101
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Ngai LL, Ma CY, Maguire O, Do AD, Robert A, Logan AC, Griffiths EA, Nemeth MJ, Green C, Pourmohamad T, van Kuijk BJ, Snel AN, Kwidama ZW, Venniker-Punt B, Cooper J, Manz MG, Gjertsen BT, Smit L, Ossenkoppele GJ, Janssen JJWM, Cloos J, Sumiyoshi T. Bimodal expression of potential drug target CLL-1 (CLEC12A) on CD34+ blasts of AML patients. Eur J Haematol 2021; 107:343-353. [PMID: 34053123 PMCID: PMC8457079 DOI: 10.1111/ejh.13672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/26/2021] [Indexed: 12/17/2022]
Abstract
Objectives This study aims to retrospectively assess C‐lectin‐like molecule 1 (CLL‐1) bimodal expression on CD34+ blasts in acute myeloid leukemia (AML) patients (total N = 306) and explore potential CLL‐1 bimodal associations with leukemia and patient‐specific characteristics. Methods Flow cytometry assays were performed to assess the deeper immunophenotyping of CLL‐1 bimodality. Cytogenetic analysis was performed to characterize the gene mutation on CLL‐1‐negative subpopulation of CLL‐1 bimodal AML samples. Results The frequency of a bimodal pattern of CLL‐1 expression of CD34+ blasts ranged from 8% to 65% in the different cohorts. Bimodal CLL‐1 expression was most prevalent in patients with MDS‐related AML (P = .011), ELN adverse risk (P = .002), NPM1 wild type (WT, P = .049), FLT3 WT (P = .035), and relatively low percentages of leukemia‐associated immunophenotypes (P = .006). Additional immunophenotyping analysis revealed the CLL‐1− subpopulation may consist of pre‐B cells, immature myeloblasts, and hematopoietic stem cells. Furthermore, (pre)‐leukemic mutations were detected in both CLL‐1+ and CLL‐1− subfractions of bimodal samples (N = 3). Conclusions C‐lectin‐like molecule 1 bimodality occurs in about 25% of AML patients and the CLL‐1− cell population still contains malignant cells, hence it may potentially limit the effectiveness of CLL‐1‐targeted therapies and warrant further investigation.
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Affiliation(s)
- Lok Lam Ngai
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Connie Y Ma
- Department of Development of Science, Genentech, South San Francisco, CA, USA
| | - Orla Maguire
- Flow and Image Cytometry Shared Resource, Buffalo, NY, USA
| | - An D Do
- Department of Development of Science, Genentech, South San Francisco, CA, USA
| | - Alberto Robert
- Department of Development of Science, Genentech, South San Francisco, CA, USA
| | - Aaron C Logan
- Department of Medicine, UCSF, San Francisco, CA, USA
| | | | | | - Cherie Green
- Department of Development of Science, Genentech, South San Francisco, CA, USA
| | | | - Bo J van Kuijk
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Alexander N Snel
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Zinia W Kwidama
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Bianca Venniker-Punt
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - James Cooper
- Department of Early Clinical Development, Genentech, South San Francisco, CA, USA
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University and University Hospital, Zurich, Switzerland
| | - Bjørn T Gjertsen
- Section for Hematology, Institute of Clinical Science, University of Bergen, Bergen, Norway
| | - Linda Smit
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gert J Ossenkoppele
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jeroen J W M Janssen
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Teiko Sumiyoshi
- Department of Development of Science, Genentech, South San Francisco, CA, USA
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102
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Wolffgramm J, Buchmuller B, Palei S, Muñoz‐López Á, Kanne J, Janning P, Schweiger MR, Summerer D. Light-Activation of DNA-Methyltransferases. Angew Chem Int Ed Engl 2021; 60:13507-13512. [PMID: 33826797 PMCID: PMC8251764 DOI: 10.1002/anie.202103945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 12/27/2022]
Abstract
5-Methylcytosine (5mC), the central epigenetic mark of mammalian DNA, plays fundamental roles in chromatin regulation. 5mC is written onto genomes by DNA methyltransferases (DNMT), and perturbation of this process is an early event in carcinogenesis. However, studying 5mC functions is limited by the inability to control individual DNMTs with spatiotemporal resolution in vivo. We report light-control of DNMT catalysis by genetically encoding a photocaged cysteine as a catalytic residue. This enables translation of inactive DNMTs, their rapid activation by light-decaging, and subsequent monitoring of de novo DNA methylation. We provide insights into how cancer-related DNMT mutations alter de novo methylation in vivo, and demonstrate local and tuneable cytosine methylation by light-controlled DNMTs fused to a programmable transcription activator-like effector domain targeting pericentromeric satellite-3 DNA. We further study early events of transcriptome alterations upon DNMT-catalyzed cytosine methylation. Our study sets a basis to dissect the order and kinetics of diverse chromatin-associated events triggered by normal and aberrant DNA methylation.
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Affiliation(s)
- Jan Wolffgramm
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Shubhendu Palei
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Álvaro Muñoz‐López
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Julian Kanne
- Department of Epigenetics and Tumor Biology, Medical FacultyUniversity of CologneKerpener Str. 6250937KölnGermany
| | - Petra Janning
- Max-Planck-Institute for Molecular PhysiologyOtto-Hahn-Str. 1144227DortmundGermany
| | - Michal R. Schweiger
- Department of Epigenetics and Tumor Biology, Medical FacultyUniversity of CologneKerpener Str. 6250937KölnGermany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
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103
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Wolffgramm J, Buchmuller B, Palei S, Muñoz‐López Á, Kanne J, Janning P, Schweiger MR, Summerer D. Light‐Activation of DNA‐Methyltransferases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jan Wolffgramm
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Shubhendu Palei
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Álvaro Muñoz‐López
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Julian Kanne
- Department of Epigenetics and Tumor Biology, Medical Faculty University of Cologne Kerpener Str. 62 50937 Köln Germany
| | - Petra Janning
- Max-Planck-Institute for Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Michal R. Schweiger
- Department of Epigenetics and Tumor Biology, Medical Faculty University of Cologne Kerpener Str. 62 50937 Köln Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
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104
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Yang SX, Hollingshead M, Rubinstein L, Nguyen D, Larenjeira ABA, Kinders RJ, Difilippantonio M, Doroshow JH. TET2 and DNMT3A mutations and exceptional response to 4'-thio-2'-deoxycytidine in human solid tumor models. J Hematol Oncol 2021; 14:83. [PMID: 34039392 PMCID: PMC8157655 DOI: 10.1186/s13045-021-01091-5] [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: 01/12/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
Background Challenges remain on the selection of patients who potentially respond to a class of drugs that target epigenetics for cancer treatment. This study aims to investigate TET2/DNMT3A mutations and antitumor activity of a novel epigenetic agent in multiple human cancer cell lines and animal models. Methods Seventeen cancer cell lines and multiple xenograft models bearing representative human solid tumors were subjected to 4′-thio-2′-deoxycytidine (T-dCyd) or control treatment. Gene mutations in cell lines were examined by whole exome and/or Sanger sequencing. Specific gene expression was measured in cells and xenograft tumor samples by Western blotting and immunohistochemistry. TET2/DNMT3A mutation status in 47,571 human tumor samples was analyzed at cBioPortal for Cancer Genomics. Results Cell survival was significantly inhibited by T-dCyd in breast BT549, lung NCI-H23, melanoma SKMEL5 and renal ACHN cancer lines harboring deleterious TET2 and nonsynonymous DNMT3A mutations compared to 13 lines without such mutation pattern (P = 0.007). The treatment upregulated p21 and induced cell cycle arrest in NCI-H23 cells, and dramatically inhibited their xenograft tumor growth versus wildtype models. T-dCyd administrations led to a significant p21 increase and near eradication of tumor cells in the double-mutant xenografts by histological evaluation. TET2/DNMT3A was co-mutated in human lung, breast, skin and kidney cancers and frequently in angioimmunoblastic and peripheral T cell lymphomas and several types of leukemia. Conclusions Cell and animal models with concurrent mutations in TET2 and DNMT3A were sensitive to T-dCyd treatment. The mutations were detectable in human solid tumors and frequently occur in some hematological malignancies. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-021-01091-5.
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Affiliation(s)
- Sherry X Yang
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Melinda Hollingshead
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Larry Rubinstein
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dat Nguyen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angelo B A Larenjeira
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Michael Difilippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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105
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Que Y, Li H, Lin L, Zhu X, Xiao M, Wang Y, Zhu L, Li D. Study on the Immune Escape Mechanism of Acute Myeloid Leukemia With DNMT3A Mutation. Front Immunol 2021; 12:653030. [PMID: 34093541 PMCID: PMC8173207 DOI: 10.3389/fimmu.2021.653030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3A (DNMT3A)-mutated acute myeloid leukemia (AML) has a poor prognosis, but the exact mechanism is still unclear. Here, we aimed to explore the mechanism of immune escape in AML with DNMT3A mutation. We constructed a DNMT3A knockout clone and DNMT3A-R882H-mutated clones. RNA-seq results showed that transcription factors and macrophage inflammatory proteins were significantly downregulated in the DNMT3A mutant clones. KEGG enrichment and gene set enrichment analysis (GSEA) showed that a large number of genes were enriched in inflammatory immune-related pathways, such as the toll-like receptor signaling pathway. Therefore, we co-cultured AML cells with macrophages. The DNMT3A-mutated AML cells attenuated M1 macrophage polarization and resisted its killing effect in vitro and in vivo. In xenografts, the tumor volumes in the experimental group were significantly larger than those in the control group, and the proportion of M2 macrophages was significantly higher. After the co-culture, the increase in pro-inflammatory cytokine expression in the mutant cells was significantly lower than that in the control group, while that in immunosuppressive factors was not significantly different. In co-cultivated supernatants, the concentration of inflammatory factors in the experimental group was significantly lower than that in the control group, while that of immunosuppressive factors was significantly higher. Resistin significantly promoted the expression of inflammatory proteins in AML cells. It relieved the inhibitory effect of DNMT3A mutation, promoted the phenotypic recovery of the co-cultured macrophages, eliminated resistance, and regulated the immune microenvironment. Thus, resistin may serve as an ancillary drug for patients with DNMT3A-mutated AML.
