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Carnie CJ, Götz MJ, Palma-Chaundler CS, Weickert P, Wanders A, Serrano-Benitez A, Li HY, Gupta V, Awwad SW, Blum CJ, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D'Alessandro G, Richards SL, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson SP. Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS. EMBO J 2024; 43:2397-2423. [PMID: 38760575 PMCID: PMC11183266 DOI: 10.1038/s44318-024-00108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation is cytotoxic. Combining results from a subsequent genetic screen in DCTD-deficient cells with the identification of the DNMT1-DPC-proximal proteome, we uncover the ubiquitin and SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to SUMOylated DNMT1-DPCs and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism, potentially laying the foundations for future identification of predictive biomarkers for decitabine treatment.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Amy Wanders
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hao-Yi Li
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sean L Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nadia Gueorguieva
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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2
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Saga T, Kanagawa M, Harada T, Lang L, Yamawaki F, Ishihara T. Prognostic Value of Pretreatment Fetal Hemoglobin Levels in Patients with Myelodysplastic Syndromes and Acute Myeloid Leukemia Treated with Azacitidine: A Single-center Retrospective Study. Intern Med 2024; 63:781-790. [PMID: 37495538 PMCID: PMC11008988 DOI: 10.2169/internalmedicine.1216-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/05/2023] [Indexed: 07/28/2023] Open
Abstract
Objective Azacitidine (AZA) has been the standard of care for elderly patients with high-risk myelodysplastic syndromes (MDS). However, reliable clinical predictors of outcome have yet to be identified. The prognostic value of fetal hemoglobin (HbF) levels has been reported for decitabine therapy. We evaluated pretreatment HbF levels in AZA monotherapy as a prognostic marker in MDS/acute myeloid leukemia (AML). Methods This study included chemotherapy-naïve patients who had received seven-day treatment schedules of AZA and whose HbF levels were measured at the onset of treatment between March 2011 and July 2020. Patients were grouped into HbF-normal (<1.0%) or HbF-elevated (≥1.0%) groups. Responses were classified according to the International Working Group 2006 criteria. Patients Twenty-nine patients were included and classified as having either MDS (n=21), chronic myelomonocytic leukemia (n=5), myelodysplastic/myeloproliferative neoplasm unclassifiable (n=1), or AML with <30% marrow blasts (n=2) based on the World Health Organization 2016 diagnostic criteria. According to the revised International Prognostic Scoring System classification, 20/29 patients were at intermediate, high, or very high risk. Pretreatment HbF levels were elevated in 13/29 patients. Results The median follow-up duration was 13.0 (range 1.5-93.5) months. The HbF-elevated group was associated with a significantly higher hematologic improvement rate (76.9% vs. 25%, p=0.009) and better overall survival (median, 21.0 vs. 13.0 months, p=0.048) than the HbF-normal group. Conclusion These results suggest that elevated pretreatment HbF levels can predict better outcomes in patients with MDS/AML treated with AZA.
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Affiliation(s)
- Tomoyuki Saga
- Department of Hematology, Kin-ikyo Chuo Hospital, Japan
| | | | - Tomoya Harada
- Department of Hematology, Kin-ikyo Chuo Hospital, Japan
| | - Lang Lang
- Department of Hematology, Kin-ikyo Chuo Hospital, Japan
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3
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Schmutz M, Zucknick M, Schlenk RF, Mertens D, Benner A, Weichenhan D, Mücke O, Döhner K, Plass C, Bullinger L, Claus R. Predictive value of DNA methylation patterns in AML patients treated with an azacytidine containing induction regimen. Clin Epigenetics 2023; 15:171. [PMID: 37885041 PMCID: PMC10601277 DOI: 10.1186/s13148-023-01580-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a heterogeneous disease with a poor prognosis. Dysregulation of the epigenetic machinery is a significant contributor to disease development. Some AML patients benefit from treatment with hypomethylating agents (HMAs), but no predictive biomarkers for therapy response exist. Here, we investigated whether unbiased genome-wide assessment of pre-treatment DNA-methylation profiles in AML bone marrow blasts can help to identify patients who will achieve a remission after an azacytidine-containing induction regimen. RESULTS A total of n = 155 patients with newly diagnosed AML treated in the AMLSG 12-09 trial were randomly assigned to a screening and a refinement and validation cohort. The cohorts were divided according to azacytidine-containing induction regimens and response status. Methylation status was assessed for 664,227 500-bp-regions using methyl-CpG immunoprecipitation-seq, resulting in 1755 differentially methylated regions (DMRs). Top regions were distilled and included genes such as WNT10A and GATA3. 80% of regions identified as a hit were represented on HumanMethlyation 450k Bead Chips. Quantitative methylation analysis confirmed 90% of these regions (36 of 40 DMRs). A classifier was trained using penalized logistic regression and fivefold cross validation containing 17 CpGs. Validation based on mass spectra generated by MALDI-TOF failed (AUC 0.59). However, discriminative ability was maintained by adding neighboring CpGs. A recomposed classifier with 12 CpGs resulted in an AUC of 0.77. When evaluated in the non-azacytidine containing group, the AUC was 0.76. CONCLUSIONS Our analysis evaluated the value of a whole genome methyl-CpG screening assay for the identification of informative methylation changes. We also compared the informative content and discriminatory power of regions and single CpGs for predicting response to therapy. The relevance of the identified DMRs is supported by their association with key regulatory processes of oncogenic transformation and support the idea of relevant DMRs being enriched at distinct loci rather than evenly distribution across the genome. Predictive response to therapy could be established but lacked specificity for treatment with azacytidine. Our results suggest that a predictive epigenotype carries its methylation information at a complex, genome-wide level, that is confined to regions, rather than to single CpGs. With increasing application of combinatorial regimens, response prediction may become even more complicated.
