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Kosvyra Α, Karadimitris Α, Papaioannou Μ, Chouvarda I. Machine learning and integrative multi-omics network analysis for survival prediction in acute myeloid leukemia. Comput Biol Med 2024; 178:108735. [PMID: 38875909 DOI: 10.1016/j.compbiomed.2024.108735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/14/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common malignant myeloid disorder in adults and the fifth most common malignancy in children, necessitating advanced technologies for outcome prediction. METHOD This study aims to enhance prognostic capabilities in AML by integrating multi-omics data, especially gene expression and methylation, through network-based feature selection methodologies. By employing artificial intelligence and network analysis, we are exploring different methods to build a machine learning model for predicting AML patient survival. We evaluate the effectiveness of combining omics data, identify the most informative method for network integration and compare the performance with standard feature selection methods. RESULTS Our findings demonstrate that integrating gene expression and methylation data significantly improves prediction accuracy compared to single omics data. Among network integration methods, our study identifies the best approach that improves informative feature selection for predicting patient outcomes in AML. Comparative analyses demonstrate the superior performance of the proposed network-based methods over standard techniques. CONCLUSIONS This research presents an innovative and robust methodology for building a survival prediction model tailored to AML patients. By leveraging multilayer network analysis for feature selection, our approach contributes to improving the understanding and prognostic capabilities in AML and laying the foundation for more effective personalized therapeutic interventions in the future.
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Affiliation(s)
- Α Kosvyra
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Α Karadimitris
- Centre for Haematology and Hugh and Josseline Langmuir Centre for Myeloma Research, Department of Immunology and Inflammation, Imperial College London, Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, Du Cane Road, London, W12 0NN, UK
| | - Μ Papaioannou
- Hematology Unit, 1st Dept of Internal Medicine, AHEPA Hospital, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Levra Levron C, Elettrico L, Duval C, Piacenti G, Proserpio V, Donati G. Bridging tissue repair and epithelial carcinogenesis: epigenetic memory and field cancerization. Cell Death Differ 2024:10.1038/s41418-023-01254-6. [PMID: 38228801 DOI: 10.1038/s41418-023-01254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
The epigenome coordinates spatial-temporal specific gene expression during development and in adulthood, for the maintenance of homeostasis and upon tissue repair. The upheaval of the epigenetic landscape is a key event in the onset of many pathologies including tumours, where epigenetic changes cooperate with genetic aberrations to establish the neoplastic phenotype and to drive cell plasticity during its evolution. DNA methylation, histone modifiers and readers or other chromatin components are indeed often altered in cancers, such as carcinomas that develop in epithelia. Lining the surfaces and the cavities of our body and acting as a barrier from the environment, epithelia are frequently subjected to acute or chronic tissue damages, such as mechanical injuries or inflammatory episodes. These events can activate plasticity mechanisms, with a deep impact on cells' epigenome. Despite being very effective, tissue repair mechanisms are closely associated with tumour onset. Here we review the similarities between tissue repair and carcinogenesis, with a special focus on the epigenetic mechanisms activated by cells during repair and opted by carcinoma cells in multiple epithelia. Moreover, we discuss the recent findings on inflammatory and wound memory in epithelia and describe the epigenetic modifications that characterise them. Finally, as wound memory in epithelial cells promotes carcinogenesis, we highlight how it represents an early step for the establishment of field cancerization.
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Affiliation(s)
- Chiara Levra Levron
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Luca Elettrico
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Carlotta Duval
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Gabriele Piacenti
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy.