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Affiliation(s)
- Yimei Que
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huimin Li
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liman Lin
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojian Zhu
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Wang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zhu
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dengju Li
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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106
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Li J, Wang C, Liu J, Yu Y, Liu Y, Peng Q, Liu H, Guan X. A feedback loop: Interactions between Inflammatory Signals and Clonal Hematopoiesis in Cardiovascular Disease. Mol Biol Rep 2021; 48:3785-3798. [PMID: 33987748 PMCID: PMC8117808 DOI: 10.1007/s11033-021-06370-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/23/2021] [Indexed: 12/16/2022]
Abstract
Age and inflammation are powerful drivers of cardiovascular disease. With the growing recognition that traditional cardiovascular risk factors are not fully accurate predictors of cardiovascular disease, recent studies have revealed the prevalence of positive selection of somatic cell mutations in hematopoietic stem cells in the elderly population, which can cause clonal hematopoiesis. Interestingly, clonal hematopoiesis is not only associated with cancer and death, but also closely related to the risk of increased cardiovascular disease due to mutations in TET2, DNMT3A, ASXL1, and JAK2. However, the mechanism of the interaction of clonal hematopoiesis and cardiovascular disease is only partially understood. In mice, somatic mutations have led to significantly increased expression of inflammatory genes in innate immune cells, which may explain the relationship between mutations and cardiovascular disease. Here, we further discuss the association between inflammatory signaling, clonal hematopoiesis, and cardiovascular disease,and using two hypotheses to propose a feedback loop between inflammatory signaling and clonal hematopoiesis for getting insight into the pathogenesis of cardiovascular diseases in depth. Therapies targeting mutant clones or increased inflammatory mediators may be useful for ameliorating the risk of cardiovascular disease.
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Affiliation(s)
- Jiashan Li
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Chao Wang
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Jiaru Liu
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Ying Yu
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Yuee Liu
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qi Peng
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Huihui Liu
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xiuru Guan
- First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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107
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Khrabrova DA, Yakubovskaya MG, Gromova ES. AML-Associated Mutations in DNA Methyltransferase DNMT3A. BIOCHEMISTRY (MOSCOW) 2021; 86:307-318. [PMID: 33838631 DOI: 10.1134/s000629792103007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In mammals, DNA methylation is an essential epigenetic modification necessary for the maintenance of genome stability, regulation of gene expression, and other processes. Carcinogenesis is accompanied by multiple changes in the DNA methylation pattern and DNA methyltransferase (DNMT) genes; these changes are often associated with poor disease prognosis. Human DNA methyltransferase DNMT3A is responsible for de novo DNA methylation. Missense mutations in the DNMT3A gene occur frequently at the early stages of tumor development and are often observed in hematologic malignances, especially in acute myeloid leukemia (AML), with a prevalence of the R882H mutation. This mutation is the only one that has been extensively studied using both model DNA substrates and cancer cell lines. Biochemical characterization of other DNMT3A mutants is necessary to assess their potential effects on the DNMT3A functioning. In this review, we describe DNMT3A mutations identified in AML with special emphasis on the missense mutations in the DNMT3A catalytic domain. The impact of R882H and less common missense mutations on the DNMT3A activity toward model DNA substrates and in cancer cell lines is discussed together with the underlying molecular mechanisms. Understanding general features of these mechanisms will be useful for further development of novel approaches for early diagnostics of hematologic diseases and personalized cancer therapy.
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Affiliation(s)
- Dariya A Khrabrova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Marianna G Yakubovskaya
- Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Elizaveta S Gromova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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108
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Lim JY, Duttke SH, Baker TS, Lee J, Gambino KJ, Venturini NJ, Ho JSY, Zheng S, Fstkchyan YS, Pillai V, Fajgenbaum DC, Marazzi I, Benner C, Byun M. DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells. J Exp Med 2021; 218:212086. [PMID: 33970190 PMCID: PMC8111463 DOI: 10.1084/jem.20202733] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/04/2021] [Accepted: 04/02/2021] [Indexed: 01/04/2023] Open
Abstract
DNMT3A encodes an enzyme that carries out de novo DNA methylation, which is essential for the acquisition of cellular identity and specialized functions during cellular differentiation. DNMT3A is the most frequently mutated gene in age-related clonal hematopoiesis. As such, mature immune cells harboring DNMT3A mutations can be readily detected in elderly persons. Most DNMT3A mutations associated with clonal hematopoiesis are heterozygous and predicted to cause loss of function, indicating that haploinsufficiency is the predominant pathogenic mechanism. Yet, the impact of DNMT3A haploinsufficiency on the function of mature immune cells is poorly understood. Here, we demonstrate that DNMT3A haploinsufficiency impairs the gain of DNA methylation at decommissioned enhancers, while simultaneously and unexpectedly impairing DNA demethylation of newly activated enhancers in mature human myeloid cells. The DNA methylation defects alter the activity of affected enhancers, leading to abnormal gene expression and impaired immune response. These findings provide insights into the mechanism of immune dysfunction associated with clonal hematopoiesis and acquired DNMT3A mutations.
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Affiliation(s)
- Jung-Yeon Lim
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Turner S Baker
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jihye Lee
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kristyne J Gambino
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicholas J Venturini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yesai S Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Minji Byun
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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Stuckey R, Gómez-Casares MT. Recent Advances in the Use of Molecular Analyses to Inform the Diagnosis and Prognosis of Patients with Polycythaemia Vera. Int J Mol Sci 2021; 22:5042. [PMID: 34068690 PMCID: PMC8126083 DOI: 10.3390/ijms22095042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 01/07/2023] Open
Abstract
Genetic studies in the past decade have improved our understanding of the molecular basis of the BCR-ABL1-negative myeloproliferative neoplasm (MPN) polycythaemia vera (PV). Such breakthroughs include the discovery of the JAK2V617F driver mutation in approximately 95% of patients with PV, as well as some very rare cases of familial hereditary MPN caused by inherited germline mutations. Patients with PV often progress to fibrosis or acute myeloid leukaemia, both associated with very poor clinical outcome. Moreover, thrombosis and major bleeding are the principal causes of morbidity and mortality. As a result of increasingly available and economical next-generation sequencing technologies, mutational studies have revealed the prognostic relevance of a few somatic mutations in terms of thrombotic risk and risk of transformation, helping to improve the risk stratification of patients with PV. Finally, knowledge of the molecular basis of PV has helped identify targets for directed therapy. The constitutive activation of the tyrosine kinase JAK2 is targeted by ruxolitinib, a JAK1/JAK2 tyrosine kinase inhibitor for PV patients who are resistant or intolerant to cytoreductive treatment with hydroxyurea. Other molecular mechanisms have also been revealed, and numerous agents are in various stages of development. Here, we will provide an update of the recent published literature on how molecular testing can improve the diagnosis and prognosis of patients with PV and present recent advances that may have prognostic value in the near future.
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Affiliation(s)
- Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas, Spain
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110
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Kang DS, Kim HS, Jung JH, Lee CM, Ahn YS, Seo YR. Formaldehyde exposure and leukemia risk: a comprehensive review and network-based toxicogenomic approach. Genes Environ 2021; 43:13. [PMID: 33845901 PMCID: PMC8042688 DOI: 10.1186/s41021-021-00183-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/19/2021] [Indexed: 12/20/2022] Open
Abstract
Formaldehyde is a widely used but highly reactive and toxic chemical. The International Agency for Research on Cancer classifies formaldehyde as a Group 1 carcinogen, based on nasopharyngeal cancer and leukemia studies. However, the correlation between formaldehyde exposure and leukemia incidence is a controversial issue. To understand the association between formaldehyde exposure and leukemia, we explored biological networks based on formaldehyde-related genes retrieved from public and commercial databases. Through the literature-based network approach, we summarized qualitative associations between formaldehyde exposure and leukemia. Our results indicate that oxidative stress-mediated genetic changes induced by formaldehyde could disturb the hematopoietic system, possibly leading to leukemia. Furthermore, we suggested major genes that are thought to be affected by formaldehyde exposure and associated with leukemia development. Our suggestions can be used to complement experimental data for understanding and identifying the leukemogenic mechanism of formaldehyde.
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Affiliation(s)
- Doo Seok Kang
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Hyun Soo Kim
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Jong-Hyeon Jung
- Faculty of Health Science, Daegu Haany University, Gyeongsan, Gyeongbuk, 38610, Republic of Korea
| | - Cheol Min Lee
- Department of Chemical and Biological Engineering, College of Natural Science and Engineering, Seokyeong University, Seoul, 02173, Republic of Korea
| | - Yeon-Soon Ahn
- Department of Preventive Medicine and Institute of Occupational and Environmental Medicine, Wonju College of Medicine, Yonsei University, Wonju, Gangwon, 26426, Republic of Korea
| | - Young Rok Seo
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, 32 Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
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111
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Point Mutation Specific Antibodies in B-Cell and T-Cell Lymphomas and Leukemias: Targeting IDH2, KRAS, BRAF and Other Biomarkers RHOA, IRF8, MYD88, ID3, NRAS, SF3B1 and EZH2. Diagnostics (Basel) 2021; 11:diagnostics11040600. [PMID: 33801781 PMCID: PMC8065453 DOI: 10.3390/diagnostics11040600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022] Open
Abstract
B-cell and T-cell lymphomas and leukemias often have distinct genetic mutations that are diagnostically defining or prognostically significant. A subset of these mutations consists of specific point mutations, which can be evaluated using genetic sequencing approaches or point mutation specific antibodies. Here, we describe genes harboring point mutations relevant to B-cell and T-cell malignancies and discuss the current availability of these targeted point mutation specific antibodies. We also evaluate the possibility of generating novel antibodies against known point mutations by computationally assessing for chemical and structural features as well as epitope antigenicity of these targets. Our results not only summarize several genetic mutations and identify existing point mutation specific antibodies relevant to hematologic malignancies, but also reveal potential underdeveloped targets which merit further study.
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112
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Gilad Y, Eliaz Y, Yu Y, Dean AM, Han SJ, Qin L, O’Malley BW, Lonard DM. A genome-scale CRISPR Cas9 dropout screen identifies synthetically lethal targets in SRC-3 inhibited cancer cells. Commun Biol 2021; 4:399. [PMID: 33767353 PMCID: PMC7994904 DOI: 10.1038/s42003-021-01929-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Steroid receptor coactivator 3 (SRC-3/NCoA3/AIB1), is a key regulator of gene transcription and it plays a central role in breast cancer (BC) tumorigenesis, making it a potential therapeutic target. Beyond its function as an important regulator of estrogen receptor transcriptional activity, SRC-3 also functions as a coactivator for a wide range of other transcription factors, suggesting SRC-3 inhibition can be beneficial in hormone-independent cancers as well. The recent discovery of a potent SRC-3 small molecule inhibitor, SI-2, enabled the further development of additional related compounds. SI-12 is an improved version of SI-2 that like SI-2 has anti-proliferative activity in various cancer types, including BC. Here, we sought to identify gene targets, that when inhibited in the presence of SI-12, would lead to enhanced BC cell cytotoxicity. We performed a genome-scale CRISPR-Cas9 screen in MCF-7 BC cells under conditions of pharmacological pressure with SI-12. A parallel screen was performed with an ER inhibitor, fulvestrant, to shed light on both common and distinct activities between SRC-3 and ERα inhibition. Bearing in mind the key role of SRC-3 in tumorigenesis of other types of cancer, we extended our study by validating potential hits identified from the MCF-7 screen in other cancer cell lines.
