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Seto A, Downs G, King O, Salehi-Rad S, Baptista A, Chin K, Grenier S, Nwachukwu B, Tierens A, Minden MD, Smith AC, Capo-Chichi JM. Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia. Cancers (Basel) 2024; 16:1693. [PMID: 38730645 PMCID: PMC11082951 DOI: 10.3390/cancers16091693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence in situ hybridization. However, small intragenic insertions, termed KMT2A partial tandem duplication (KMT2A-PTD), are particularly challenging to detect using standard molecular and cytogenetic approaches. METHODS We have validated the use of a custom hybrid-capture-based next-generation sequencing (NGS) panel for comprehensive profiling of AML patients seen at our institution. This NGS panel targets the entire consensus coding DNA sequence of KMT2A. To deduce the presence of a KMT2A-PTD, we used the relative ratio of KMT2A exons coverage. We sought to corroborate the KMT2A-PTD NGS results using (1) multiplex-ligation probe amplification (MLPA) and (2) optical genome mapping (OGM). RESULTS We analyzed 932 AML cases and identified 41 individuals harboring a KMT2A-PTD. MLPA, NGS, and OGM confirmed the presence of a KMT2A-PTD in 22 of the cases analyzed where orthogonal testing was possible. The two false-positive KMT2A-PTD calls by NGS could be explained by the presence of cryptic structural variants impacting KMT2A and interfering with KMT2A-PTD analysis. OGM revealed the nature of these previously undetected gene rearrangements in KMT2A, while MLPA yielded inconclusive results. MLPA analysis for KMT2A-PTD is limited to exon 4, whereas NGS and OGM resolved KMT2A-PTD sizes and copy number levels. CONCLUSIONS KMT2A-PTDs are complex gene rearrangements that cannot be fully ascertained using a single genomic platform. MLPA, NGS panels, and OGM are complementary technologies applied in standard-of-care testing for AML patients. MLPA and NGS panels are designed for targeted copy number analysis; however, our results showed that integration of concurrent genomic alterations is needed for accurate KMT2A-PTD identification. Unbalanced chromosomal rearrangements overlapping with KMT2A can interfere with the diagnostic sensitivity and specificity of copy-number-based KMT2A-PTD detection methodologies.
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Affiliation(s)
- Andrew Seto
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Gregory Downs
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Olivia King
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Shabnam Salehi-Rad
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Ana Baptista
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Kayu Chin
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Sylvie Grenier
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Bevoline Nwachukwu
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
| | - Anne Tierens
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Hematology and Transfusion Medicine, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Mark D. Minden
- Department of Medicine Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada;
| | - Adam C. Smith
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - José-Mario Capo-Chichi
- Genome Diagnostics & Cancer Cytogenetics Laboratories, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; (A.S.); (G.D.); (O.K.); (S.S.-R.); (A.B.); (K.C.); (S.G.); (B.N.)
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada;
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Boscaro E, Urbino I, Catania FM, Arrigo G, Secreto C, Olivi M, D'Ardia S, Frairia C, Giai V, Freilone R, Ferrero D, Audisio E, Cerrano M. Modern Risk Stratification of Acute Myeloid Leukemia in 2023: Integrating Established and Emerging Prognostic Factors. Cancers (Basel) 2023; 15:3512. [PMID: 37444622 DOI: 10.3390/cancers15133512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
An accurate estimation of AML prognosis is complex since it depends on patient-related factors, AML manifestations at diagnosis, and disease genetics. Furthermore, the depth of response, evaluated using the level of MRD, has been established as a strong prognostic factor in several AML subgroups. In recent years, this rapidly evolving field has made the prognostic evaluation of AML more challenging. Traditional prognostic factors, established in cohorts of patients treated with standard intensive chemotherapy, are becoming less accurate as new effective therapies are emerging. The widespread availability of next-generation sequencing platforms has improved our knowledge of AML biology and, consequently, the recent ELN 2022 recommendations significantly expanded the role of new gene mutations. However, the impact of rare co-mutational patterns remains to be fully disclosed, and large international consortia such as the HARMONY project will hopefully be instrumental to this aim. Moreover, accumulating evidence suggests that clonal architecture plays a significant prognostic role. The integration of clinical, cytogenetic, and molecular factors is essential, but hierarchical methods are reaching their limit. Thus, innovative approaches are being extensively explored, including those based on "knowledge banks". Indeed, more robust prognostic estimations can be obtained by matching each patient's genomic and clinical data with the ones derived from very large cohorts, but further improvements are needed.