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3
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Papadopoulou V, Schoumans J, Basset V, Solly F, Pasquier J, Blum S, Spertini O. Single-center, observational study of AML/MDS-EB with IDH1/2 mutations: genetic profile, immunophenotypes, mutational kinetics and outcomes. Hematology 2023; 28:2180704. [PMID: 36815747 DOI: 10.1080/16078454.2023.2180704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVE IDH1/2 mutations, intervening in epigenetic procedures, are frequently encountered in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). Knowledge of the genetics, immunophenotypes, and mutational kinetics of IDH1/2-mutated AML can contribute to the understanding of AML clonal architecture and inform therapeutics and monitoring. METHODS We retrospectively analyzed 50 IDH1/2-mutated AML/MDS-EB cases of our institution, to identify recurrent co-mutations, immunophenotypes, patterns of co-variance of IDH1/2 allele burdens with those of recurrent co-mutations, frequency of persistent IDH1/2 mutation as clonal hematopoiesis of indeterminate potential (CHIP) in remission and response to hypomethylating agents. RESULTS Most frequently co-mutated genes were DNMT3A, SRSF2 and NPM1. Most cases with co-existent IDH1/2 and NPM1 mutations (11/13) showed an 'APL-like' immunophenotype (CD34-HLADR-). Allele burdens of mutated IDH1/2 were identical to mutated SRSF2 allele burdens at diagnosis and remission, but not always to mutated NPM1 allele burden in remission. We show persistence of significant mutIDH1/2 allele burden in approximately one-fourth of patients with deep remissions. IDH1/2 mutations were significantly more frequent among responders to first-line HMA-based regimens than among non-responders, in patients treated for myeloid neoplasms with excess blasts. CONCLUSIONS IDH1/2 mutations are most frequently accompanied by DNMT3A, SRSF2 and NPM1 mutations. NPM1-IDH1/2 mutated AML has a mature phenotype possibly amenable to differentiation therapies. IDH1/2 and SRSF2 mutations probably arise at the same developmental stage of the disease, as their allele burdens covariate. IDH1/2 mutation represents CHIP in a substantial proportion of cases and is therefore no reliable residual disease marker. The preferential presence of IDH1/2 mutations among HMA-responders could inform therapeutic decisions if confirmed in larger series.
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Affiliation(s)
- Vasiliki Papadopoulou
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jacqueline Schoumans
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Valentin Basset
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Françoise Solly
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jérôme Pasquier
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Sabine Blum
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Olivier Spertini
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
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4
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Heyes E, Wilhelmson AS, Wenzel A, Manhart G, Eder T, Schuster MB, Rzepa E, Pundhir S, D'Altri T, Frank AK, Gentil C, Woessmann J, Schoof EM, Meggendorfer M, Schwaller J, Haferlach T, Grebien F, Porse BT. TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression. Nat Commun 2023; 14:6185. [PMID: 37794021 PMCID: PMC10550934 DOI: 10.1038/s41467-023-41927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated; CEBPADM) in acute myeloid leukemia (AML) with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. The most frequently co-mutated genes in CEBPADM AML are GATA2 and TET2, however the molecular mechanisms underlying this co-mutational spectrum are incomplete. By combining transcriptomic and epigenomic analyses of CEBPA-TET2 co-mutated patients with models thereof, we identify GATA2 as a conserved target of the CEBPA-TET2 mutational axis, providing a rationale for the mutational spectra in CEBPADM AML. Elevated CEBPA levels, driven by CEBPANT, mediate recruitment of TET2 to the Gata2 distal hematopoietic enhancer thereby increasing Gata2 expression. Concurrent loss of TET2 in CEBPADM AML induces a competitive advantage by increasing Gata2 promoter methylation, thereby rebalancing GATA2 levels. Of clinical relevance, demethylating treatment of Cebpa-Tet2 co-mutated AML restores Gata2 levels and prolongs disease latency.
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Affiliation(s)
- Elizabeth Heyes
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Anna S Wilhelmson
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Wenzel
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Manhart
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Thomas Eder
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Mikkel B Schuster
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edwin Rzepa
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Sachin Pundhir
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Teresa D'Altri
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Katrine Frank
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital Basel, Basel, Switzerland
| | | | - Florian Grebien
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria.