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Affiliation(s)
- Yosi Gilad
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Yossi Eliaz
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Yang Yu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Adam M. Dean
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - San Jung Han
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Li Qin
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Bert W. O’Malley
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - David M. Lonard
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
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113
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Clonal hematopoiesis: mechanisms driving dominance of stem cell clones. Blood 2021; 136:1590-1598. [PMID: 32746453 DOI: 10.1182/blood.2020006510] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The discovery of clonal hematopoiesis (CH) in older individuals has changed the way hematologists and stem cell biologists view aging. Somatic mutations accumulate in stem cells over time. While most mutations have no impact, some result in subtle functional differences that ultimately manifest in distinct stem cell behaviors. With a large pool of stem cells and many decades to compete, some of these differences confer advantages under specific contexts. Approximately 20 genes are recurrently found as mutated in CH, indicating they confer some advantage. The impact of these mutations has begun to be analyzed at a molecular level by modeling in cell lines and in mice. Mutations in epigenetic regulators such as DNMT3A and TET2 confer an advantage by enhancing self-renewal of stem and progenitor cells and inhibiting their differentiation. Mutations in other genes involved in the DNA damage response may simply enhance cell survival. Here, we review proposed mechanisms that lead to CH, specifically in the context of stem cell biology, based on our current understanding of the function of some of the CH-associated genes.
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Heuser M, Smith BD, Fiedler W, Sekeres MA, Montesinos P, Leber B, Merchant A, Papayannidis C, Pérez-Simón JA, Hoang CJ, O'Brien T, Ma WW, Zeremski M, O'Connell A, Chan G, Cortes JE. Clinical benefit of glasdegib plus low-dose cytarabine in patients with de novo and secondary acute myeloid leukemia: long-term analysis of a phase II randomized trial. Ann Hematol 2021; 100:1181-1194. [PMID: 33740113 PMCID: PMC8043884 DOI: 10.1007/s00277-021-04465-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/17/2022]
Abstract
This analysis from the phase II BRIGHT AML 1003 trial reports the long-term efficacy and safety of glasdegib + low-dose cytarabine (LDAC) in patients with acute myeloid leukemia ineligible for intensive chemotherapy. The multicenter, open-label study randomized (2:1) patients to receive glasdegib + LDAC (de novo, n = 38; secondary acute myeloid leukemia, n = 40) or LDAC alone (de novo, n = 18; secondary acute myeloid leukemia, n = 20). At the time of analysis, 90% of patients had died, with the longest follow-up since randomization 36 months. The combination of glasdegib and LDAC conferred superior overall survival (OS) versus LDAC alone; hazard ratio (HR) 0.495; (95% confidence interval [CI] 0.325–0.752); p = 0.0004; median OS was 8.3 versus 4.3 months. Improvement in OS was consistent across cytogenetic risk groups. In a post-hoc subgroup analysis, a survival trend with glasdegib + LDAC was observed in patients with de novo acute myeloid leukemia (HR 0.720; 95% CI 0.395–1.312; p = 0.14; median OS 6.6 vs 4.3 months) and secondary acute myeloid leukemia (HR 0.287; 95% CI 0.151–0.548; p < 0.0001; median OS 9.1 vs 4.1 months). The incidence of adverse events in the glasdegib + LDAC arm decreased after 90 days’ therapy: 83.7% versus 98.7% during the first 90 days. Glasdegib + LDAC versus LDAC alone continued to demonstrate superior OS in patients with acute myeloid leukemia; the clinical benefit with glasdegib + LDAC was particularly prominent in patients with secondary acute myeloid leukemia. ClinicalTrials.gov identifier: NCT01546038.
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Affiliation(s)
- Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - B Douglas Smith
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Walter Fiedler
- Department of Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Mikkael A Sekeres
- Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, FL, Miami, USA
| | - Pau Montesinos
- Hospital Universitari i Politècnic La Fe, Valencia, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Brian Leber
- Juravinski Hospital at Hamilton Health Sciences, Hamilton, ON, Canada
| | - Akil Merchant
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - José A Pérez-Simón
- Hospital Universitario Virgen del Rocío, Instituto de Biomedicina (IbiS)/CSIC/CIBERONC), Universidad de Sevilla, Seville, Spain
| | | | | | | | | | | | | | - Jorge E Cortes
- University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Georgia Cancer Center, Augusta, GA, USA
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115
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Ehx G, Larouche JD, Durette C, Laverdure JP, Hesnard L, Vincent K, Hardy MP, Thériault C, Rulleau C, Lanoix J, Bonneil E, Feghaly A, Apavaloaei A, Noronha N, Laumont CM, Delisle JS, Vago L, Hébert J, Sauvageau G, Lemieux S, Thibault P, Perreault C. Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes. Immunity 2021; 54:737-752.e10. [PMID: 33740418 DOI: 10.1016/j.immuni.2021.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/24/2020] [Accepted: 02/26/2021] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) has not benefited from innovative immunotherapies, mainly because of the lack of actionable immune targets. Using an original proteogenomic approach, we analyzed the major histocompatibility complex class I (MHC class I)-associated immunopeptidome of 19 primary AML samples and identified 58 tumor-specific antigens (TSAs). These TSAs bore no mutations and derived mainly (86%) from supposedly non-coding genomic regions. Two AML-specific aberrations were instrumental in the biogenesis of TSAs, intron retention, and epigenetic changes. Indeed, 48% of TSAs resulted from intron retention and translation, and their RNA expression correlated with mutations of epigenetic modifiers (e.g., DNMT3A). AML TSA-coding transcripts were highly shared among patients and were expressed in both blasts and leukemic stem cells. In AML patients, the predicted number of TSAs correlated with spontaneous expansion of cognate T cell receptor clonotypes, accumulation of activated cytotoxic T cells, immunoediting, and improved survival. These TSAs represent attractive targets for AML immunotherapy.
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Affiliation(s)
- Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Caroline Rulleau
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Sébastien Delisle
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Josée Hébert
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montreal, QC H3C 3J7, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada.
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Abstract
Myeloproliferative neoplasms are hematopoietic stem cell disorders based on somatic mutations in JAK2, calreticulin, or MPL activating JAK-STAT signaling. Modern sequencing efforts have revealed the genomic landscape of myeloproliferative neoplasms with additional genetic alterations mainly in epigenetic modifiers and splicing factors. High molecular risk mutations with adverse outcomes have been identified and clonal evolution may promote progression to fibrosis and acute myeloid leukemia. JAK2V617F is recurrently detected in clonal hematopoiesis of indeterminate potential with increased risk for vascular events. Insights into the genetics of myeloproliferative neoplasms has facilitated diagnosis and prognostication and poses novel candidates for targeted therapeutic intervention.
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117
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Kores K, Konc J, Bren U. Mechanistic Insights into Side Effects of Troglitazone and Rosiglitazone Using a Novel Inverse Molecular Docking Protocol. Pharmaceutics 2021; 13:315. [PMID: 33670968 PMCID: PMC7997210 DOI: 10.3390/pharmaceutics13030315] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
Thiazolidinediones form drugs that treat insulin resistance in type 2 diabetes mellitus. Troglitazone represents the first drug from this family, which was removed from use by the FDA due to its hepatotoxicity. As an alternative, rosiglitazone was developed, but it was under the careful watch of FDA for a long time due to suspicion, that it causes cardiovascular diseases, such as heart failure and stroke. We applied a novel inverse molecular docking protocol to discern the potential protein targets of both drugs. Troglitazone and rosiglitazone were docked into predicted binding sites of >67,000 protein structures from the Protein Data Bank and examined. Several new potential protein targets with successfully docked troglitazone and rosiglitazone were identified. The focus was devoted to human proteins so that existing or new potential side effects could be explained or proposed. Certain targets of troglitazone such as 3-oxo-5-beta-steroid 4-dehydrogenase, neutrophil collagenase, stromelysin-1, and VLCAD were pinpointed, which could explain its hepatoxicity, with additional ones indicating that its application could lead to the treatment/development of cancer. Results for rosiglitazone discerned its interaction with members of the matrix metalloproteinase family, which could lead to cancer and neurodegenerative disorders. The concerning cardiovascular side effects of rosiglitazone could also be explained. We firmly believe that our results deepen the mechanistic understanding of the side effects of both drugs, and potentially with further development and research maybe even help to minimize them. On the other hand, the novel inverse molecular docking protocol on the other hand carries the potential to develop into a standard tool to predict possible cross-interactions of drug candidates potentially leading to adverse side effects.
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Affiliation(s)
- Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (J.K.)
| | - Janez Konc
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (J.K.)
- Laboratory for Molecular Modeling, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (J.K.)
- Department of Applied Natural Sciences, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
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118
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Fathi E, Farahzadi R, Montazersaheb S, Bagheri Y. Epigenetic Modifications in Acute Lymphoblastic Leukemia: From Cellular Mechanisms to Therapeutics. Curr Gene Ther 2021; 21:60-71. [PMID: 33183201 DOI: 10.2174/1566523220999201111194554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Epigenetic modification pattern is considered as a characteristic feature in blood malignancies. Modifications in the DNA methylation modulators are recurrent in lymphoma and leukemia, so that the distinct methylation pattern defines different types of leukemia. Generally, the role of epigenetics is less understood, and most investigations are focused on genetic abnormalities and cytogenic studies to develop novel treatments for patients with hematologic disorders. Recently, understanding the underlying mechanism of acute lymphoblastic leukemia (ALL), especially epigenetic alterations as a driving force in the development of ALL opens a new era of investigation for developing promising strategy, beyond available conventional therapy. OBJECTIVE This review will focus on a better understanding of the epigenetic mechanisms in cancer development and progression, with an emphasis on epigenetic alterations in ALL including, DNA methylation, histone modification, and microRNA alterations. Other topics that will be discussed include the use of epigenetic alterations as a promising therapeutic target in order to develop novel, well-suited approaches against ALL. CONCLUSION According to the literature review, leukemogenesis of ALL is extensively influenced by epigenetic modifications, particularly DNA hyper-methylation, histone modification, and miRNA alteration.
