landscape in this disease, as well as their prognostic, predictive, and therapeutic implications. Recent Findings: Recent studies have shown how many cases of AML evolve from a premalignant period of latency characterized by the accumulation of several mutations and the emergence of one or multiple dominant clones. The pattern of co-occurring mutations and cytogenetic abnormalities at diagnosis defines risk and can determine therapeutic approaches to induce remission. Besides the genetic landscape at diagnosis, the continued presence of particular gene mutations during or after treatment carries prognostic information that should further influence strategies to maintain remission in the long term. Summary: The recent progress made in AML research is a seminal example of how basic science can translate into improving clinical practice. Our ability to characterize the genomic landscape of individual patients has not only improved our ability to diagnose and prognosticate but is also bringing the promise of precision medicine to fruition in the field

Molecular Landscape of Acute Myeloid Leukemia: Prognostic and Therapeutic Implications

Funder: University of CambridgeAbstract: Purpose of Review: The field of acute myeloid leukemia (AML) has been revolutionized in recent years by the advent of high-throughput techniques, such as next-generation sequencing. In this review, we will discuss some of the recently identified mutations that have defined a new molecular landscape in this disease, as well as their prognostic, predictive, and therapeutic implications. Recent Findings: Recent studies have shown how many cases of AML evolve from a premalignant period of latency characterized by the accumulation of several mutations and the emergence of one or multiple dominant clones. The pattern of co-occurring mutations and cytogenetic abnormalities at diagnosis defines risk and can determine therapeutic approaches to induce remission. Besides the genetic landscape at diagnosis, the continued presence of particular gene mutations during or after treatment carries prognostic information that should further influence strategies to maintain remission in the long term. Summary: The recent progress made in AML research is a seminal example of how basic science can translate into improving clinical practice. Our ability to characterize the genomic landscape of individual patients has not only improved our ability to diagnose and prognosticate but is also bringing the promise of precision medicine to fruition in the field

Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AML

This study demonstrates that EZH2 has stage-specific and diametrically opposite roles during the induction and maintenance stages of AML. However, different transcriptional programs are affected at each stage, identifying mutant EZH2 as a prognostic marker and paradoxically wild-type EZH2 as a potential therapeutic targetThe Huntly laboratory is funded by CRUK (Programme C18680/A25508), ERC (Grant 647685 COMAL), KKLF, MRC, Bloodwise, the Wellcome Trust (WT) and the Cambridge NIHR BRC. F.B. is a recipient of a Wellcome Trust PhD for Clinicians award. P.G. is funded by the Wellcome Trust (109967/Z/15/Z). We acknowledge the WT/MRC centre grant (097922/Z/11/Z) and support from WT strategic award 100140. Research in the laboratory is also supported by core funding from Wellcome and MRC to the Wellcome-MRC Cambridge Stem Cell Institute. We are grateful to Chiara Cossetti, Gabriela Grondys-Kotarba and Reiner Schulte at the CIMR Flow Cytometry Core for their invaluable help and advice with cell sorting. This research was supported by the Cambridge NIHR BRC Cell Phenotyping Hub. Patient samples were received from the UK NCRI AML trials. The authors declare no competing financial interests

Glutaminolysis is a metabolic dependency in FLT3ITD acute myeloid leukemia unmasked by FLT3 tyrosine kinase inhibition.