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
| | - Bo T Porse
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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Humphries S, Bond DR, Germon ZP, Keely S, Enjeti AK, Dun MD, Lee HJ. Crosstalk between DNA methylation and hypoxia in acute myeloid leukaemia. Clin Epigenetics 2023; 15:150. [PMID: 37705055 PMCID: PMC10500762 DOI: 10.1186/s13148-023-01566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a deadly disease characterised by the uncontrolled proliferation of immature myeloid cells within the bone marrow. Altered regulation of DNA methylation is an important epigenetic driver of AML, where the hypoxic bone marrow microenvironment can help facilitate leukaemogenesis. Thus, interactions between epigenetic regulation and hypoxia signalling will have important implications for AML development and treatment. MAIN BODY This review summarises the importance of DNA methylation and the hypoxic bone marrow microenvironment in the development, progression, and treatment of AML. Here, we focus on the role hypoxia plays on signalling and the subsequent regulation of DNA methylation. Hypoxia is likely to influence DNA methylation through altered metabolic pathways, transcriptional control of epigenetic regulators, and direct effects on the enzymatic activity of epigenetic modifiers. DNA methylation may also prevent activation of hypoxia-responsive genes, demonstrating bidirectional crosstalk between epigenetic regulation and the hypoxic microenvironment. Finally, we consider the clinical implications of these interactions, suggesting that reduced cell cycling within the hypoxic bone marrow may decrease the efficacy of hypomethylating agents. CONCLUSION Hypoxia is likely to influence AML progression through complex interactions with DNA methylation, where the therapeutic efficacy of hypomethylating agents may be limited within the hypoxic bone marrow. To achieve optimal outcomes for AML patients, future studies should therefore consider co-treatments that can promote cycling of AML cells within the bone marrow or encourage their dissociation from the bone marrow.
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Affiliation(s)
- Sam Humphries
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Danielle R Bond
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Zacary P Germon
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Anoop K Enjeti
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Department of Haematology, Calvary Mater Hospital, Waratah, NSW, 2298, Australia
- New South Wales Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, 2305, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Heather J Lee
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
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Palau A, Segerberg F, Lidschreiber M, Lidschreiber K, Naughton AJ, Needhamsen M, Jung LA, Jagodic M, Cramer P, Lehmann S, Carlsten M, Lennartsson A. Perturbed epigenetic transcriptional regulation in AML with IDH mutations causes increased susceptibility to NK cells. Leukemia 2023; 37:1830-1841. [PMID: 37495775 PMCID: PMC10457197 DOI: 10.1038/s41375-023-01972-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/05/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
Isocitrate dehydrogenase (IDH) mutations are found in 20% of acute myeloid leukemia (AML) patients. However, only 30-40% of the patients respond to IDH inhibitors (IDHi). We aimed to identify a molecular vulnerability to tailor novel therapies for AML patients with IDH mutations. We characterized the transcriptional and epigenetic landscape with the IDH2i AG-221, using an IDH2 mutated AML cell line model and AML patient cohorts, and discovered a perturbed transcriptional regulatory network involving myeloid transcription factors that were partly restored after AG-221 treatment. In addition, hypermethylation of the HLA cluster caused a down-regulation of HLA class I genes, triggering an enhanced natural killer (NK) cell activation and an increased susceptibility to NK cell-mediated responses. Finally, analyses of DNA methylation data from IDHi-treated patients showed that non-responders still harbored hypermethylation in HLA class I genes. In conclusion, this study provides new insights suggesting that IDH mutated AML is particularly sensitive to NK cell-based personalized immunotherapy.
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Affiliation(s)
- Anna Palau
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Filip Segerberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Michael Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katja Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Aonghus J Naughton
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Lisa Anna Jung
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Patrick Cramer
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
- Hematology Centre, Karolinska University Hospital, Stockholm, Sweden.
- Hematology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
| | - Mattias Carlsten
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
- Center for Cell Therapy and Allogeneic Stem Cell Transplantation, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden.