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Affiliation(s)
- Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Zucknick
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | - Richard F Schlenk
- NCT-Trial Center, National Center of Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Mertens
- Cooperation Unit "Mechanisms of Leukemogenesis", German Cancer Research Center, Heidelberg, Germany
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, Ulm University Medical Center, Ulm, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Mücke
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Bullinger
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- Department of Hematology, Oncology, and Cancer Immunology, Campus Virchow Klinikum, Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rainer Claus
- Hematology and Oncology, Medical Faculty, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany.
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Pathology, Medical Faculty, University of Augsburg, Augsburg, Germany.
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Yabushita T, Chinen T, Nishiyama A, Asada S, Shimura R, Isobe T, Yamamoto K, Sato N, Enomoto Y, Tanaka Y, Fukuyama T, Satoh H, Kato K, Saitoh K, Ishikawa T, Soga T, Nannya Y, Fukagawa T, Nakanishi M, Kitagawa D, Kitamura T, Goyama S. Mitotic perturbation is a key mechanism of action of decitabine in myeloid tumor treatment. Cell Rep 2023; 42:113098. [PMID: 37714156 DOI: 10.1016/j.celrep.2023.113098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/22/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023] Open
Abstract
Decitabine (DAC) is clinically used to treat myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Our genome-wide CRISPR-dCas9 activation screen using MDS-derived AML cells indicates that mitotic regulation is critical for DAC resistance. DAC strongly induces abnormal mitosis (abscission failure or tripolar mitosis) in human myeloid tumors at clinical concentrations, especially in those with TP53 mutations or antecedent hematological disorders. This DAC-induced mitotic disruption and apoptosis are significantly attenuated in DNMT1-depleted cells. In contrast, overexpression of Dnmt1, but not the catalytically inactive mutant, enhances DAC-induced mitotic defects in myeloid tumors. We also demonstrate that DAC-induced mitotic disruption is enhanced by pharmacological inhibition of the ATR-CLSPN-CHK1 pathway. These data challenge the current assumption that DAC inhibits leukemogenesis through DNMT1 inhibition and subsequent DNA hypomethylation and highlight the potent activity of DAC to disrupt mitosis through aberrant DNMT1-DNA covalent bonds.
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Affiliation(s)
- Tomohiro Yabushita
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Asada
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Ruka Shimura
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoya Isobe
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan; Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keita Yamamoto
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Naru Sato
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Enomoto
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomofusa Fukuyama
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Hematology, International University of Health and Welfare Hospital, Tochigi, Japan
| | - Hitoshi Satoh
- Division of Medical Genome Sciences, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Keiko Kato
- Infinity Lab, INC, Yamagata, Japan; Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Kaori Saitoh
- Infinity Lab, INC, Yamagata, Japan; Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Takamasa Ishikawa
- Infinity Lab, INC, Yamagata, Japan; Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Yasuhito Nannya
- Division of Hematopoietic Disease Control, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo, Japan
| | - Susumu Goyama
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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5
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Kagan AB, Garrison DA, Anders NM, Webster J, Baker SD, Yegnasubramanian S, Rudek MA. DNA methyltransferase inhibitor exposure-response: Challenges and opportunities. Clin Transl Sci 2023; 16:1309-1322. [PMID: 37345219 PMCID: PMC10432879 DOI: 10.1111/cts.13548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Although DNA methyltransferase inhibitors (DNMTis), such as azacitidine and decitabine, are used extensively in the treatment of myelodysplastic syndromes and acute myeloid leukemia, there remain unanswered questions about DNMTi's mechanism of action and predictors of clinical response. Because patients often remain on single-agent DNMTis or DNMTi-containing regimens for several months before knowing whether clinical benefit can be achieved, the development and clinical validation of response-predictive biomarkers represents an important unmet need in oncology. In this review, we will summarize the clinical studies that led to the approval of azacitidine and decitabine, as well as the real-world experience with these drugs. We will then focus on biomarker development for DNMTis-specifically, efforts at determining exposure-response relationships and challenges that remain impacting the broader clinical translation of these methods. We will highlight recent progress in liquid-chromatography tandem mass spectrometry technology that has allowed for the simultaneous measurement of decitabine genomic incorporation and global DNA methylation, which has significant potential as a mechanism-of-action based biomarker in patients on DNMTis. Last, we will cover important research questions that need to be addressed in order to optimize this potential biomarker for clinical use.