FLT3 internal tandem duplication (FLT3ITD) mutations are common in acute myeloid leukemia (AML) associated with poor patient prognosis. Although new-generation FLT3 tyrosine kinase inhibitors (TKI) have shown promising results, the outcome of FLT3ITD AML patients remains poor and demands the identification of novel, specific, and validated therapeutic targets for this highly aggressive AML subtype. Utilizing an unbiased genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screen, we identify GLS, the first enzyme in glutamine metabolism, as synthetically lethal with FLT3-TKI treatment. Using complementary metabolomic and gene-expression analysis, we demonstrate that glutamine metabolism, through its ability to support both mitochondrial function and cellular redox metabolism, becomes a metabolic dependency of FLT3ITD AML, specifically unmasked by FLT3-TKI treatment. We extend these findings to AML subtypes driven by other tyrosine kinase (TK) activating mutations and validate the role of GLS as a clinically actionable therapeutic target in both primary AML and in vivo models. Our work highlights the role of metabolic adaptations as a resistance mechanism to several TKI and suggests glutaminolysis as a therapeutically targetable vulnerability when combined with specific TKI in FLT3ITD and other TK activating mutation-driven leukemias.P.G. is funded by the Wellcome Trust (109967/Z/15/Z) and was previously supported by the Academy of medical Sciences and Lady Tata Memorial Trust. The Huntly lab is funded by European Research Council, MRC, Bloodwise, the Kay Kendall Leukaemia Fund, the Cambridge NIHR Biomedical Research Centre, and core support grants to the Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute. C.F. and A.S.H.C are funded by the Medical Research Council, Core Grant to the Cancer Unit. P.M-P. is supported by a grant from Cancer Research UK (C56179/A21617). D.S. is a Postdoctoral Fellow of the Mildred-Scheel Organisation, German Cancer Aid. This research was supported by the CIMR Flow Cytometry Core Facility. We would like to thank the Welcome Trust Sanger Institute facility for the MiSeq run

Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy.

Like normal hematopoietic stem cells, leukemic stem cells depend on their bone marrow (BM) microenvironment for survival, but the underlying mechanisms remain largely unknown. We have studied the contribution of nestin+ BM mesenchymal stem cells (BMSCs) to MLL-AF9-driven acute myeloid leukemia (AML) development and chemoresistance in vivo. Unlike bulk stroma, nestin+ BMSC numbers are not reduced in AML, but their function changes to support AML cells, at the expense of non-mutated hematopoietic stem cells (HSCs). Nestin+ cell depletion delays leukemogenesis in primary AML mice and selectively decreases AML, but not normal, cells in chimeric mice. Nestin+ BMSCs support survival and chemotherapy relapse of AML through increased oxidative phosphorylation, tricarboxylic acid (TCA) cycle activity, and glutathione (GSH)-mediated antioxidant defense. Therefore, AML cells co-opt energy sources and antioxidant defense mechanisms from BMSCs to survive chemotherapy.D.F. was supported by Associazione Italiana Ricerca sul Cancro (AIRCFellowship 20930 for Abroad) and scholarships from Società Italiana di Ematologia (SIE) and Associazione "Amici di Beat Leukemia Dr. Alessandro Cevenini ONLUS" and AIL Bologna ODV. A.S.-A. was supported by a European Hematology Association Research Fellowship and C.L.F-C. by a fellowship from Boehringer Foundation. This work was supported by core support grants from the Wellcome Trust (203151/Z/16/Z) and the MRC to the Cambridge Stem Cell Institute, and the Instituto de Salud Carlos III (ISCIII), Ministerio de Ciencia, Innovación y Universidades (MCNU) and Pro CNIC Foundation to CNIC, which is a Severo Ochoa Center of Excellence (SEV-2015-0505). This work was supported by MCNU (Plan Nacional grant SAF-2011-30308 to S.M.-F.; Ramón y Cajal Program grants RYC-2011-09726 to A.S.-A. and RYC-2009-04703 to S.M.-F.); Marie Curie Career Integration Program grants (FP7-PEOPLE-2011-RG-294262/294096) to A.S.-A. and S.M.-F.; Spanish Ministry of Science, Innovation and Universities (BIO2015-67580-P and PGC2018- 097019-B-I00), Carlos III Institute of Health-Fondo de Investigación Sanitaria grant PRB3(IPT17/0019 - ISCIII-SGEFI / ERDF, ProteoRed), Fundació MaratóTV3 (grant 122/C/2015) and “la Caixa” Banking Foundation (project code HR17-00247) to J.V.; the Medical Research Council grant MRC_MC_UU_12022/6 to C.F; an ERC award (COMAL: 647685) and a CRUK Programme Award to B.J.H; the Swiss National Science Foundation (SNF, 31003A_173224/1 & 31003A_173224/1) and the Gertrude von Meissner Foundation (Basel, Switzerland) to J.S.; ISCIII Spanish Cell Therapy Network TerCel, ConSEPOC-Comunidad de Madrid grant (S2010/BMD-2542), National Health Service Blood and Transplant (United Kingdom), European Union’s Horizon 2020 research (ERC- 2014-CoG-648765) and a Programme Foundation Award (C61367/A26670) from Cancer Research UK to S.M.-F., who was also supported in part by an International Early Career Scientist grant of the Howard Hughes Medical Institute

Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes

Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies

The role of the Dnmt3aR882H mutation in the evolution of clonal haematopoiesis.