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Affiliation(s)
- Eleonora Boscaro
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Irene Urbino
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Federica Maria Catania
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Giulia Arrigo
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Carolina Secreto
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Matteo Olivi
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Stefano D'Ardia
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Chiara Frairia
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Valentina Giai
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Roberto Freilone
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Dario Ferrero
- Division of Hematology, Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Turin, Italy
| | - Ernesta Audisio
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Marco Cerrano
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
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Halprin C, Kitahara S, Vail E, Eno CC. Detecting the "Undetectable" Alterations: Use of NGS to uncover high-risk alterations. Cancer Genet 2022; 264-265:5-7. [DOI: 10.1016/j.cancergen.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/25/2022]
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Gerding WM, Tembrink M, Nilius‐Eliliwi V, Mika T, Dimopoulos F, Ladigan‐Badura S, Eckhardt M, Pohl M, Wünnenberg M, Farshi P, Reimer P, Schroers R, Nguyen HP, Vangala DB. Optical genome mapping reveals additional prognostic information compared to conventional cytogenetics in
AML
/
MDS
patients. Int J Cancer 2022; 150:1998-2011. [DOI: 10.1002/ijc.33942] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Wanda M. Gerding
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
| | - Marco Tembrink
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
| | - Verena Nilius‐Eliliwi
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Thomas Mika
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Fotios Dimopoulos
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Swetlana Ladigan‐Badura
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Matthias Eckhardt
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Michael Pohl
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Max Wünnenberg
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Pakhshan Farshi
- Department of Hematology and Oncology Kliniken Essen‐Mitte Essen Germany
| | - Peter Reimer
- Department of Hematology and Oncology Kliniken Essen‐Mitte Essen Germany
| | - Roland Schroers
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Huu Phuc Nguyen
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
| | - Deepak B. Vangala
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
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NKL Homeobox Genes NKX2-3 and NKX2-4 Deregulate Megakaryocytic-Erythroid Cell Differentiation in AML. Int J Mol Sci 2021; 22:ijms222111434. [PMID: 34768865 PMCID: PMC8583893 DOI: 10.3390/ijms222111434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
NKL homeobox genes encode transcription factors that impact normal development and hematopoietic malignancies if deregulated. Recently, we established an NKL-code that describes the physiological expression pattern of eleven NKL homeobox genes in the course of hematopoiesis, allowing evaluation of aberrantly activated NKL genes in leukemia/lymphoma. Here, we identify ectopic expression of NKL homeobox gene NKX2-4 in an erythroblastic acute myeloid leukemia (AML) cell line OCI-M2 and describe investigation of its activating factors and target genes. Comparative expression profiling data of AML cell lines revealed in OCI-M2 an aberrantly activated program for endothelial development including master factor ETV2 and the additional endothelial signature genes HEY1, IRF6, and SOX7. Corresponding siRNA-mediated knockdown experiments showed their role in activating NKX2-4 expression. Furthermore, the ETV2 locus at 19p13 was genomically amplified, possibly underlying its aberrant expression. Target gene analyses of NKX2-4 revealed activated ETV2, HEY1, and SIX5 and suppressed FLI1. Comparative expression profiling analysis of public datasets for AML patients and primary megakaryocyte–erythroid progenitor cells showed conspicuous similarities to NKX2-4 activating factors and the target genes we identified, supporting the clinical relevance of our findings and developmental disturbance by NKX2-4. Finally, identification and target gene analysis of aberrantly expressed NKX2-3 in AML patients and a megakaryoblastic AML cell line ELF-153 showed activation of FLI1, contrasting with OCI-M2. FLI1 encodes a master factor for myelopoiesis, driving megakaryocytic differentiation and suppressing erythroid differentiation, thus representing a basic developmental target of these homeo-oncogenes. Taken together, we have identified aberrantly activated NKL homeobox genes NKX2-3 and NKX2-4 in AML, deregulating genes involved in megakaryocytic and erythroid differentiation processes, and thereby contributing to the formation of specific AML subtypes.