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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Gruber E, Kats LM. The curious case of IDH mutant acute myeloid leukaemia: biochemistry and therapeutic approaches. Biochem Soc Trans 2023; 51:1675-1686. [PMID: 37526143 PMCID: PMC10586776 DOI: 10.1042/bst20230017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
Of the many genetic alterations that occur in cancer, relatively few have proven to be suitable for the development of targeted therapies. Mutations in isocitrate dehydrogenase (IDH) 1 and -2 increase the capacity of cancer cells to produce a normally scarce metabolite, D-2-hydroxyglutarate (2-HG), by several orders of magnitude. The discovery of the unusual biochemistry of IDH mutations spurred a flurry of activity that revealed 2-HG as an 'oncometabolite' with pleiotropic effects in malignant cells and consequences for anti-tumour immunity. Over the next decade, we learned that 2-HG dysregulates a wide array of molecular pathways, among them a large family of dioxygenases that utilise the closely related metabolite α-ketoglutarate (α-KG) as an essential co-substrate. 2-HG not only contributes to malignant transformation, but some cancer cells become addicted to it and sensitive to inhibitors that block its synthesis. Moreover, high 2-HG levels and loss of wild-type IDH1 or IDH2 activity gives rise to synthetic lethal vulnerabilities. Herein, we review the biology of IDH mutations with a particular focus on acute myeloid leukaemia (AML), an aggressive disease where selective targeting of IDH-mutant cells is showing significant promise.
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Affiliation(s)
- Emily Gruber
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Lev M. Kats
- Peter MacCallum Cancer Centre and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
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8
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Venneker S, Bovée JVMG. IDH Mutations in Chondrosarcoma: Case Closed or Not? Cancers (Basel) 2023; 15:3603. [PMID: 37509266 PMCID: PMC10377514 DOI: 10.3390/cancers15143603] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Chondrosarcomas are malignant cartilage-producing tumours that frequently harbour isocitrate dehydrogenase 1 and -2 (IDH) gene mutations. Several studies have confirmed that these mutations are key players in the early stages of cartilage tumour development, but their role in later stages remains ambiguous. The prognostic value of IDH mutations remains unclear and preclinical studies have not identified effective treatment modalities (in)directly targeting these mutations. In contrast, the IDH mutation status is a prognostic factor in other cancers, and IDH mutant inhibitors as well as therapeutic strategies targeting the underlying vulnerabilities induced by IDH mutations seem effective in these tumour types. This discrepancy in findings might be ascribed to a difference in tumour type, elevated D-2-hydroxyglutarate levels, and the type of in vitro model (endogenous vs. genetically modified) used in preclinical studies. Moreover, recent studies suggest that the (epi)genetic landscape in which the IDH mutation functions is an important factor to consider when investigating potential therapeutic strategies or patient outcomes. These findings imply that the dichotomy between IDH wildtype and mutant is too simplistic and additional subgroups indeed exist within chondrosarcoma. Future studies should focus on the identification, characterisation, and tailoring of treatments towards these biological subgroups within IDH wildtype and mutant chondrosarcoma.