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Affiliation(s)
- Ezzatollah Fathi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Raheleh Farahzadi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yasin Bagheri
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
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119
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Venugopal K, Feng Y, Shabashvili D, Guryanova OA. Alterations to DNMT3A in Hematologic Malignancies. Cancer Res 2021; 81:254-263. [PMID: 33087320 PMCID: PMC7855745 DOI: 10.1158/0008-5472.can-20-3033] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
In the last decade, large-scale genomic studies in patients with hematologic malignancies identified recurrent somatic alterations in epigenetic modifier genes. Among these, the de novo DNA methyltransferase DNMT3A has emerged as one of the most frequently mutated genes in adult myeloid as well as lymphoid malignancies and in clonal hematopoiesis. In this review, we discuss recent advances in our understanding of the biochemical and structural consequences of DNMT3A mutations on DNA methylation catalysis and binding interactions and summarize their effects on epigenetic patterns and gene expression changes implicated in the pathogenesis of hematologic malignancies. We then review the role played by mutant DNMT3A in clonal hematopoiesis, accompanied by its effect on immune cell function and inflammatory responses. Finally, we discuss how this knowledge informs therapeutic approaches for hematologic malignancies with mutant DNMT3A.
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Affiliation(s)
- Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Yang Feng
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Daniil Shabashvili
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida.
- University of Florida Health Cancer Center, Gainesville, Florida
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120
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Mallona I, Ilie IM, Karemaker ID, Butz S, Manzo M, Caflisch A, Baubec T. Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Res 2021; 49:145-157. [PMID: 33290556 PMCID: PMC7797059 DOI: 10.1093/nar/gkaa1168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/22/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding side chain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent enzymatic activity provides additional insights into the complex regulation of DNA methylation patterns.
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Affiliation(s)
- Izaskun Mallona
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich 8057, Switzerland
| | - Ioana Mariuca Ilie
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Ino Dominiek Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
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121
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Abstract
PURPOSE OF REVIEW Nucleophosmin (NPM1) mutations are encountered in myeloid neoplasia and are present in ~ 30% of de novo acute myeloid leukemia cases. This review summarizes features of mutant NPM1-related disease, with a particular emphasis on recent discoveries relevant to disease monitoring, prognostication, and therapeutic intervention. RECENT FINDINGS Recent studies have shown that HOX/MEIS gene overexpression is central to the survival of NPM1-mutated cells. Two distinct classes of small molecule drugs, BH3 mimetics and menin-MLL interaction inhibitors, have demonstrated exquisite leukemic cell toxicity in preclinical AML models associated with HOX/MEIS overexpression, and the former of these has shown efficacy in older treatment-naïve NPM1-mutated AML patients. The results of ongoing clinical trials further investigating these compounds will be of particular importance and may alter the clinical management of patients with NPM1-mutated myeloid neoplasms. Significant scientific advancements over the last decade, including improved sequencing and disease monitoring techniques, have fostered a much deeper understanding of mutant NPM1 disease biology, prognostication, and opportunities for therapeutic intervention. These discoveries have led to the development of clinical assays that permit the detection and monitoring of mutant NPM1 and have paved the way for future investigation of targeted therapeutics using emerging cutting-edge techniques.
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Affiliation(s)
- Sanjay S Patel
- Division of Hematopathology, Weill Cornell Medical College, New York, NY, USA
| | - Michael J Kluk
- Division of Hematopathology, Weill Cornell Medical College, New York, NY, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children's Hospital, 300 Longwood Avenue, Bader 126.2, Boston, MA, 02115, USA.
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122
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Abstract
Although we are just beginning to understand the mechanisms that regulate the epigenome, aberrant epigenetic programming has already emerged as a hallmark of hematologic malignancies including acute myeloid leukemia (AML) and B-cell lymphomas. Although these diseases arise from the hematopoietic system, the epigenetic mechanisms that drive these malignancies are quite different. Yet, in all of these tumors, somatic mutations in transcription factors and epigenetic modifiers are the most commonly mutated set of genes and result in multilayered disruption of the epigenome. Myeloid and lymphoid neoplasms generally manifest epigenetic allele diversity, which contributes to tumor cell population fitness regardless of the underlying genetics. Epigenetic therapies are emerging as one of the most promising new approaches for these patients. However, effective targeting of the epigenome must consider the need to restore the various layers of epigenetic marks, appropriate biological end points, and specificity of therapeutic agents to truly realize the potential of this modality.
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Affiliation(s)
- Cihangir Duy
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Wendy Béguelin
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
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123
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Zaro BW, Noh JJ, Mascetti VL, Demeter J, George B, Zukowska M, Gulati GS, Sinha R, Flynn RA, Banuelos A, Zhang A, Wilkinson AC, Jackson P, Weissman IL. Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells. eLife 2020; 9:e62210. [PMID: 33236985 PMCID: PMC7688314 DOI: 10.7554/elife.62210] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
The balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for a healthy blood supply; imbalances underlie hematological diseases. The importance of HSCs and their progenitors have led to their extensive characterization at genomic and transcriptomic levels. However, the proteomics of hematopoiesis remains incompletely understood. Here we report a proteomics resource from mass spectrometry of mouse young adult and old adult mouse HSCs, multipotent progenitors and oligopotent progenitors; 12 cell types in total. We validated differential protein levels, including confirmation that Dnmt3a protein levels are undetected in young adult mouse HSCs until forced into cycle. Additionally, through integrating proteomics and RNA-sequencing datasets, we identified a subset of genes with apparent post-transcriptional repression in young adult mouse HSCs. In summary, we report proteomic coverage of young and old mouse HSCs and progenitors, with broader implications for understanding mechanisms for stem cell maintenance, niche interactions and fate determination.
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Affiliation(s)
- Balyn W Zaro
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Joseph J Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Victoria L Mascetti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Benson George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Monika Zukowska
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Ryan A Flynn
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Allison Banuelos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Peter Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology and the Stanford UC-Berkeley Stem Cell InstituteStanfordUnited States
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
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Bioinformatics Analysis Identifies Key Genes and Pathways in Acute Myeloid Leukemia Associated with DNMT3A Mutation. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9321630. [PMID: 33299888 PMCID: PMC7707947 DOI: 10.1155/2020/9321630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/22/2020] [Accepted: 08/01/2020] [Indexed: 02/01/2023]
Abstract
Background DNA methyltransferase 3 alpha (DNMT3A) mutation was one of the most frequent genetic alterations in acute myeloid leukemia (AML), which was associated with poor prognosis and appeared to be a potential biomarker. Herein, we aimed to identify the key genes and pathways involved in adult AML with DNMT3A mutations and to find possible therapeutic targets for improving treatment. Methods The RNA sequencing datasets of 170 adult AML patients were obtained from The Cancer Genome Atlas (TCGA) database. EdgeR of the R platform was used to identify the differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by Metascape and DAVID. And protein-protein interaction (PPI) network and clustering modules were analyzed with the STRING database and Cytoscape software. Results Mutated DNMT3A resulted in a shorter overall survival (OS) in AML patients and obviously associated with age, blast percentage in peripheral blood, and FLT3 mutation. A total of 283 DEGs were detected, of which 95 were upregulated and 188 were downregulated. GO term analysis showed that DEGs were significantly enriched in neutrophil degranulation, myeloid cell differentiation, stem cell proliferation, positive regulation of neurological system process, leukocyte migration, and tissue morphogenesis. KEGG pathway enrichment analysis indicated that the pathway of cancer, PI3K-Akt signaling pathway, and transcriptional misregulation in cancer may play a crucial role in DNMT3A mutation AML. Seven hub genes (BMP4, MPO, THBS1, APP, ELANE, HOXA7, and VWF) had a significant prognostic value. Conclusion Bioinformatics analysis in the present study provided novel targets for early diagnosis and new strategies for treatment for AML with DNMT3A mutation.
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Chebly A, Chouery E, Ropio J, Kourie HR, Beylot-Barry M, Merlio JP, Tomb R, Chevret E. Diagnosis and treatment of lymphomas in the era of epigenetics. Blood Rev 2020; 48:100782. [PMID: 33229141 DOI: 10.1016/j.blre.2020.100782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/05/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Lymphomas represent a heterogeneous group of cancers characterized by clonal lymphoproliferation. Over the past decades, frequent epigenetic dysregulations have been identified in hematologic malignancies including lymphomas. Many of these impairments occur in genes with established roles and well-known functions in the regulation and maintenance of the epigenome. In hematopoietic cells, these dysfunctions can result in abnormal DNA methylation, erroneous chromatin state and/or altered miRNA expression, affecting many different cellular functions. Nowadays, it is evident that epigenetic dysregulations in lymphoid neoplasms are mainly caused by genetic alterations in genes encoding for enzymes responsible for histone or chromatin modifications. We summarize herein the recent epigenetic modifiers findings in lymphomas. We focus also on the most commonly mutated epigenetic regulators and emphasize on actual epigenetic therapies.
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Affiliation(s)
- Alain Chebly
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Eliane Chouery
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Joana Ropio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Porto University, Institute of Biomedical Sciences of Abel Salazar, 4050-313 Porto, Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Institute of Molecular Pathology and Immunology (Ipatimup), Cancer Biology group, 4200-465 Porto, Portugal
| | - Hampig Raphael Kourie
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Hematology-Oncology Department, Beirut, Lebanon
| | - Marie Beylot-Barry
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Dermatology Department, 33000 Bordeaux, France
| | - Jean-Philippe Merlio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Tumor Bank and Tumor Biology Laboratory, 33600 Pessac, France
| | - Roland Tomb
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Dermatology Department, Beirut, Lebanon
| | - Edith Chevret
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France.
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Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma. Cancers (Basel) 2020; 12:cancers12113304. [PMID: 33182397 PMCID: PMC7697455 DOI: 10.3390/cancers12113304] [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: 09/28/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The use of next generation technologies has helped to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. Nonetheless, the sequencing of all protein-coding genes of an individual may lead to doubtful assignments of causality for non-pathological variants, so it is mandatory to perform comprehensive studies and screening of additional patients for new mutations. Here we describe a novel DNMT3A germline variant identified by whole-exome sequencing in a patient with multiple paragangliomas and papillary thyroid carcinoma. The increased methylation of DNMT3A target genes observed in the proband’s sample points towards a gain-of-function effect of the variant, contrasting with the inactivation caused by loss-of-function alterations commonly seen in other neoplasia and in patients with Tatton-Brown-Rahman syndrome. This finding stresses the diverse molecular outcomes and suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants. Abstract Over the past few years, next generation technologies have been applied to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. We recently found germline DNMT3A gain-of-function variants in two patients with head and neck paragangliomas causing a characteristic hypermethylated DNA profile. Here, whole-exome sequencing identifies a novel germline DNMT3A variant (p.Gly332Arg) in a patient with bilateral carotid paragangliomas, papillary thyroid carcinoma and idiopathic intellectual disability. The variant, located in the Pro-Trp-Trp-Pro (PWWP) domain of the protein involved in chromatin targeting, affects a residue mutated in papillary thyroid tumors and located between the two residues found mutated in microcephalic dwarfism patients. Structural modelling of the variant in the DNMT3A PWWP domain predicts that the interaction with H3K36me3 will be altered. An increased methylation of DNMT3A target genes, compatible with a gain-of-function effect of the alteration, was observed in saliva DNA from the proband and in one independent acute myeloid leukemia sample carrying the same p.Gly332Arg variant. Although further studies are needed to support a causal role of DNMT3A variants in paraganglioma, the description of a new DNMT3A alteration in a patient with multiple clinical features suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants.