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6
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Hanbazazh M, Harada S, Reddy V, Mackinnon AC, Harbi D, Morlote D. The Interpretation of Sequence Variants in Myeloid Neoplasms. Am J Clin Pathol 2021; 156:728-748. [PMID: 34155503 DOI: 10.1093/ajcp/aqab039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To provide an overview of the challenges encountered during the interpretation of sequence variants detected by next-generation sequencing (NGS) in myeloid neoplasms, as well as the limitations of the technology with the goal of preventing the over- or undercalling of alterations that may have a significant effect on patient management. METHODS Review of the peer-reviewed literature on the interpretation, reporting, and technical challenges of NGS assays for myeloid neoplasms. RESULTS NGS has been integrated widely and rapidly into the standard evaluating of myeloid neoplasms. Review of the literature reveals that myeloid sequence variants are challenging to detect and interpret. Large insertions and guanine-cytosine-heavy areas prove technically challenging while frameshift and truncating alterations may be classified as variants of uncertain significance by tertiary analysis informatics pipelines due to their absence in the literature and databases. CONCLUSIONS The analysis and interpretation of NGS results in myeloid neoplasia are challenging due to the varied number of detectable gene alterations. Familiarity with the genomic landscape of myeloid malignancies and knowledge of the tools available for the interpretation of sequence variants are essential to facilitate translation into clinical and therapy decisions.
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Affiliation(s)
- Mehenaz Hanbazazh
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shuko Harada
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishnu Reddy
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexander Craig Mackinnon
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Djamel Harbi
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diana Morlote
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
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7
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Dai B, Yu H, Ma T, Lei Y, Wang J, Zhang Y, Lu J, Yan H, Jiang L, Chen B. The Application of Targeted RNA Sequencing for KMT2A-Partial Tandem Duplication Identification and Integrated Analysis of Molecular Characterization in Acute Myeloid Leukemia. J Mol Diagn 2021; 23:1478-1490. [PMID: 34384895 DOI: 10.1016/j.jmoldx.2021.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 12/25/2022] Open
Abstract
The partial tandem duplication of histone-lysine N-methyltransferase 2A (KMT2A-PTD) is an important genetic alteration in acute myeloid leukemia (AML) and is associated with poor clinical outcome. Accurate and rapid detection of KMT2A-PTD is important for outcome prediction and clinical management, but next-generation sequencing-based quantitative research is still lacking. In this study, we developed a targeted RNA-based next-generation sequencing panel, together with single primer enrichment and unique molecular identifiers, to identify KMT2A-PTD as well as AML-related gene fusions and other driver mutations. Our panel showed high sensitivity, accuracy, and reproducibility in detecting the fusion ratio of KMT2A-PTD. We characterized the mutation profile of KMT2A-PTD-positive patients with AML and found different distribution patterns of driver mutations according to KMT2A-PTD fusion ratio level. Survival analyses revealed that the fusion ratio of KMT2A-PTD did not affect clinical outcome, but a novel molecular combination, namely, KMT2A-PTD/DNMT3A/FMS-like tyrosine kinase 3-internal tandem duplication, was associated with poor prognosis. Finally, we proved that the dynamic changes in the KMT2A-PTD fusion ratio were consistent with the overall process of disease progression. In summary, we applied the unique molecular identifier-based RNA panel to quantitatively detect KMT2A-PTD and elucidate its clinical relevance, which complemented the integrative network of various genetic alterations in AML.