DNMT3A mutations are very frequent events in clonal haematopoiesis of indeter- minate potential (CHIP), and considered one of the earliest genetic events during the development of haematopoietic malignancies. Individuals with CHIP, in spite of having a normal full blood count are at increased risk of cardiovascular and pulmonary diseases as well as haematological neoplasms. Somatic mutations in DNMT3A are drivers of CHIP, but decades may elapse between the acquisition of a mutation and CHIP. Besides, only a minority of these individuals will go onto developing a haematological cancer, this wide interindividual heterogeneity suggests that environmental factors influence clonal expansion. It is in particular emerging, that individuals with CHIP have a proinflamma- tory phenotype, additionally, chronic inflammation is typically considered deleterious to normal haematopoiesis, as it leads to haematopoietic stem cells (HSCs) exhaustion. R882H Using a conditional knock-in mouse model heterozygous for Dnmt3a mon DNMT3A mutation, we have assessed the responses of Long-Term Haematopoietic Stem Cells (LT-HSCs) to inflammatory "stress" in vitro and in vivo. We have also em- ployed bulk LT-HSCs genomics studies to interrogate differences in the transcriptional landscape in response to inflammation. We have demonstrated that Dnmt3a-mutant LT- HSCs have a globally abnormal response to inflammation, characterised by faster exit from quiescence and subsequent hyper-proliferation. Interestingly, as well as a larger differentiated output, Dnmt3aR882H HSCs were also better preserving their progenitor compartment and their self-renewal ability compared to wild-type HSCs exposed to the same stimulus, giving some insight into potential mechanisms that lead to clonal expan- sion within an inflammatory microenvironment. We linked this phenotype to the reduced expression of two TP53 target genes: Niam/Tbrg1, involved in the TP53-mediated activation of the p21 pathway that leads to G1 growth arrest upon exposure to "stress", and Necdin/Ndn a regulator of LT-HSCs quiescence. We then went on to demonstrate that TP53 and DNMT3A might function redundantly within the same functional pathway, and that Dnmt3a loss-of-function can lead to re- duced stem cell quiescence in vivo, and increased genomic instability when Dnmt3aR882H progenitors are challenged with genotoxic “stressors”. Interestingly, in spite of accumu- lating more DNA damage, Dnmt3aR882H cells did not lose clonogenic ability and showed similar viability to wild-type cells, suggesting that these cells are more tolerant to the accumulation of DNA damage. Subtle changes of this nature are likely to play an im- portant role in a phenomenon that develops over the lifetime of an individual, and could create a permissive state for the retention and accumulation of subsequent mutations, eventually leading to transformation.This project was funded by Wellcom

The RNA editing landscape in acute myeloid leukemia reveals associations with disease mutations and clinical outcome.

Several studies have documented aberrant RNA editing patterns across multiple tumors across large patient cohorts from The Cancer Genome Atlas (TCGA). However, studies on understanding the role of RNA editing in acute myeloid leukemia (AML) have been limited to smaller sample sizes. Using high throughput transcriptomic data from the TCGA, we demonstrated higher levels of editing as a predictor of poor outcome within the AML patient samples. Moreover, differential editing patterns were observed across individual AML genotypes. We also could demonstrate a negative association between the degree of editing and mRNA abundance for some transcripts, identifying the potential regulatory potential of RNA-editing in altering gene expression in AML. Further edQTL analysis suggests potential cis-regulatory mechanisms in RNA editing variation. Our work suggests a functional and regulatory role of RNA editing in the pathogenesis of AML and we extended our analysis to gain insight into the factors influencing altered levels of editing