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127
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Biological and genetic landscape of breast implant-associated anaplastic large cell lymphoma (BIA-ALCL). Eur J Surg Oncol 2020; 47:942-951. [PMID: 33158639 DOI: 10.1016/j.ejso.2020.10.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 12/30/2022] Open
Abstract
Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is an uncommon form of non-Hodgkin lymphoma (cancer of the immune system) that can develop around breast implants. Breast implants are among the most commonly used medical devices for cosmetic or reconstructive purposes. In the past few years, the number of women with breast implants diagnosed with anaplastic large cell lymphoma (ALCL) has increased, and several studies have suggested a direct association between breast implants and an increased risk of this disease. Although it has been hypothesized that chronic stimulation of the immune system caused by implant materials and biofilms as well as a possible genetic predisposition play an important role in this disease, the cellular and molecular causes of BIA-ALCL are not fully understood. This review aims to describe the current understanding around the environmental and molecular drivers of BIA-ALCL as well as the genetic and chromosomal abnormalities identified in this disease to date.
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128
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Abstract
Acute myeloid leukemia (AML) is a clinically, morphologically, and genetically heterogeneous disorder. Like many malignancies, the genomic landscape of pediatric AML has been mapped recently through sequencing of large cohorts of patients. Much has been learned about the biology of AML through studies of specific recurrent genetic lesions. Further, genetic lesions have been linked to specific clinical features, response to therapy, and outcome, leading to improvements in risk stratification. Lastly, targeted therapeutic approaches have been developed for the treatment of specific genetic lesions, some of which are already having a positive impact on outcomes. While the advances made based on the discoveries of sequencing studies are significant, much work is left. The biologic, clinical, and prognostic impact of a number of genetic lesions, including several seemingly unique to pediatric patients, remains undefined. While targeted approaches are being explored, for most, the efficacy and tolerability when incorporated into standard therapy is yet to be determined. Furthermore, the challenge of how to study small subpopulations with rare genetic lesions in an already rare disease will have to be considered. In all, while questions and challenges remain, precisely defining the genomic landscape of AML, holds great promise for ultimately leading to improved outcomes for affected patients.
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Affiliation(s)
- Shannon E Conneely
- Division of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates Avenue, Feigin Tower, Suite 1025, Houston, TX, 77030, USA
| | - Rachel E Rau
- Division of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates Avenue, Feigin Tower, Suite 1025, Houston, TX, 77030, USA.
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Azizi A, Ediriwickrema A, Dutta R, Patel SA, Shomali W, Medeiros B, Iberri D, Gotlib J, Mannis G, Greenberg P, Majeti R, Zhang T. Venetoclax and hypomethylating agent therapy in high risk myelodysplastic syndromes: a retrospective evaluation of a real-world experience. Leuk Lymphoma 2020; 61:2700-2707. [PMID: 32543932 DOI: 10.1080/10428194.2020.1775214] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Treatment with hypomethylating agents (HMAs) azacitidine or decitabine is the current standard of care for high risk myelodysplastic syndromes (MDSs) but is associated with low rates of response. The limited number of treatment options for patients with high risk MDS highlights a need for new therapeutic options. Venetoclax is an inhibitor of the BCL-2 protein which, when combined with an HMA, has shown high response rates in unfit and previously untreated acute myeloid leukemia. We performed a retrospective study of high risk MDS patients receiving combination HMA plus venetoclax in order to determine their effectiveness in this context. We show that in our cohort, the combination results in high response rates but is associated with a high frequency of myelosuppression. These data highlight the efficacy of combination HMA plus venetoclax in high risk MDS, warranting further prospective evaluation in clinical trials.
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Affiliation(s)
- Armon Azizi
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Asiri Ediriwickrema
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Ritika Dutta
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Shyam A Patel
- Department of Medicine, Division of Hematology-Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - William Shomali
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Bruno Medeiros
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - David Iberri
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Jason Gotlib
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Gabriel Mannis
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Peter Greenberg
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Tian Zhang
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
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Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev 2020; 34:1546-1558. [PMID: 33004415 PMCID: PMC7608744 DOI: 10.1101/gad.341925.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
The de novo DNA methyltransferases Dnmt3a and Dnmt3b play crucial roles in developmental and cellular processes. Their enzymatic activities are stimulated by a regulatory protein Dnmt3L (Dnmt3-like) in vitro. However, genetic evidence indicates that Dnmt3L functions predominantly as a regulator of Dnmt3a in germ cells. How Dnmt3a and Dnmt3b activities are regulated during embryonic development and in somatic cells remains largely unknown. Here we show that Dnmt3b3, a catalytically inactive Dnmt3b isoform expressed in differentiated cells, positively regulates de novo methylation by Dnmt3a and Dnmt3b with a preference for Dnmt3b. Dnmt3b3 is equally potent as Dnmt3L in stimulating the activities of Dnmt3a2 and Dnmt3b2 in vitro. Like Dnmt3L, Dnmt3b3 forms a complex with Dnmt3a2 with a stoichiometry of 2:2. However, rescue experiments in Dnmt3a/3b/3l triple-knockout (TKO) mouse embryonic stem cells (mESCs) reveal that Dnmt3b3 prefers Dnmt3b2 over Dnmt3a2 in remethylating genomic sequences. Dnmt3a2, an active isoform that lacks the N-terminal uncharacterized region of Dnmt3a1 including a nuclear localization signal, has very low activity in TKO mESCs, indicating that an accessory protein is absolutely required for its function. Our results suggest that Dnmt3b3 and perhaps similar Dnmt3b isoforms facilitate de novo DNA methylation during embryonic development and in somatic cells.
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Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhengzhou Ying
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lance Babcock
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Esha Gupta
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nat Commun 2020; 11:5327. [PMID: 33087716 PMCID: PMC7577981 DOI: 10.1038/s41467-020-19119-8] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/22/2020] [Indexed: 02/04/2023] Open
Abstract
Clonal diversity is a consequence of cancer cell evolution driven by Darwinian selection. Precise characterization of clonal architecture is essential to understand the evolutionary history of tumor development and its association with treatment resistance. Here, using a single-cell DNA sequencing, we report the clonal architecture and mutational histories of 123 acute myeloid leukemia (AML) patients. The single-cell data reveals cell-level mutation co-occurrence and enables reconstruction of mutational histories characterized by linear and branching patterns of clonal evolution, with the latter including convergent evolution. Through xenotransplantion, we show leukemia initiating capabilities of individual subclones evolving in parallel. Also, by simultaneous single-cell DNA and cell surface protein analysis, we illustrate both genetic and phenotypic evolution in AML. Lastly, single-cell analysis of longitudinal samples reveals underlying evolutionary process of therapeutic resistance. Together, these data unravel clonal diversity and evolution patterns of AML, and highlight their clinical relevance in the era of precision medicine. Understanding the evolutionary trajectory of cancer samples may enable understanding resistance to treatment. Here, the authors used single cell sequencing of a cohort of acute myeloid leukemia tumours and identify features of linear and branching evolution in tumours.
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132
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Heller G, Nebenfuehr S, Bellutti F, Ünal H, Zojer M, Scheiblecker L, Sexl V, Kollmann K. The Effect of CDK6 Expression on DNA Methylation and DNMT3B Regulation. iScience 2020; 23:101602. [PMID: 33205015 PMCID: PMC7648139 DOI: 10.1016/j.isci.2020.101602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/31/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
CDK6 is frequently overexpressed in various cancer types and functions as a positive regulator of the cell cycle and as a coregulator of gene transcription. We provide evidence that CDK6 is involved in the process of DNA methylation, at least in ALL. We observe a positive correlation of CDK6 and DNMT expression in a large number of ALL samples. ChIP-seq analysis reveals CDK6 binding to genomic regions associated with DNA methyltransferases (DNMTs). ATAC-seq shows a strong reduction in chromatin accessibility for DNMT3B in CDK6-deficient BCR-ABL + Cdk6-/- cells, accompanied by lower levels of DNMT3B mRNA and less chromatin-bound DNMT3B, as shown by RNA-seq and chromatome analysis. Motif analysis suggests that ETS family members interact with CDK6 to regulate DNMT3B. Reduced representation bisulfite sequencing analysis uncovers reversible and cell line-specific changes in DNA methylation patterns upon CDK6 loss. The results reveal a function of CDK6 as a regulator of DNA methylation in transformed cells.
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Affiliation(s)
- Gerwin Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, 1090 Vienna, Austria.,Comprehensive Cancer Center, Vienna, Austria.,Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Sofie Nebenfuehr
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Florian Bellutti
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Huriye Ünal
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Markus Zojer
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Lisa Scheiblecker
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Veronika Sexl
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Karoline Kollmann
- Department for Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
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133
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Bai G, Ross H, Zhang Y, Lee K, Ro JY. The Role of DNA Methylation in Transcriptional Regulation of Pro-Nociceptive Genes in Rat Trigeminal Ganglia. Epigenet Insights 2020; 13:2516865720938677. [PMID: 32974606 PMCID: PMC7495519 DOI: 10.1177/2516865720938677] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022] Open
Abstract
Epigenetic modulation by DNA methylation is associated with aberrant gene
expression in sensory neurons, which consequently leads to pathological pain
responses. In this study, we sought to investigate whether peripheral
inflammation alters global DNA methylation in trigeminal ganglia (TG) and
results in abnormal expression of pro-nociceptive genes. Our results show that
peripheral inflammation remotely reduced the level of global DNA methylation in
rat TG with a concurrent reduction in DNMT1 and
DNMT3a expression. Using unbiased steps, we selected the
following pro-nociceptive candidate genes that are potentially regulated by DNA
methylation: TRPV1, TRPA1, P2X3, and PIEZO2.
Inhibition of DNMT with 5-Aza-dC in dissociated TG cells produced dose-dependent
upregulation of TRPV1, TRPA1, and P2X3.
Systemic treatment of animals with 5-Aza-dC significantly increased the
expression of TRPV1, TRPA1, and PIEZO2 in TG.