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Affiliation(s)
- Bing Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yu
- Jiangsu Key Laboratory of Zoonosis and Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonose, Yangzhou University, Yangzhou, China
| | - Tingting Ma
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiyue Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Bing Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Antherieu G, Bidet A, Huet S, Hayette S, Migeon M, Boureau L, Sujobert P, Thomas X, Ghesquières H, Pigneux A, Heiblig M. Allogenic Stem Cell Transplantation Abrogates Negative Impact on Outcome of AML Patients with KMT2A Partial Tandem Duplication. Cancers (Basel) 2021; 13:cancers13092272. [PMID: 34068470 PMCID: PMC8126020 DOI: 10.3390/cancers13092272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023] Open
Abstract
Recently, a new subset of acute myeloid leukemia (AML) presenting a direct partial tandem duplication (PTD) of the KMT2A gene was described. The consequences of this alteration in terms of outcome and response to treatment remain unclear. We analyzed retrospectively a cohort of KMT2A-PTD-mutated patients with newly diagnosed AML. With a median follow-up of 3.6 years, the median overall survival was 12.1 months. KMT2A-PTD-mutated patients were highly enriched in mutations affecting epigenetic actors and the RTK/RAS signaling pathway. Integrating KMT2A-PTD in ELN classification abrogates its predictive value on survival suggesting that this mutation may overcome other genomic marker effects. In patients receiving intensive chemotherapy, hematopoietic stem cell transplantation (HSCT) significantly improved the outcome compared to non-transplanted patients. In the multivariate analysis, only HSCT at any time in complete remission (HR = 2.35; p = 0.034) and FLT3-ITD status (HR = 0.29; p = 0.014) were independent variables associated with overall survival, whereas age was not. In conclusion, our results emphasize that KMT2A-PTD should be considered as a potential adverse prognostic factor. However, as KMT2A-PTD-mutated patients are usually considered an intermediate risk group, upfront HSCT should be considered in first CR due to the high relapse rate observed in this subset of patients.
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Affiliation(s)
- Gabriel Antherieu
- Department of Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (G.A.); (X.T.); (H.G.)
| | - Audrey Bidet
- Hematology Biology, Molecular Hematology, Bordeaux University Hospital, 33600 Pessac, France; (A.B.); (M.M.); (L.B.)
| | - Sarah Huet
- Department of Molecular Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (S.H.); (S.H.); (P.S.)
| | - Sandrine Hayette
- Department of Molecular Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (S.H.); (S.H.); (P.S.)
| | - Marina Migeon
- Hematology Biology, Molecular Hematology, Bordeaux University Hospital, 33600 Pessac, France; (A.B.); (M.M.); (L.B.)
| | - Lisa Boureau
- Hematology Biology, Molecular Hematology, Bordeaux University Hospital, 33600 Pessac, France; (A.B.); (M.M.); (L.B.)
| | - Pierre Sujobert
- Department of Molecular Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (S.H.); (S.H.); (P.S.)
| | - Xavier Thomas
- Department of Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (G.A.); (X.T.); (H.G.)
| | - Hervé Ghesquières
- Department of Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (G.A.); (X.T.); (H.G.)
| | - Arnaud Pigneux
- Hematology and Cell Therapy, Bordeaux University Hospital, 33600 Pessac, France;
| | - Mael Heiblig
- Department of Hematology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre Bénite, France; (G.A.); (X.T.); (H.G.)
