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Maifrede S, Le BV, Nieborowska-Skorska M, Golovine K, Sullivan-Reed K, Dunuwille WMB, Nacson J, Hulse M, Keith K, Madzo J, Caruso LB, Gazze Z, Lian Z, Padella A, Chitrala KN, Bartholdy BA, Matlawska-Wasowska K, Di Marcantonio D, Simonetti G, Greiner G, Sykes SM, Valent P, Paietta EM, Tallman MS, Fernandez HF, Litzow MR, Minden MD, Huang J, Martinelli G, Vassiliou GS, Tempera I, Piwocka K, Johnson N, Challen GA, Skorski T. TET2 and DNMT3A Mutations Exert Divergent Effects on DNA Repair and Sensitivity of Leukemia Cells to PARP Inhibitors. Cancer Res 2021; 81:5089-5101. [PMID: 34215619 PMCID: PMC8487956 DOI: 10.1158/0008-5472.can-20-3761] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Somatic variants in TET2 and DNMT3A are founding mutations in hematological malignancies that affect the epigenetic regulation of DNA methylation. Mutations in both genes often co-occur with activating mutations in genes encoding oncogenic tyrosine kinases such as FLT3ITD, BCR-ABL1, JAK2V617F , and MPLW515L , or with mutations affecting related signaling pathways such as NRASG12D and CALRdel52 . Here, we show that TET2 and DNMT3A mutations exert divergent roles in regulating DNA repair activities in leukemia cells expressing these oncogenes. Malignant TET2-deficient cells displayed downregulation of BRCA1 and LIG4, resulting in reduced activity of BRCA1/2-mediated homologous recombination (HR) and DNA-PK-mediated non-homologous end-joining (D-NHEJ), respectively. TET2-deficient cells relied on PARP1-mediated alternative NHEJ (Alt-NHEJ) for protection from the toxic effects of spontaneous and drug-induced DNA double-strand breaks. Conversely, DNMT3A-deficient cells favored HR/D-NHEJ owing to downregulation of PARP1 and reduction of Alt-NHEJ. Consequently, malignant TET2-deficient cells were sensitive to PARP inhibitor (PARPi) treatment in vitro and in vivo, whereas DNMT3A-deficient cells were resistant. Disruption of TET2 dioxygenase activity or TET2-Wilms' tumor 1 (WT1)-binding ability was responsible for DNA repair defects and sensitivity to PARPi associated with TET2 deficiency. Moreover, mutation or deletion of WT1 mimicked the effect of TET2 mutation on DSB repair activity and sensitivity to PARPi. Collectively, these findings reveal that TET2 and WT1 mutations may serve as biomarkers of synthetic lethality triggered by PARPi, which should be explored therapeutically. SIGNIFICANCE: TET2 and DNMT3A mutations affect distinct DNA repair mechanisms and govern the differential sensitivities of oncogenic tyrosine kinase-positive malignant hematopoietic cells to PARP inhibitors.
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Affiliation(s)
- Silvia Maifrede
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Bac Viet Le
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
- Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Konstantin Golovine
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Wangisa M B Dunuwille
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, Missouri
| | - Joseph Nacson
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael Hulse
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Kelsey Keith
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Lisa Beatrice Caruso
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Zachary Gazze
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Zhaorui Lian
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Antonella Padella
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Kumaraswamy N Chitrala
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Ksenia Matlawska-Wasowska
- Division of Hematology-Oncology, Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Daniela Di Marcantonio
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania
| | - Giorgia Simonetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Stephen M Sykes
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania
| | - Peter Valent
- Division of Hematology and Hemostaseology and Ludwig-Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Elisabeth M Paietta
- Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, New York
| | - Martin S Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hugo F Fernandez
- Moffitt Malignant Hematology and Cellular Therapy at Memorial Healthcare System, Pembroke Pines, Florida
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mark D Minden
- Princess Margaret Cancer Center, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Jian Huang
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Italo Tempera
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | | | - Neil Johnson
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Grant A Challen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, Missouri.
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
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