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Affiliation(s)
- Sanne Venneker
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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9
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Lachowiez CA, Loghavi S, Zeng Z, Tanaka T, Kim YJ, Uryu H, Turkalj S, Jakobsen NA, Luskin MR, Duose DY, Tidwell RSS, Short NJ, Borthakur G, Kadia TM, Masarova L, Tippett GD, Bose P, Jabbour EJ, Ravandi F, Daver NG, Garcia-Manero G, Kantarjian H, Garcia JS, Vyas P, Takahashi K, Konopleva M, DiNardo CD. A Phase Ib/II Study of Ivosidenib with Venetoclax ± Azacitidine in IDH1-Mutated Myeloid Malignancies. Blood Cancer Discov 2023; 4:276-293. [PMID: 37102976 PMCID: PMC10320628 DOI: 10.1158/2643-3230.bcd-22-0205] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/26/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
The safety and efficacy of combining the isocitrate dehydrogenase-1 (IDH1) inhibitor ivosidenib (IVO) with the BCL2 inhibitor venetoclax (VEN; IVO + VEN) ± azacitidine (AZA; IVO + VEN + AZA) were evaluated in four cohorts of patients with IDH1-mutated myeloid malignancies (n = 31). Most (91%) adverse events were grade 1 or 2. The maximal tolerated dose was not reached. Composite complete remission with IVO + VEN + AZA versus IVO + VEN was 90% versus 83%. Among measurable residual disease (MRD)-evaluable patients (N = 16), 63% attained MRD--negative remissions; IDH1 mutation clearance occurred in 64% of patients receiving ≥5 treatment cycles (N = 14). Median event-free survival and overall survival were 36 [94% CI, 23-not reached (NR)] and 42 (95% CI, 42-NR) months. Patients with signaling gene mutations appeared to particularly benefit from the triplet regimen. Longitudinal single-cell proteogenomic analyses linked cooccurring mutations, antiapoptotic protein expression, and cell maturation to therapeutic sensitivity of IDH1-mutated clones. No IDH isoform switching or second-site IDH1 mutations were observed, indicating combination therapy may overcome established resistance pathways to single-agent IVO. SIGNIFICANCE IVO + VEN + AZA is safe and active in patients with IDH1-mutated myeloid malignancies. Combination therapy appears to overcome resistance mechanisms observed with single-agent IDH-inhibitor use, with high MRD-negative remission rates. Single-cell DNA ± protein and time-of-flight mass-cytometry analysis revealed complex resistance mechanisms at relapse, highlighting key pathways for future therapeutic intervention. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Curtis A Lachowiez
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Sanam Loghavi
- The University of Texas MD Anderson Cancer Center, Department of Hematopathology, Houston, Texas
| | - Zhihong Zeng
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Tomoyuki Tanaka
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Yi June Kim
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Hidetaka Uryu
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Clinical Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Clinical Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Marlise R Luskin
- Dana-Farber Cancer Institute, Leukemia Program, Boston, Massachusetts
| | - Dzifa Y Duose
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, Texas
| | - Rebecca S S Tidwell
- The University of Texas MD Anderson Cancer Center, Department of Biostatistics, Houston, Texas
| | - Nicholas J Short
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Tapan M Kadia
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Lucia Masarova
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - George D Tippett
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Prithviraj Bose
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Elias J Jabbour
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Farhad Ravandi
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Naval G Daver
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | | | - Hagop Kantarjian
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | | | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Clinical Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Koichi Takahashi
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Marina Konopleva
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
| | - Courtney D DiNardo
- The University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, Texas
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10
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Saulle E, Spinello I, Quaranta MT, Labbaye C. Advances in Understanding the Links between Metabolism and Autophagy in Acute Myeloid Leukemia: From Biology to Therapeutic Targeting. Cells 2023; 12:1553. [PMID: 37296673 PMCID: PMC10252746 DOI: 10.3390/cells12111553] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Autophagy is a highly conserved cellular degradation process that regulates cellular metabolism and homeostasis under normal and pathophysiological conditions. Autophagy and metabolism are linked in the hematopoietic system, playing a fundamental role in the self-renewal, survival, and differentiation of hematopoietic stem and progenitor cells, and in cell death, particularly affecting the cellular fate of the hematopoietic stem cell pool. In leukemia, autophagy sustains leukemic cell growth, contributes to survival of leukemic stem cells and chemotherapy resistance. The high frequency of disease relapse caused by relapse-initiating leukemic cells resistant to therapy occurs in acute myeloid leukemia (AML), and depends on the AML subtypes and treatments used. Targeting autophagy may represent a promising strategy to overcome therapeutic resistance in AML, for which prognosis remains poor. In this review, we illustrate the role of autophagy and the impact of its deregulation on the metabolism of normal and leukemic hematopoietic cells. We report updates on the contribution of autophagy to AML development and relapse, and the latest evidence indicating autophagy-related genes as potential prognostic predictors and drivers of AML. We review the recent advances in autophagy manipulation, combined with various anti-leukemia therapies, for an effective autophagy-targeted therapy for AML.