Furthermore, the overexpression of DNMT3a, as delivered by a lentiviral vector,
significantly downregulated TRPV1 and PIEZO2
expression and also reliably decreased TRPA1 and
P2X3 transcripts. MeDIP revealed that this overexpression
also significantly enhanced methylation of CGIs associated with
TRPV1 and TRPA1. In addition, bisulfite
sequencing data indicated that the CGI associated with TRPA1
was methylated in a pattern catalyzed by DNMT3a. Taken together, our results
show that all 4 pro-nociceptive genes are subject to epigenetic modulation via
DNA methylation, likely via DNMT3a under inflammatory conditions. These findings
provide the first evidence for the functional importance of DNA methylation as
an epigenetic factor in the transcription of pro-nociceptive genes in TG that
are implicated in pathological orofacial pain responses.
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Affiliation(s)
- Guang Bai
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - Holly Ross
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - Youping Zhang
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - KiSeok Lee
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - Jin Y Ro
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
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134
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DiNardo CD, Beird HC, Estecio M, Hardikar S, Takahashi K, Bannon SA, Borthakur G, Jabbour E, Gumbs C, Khoury JD, Routbort M, Gong T, Kondo K, Kantarjian H, Garcia-Manero G, Chen T, Futreal PA. Germline DNMT3A mutation in familial acute myeloid leukaemia. Epigenetics 2020; 16:567-576. [PMID: 32856987 DOI: 10.1080/15592294.2020.1809871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a heterogeneous myeloid malignancy characterized by recurrent clonal events, including mutations in epigenetically relevant genes such as DNMT3A, ASXL1, IDH1/2, and TET2. Next-generation sequencing analysis of a mother and son pair who both developed adult-onset diploid AML identified a novel germline missense mutation DNMT3A p.P709S. The p.P709S protein-altering variant resides in the highly conserved catalytic DNMT3A methyltransferase domain. Functional studies demonstrate that the p.P709S variant confers dominant negative effects when interacting with wildtype DNMT3A. LINE-1 pyrosequencing and reduced representation bisulphite sequencing (RBBS) analysis demonstrated global DNA hypomethylation in germline samples, not present in the leukaemic samples. Somatic acquisition of IDH2 p.R172K mutations, in concert with additional acquired clonal DNMT3A events in both patients at the time of AML diagnosis, confirms the important pathogenic interaction of epigenetically active genes, and implies a strong selection and regulation of methylation in leukaemogenesis. Improved characterization of germline mutations may enable us to better predict malignant clonal evolution, improving our ability to provide customized treatment or future preventative strategies.
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Affiliation(s)
- Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcos Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah A Bannon
- Department of Clinical Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Routbort
- Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Gong
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimie Kondo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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135
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Jacquelin S, Kramer F, Mullally A, Lane SW. Murine Models of Myelofibrosis. Cancers (Basel) 2020; 12:cancers12092381. [PMID: 32842500 PMCID: PMC7563264 DOI: 10.3390/cancers12092381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 01/22/2023] Open
Abstract
Myelofibrosis (MF) is subtype of myeloproliferative neoplasm (MPN) characterized by a relatively poor prognosis in patients. Understanding the factors that drive MF pathogenesis is crucial to identifying novel therapeutic approaches with the potential to improve patient care. Driver mutations in three main genes (janus kinase 2 (JAK2), calreticulin (CALR), and myeloproliferative leukemia virus oncogene (MPL)) are recurrently mutated in MPN and are sufficient to engender MPN using animal models. Interestingly, animal studies have shown that the underlying molecular mutation and the acquisition of additional genetic lesions is associated with MF outcome and transition from early stage MPN such as essential thrombocythemia (ET) and polycythemia vera (PV) to secondary MF. In this issue, we review murine models that have contributed to a better characterization of MF pathobiology and identification of new therapeutic opportunities in MPN.
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Affiliation(s)
- Sebastien Jacquelin
- Cancer program QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
- Correspondence: (S.J.); (S.W.L.)
| | - Frederike Kramer
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (F.K.); (A.M.)
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (F.K.); (A.M.)
| | - Steven W. Lane
- Cancer program QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
- Cancer Care Services, The Royal Brisbane and Women’s Hospital, Brisbane 4029, Australia
- University of Queensland, St Lucia, QLD 4072, Australia
- Correspondence: (S.J.); (S.W.L.)
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136
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Mhaidly R, Krug A, Gaulard P, Lemonnier F, Ricci JE, Verhoeyen E. New preclinical models for angioimmunoblastic T-cell lymphoma: filling the GAP. Oncogenesis 2020; 9:73. [PMID: 32796826 PMCID: PMC7427806 DOI: 10.1038/s41389-020-00259-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Mouse models are essential to study and comprehend normal and malignant hematopoiesis. The ideal preclinical model should mimic closely the human malignancy. This means that these mice should recapitulate the clinical behavior of the human diseases such as cancer and therapeutic responses with high reproducibility. In addition, the genetic mutational status, the cell phenotype, the microenvironment of the tumor and the time until tumor development occurs, should be mimicked in a preclinical model. This has been particularly challenging for human angioimmunoblastic lymphoma (AITL), one of the most prominent forms of peripheral T-cell lymphomas. A complex network of interactions between AITL tumor cells and the various cells of the tumor microenvironment has impeded the study of AITL pathogenesis in vitro. Very recently, new mouse models that recapitulate faithfully the major features of human AITL disease have been developed. Here, we provide a summary of the pathology, the transcriptional profile and genetic and immune-phenotypic features of human AITL. In addition, we give an overview of preclinical models that recapitulate more or less faithfully human AITL characteristics and pathology. These recently engineered mouse models were essential in the evaluation of novel therapeutic agents for possible treatment of AITL, a malignancy in urgent need of new treatment options.
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Affiliation(s)
- Rana Mhaidly
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France
- Institut Curie, Stress and Cancer Laboratory, Equipe Labellisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'ULM, F-75248, Paris, France
- Inserm, U830, 26, rue d'ULM, Paris, F-75005, France
| | - Adrien Krug
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France
| | - Philippe Gaulard
- Université Paris-Est Créteil; Institut Mondor de Recherche Biomédicale, INSERMU955; Institut Mondor de Recherche Biomédicale, INSERMU955, Université Paris Est Créteil, Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance publique des Hôpitaux de Paris, Créteil, France
| | - François Lemonnier
- Université Paris-Est Créteil; Institut Mondor de Recherche Biomédicale, INSERMU955; Institut Mondor de Recherche Biomédicale, INSERMU955, Université Paris Est Créteil, Créteil, France
- Unité Hémopathies Lymphoïdes, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris, Créteil, France
| | | | - Els Verhoeyen
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France.
- CIRI, Université de Lyon, INSERM U1111, ENS de Lyon, Université Lyon1, CNRS, UMR 5308, 69007, Lyon, France.
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137
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Tovy A, Reyes JM, Gundry MC, Brunetti L, Lee-Six H, Petljak M, Park HJ, Guzman AG, Rosas C, Jeffries AR, Baple E, Mill J, Crosby AH, Sency V, Xin B, Machado HE, Castillo D, Weitzel JN, Li W, Stratton MR, Campbell PJ, Wang H, Sanders MA, Goodell MA. Tissue-Biased Expansion of DNMT3A-Mutant Clones in a Mosaic Individual Is Associated with Conserved Epigenetic Erosion. Cell Stem Cell 2020; 27:326-335.e4. [PMID: 32673568 PMCID: PMC7494054 DOI: 10.1016/j.stem.2020.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/10/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) is the most commonly mutated gene in clonal hematopoiesis (CH). Somatic DNMT3A mutations arise in hematopoietic stem cells (HSCs) many years before malignancies develop, but difficulties in comparing their impact before malignancy with wild-type cells have limited the understanding of their contributions to transformation. To circumvent this limitation, we derived normal and DNMT3A mutant lymphoblastoid cell lines from a germline mosaic individual in whom these cells co-existed for nearly 6 decades. Mutant cells dominated the blood system, but not other tissues. Deep sequencing revealed similar mutational burdens and signatures in normal and mutant clones, while epigenetic profiling uncovered the focal erosion of DNA methylation at oncogenic regulatory regions in mutant clones. These regions overlapped with those sensitive to DNMT3A loss after DNMT3A ablation in HSCs and in leukemia samples. These results suggest that DNMT3A maintains a conserved DNA methylation pattern, the erosion of which provides a distinct competitive advantage to hematopoietic cells.
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Affiliation(s)
- Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Michael C Gundry
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Henry Lee-Six
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Mia Petljak
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Hyun Jung Park
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Anna G Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Aaron R Jeffries
- RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Emma Baple
- RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Jonathan Mill
- RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Valerie Sency
- DDC Clinic Center for Special Needs Children, Middlefield, OH, USA; Department of Pediatrics, Rainbow Babies & Children's Hospital, Cleveland, OH, USA; Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH, USA
| | - Baozhong Xin
- DDC Clinic Center for Special Needs Children, Middlefield, OH, USA; Department of Pediatrics, Rainbow Babies & Children's Hospital, Cleveland, OH, USA; Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH, USA
| | - Heather E Machado
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael R Stratton
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Peter J Campbell
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Heng Wang
- DDC Clinic Center for Special Needs Children, Middlefield, OH, USA; Department of Pediatrics, Rainbow Babies & Children's Hospital, Cleveland, OH, USA; Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH, USA
| | - Mathijs A Sanders
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK; Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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138
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Caponetti GC, Bagg A. Mutations in myelodysplastic syndromes: Core abnormalities and CHIPping away at the edges. Int J Lab Hematol 2020; 42:671-684. [PMID: 32757473 DOI: 10.1111/ijlh.13284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022]
Abstract
The myelodysplastic syndromes (MDS) are a heterogeneous constellation of hematologic malignancies characterized by aberrant differentiation and clonal expansion of abnormal myeloid cells that initially manifest with ineffective hematopoiesis and consequent cytopenias. The prognosis of MDS is variable and depends on clinical and hematologic parameters, cytogenetic and molecular findings, as well as comorbidities. Gene sequencing studies have uncovered remarkable genomic complexity within MDS, based on the presence of recurrent and sometimes co-operating mutations in genes encoding proteins that play a role in numerous biologic pathways. Although the treatment of MDS is currently limited to the use of hypomethylating, immunomodulatory, or erythropoiesis-stimulating agents, improved understanding of the molecular underpinnings of its pathophysiology has led to the development of multiple targeted treatments that are poised to be added to the therapeutic armamentarium. This review will focus on the role of mutations in the pathogenesis, diagnosis, and prognosis of MDS and how the discovery of clonal hematopoiesis of indeterminate potential (CHIP) might impact the utility of detecting mutations in the diagnosis of MDS.
