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Yang F, Anekpuritanang T, Press RD. Clinical Utility of Next-Generation Sequencing in Acute Myeloid Leukemia. Mol Diagn Ther 2021; 24:1-13. [PMID: 31848884 DOI: 10.1007/s40291-019-00443-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous disease that, even with current advancements in therapy, continues to have a poor prognosis. Recurrent somatic mutations have been identified in a core set of pathogenic genes including FLT3 (25-30% prevalence), NPM1 (25-30%), DNMT3A (25-30%), IDH1/2 (5-15%), and TET2 (5-15%), with direct diagnostic, prognostic, and targeted therapeutic implications. Advances in the understanding of the complex mechanisms of AML leukemogenesis have led to the development and recent US Food and Drug Administration (FDA) approval of several targeted therapies: midostaurin and gilteritinib targeting activated FLT3, and ivosidenib and enasidenib targeting mutated IDH1/2. Several additional drug candidates targeting other recurrently mutated gene pathways in AML are also being actively developed. Furthermore, outside of the realm of predicting responses to targeted therapies, many other mutated genes, which comprise the so-called long tail of oncogenic drivers in AML, have been shown to provide clinically useful diagnostic and prognostic information for AML patients. Many of these recurrently mutated genes have also been shown to be excellent biomarkers for post-treatment minimal residual disease (MRD) monitoring for assessing treatment response and predicting future relapse. In addition, the identification of germline mutations in a set of genes predisposing to myeloid malignancies may directly inform treatment decisions (particularly stem cell transplantation) and impact other family members. Recent advances in sequencing technology have made it practically and economically feasible to evaluate many genes simultaneously using next-generation sequencing (NGS). Mutation screening with NGS panels has been recommended by national and international professional guidelines as the standard of care for AML patients. NGS-based detection of the heterogeneous genes commonly mutated in AML has practical clinical utility for disease diagnosis, prognosis, prediction of targeted therapy response, and MRD monitoring.
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Affiliation(s)
- Fei Yang
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Tauangtham Anekpuritanang
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA.,Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Richard D Press
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA. .,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
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Guan Y, Hasipek M, Tiwari AD, Maciejewski JP, Jha BK. TET-dioxygenase deficiency in oncogenesis and its targeting for tumor-selective therapeutics. Semin Hematol 2021; 58:27-34. [PMID: 33509440 PMCID: PMC7938524 DOI: 10.1053/j.seminhematol.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/04/2020] [Accepted: 12/19/2020] [Indexed: 02/08/2023]
Abstract
TET2 is one of the most frequently mutated genes in myeloid neoplasms. TET2 loss-of-function perturbs myeloid differentiation and causes clonal expansion. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, targeted therapies are lagging. Here we review known biochemical mechanisms and candidate therapies that emerge from this. Specifically, we discuss the potential utility of vitamin C to compensate for TET-dioxygenase deficiency, to thereby restore the biochemical function. An alternative approach exploits the TET-deficient state for synthetic lethality, exploiting the fact that a minimum level of TET-dioxygenase activity is required for cell survival, rendering TET2-mutant malignant cells selectively vulnerable to inhibitors of TET-function.
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Affiliation(s)
- Yihong Guan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Metis Hasipek
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Anand D Tiwari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
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Hartmann L, Nadarajah N, Meggendorfer M, Höllein A, Vetro C, Kern W, Haferlach T, Haferlach C, Stengel A. Molecular characterization of a second myeloid neoplasm developing after treatment for acute myeloid leukemia. Leukemia 2019; 34:811-820. [PMID: 31719678 DOI: 10.1038/s41375-019-0633-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Therapy-related myeloid neoplasms (tMN) following successful treatment of acute myeloid leukemia (AML) are rare and poorly characterized. To evaluate the presence of a common ancestral clone, we performed whole-exome sequencing of 25 patients at AML diagnosis, tMN diagnosis (tMDS: 13; tAML: 12), and matched remission samples, identifying 607 mutations affecting 504 different genes (46 recurrently mutated). Number of mutations was higher in tAML vs. tMDS cases (median 19 vs 13 mutations, p = 0.05). Focusing on 24 genes commonly mutated in hematological malignancies, 19/25 (76%) patients were found to share mutations between AML and tMN, mostly affecting epigenetic modifiers (21/32; 66%), splicing factors (6/32; 19%), and chromatin modifiers (3/32; 9%). Analysis of remission samples identified 13 persisting mutations in 10/22 patients, affecting DNMT3A (n = 6), TET2 (n = 5), IDH1 and SRSF2 (n = 1, each). Comparison of cytogenetics revealed that 9/12 patients with a normal karyotype (NK) in AML harbored aberrations in tMN, four aberrant AML cases presented with NK in tMN, four other patients showed unrelated cytogenetic aberrations. Our study provides novel insights into the pathogenesis of tMN, hypothesizing the presence of a common ancestral clone in AML and tMN. Mutations mostly affected epigenetic modifiers, which have previously been linked to clonal hematopoiesis.