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Affiliation(s)
- Ernestina Saulle
- Correspondence: (E.S.); (C.L.); Tel.: +39-0649902422 (E.S.); +39-0649902418 (C.L.)
| | | | | | - Catherine Labbaye
- Correspondence: (E.S.); (C.L.); Tel.: +39-0649902422 (E.S.); +39-0649902418 (C.L.)
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11
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Fortin J, Chiang MF, Meydan C, Foox J, Ramachandran P, Leca J, Lemonnier F, Li WY, Gams MS, Sakamoto T, Chu M, Tobin C, Laugesen E, Robinson TM, You-Ten A, Butler DJ, Berger T, Minden MD, Levine RL, Guidos CJ, Melnick AM, Mason CE, Mak TW. Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells. Proc Natl Acad Sci U S A 2023; 120:e2208176120. [PMID: 36652477 PMCID: PMC9942850 DOI: 10.1073/pnas.2208176120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have distinct, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that Idh2R172K and Tet2 loss-of-function have divergent consequences on the expression and activity of key hematopoietic and leukemogenic regulators. Notably, chromatin accessibility and transcriptional deregulation in Idh2R172K cells were partially disconnected from DNA methylation alterations. These results highlight unanticipated divergent effects of IDH1/2 and TET2 mutations, providing support for the optimization of genotype-specific therapies.
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Affiliation(s)
- Jerome Fortin
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- 2To whom correspondence may be addressed. , , or
| | - Ming-Feng Chiang
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Cem Meydan
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
- dWorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY10065
| | - Jonathan Foox
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
| | | | - Julie Leca
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - François Lemonnier
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- eInstitut Mondor de Recherche Biomédicale, INSERMU955, Université Paris Est Créteil, Créteil94010, France
| | - Wanda Y. Li
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- fCentre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Miki S. Gams
- gDepartment of Immunology, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ONM5G 0A4, Canada
| | - Takashi Sakamoto
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- hDepartment of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Mandy Chu
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Chantal Tobin
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Eric Laugesen
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Troy M. Robinson
- iHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- jLouis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Annick You-Ten
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Daniel J. Butler
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
| | - Thorsten Berger
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Mark D. Minden
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Ross L. Levine
- iHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- kCenter for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY10065
- lCenter for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Cynthia J. Guidos
- gDepartment of Immunology, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ONM5G 0A4, Canada
| | - Ari M. Melnick
- mDepartment of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY10021
| | - Christopher E. Mason
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
- dWorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY10065
| | - Tak W. Mak
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- fCentre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- nDepartment of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- 2To whom correspondence may be addressed. , , or
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12
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Steinhäuser S, Silva P, Lenk L, Beder T, Hartmann A, Hänzelmann S, Fransecky L, Neumann M, Bastian L, Lipinski S, Richter K, Bultmann M, Hübner E, Xia S, Röllig C, Vogiatzi F, Schewe DM, Yumiceba V, Schultz K, Spielmann M, Baldus CD. Isocitrate dehydrogenase 1 mutation drives leukemogenesis by PDGFRA activation due to insulator disruption in acute myeloid leukemia (AML). Leukemia 2023; 37:134-142. [PMID: 36411356 PMCID: PMC9883162 DOI: 10.1038/s41375-022-01751-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/22/2022]
Abstract
Acute myeloid leukemia (AML) is characterized by complex molecular alterations and driver mutations. Elderly patients show increased frequencies of IDH mutations with high chemoresistance and relapse rates despite recent therapeutic advances. Besides being associated with global promoter hypermethylation, IDH1 mutation facilitated changes in 3D DNA-conformation by CTCF-anchor methylation and upregulated oncogene expression in glioma, correlating with poor prognosis. Here, we investigated the role of IDH1 p.R132H mutation in altering 3D DNA-architecture and subsequent oncogene activation in AML. Using public RNA-Seq data, we identified upregulation of tyrosine kinase PDGFRA in IDH1-mutant patients, correlating with poor prognosis. DNA methylation analysis identified CpG hypermethylation within a CTCF-anchor upstream of PDGFRA in IDH1-mutant patients. Increased PDGFRA expression, PDGFRA-CTCF methylation and decreased CTCF binding were confirmed in AML CRISPR cells with heterozygous IDH1 p.R132H mutation and upon exogenous 2-HG treatment. IDH1-mutant cells showed higher sensitivity to tyrosine kinase inhibitor dasatinib, which was supported by reduced blast count in a patient with refractory IDH1-mutant AML after dasatinib treatment. Our data illustrate that IDH1 p.R132H mutation leads to CTCF hypermethylation, disrupting DNA-looping and insulation of PDGFRA, resulting in PDGFRA upregulation in IDH1-mutant AML. Treatment with dasatinib may offer a novel treatment strategy for IDH1-mutant AML.