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Affiliation(s)
- Gabriel C Caponetti
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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139
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Li Y, Jiang B, He Z, Zhu H, He R, Fan S, Wu X, Xie L, He X. circIQCH sponges miR-145 to promote breast cancer progression by upregulating DNMT3A expression. Aging (Albany NY) 2020; 12:15532-15545. [PMID: 32756009 PMCID: PMC7467367 DOI: 10.18632/aging.103746] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/25/2020] [Indexed: 12/16/2022]
Abstract
As a unique type of RNA, circular RNAs (circRNAs) are important regulators of multiple biological processes in the progression of cancer. However, the potential role of most circRNAs in breast cancer lung metastasis is still unknown. In this study, we characterized and further investigated circIQCH (hsa_circ_0104345) by analyzing the circRNA microarray profiling in our previous study. circIQCH was upregulated in breast cancer tissues, especially in the metastatic sites. CCK-8, transwell, wound-healing and mouse xenograft assays were carried out to investigate the functions of circIQCH. Knockdown of circIQCH inhibited breast cancer cell proliferation and migration to lung. Moreover, luciferase reporter assays and RNA immunoprecipitation assays were performed to elucidate the underlying molecular mechanism of circIQCH. The results showed that circIQCH sponges miR-145 and promotes breast cancer progression by upregulating DNMT3A. In summary, our study demonstrated the pivotal role of circIQCH-miR-145-DNMT3A axis in breast cancer growth and metastasis via the mechanism of competing endogenous RNAs. Thus, circIQCH could be a potential therapeutic target for breast cancer.
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Affiliation(s)
- Yuehua Li
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang 421001, Hunan Province, China
- Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang 421001, Hunan Province, China
| | - Baohong Jiang
- Department of Pharmacy, The First Affiliated Hospital, University of South China, Hengyang 421001, Hunan Province, China
| | - Zhengxi He
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Hongbo Zhu
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang 421001, Hunan Province, China
| | - Rongfang He
- Department of Pathology, The First Affiliated Hospital, University of South China, Hengyang 421001, Hunan Province, China
| | - Shanji Fan
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital, University of South China, Hengyang, 421001 Hunan Province, China
| | - Xiaoping Wu
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang 421001, Hunan Province, China
| | - Liming Xie
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang 421001, Hunan Province, China
| | - Xiusheng He
- Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang 421001, Hunan Province, China
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140
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Blecua P, Martinez‐Verbo L, Esteller M. The DNA methylation landscape of hematological malignancies: an update. Mol Oncol 2020; 14:1616-1639. [PMID: 32526054 PMCID: PMC7400809 DOI: 10.1002/1878-0261.12744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
The rapid advances in high-throughput sequencing technologies have made it more evident that epigenetic modifications orchestrate a plethora of complex biological processes. During the last decade, we have gained significant knowledge about a wide range of epigenetic changes that crucially contribute to some of the most aggressive forms of leukemia, lymphoma, and myelodysplastic syndromes. DNA methylation is a key epigenetic player in the abnormal initiation, development, and progression of these malignancies, often acting in synergy with other epigenetic alterations. It also contributes to the acquisition of drug resistance. In this review, we summarize the role of DNA methylation in hematological malignancies described in the current literature. We discuss in detail the dual role of DNA methylation in normal and aberrant hematopoiesis, as well as the involvement of this type of epigenetic change in other aspects of the disease. Finally, we present a comprehensive overview of the main clinical implications, including a discussion of the therapeutic strategies that regulate or reverse aberrant DNA methylation patterns in hematological malignancies, including their combination with (chemo)immunotherapy.
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Affiliation(s)
- Pedro Blecua
- Cancer Epigenetics GroupJosep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain
| | - Laura Martinez‐Verbo
- Cancer Epigenetics GroupJosep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain
| | - Manel Esteller
- Cancer Epigenetics GroupJosep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC)MadridSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
- Physiological Sciences DepartmentSchool of Medicine and Health SciencesUniversity of BarcelonaSpain
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141
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Midic D, Rinke J, Perner F, Müller V, Hinze A, Pester F, Landschulze J, Ernst J, Gruhn B, Matziolis G, Heidel FH, Hochhaus A, Ernst T. Prevalence and dynamics of clonal hematopoiesis caused by leukemia-associated mutations in elderly individuals without hematologic disorders. Leukemia 2020; 34:2198-2205. [PMID: 32457355 PMCID: PMC7387320 DOI: 10.1038/s41375-020-0869-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 04/29/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022]
Abstract
Clonal hematopoiesis is frequently observed in elderly people. To investigate the prevalence and dynamics of genetic alterations among healthy elderly individuals, a cohort of 50 people >80 years was genotyped for commonly mutated leukemia-associated genes by targeted deep next-generation sequencing. A total of 16 somatic mutations were identified in 13/50 (26%) individuals. Mutations occurred at low variant allele frequencies (median 11.7%) and remained virtually stable over 3 years without development of hematologic malignancies in affected individuals. With DNMT3A mutations most frequently detected, another cohort of 160 healthy people spanning all age groups was sequenced specifically for DNMT3A revealing an overall mutation rate of 6.2% (13/210) and an age-dependent increase of mutation prevalence. A significant difference (p = 0.017) in the DNMT3A expression pattern was detected between younger and healthy elderly people as determined by qRT-PCR. To evaluate the selection of clonal hematopoietic stem cells (HSCs), bone marrow of two healthy individuals with mutant DNMT3A was transplanted in a humanized mouse model. Xenografts displayed stable kinetics of DNMT3A mutations over 8 months. These findings indicate that the appearance of low-level clones with leukemia-associated mutations is a common age-associated phenomenon, but insufficient to initiate clonal selection and expansion without the additional influence of other factors.
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Affiliation(s)
- Danica Midic
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Jenny Rinke
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Florian Perner
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Violetta Müller
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Anna Hinze
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | | | | | - Jana Ernst
- Klinik für Kinder- und Jugendmedizin, Universitätsklinikum Jena, Jena, Germany
| | - Bernd Gruhn
- Klinik für Kinder- und Jugendmedizin, Universitätsklinikum Jena, Jena, Germany
| | - Georg Matziolis
- Orthopädische Klinik der Waldkliniken Eisenberg, Eisenberg, Germany
| | - Florian H Heidel
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Jena, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Thomas Ernst
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany.
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142
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Lauber C, Correia N, Trumpp A, Rieger MA, Dolnik A, Bullinger L, Roeder I, Seifert M. Survival differences and associated molecular signatures of DNMT3A-mutant acute myeloid leukemia patients. Sci Rep 2020; 10:12761. [PMID: 32728112 PMCID: PMC7391693 DOI: 10.1038/s41598-020-69691-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/13/2020] [Indexed: 12/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a very heterogeneous and highly malignant blood cancer. Mutations of the DNA methyltransferase DNMT3A are among the most frequent recurrent genetic lesions in AML. The majority of DNMT3A-mutant AML patients shows fast relapse and poor survival, but also patients with long survival or long-term remission have been reported. Underlying molecular signatures and mechanisms that contribute to these survival differences are only poorly understood and have not been studied in detail so far. We applied hierarchical clustering to somatic gene mutation profiles of 51 DNMT3A-mutant patients from The Cancer Genome Atlas (TCGA) AML cohort revealing two robust patient subgroups with profound differences in survival. We further determined molecular signatures that distinguish both subgroups. Our results suggest that FLT3 and/or NPM1 mutations contribute to survival differences of DNMT3A-mutant patients. We observed an upregulation of genes of the p53, VEGF and DNA replication pathway and a downregulation of genes of the PI3K-Akt pathway in short- compared to long-lived patients. We identified that the majority of measured miRNAs was downregulated in the short-lived group and we found differentially expressed microRNAs between both subgroups that have not been reported for AML so far (miR-153-2, miR-3065, miR-95, miR-6718) suggesting that miRNAs could be important for prognosis. In addition, we learned gene regulatory networks to predict potential major regulators and found several genes and miRNAs with known roles in AML pathogenesis, but also interesting novel candidates involved in the regulation of hematopoiesis, cell cycle, cell differentiation, and immunity that may contribute to the observed survival differences of both subgroups and could therefore be important for prognosis. Moreover, the characteristic gene mutation and expression signatures that distinguished short- from long-lived patients were also predictive for independent DNMT3A-mutant AML patients from other cohorts and could also contribute to further improve the European LeukemiaNet (ELN) prognostic scoring system. Our study represents the first in-depth computational approach to identify molecular factors associated with survival differences of DNMT3A-mutant AML patients and could trigger additional studies to develop robust molecular markers for a better stratification of AML patients with DNMT3A mutations.
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Affiliation(s)
- Chris Lauber
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Nádia Correia
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael A Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Anna Dolnik
- Department of Hematology, Oncology and Tumorimmunology, Charité University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany. .,National Center for Tumor Diseases (NCT), Dresden, Germany.
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143
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Hoang NM, Rui L. DNA methyltransferases in hematological malignancies. J Genet Genomics 2020; 47:361-372. [PMID: 32994141 PMCID: PMC7704698 DOI: 10.1016/j.jgg.2020.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
DNA methyltransferases (DNMTs) are an evolutionarily conserved family of DNA methylases, transferring a methyl group onto the fifth carbon of a cytosine residue. The mammalian DNMT family includes three major members that have functional methylation activities, termed DNMT1, DNMT3A, and DNMT3B. DNMT3A and DNMT3B are responsible for methylation establishment, whereas DNMT1 maintains methylation during DNA replication. Accumulating evidence demonstrates that regulation of DNA methylation by DNMTs is critical for normal hematopoiesis. Aberrant DNA methylation due to DNMT dysregulation and mutations is known as an important molecular event of hematological malignancies, such as DNMT3A mutations in acute myeloid leukemia. In this review, we first describe the basic methylation mechanisms of DNMTs and their functions in lymphocyte maturation and differentiation. We then discuss the current understanding of DNA methylation heterogeneity in leukemia and lymphoma to highlight the importance of studying DNA methylation targets. We also discuss DNMT mutations and pathogenic roles in human leukemia and lymphoma. We summarize the recent understanding of how DNMTs interact with transcription factors or cofactors to repress the expression of tumor suppressor genes. Finally, we highlight current clinical studies using DNMT inhibitors for the treatment of these hematological malignancies.
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Affiliation(s)
- Nguyet-Minh Hoang
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA
| | - Lixin Rui
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA.
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144
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Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J. Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat Commun 2020; 11:3355. [PMID: 32620778 PMCID: PMC7335073 DOI: 10.1038/s41467-020-17109-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases, DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.
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Affiliation(s)
- Linfeng Gao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sara A Grimm
- Division of Intramural Research, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Wendan Ren
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Sabrina Adam
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Dongliang Chen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Hiwot Anteneh
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Paul A Wade
- Division of Intramural Research, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Jikui Song
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA.