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Affiliation(s)
- Luise Hartmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Alexander Höllein
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Calogero Vetro
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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Identification of Two DNMT3A Mutations Compromising Protein Stability and Methylation Capacity in Acute Myeloid Leukemia. JOURNAL OF ONCOLOGY 2019; 2019:5985923. [PMID: 31827512 PMCID: PMC6881567 DOI: 10.1155/2019/5985923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022]
Abstract
Somatic mutations of DNMT3A occur in about 20% of acute myeloid leukemia (AML) patients. They mostly consist in heterozygous missense mutations targeting a hotspot site at R882 codon, which exhibit a dominant negative effect and are associated with high myeloblast count, advanced age, and poor prognosis. Other types of mutations such as truncations, insertions, or single-nucleotide deletion also affect the DNMT3A gene, though with lower frequency. The present study aimed to characterize two DNMT3A gene mutations identified by next-generation sequencing (NGS), through analysis of protein stability and DNA methylation status at CpG islands. The first mutation was a single-nucleotide variant of DNMT3A at exon 20 causing a premature STOP codon (c.2385G > A; p.Trp795 ∗ ; NM_022552.4). The DNMT3A mutation load increased from 4.5% to 38.2% during guadecitabine treatment, with a dominant negative effect on CpG methylation and on protein expression. The second mutation was a novel insertion of 35 nucleotides in exon 22 of DNMT3A (NM_022552.4) that introduced a STOP codon too, after the amino acid Glu863 caused by a frameshift insertion (c.2586_2587insTCATGAATGAGAAAGAGGACATCTTATGGTGCACT; p. Thr862_Glu863fsins). The mutation, which was associated with reduced DNMT3A expression and CpG methylation, persisted at relapse with minor changes in the methylation profile and at protein level. Our data highlight the need to better understand the consequences of DNMT3A mutations other than R882 substitutions in the leukemogenic process in order to tailor patient treatments, thus avoiding therapeutic resistance and disease relapse.
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NPM1 mutated AML can relapse with wild-type NPM1: persistent clonal hematopoiesis can drive relapse. Blood Adv 2019; 2:3118-3125. [PMID: 30455361 DOI: 10.1182/bloodadvances.2018023432] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/23/2018] [Indexed: 01/07/2023] Open
Abstract
Acute myeloid leukemia (AML) with NPM1 mutation (NPM1 mut) defines a World Health Organization entity. Absence of minimal residual disease (MRD) following induction chemotherapy is associated with an excellent prognosis. Data are conflicting on NPM1 mut AML relapsing with wild-type NPM1 (NPM1 wt ). We analyzed 104 paired samples of NPM1 mut AML patients with relapse and identified 14/104 that relapsed with NPM1 wt AML. Blood counts at diagnosis differed significantly between patients with NPM1 mut and NPM1 wt relapse (median white blood cell count, 30 vs 3 × 109/L, P = .008; platelet count, 66 vs 128 × 109/l, P = .018). NPM1 mut relapse occurred significantly earlier than NPM1 wt relapse (14 vs 43 months, P = .004). At diagnosis, FLT3-ITD were more frequent in patients with NPM1 mut relapse (P = .029), whereas DNMT3A mutations were more frequent in patients with NPM1 wt relapse (P = .035). Sequencing analysis of paired samples at diagnosis, molecular remission, and NPM1 wt relapse identified cooccurring mutations that persist from diagnosis throughout remission and at relapse, suggestive of a preexisting clonal hematopoiesis. We provide evidence that AML relapsing with NPM1 wt is a distinct disease and that initial leukemia and relapse potentially arise from a premalignant clonal hematopoiesis.
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Martignoles JA, Delhommeau F, Hirsch P. Genetic Hierarchy of Acute Myeloid Leukemia: From Clonal Hematopoiesis to Molecular Residual Disease. Int J Mol Sci 2018; 19:E3850. [PMID: 30513905 PMCID: PMC6321602 DOI: 10.3390/ijms19123850] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 02/06/2023] Open
Abstract
Recent advances in the field of cancer genome analysis revolutionized the picture we have of acute myeloid leukemia (AML). Pan-genomic studies, using either single nucleotide polymorphism arrays or whole genome/exome next generation sequencing, uncovered alterations in dozens of new genes or pathways, intimately connected with the development of leukemia. From a simple two-hit model in the late nineties, we are now building clonal stories that involve multiple unexpected cellular functions, leading to full-blown AML. In this review, we will address several seminal concepts that result from these new findings. We will describe the genetic landscape of AML, the association and order of events that define multiple sub-entities, both in terms of pathogenesis and in terms of clinical practice. Finally, we will discuss the use of this knowledge in the settings of new strategies for the evaluation of measurable residual diseases (MRD), using clone-specific multiple molecular targets.
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Affiliation(s)
- Jean-Alain Martignoles
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Hématologie Biologique, F-75012 Paris, France.
| | - François Delhommeau
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Hématologie Biologique, F-75012 Paris, France.
| | - Pierre Hirsch
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Hématologie Biologique, F-75012 Paris, France.
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