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Affiliation(s)
- Sophie Steinhäuser
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Patricia Silva
- Department of Hematology and Oncology, Charité University Hospital, Berlin, Germany
| | - Lennart Lenk
- Department of Pediatrics I, ALL-BFM Study Group, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Thomas Beder
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alina Hartmann
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sonja Hänzelmann
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lars Fransecky
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Martin Neumann
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lorenz Bastian
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Simone Lipinski
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Kathrin Richter
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Miriam Bultmann
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Emely Hübner
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Shuli Xia
- Kennedy Krieger Institute, Baltimore, MD, USA
- School of Medicine, Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Christoph Röllig
- Department of Internal Medicine I, University Hospital Carl-Gustav-Carus, Dresden, Germany
| | - Fotini Vogiatzi
- Department of Pediatrics I, ALL-BFM Study Group, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Veronica Yumiceba
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Kristin Schultz
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Malte Spielmann
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Claudia Dorothea Baldus
- Department of Inner Medicine II (Hematology/Oncology), University Hospital Schleswig-Holstein, Kiel, Germany.
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany.
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13
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Effects of cancer-associated point mutations on the structure, function, and stability of isocitrate dehydrogenase 2. Sci Rep 2022; 12:18830. [PMID: 36335201 PMCID: PMC9637083 DOI: 10.1038/s41598-022-23659-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Mutations in isocitrate dehydrogenase (IDH) are frequently found in low-grade gliomas, secondary glioblastoma, chondrosarcoma, acute myeloid leukemias, and intrahepatic cholangiocarcinoma. However, the molecular mechanisms of how IDH2 mutations induce carcinogenesis remain unclear. Using overlapping PCR, transfection, immunoblotting, immunoprecipitation, measurements of enzyme activity, glucose, lactic acid, ATP, and reactive oxygen species (ROS), cell viability, protein degradation assays post-inhibition of the 26S proteasome (bortezomib) or HSP90 (17-AAG), and a homology model, we demonstrated that the properties of ten cancer-associated IDH2 variants (R140G/Q/W and R172S/K/M/W/G/C/P) arising from point mutations are closely related to their structure and stability. Compared with wild-type IDH2, the R172 and R140 point mutations resulted in a decrease in IDH2 activity, ROS, and lactate levels and an increase in glucose and ATP levels under normal and hypoxic conditions, indicating that mutant IDH2 increases cell dependency on mitochondrial oxidative phosphorylation, and reduces glycolysis under hypoxia. Overexpression of most of IDH2 point mutants showed anti-proliferative effects in the 293T and BV2 cell lines by inhibition of PI3K/AKT signaling and cyclin D1 expression and/or induced the expression of TNF-α and IL-6. Furthermore, bortezomib treatment resulted in dramatic degradation of IDH2 mutants, including R140G, R140Q, R140W, R172S and R172K, whereas it had little impact on the expression of WT and other mutants (R172M, R172W, R172G, R172C and R172P). In addition, targeting HSP90 minimally affected the expression of mutated IDH2 due to a lack of interaction between HSP90 and IDH2. The homology model further revealed that changes in conformation and IDH2 protein stability appeared to be associated with these point mutations. Taken together, our findings provide information important for understanding the molecular mechanisms of IDH2 mutations in tumors.