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
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145
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Lee J, Godfrey AL, Nangalia J. Genomic heterogeneity in myeloproliferative neoplasms and applications to clinical practice. Blood Rev 2020; 42:100708. [PMID: 32571583 DOI: 10.1016/j.blre.2020.100708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/22/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022]
Abstract
The myeloproliferative neoplasms (MPN) polycythaemia vera, essential thrombocythaemia and primary myelofibrosis are chronic myeloid disorders associated most often with mutations in JAK2, MPL and CALR, and in some patients with additional acquired genomic lesions. Whilst the molecular mechanisms downstream of these mutations are now clearer, it is apparent that clinical phenotype in MPN is a product of complex interactions, acting between individual mutations, between disease subclones, and between the tumour and background host factors. In this review we first discuss MPN phenotypic driver mutations and the factors that interact with them to influence phenotype. We consider the importance of ongoing studies of clonal haematopoiesis, which may inform a better understanding of why MPN develop in specific individuals. We then consider how best to deploy genomic testing in a clinical environment and the challenges as well as opportunities that may arise from more routine, comprehensive genomic analysis of patients with MPN.
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Affiliation(s)
- Joe Lee
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anna L Godfrey
- Haematopathology and Oncology Diagnostics Service/ Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Hills Rd, Cambridge CB2 0QQ, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Haematopathology and Oncology Diagnostics Service/ Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Hills Rd, Cambridge CB2 0QQ, UK.
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146
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Zhang TJ, Zhang LC, Xu ZJ, Zhou JD. Expression and prognosis analysis of DNMT family in acute myeloid leukemia. Aging (Albany NY) 2020; 12:14677-14690. [PMID: 32597790 PMCID: PMC7425446 DOI: 10.18632/aging.103520] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/04/2020] [Indexed: 04/08/2023]
Abstract
DNA methyltransferases (DNMTs) by regulating DNA methylation play crucial roles in the progression of hematologic malignancies, especially for acute myeloid leukemia (AML). Accumulating investigations have identified the high incidence of DNMT3A mutation in AML, and it is correlated with poor prognosis. Although a few studies have shown the expression of DNMTs and their clinical significance in AML, the results remain to be discussed. Herein, we systemically analyzed the DNMTs expression and their relationship with clinic-pathological features and prognosis in AML patients. DNMTs expression especially for DNMT3A/3B was closely associated with AML among various human cancers. DNMT3A expression was increased in AML patients, whereas DNMT3B expression was decreased. Significant associations between DNMT3A/B expression and clinic-pathological features/gene mutations were observed. Kaplan-Meier analysis showed that DNMT3A expression was associated with better overall survival (OS) and leukemia-free survival (LFS) among whole-cohort AML, and independently affected OS determined by Cox repression multivariate analysis. Notably, patients that received hematopoietic stem cell transplantation (HSCT) showed significantly better OS and LFS in DNMT3A lower-expressed groups, whereas patients in DNMT3A higher-expressed groups did not. By bioinformatics analysis, DNMT3A expression was found to be positively correlated with several leukemia-associated genes/microRNAs, and DNMT3A was identified as direct targets of miR-429 and miR-29b in AML. Collectively, our study demonstrated that DNMT3A/3B showed significant expression differences in AML. DNMT3A expression acted as a potential prognostic biomarker and may guide treatment choice between chemotherapy and HSCT in AML.
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Affiliation(s)
- Ting-Juan Zhang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang, Zhenjiang, Jiangsu, People’s Republic of China
| | - Liu-Chao Zhang
- Department of Medical Laboratory, Shanghai Deji Hospital, Qingdao University, Shanghai, People’s Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang, Zhenjiang, Jiangsu, People’s Republic of China
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang, Zhenjiang, Jiangsu, People’s Republic of China
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147
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Veninga A, De Simone I, Heemskerk JWM, Cate HT, van der Meijden PEJ. Clonal hematopoietic mutations linked to platelet traits and the risk of thrombosis or bleeding. Haematologica 2020; 105:2020-2031. [PMID: 32554558 PMCID: PMC7395290 DOI: 10.3324/haematol.2019.235994] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
Platelets are key elements in thrombosis, particularly in atherosclerosis-associated arterial thrombosis (atherothrombosis), and hemostasis. Megakaryocytes in the bone marrow, differentiated from hematopoietic stem cells are generally considered as a uniform source of platelets. However, recent insights into the causes of malignancies, including essential thrombocytosis, indicate that not only inherited but also somatic mutations in hematopoietic cells are linked to quantitative or qualitative platelet abnormalities. In particular cases, these form the basis of thrombo-hemorrhagic complications regularly observed in patient groups. This has led to the concept of clonal hematopoiesis of indeterminate potential (CHIP), defined as somatic mutations caused by clonal expansion of mutant hematopoietic cells without evident disease. This concept also provides clues regarding the importance of platelet function in relation to cardiovascular disease. In this summative review, we present an overview of genes associated with clonal hematopoiesis and altered platelet production and/or functionality, like mutations in JAK2 We consider how reported CHIP genes can influence the risk of cardiovascular disease, by exploring the consequences for platelet function related to (athero)thrombosis, or the risk of bleeding. More insight into the functional consequences of the CHIP mutations may favor personalized risk assessment, not only with regard to malignancies but also in relation to thrombotic vascular disease.
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Affiliation(s)
- Alicia Veninga
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht
| | - Ilaria De Simone
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht
| | - Johan W M Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht
| | - Hugo Ten Cate
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht.,Thrombosis Expertise Center, Heart and Vascular Center, Maastricht University Medical Center, Maastricht.,Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Paola E J van der Meijden
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht .,Thrombosis Expertise Center, Heart and Vascular Center, Maastricht University Medical Center, Maastricht
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148
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Lee D, Lee S, Kim S. PRISM: methylation pattern-based, reference-free inference of subclonal makeup. Bioinformatics 2020; 35:i520-i529. [PMID: 31510697 PMCID: PMC6612819 DOI: 10.1093/bioinformatics/btz327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Motivation Characterizing cancer subclones is crucial for the ultimate conquest of cancer. Thus, a number of bioinformatic tools have been developed to infer heterogeneous tumor populations based on genomic signatures such as mutations and copy number variations. Despite accumulating evidence for the significance of global DNA methylation reprogramming in certain cancer types including myeloid malignancies, none of the bioinformatic tools are designed to exploit subclonally reprogrammed methylation patterns to reveal constituent populations of a tumor. In accordance with the notion of global methylation reprogramming, our preliminary observations on acute myeloid leukemia (AML) samples implied the existence of subclonally occurring focal methylation aberrance throughout the genome. Results We present PRISM, a tool for inferring the composition of epigenetically distinct subclones of a tumor solely from methylation patterns obtained by reduced representation bisulfite sequencing. PRISM adopts DNA methyltransferase 1-like hidden Markov model-based in silico proofreading for the correction of erroneous methylation patterns. With error-corrected methylation patterns, PRISM focuses on a short individual genomic region harboring dichotomous patterns that can be split into fully methylated and unmethylated patterns. Frequencies of such two patterns form a sufficient statistic for subclonal abundance. A set of statistics collected from each genomic region is modeled with a beta-binomial mixture. Fitting the mixture with expectation-maximization algorithm finally provides inferred composition of subclones. Applying PRISM for two AML samples, we demonstrate that PRISM could infer the evolutionary history of malignant samples from an epigenetic point of view. Availability and implementation PRISM is freely available on GitHub (https://github.com/dohlee/prism). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dohoon Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Sangseon Lee
- Department of Computer Science and Engineering, Seoul National University, Seoul, Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Department of Computer Science and Engineering, Seoul National University, Seoul, Korea.,Bioinformatics Institute, Seoul National University, Seoul, Korea
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149
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Abstract
PURPOSE OF REVIEW The field of acute myeloid leukemia (AML) has been revolutionized in recent years by the advent of high-throughput techniques, such as next-generation sequencing. In this review, we will discuss some of the recently identified mutations that have defined a new molecular landscape in this disease, as well as their prognostic, predictive, and therapeutic implications. RECENT FINDINGS Recent studies have shown how many cases of AML evolve from a premalignant period of latency characterized by the accumulation of several mutations and the emergence of one or multiple dominant clones. The pattern of co-occurring mutations and cytogenetic abnormalities at diagnosis defines risk and can determine therapeutic approaches to induce remission. Besides the genetic landscape at diagnosis, the continued presence of particular gene mutations during or after treatment carries prognostic information that should further influence strategies to maintain remission in the long term. The recent progress made in AML research is a seminal example of how basic science can translate into improving clinical practice. Our ability to characterize the genomic landscape of individual patients has not only improved our ability to diagnose and prognosticate but is also bringing the promise of precision medicine to fruition in the field.
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Affiliation(s)
- Ludovica Marando
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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150
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Emperle M, Adam S, Kunert S, Dukatz M, Baude A, Plass C, Rathert P, Bashtrykov P, Jeltsch A. Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns. Nucleic Acids Res 2020; 47:11355-11367. [PMID: 31620784 PMCID: PMC6868496 DOI: 10.1093/nar/gkz911] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 02/01/2023] Open
Abstract
Somatic DNMT3A mutations at R882 are frequently observed in AML patients including the very abundant R882H, but also R882C, R882P and R882S. Using deep enzymology, we show here that DNMT3A-R882H has more than 70-fold altered flanking sequence preferences when compared with wildtype DNMT3A. The R882H flanking sequence preferences mainly differ on the 3' side of the CpG site, where they resemble DNMT3B, while 5' flanking sequence preferences resemble wildtype DNMT3A, indicating that R882H behaves like a DNMT3A/DNMT3B chimera. Investigation of the activity and flanking sequence preferences of other mutations of R882 revealed that they cause similar effects. Bioinformatic analyses of genomic methylation patterns focusing on flanking sequence effects after expression of wildtype DNMT3A and R882H in human cells revealed that genomic methylation patterns reflect the details of the altered flanking sequence preferences of R882H. Concordantly, R882H specific hypermethylation in AML patients was strongly correlated with the R882H flanking sequence preferences. R882H specific DNA hypermethylation events in AML patients were accompanied by R882H specific mis-regulation of several genes with strong cancer connection, which are potential downstream targets of R882H. In conclusion, our data provide novel and detailed mechanistic understanding of the pathogenic mechanism of the DNMT3A R882H somatic cancer mutation.
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Affiliation(s)
- Max Emperle
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Sabrina Adam
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Stefan Kunert
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Michael Dukatz
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Annika Baude
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, 28069120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, 28069120 Heidelberg, Germany
| | - Philipp Rathert
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
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