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Lehner KM, Gopalakrishnapillai A, Kolb EA, Barwe SP. Bone Marrow Microenvironment-Induced Chemoprotection in KMT2A Rearranged Pediatric AML Is Overcome by Azacitidine-Panobinostat Combination. Cancers (Basel) 2023; 15:3112. [PMID: 37370721 DOI: 10.3390/cancers15123112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Advances in therapies of pediatric acute myeloid leukemia (AML) have been minimal in recent decades. Although 82% of patients will have an initial remission after intensive therapy, approximately 40% will relapse. KMT2A is the most common chromosomal translocation in AML and has a poor prognosis resulting in high relapse rates and low chemotherapy efficacy. Novel targeted approaches are needed to increase sensitivity to chemotherapy. Recent studies have shown how interactions within the bone marrow (BM) microenvironment help AML cells evade chemotherapy and contribute to relapse by promoting leukemic blast survival. This study investigates how DNA hypomethylating agent azacitidine and histone deacetylase inhibitor panobinostat synergistically overcome BM niche-induced chemoprotection modulated by stromal, endothelial, and mesenchymal stem cells and the extracellular matrix (ECM). We show that direct contact between AML cells and BM components mediates chemoprotection. We demonstrate that azacitidine and panobinostat synergistically sensitize MV4;11 cells and KMT2A rearranged pediatric patient-derived xenograft lines to cytarabine in multicell coculture. Treatment with the epigenetic drug combination reduced leukemic cell association with multicell monolayer and ECM in vitro and increased mobilization of leukemic cells from the BM in vivo. Finally, we show that pretreatment with the epigenetic drug combination improves the efficacy of chemotherapy in vivo.
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Affiliation(s)
- Kara M Lehner
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children's Hospital, Wilmington, DE 19803, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Anilkumar Gopalakrishnapillai
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children's Hospital, Wilmington, DE 19803, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Edward Anders Kolb
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children's Hospital, Wilmington, DE 19803, USA
| | - Sonali P Barwe
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children's Hospital, Wilmington, DE 19803, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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Górecki M, Kozioł I, Kopystecka A, Budzyńska J, Zawitkowska J, Lejman M. Updates in KMT2A Gene Rearrangement in Pediatric Acute Lymphoblastic Leukemia. Biomedicines 2023; 11:biomedicines11030821. [PMID: 36979800 PMCID: PMC10045821 DOI: 10.3390/biomedicines11030821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/10/2023] Open
Abstract
The KMT2A (formerly MLL) encodes the histone lysine-specific N-methyltransferase 2A and is mapped on chromosome 11q23. KMT2A is a frequent target for recurrent translocations in acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), or mixed lineage (biphenotypic) leukemia (MLL). Over 90 KMT2A fusion partners have been identified until now, including the most recurring ones—AFF1, MLLT1, and MLLT3—which encode proteins regulating epigenetic mechanisms. The presence of distinct KMT2A rearrangements is an independent dismal prognostic factor, while very few KMT2A rearrangements display either a good or intermediate outcome. KMT2A-rearranged (KMT2A-r) ALL affects more than 70% of new ALL diagnoses in infants (<1 year of age), 5–6% of pediatric cases, and 15% of adult cases. KMT2A-rearranged (KMT2A-r) ALL is characterized by hyperleukocytosis, a relatively high incidence of central nervous system (CNS) involvement, an aggressive course with early relapse, and early relapses resulting in poor prognosis. The exact pathways of fusions and the effects on the final phenotypic activity of the disease are still subjects of much research. Future trials could consider the inclusion of targeted immunotherapeutic agents and prioritize the identification of prognostic factors, allowing for the less intensive treatment of some infants with KMT2A ALL. The aim of this review is to summarize our knowledge and present current insight into the mechanisms of KMT2A-r ALL, portray their characteristics, discuss the clinical outcome along with risk stratification, and present novel therapeutic strategies.
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Affiliation(s)
- Mateusz Górecki
- Student Scientific Society of Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Ilona Kozioł
- Student Scientific Society of the Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Agnieszka Kopystecka
- Student Scientific Society of the Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Julia Budzyńska
- Student Scientific Society of the Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Joanna Zawitkowska
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence:
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Cheung LC, Aya-Bonilla C, Cruickshank MN, Chiu SK, Kuek V, Anderson D, Chua GA, Singh S, Oommen J, Ferrari E, Hughes AM, Ford J, Kunold E, Hesselman MC, Post F, Faulk KE, Breese EH, Guest EM, Brown PA, Loh ML, Lock RB, Kees UR, Jafari R, Malinge S, Kotecha RS. Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy. Leukemia 2023; 37:61-71. [PMID: 36380143 PMCID: PMC9883157 DOI: 10.1038/s41375-022-01746-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.