- Correspondence: ; Tel.: +33-478-862-240; Fax: +33-472-678-880
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9
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Ruhnke L, Stölzel F, Wagenführ L, Altmann H, Platzbecker U, Herold S, Rump A, Schröck E, Bornhäuser M, Schetelig J, von Bonin M. Case Report: ANXA2 Associated Life-Threatening Coagulopathy With Hyperfibrinolysis in a Patient With Non-APL Acute Myeloid Leukemia. Front Oncol 2021; 11:666014. [PMID: 33937079 PMCID: PMC8082174 DOI: 10.3389/fonc.2021.666014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/15/2021] [Indexed: 11/21/2022] Open
Abstract
Patients with acute promyelocytic leukemia (APL) often present with potentially life-threatening hemorrhagic diathesis. The underlying pathomechanisms of APL-associated coagulopathy are complex. However, two pathways considered to be APL-specific had been identified: 1) annexin A2 (ANXA2)-associated hyperfibrinolysis and 2) podoplanin (PDPN)-mediated platelet activation and aggregation. In contrast, since disseminated intravascular coagulation (DIC) is far less frequent in patients with non-APL acute myeloid leukemia (AML), the pathophysiology of AML-associated hemorrhagic disorders is not well understood. Furthermore, the potential threat of coagulopathy in non-APL AML patients may be underestimated. Herein, we report a patient with non-APL AML presenting with severe coagulopathy with hyperfibrinolysis. Since his clinical course resembled a prototypical APL-associated hemorrhagic disorder, we hypothesized pathophysiological similarities. Performing multiparametric flow cytometry (MFC) and immunofluorescence imaging (IF) studies, we found the patient’s bone-marrow mononuclear cells (BM-MNC) to express ANXA2 - a biomarker previously thought to be APL-specific. In addition, whole-exome sequencing (WES) on sorted BM-MNC (leukemia-associated immunophenotype (LAIP)1: ANXAlo, LAIP2: ANXAhi) demonstrated high intra-tumor heterogeneity. Since ANXA2 regulation is not well understood, further research to determine the coagulopathy-initiating events in AML and APL is indicated. Moreover, ANXA2 and PDPN MFC assessment as a tool to determine the risk of life-threatening DIC in AML and APL patients should be evaluated.
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Affiliation(s)
- Leo Ruhnke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Lisa Wagenführ
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Heidi Altmann
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,German Cancer Consortium (DKTK) partner site Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic I, Hematology and Cellular Therapy, Leipzig University Hospital, Leipzig, Germany
| | - Sylvia Herold
- Institute of Pathology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Andreas Rump
- National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,German Cancer Consortium (DKTK) partner site Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Clinical Genetics, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Evelin Schröck
- National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,German Cancer Consortium (DKTK) partner site Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Clinical Genetics, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,German Cancer Consortium (DKTK) partner site Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Malte von Bonin
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany.,German Cancer Consortium (DKTK) partner site Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Kishtagari A, Levine RL. The Role of Somatic Mutations in Acute Myeloid Leukemia Pathogenesis. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a034975. [PMID: 32398288 DOI: 10.1101/cshperspect.a034975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute myeloid leukemia (AML) is characterized by attenuation of lineage differentiation trajectories that results in impaired hematopoiesis and enhanced self-renewal. To date, sequencing studies have provided a rich landscape of information on the somatic mutations that contribute to AML pathogenesis. These studies show that most AML genomes harbor relatively fewer mutations, which are acquired in a stepwise manner. Our understanding of the genetic basis of leukemogenesis informs a broader understanding of what initiates and maintains the AML clone and informs the development of prognostic models and mechanism-based therapeutic strategies. Here, we explore the current knowledge of genetic and epigenetic aberrations in AML pathogenesis and how recent studies are expanding our knowledge of leukemogenesis and using this to accelerate therapeutic development for AML patients.