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14
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Seo W, Silwal P, Song IC, Jo EK. The dual role of autophagy in acute myeloid leukemia. J Hematol Oncol 2022; 15:51. [PMID: 35526025 PMCID: PMC9077970 DOI: 10.1186/s13045-022-01262-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/14/2022] [Indexed: 01/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a severe hematologic malignancy prevalent in older patients, and the identification of potential therapeutic targets for AML is problematic. Autophagy is a lysosome-dependent catabolic pathway involved in the tumorigenesis and/or treatment of various cancers. Mounting evidence has suggested that autophagy plays a critical role in the initiation and progression of AML and anticancer responses. In this review, we describe recent updates on the multifaceted functions of autophagy linking to genetic alterations of AML. We also summarize the latest evidence for autophagy-related genes as potential prognostic predictors and drivers of AML tumorigenesis. We then discuss the crosstalk between autophagy and tumor cell metabolism into the impact on both AML progression and anti-leukemic treatment. Moreover, a series of autophagy regulators, i.e., the inhibitors and activators, are described as potential therapeutics for AML. Finally, we describe the translation of autophagy-modulating therapeutics into clinical practice. Autophagy in AML is a double-edged sword, necessitating a deeper understanding of how autophagy influences dual functions in AML tumorigenesis and anti-leukemic responses.
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Affiliation(s)
- Wonhyoung Seo
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon, 35015, Korea.,Department of Microbiology, Chungnam National University College of Medicine, Daejeon, 35015, Korea.,Department of Medical Science, Chungnam National University College of Medicine, Daejeon, 35015, Korea
| | - Prashanta Silwal
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon, 35015, Korea.,Department of Microbiology, Chungnam National University College of Medicine, Daejeon, 35015, Korea
| | - Ik-Chan Song
- Division of Hematology/Oncology, Department of Internal Medicine, Chungnam National University College of Medicine, Daejeon, 35015, Korea
| | - Eun-Kyeong Jo
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon, 35015, Korea. .,Department of Microbiology, Chungnam National University College of Medicine, Daejeon, 35015, Korea. .,Department of Medical Science, Chungnam National University College of Medicine, Daejeon, 35015, Korea.
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15
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Dissecting TET2 Regulatory Networks in Blood Differentiation and Cancer. Cancers (Basel) 2022; 14:cancers14030830. [PMID: 35159097 PMCID: PMC8834528 DOI: 10.3390/cancers14030830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Bone marrow disorders such as leukemia and myelodysplastic syndromes are characterized by abnormal healthy blood cells production and function. Uncontrolled growth and impaired differentiation of white blood cells hinder the correct development of healthy cells in the bone marrow. One of the most frequent alterations that appear to initiate this deregulation and persist in leukemia patients are mutations in epigenetic regulators such as TET2. This review summarizes the latest molecular findings regarding TET2 functions in hematopoietic cells and their potential implications in blood cancer origin and evolution. Our goal was to encompass and interlink up-to-date discoveries of the convoluted TET2 functional network to provide a more precise overview of the leukemic burden of this protein. Abstract Cytosine methylation (5mC) of CpG is the major epigenetic modification of mammalian DNA, playing essential roles during development and cancer. Although DNA methylation is generally associated with transcriptional repression, its role in gene regulation during cell fate decisions remains poorly understood. DNA demethylation can be either passive or active when initiated by TET dioxygenases. During active demethylation, transcription factors (TFs) recruit TET enzymes (TET1, 2, and 3) to specific gene regulatory regions to first catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and subsequently to higher oxidized cytosine derivatives. Only TET2 is frequently mutated in the hematopoietic system from the three TET family members. These mutations initially lead to the hematopoietic stem cells (HSCs) compartment expansion, eventually evolving to give rise to a wide range of blood malignancies. This review focuses on recent advances in characterizing the main TET2-mediated molecular mechanisms that activate aberrant transcriptional programs in blood cancer onset and development. In addition, we discuss some of the key outstanding questions in the field.
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