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Affiliation(s)
- Laurence C Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Carlos Aya-Bonilla
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | | | - Sung K Chiu
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Vincent Kuek
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Denise Anderson
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Sajla Singh
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Joyce Oommen
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Emanuela Ferrari
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Anastasia M Hughes
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Jette Ford
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Elena Kunold
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Maria C Hesselman
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Frederik Post
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Kelly E Faulk
- University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, USA
| | - Erin H Breese
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin M Guest
- Division of Hematology, Oncology, Blood and Marrow Transplantation, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Patrick A Brown
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD, USA
| | - Mignon L Loh
- Division of Pediatric Hematology, Oncology, Bone Marrow Transplant and Cellular Therapy, Seattle Children's Hospital, Seattle, WA, USA
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre/School of Women's and Children's Health/UNSW Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Ursula R Kees
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rozbeh Jafari
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Sébastien Malinge
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Medical School, Curtin University, Perth, WA, Australia.
- The University of Western Australia, Perth, WA, Australia.
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.
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Lopes BA, Poubel CP, Teixeira CE, Caye-Eude A, Cavé H, Meyer C, Marschalek R, Boroni M, Emerenciano M. Novel Diagnostic and Therapeutic Options for KMT2A-Rearranged Acute Leukemias. Front Pharmacol 2022; 13:749472. [PMID: 35734412 PMCID: PMC9208280 DOI: 10.3389/fphar.2022.749472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
The KMT2A (MLL) gene rearrangements (KMT2A-r) are associated with a diverse spectrum of acute leukemias. Although most KMT2A-r are restricted to nine partner genes, we have recently revealed that KMT2A-USP2 fusions are often missed during FISH screening of these genetic alterations. Therefore, complementary methods are important for appropriate detection of any KMT2A-r. Here we use a machine learning model to unravel the most appropriate markers for prediction of KMT2A-r in various types of acute leukemia. A Random Forest and LightGBM classifier was trained to predict KMT2A-r in patients with acute leukemia. Our results revealed a set of 20 genes capable of accurately estimating KMT2A-r. The SKIDA1 (AUC: 0.839; CI: 0.799–0.879) and LAMP5 (AUC: 0.746; CI: 0.685–0.806) overexpression were the better markers associated with KMT2A-r compared to CSPG4 (also named NG2; AUC: 0.722; CI: 0.659–0.784), regardless of the type of acute leukemia. Of importance, high expression levels of LAMP5 estimated the occurrence of all KMT2A-USP2 fusions. Also, we performed drug sensitivity analysis using IC50 data from 345 drugs available in the GDSC database to identify which ones could be used to treat KMT2A-r leukemia. We observed that KMT2A-r cell lines were more sensitive to 5-Fluorouracil (5FU), Gemcitabine (both antimetabolite chemotherapy drugs), WHI-P97 (JAK-3 inhibitor), Foretinib (MET/VEGFR inhibitor), SNX-2112 (Hsp90 inhibitor), AZD6482 (PI3Kβ inhibitor), KU-60019 (ATM kinase inhibitor), and Pevonedistat (NEDD8-activating enzyme (NAE) inhibitor). Moreover, IC50 data from analyses of ex-vivo drug sensitivity to small-molecule inhibitors reveals that Foretinib is a promising drug option for AML patients carrying FLT3 activating mutations. Thus, we provide novel and accurate options for the diagnostic screening and therapy of KMT2A-r leukemia, regardless of leukemia subtype.
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Affiliation(s)
- Bruno A. Lopes
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Caroline Pires Poubel
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Cristiane Esteves Teixeira
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Aurélie Caye-Eude
- Département de Génétique, UF de Génétique moléculaire, Assistance Publique des Hópitaux de Paris (AP-HP), Hópital Robert Debré, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Hélène Cavé
- Département de Génétique, UF de Génétique moléculaire, Assistance Publique des Hópitaux de Paris (AP-HP), Hópital Robert Debré, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Claus Meyer
- DCAL/Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Rolf Marschalek
- DCAL/Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Mariana Emerenciano
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- *Correspondence: Mariana Emerenciano,
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