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Affiliation(s)
- Ashwin Kishtagari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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11
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Grieselhuber NR, Mims AS. Novel Targeted Therapeutics in Acute Myeloid Leukemia: an Embarrassment of Riches. Curr Hematol Malig Rep 2021; 16:192-206. [PMID: 33738705 DOI: 10.1007/s11899-021-00621-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW Acute myeloid leukemia (AML) is an aggressive malignancy of the bone marrow that has a poor prognosis with traditional cytotoxic chemotherapy, especially in elderly patients. In recent years, small molecule inhibitors targeting AML-associated IDH1, IDH2, and FLT3 mutations have been FDA approved. However, the majority of AML cases do not have a targetable mutation. A variety of novel agents targeting both previously untargetable mutations and general pathways in AML are currently being investigated. Herein, we review selected new targeted therapies currently in early-phase clinical investigation in AML. RECENT FINDINGS The DOT1L inhibitor pinometostat in KMT2A-rearranged AML, the menin inhibitors KO-539 and SYNDX-5613 in KMT2Ar and NPM1-mutated AML, and the mutant TP53 inhibitor APR-246 are examples of novel agents targeting specific mutations in AML. In addition, BET inhibitors, polo-like kinase inhibitors, and MDM2 inhibitors are promising new drug classes for AML which do not depend on the presence of a particular mutation. AML remains in incurable disease for many patients but advances in genomics, epigenetics, and drug discovery have led to the development of many potential novel therapeutic agents, many of which are being investigated in ongoing clinical trials. Additional studies will be necessary to determine how best to incorporate these novel agents into routine clinical treatment of AML.
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Affiliation(s)
- Nicole R Grieselhuber
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Alice S Mims
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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12
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Testa U, Castelli G, Pelosi E. Isocitrate Dehydrogenase Mutations in Myelodysplastic Syndromes and in Acute Myeloid Leukemias. Cancers (Basel) 2020; 12:E2427. [PMID: 32859092 PMCID: PMC7564409 DOI: 10.3390/cancers12092427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease generated by the acquisition of multiple genetic and epigenetic aberrations which impair the proliferation and differentiation of hematopoietic progenitors and precursors. In the last years, there has been a dramatic improvement in the understanding of the molecular alterations driving cellular signaling and biochemical changes determining the survival advantage, stimulation of proliferation, and impairment of cellular differentiation of leukemic cells. These molecular alterations influence clinical outcomes and provide potential targets for drug development. Among these alterations, an important role is played by two mutant enzymes of the citric acid cycle, isocitrate dehydrogenase (IDH), IDH1 and IDH2, occurring in about 20% of AMLs, which leads to the production of an oncogenic metabolite R-2-hydroxy-glutarate (R-2-HG); this causes a DNA hypermethylation and an inhibition of hematopoietic stem cell differentiation. IDH mutations differentially affect prognosis of AML patients following the location of the mutation and other co-occurring genomic abnormalities. Recently, the development of novel therapies based on the specific targeting of mutant IDH may contribute to new effective treatments of these patients. In this review, we will provide a detailed analysis of the biological, clinical, and therapeutic implications of IDH mutations.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.C.); (E.P.)
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13
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Yu J, Li Y, Zhang D, Wan D, Jiang Z. Clinical implications of recurrent gene mutations in acute myeloid leukemia. Exp Hematol Oncol 2020; 9:4. [PMID: 32231866 PMCID: PMC7099827 DOI: 10.1186/s40164-020-00161-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous clonal malignancy characterized by recurrent gene mutations. Genomic heterogeneity, patients’ individual variability, and recurrent gene mutations are the major obstacles among many factors that impact treatment efficacy of the AML patients. With the application of cost- and time-effective next-generation sequencing (NGS) technologies, an enormous diversity of genetic mutations has been identified. The recurrent gene mutations and their important roles in acute myeloid leukemia (AML) pathogenesis have been studied extensively. In this review, we summarize the recent development on the gene mutation in patients with AML.
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Affiliation(s)
- Jifeng Yu
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China.,2Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Yingmei Li
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Danfeng Zhang
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Dingming Wan
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Zhongxing Jiang
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
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