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Affiliation(s)
- Amanda B. Kagan
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Dominique A. Garrison
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Nicole M. Anders
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Jonathan A. Webster
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Sharyn D. Baker
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Michelle A. Rudek
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
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Liu J, Min S, Kim D, Park J, Park E, Koh Y, Shin DY, Kim TK, Byun JM, Yoon SS, Hong J. Epigenetic priming improves salvage chemotherapy in diffuse large B-cell lymphoma via endogenous retrovirus-induced cGAS-STING activation. Clin Epigenetics 2023; 15:75. [PMID: 37138342 PMCID: PMC10155448 DOI: 10.1186/s13148-023-01493-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Although most patients with diffuse large B-cell lymphoma (DLBCL) achieve complete remission after first-line rituximab-containing immunochemotherapy, up to 40% of patients relapse and require salvage therapy. Among those patients, a substantial proportion remain refractory to salvage therapy due to insufficient efficacy or intolerance of toxicities. A hypomethylating agent, 5-azacytidine, showed a chemosensitizing effect when primed before chemotherapy in lymphoma cell lines and newly diagnosed DLBCL patients. However, its potential to improve outcomes of salvage chemotherapy in DLBCL has not been investigated. RESULTS In this study, we demonstrated the mechanism of 5-azacytidine priming as a chemosensitizer in a platinum-based salvage regimen. This chemosensitizing effect was associated with endogenous retrovirus (ERV)-induced viral mimicry responses via the cGAS-STING axis. We found deficiency of cGAS impaired the chemosensitizing effect of 5-azacytidine. Furthermore, combining vitamin C and 5-azacytidine to synergistically activate STING could be a potential remedy for insufficient priming induced by 5-azacytidine alone. CONCLUSIONS Taken together, the chemosensitizing effect of 5-azacytidine could be exploited to overcome the limitations of the current platinum-containing salvage chemotherapy in DLBCL and the status of cGAS-STING has the potential to predict the efficacy of 5-azacytidine priming.
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Affiliation(s)
- Jun Liu
- College of Medicine, Zhejiang University, Hangzhou, China
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Suji Min
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dongchan Kim
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunchae Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngil Koh
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ja Min Byun
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junshik Hong
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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7
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Smith DA, Sadler MC, Altman RB. Promises and challenges in pharmacoepigenetics. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e18. [PMID: 37560024 PMCID: PMC10406571 DOI: 10.1017/pcm.2023.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 08/11/2023]
Abstract
Pharmacogenetics, the study of how interindividual genetic differences affect drug response, does not explain all observed heritable variance in drug response. Epigenetic mechanisms, such as DNA methylation, and histone acetylation may account for some of the unexplained variances. Epigenetic mechanisms modulate gene expression and can be suitable drug targets and can impact the action of nonepigenetic drugs. Pharmacoepigenetics is the field that studies the relationship between epigenetic variability and drug response. Much of this research focuses on compounds targeting epigenetic mechanisms, called epigenetic drugs, which are used to treat cancers, immune disorders, and other diseases. Several studies also suggest an epigenetic role in classical drug response; however, we know little about this area. The amount of information correlating epigenetic biomarkers to molecular datasets has recently expanded due to technological advances, and novel computational approaches have emerged to better identify and predict epigenetic interactions. We propose that the relationship between epigenetics and classical drug response may be examined using data already available by (1) finding regions of epigenetic variance, (2) pinpointing key epigenetic biomarkers within these regions, and (3) mapping these biomarkers to a drug-response phenotype. This approach expands on existing knowledge to generate putative pharmacoepigenetic relationships, which can be tested experimentally. Epigenetic modifications are involved in disease and drug response. Therefore, understanding how epigenetic drivers impact the response to classical drugs is important for improving drug design and administration to better treat disease.
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Affiliation(s)
- Delaney A Smith
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Marie C Sadler
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- University Center for Primary Care and Public Health, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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8
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Aumer T, Gremmelmaier CB, Runtsch LS, Pforr JC, Yeşiltaç GN, Kaiser S, Traube FR. Comprehensive comparison between azacytidine and decitabine treatment in an acute myeloid leukemia cell line. Clin Epigenetics 2022; 14:113. [PMID: 36089606 PMCID: PMC9465881 DOI: 10.1186/s13148-022-01329-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
Azacytidine (AzaC) and decitabine (AzadC) are cytosine analogs that covalently trap DNA methyltransferases, which place the important epigenetic mark 5-methyl-2'-deoxycytidine by methylating 2'-deoxycytidine (dC) at the C5 position. AzaC and AzadC are used in the clinic as antimetabolites to treat myelodysplastic syndrome and acute myeloid leukemia and are explored against other types of cancer. Although their principal mechanism of action is known, the downstream effects of AzaC and AzadC treatment are not well understood and the cellular prerequisites that determine sensitivity toward AzaC and AzadC remain elusive. Here, we investigated the effects and phenotype of AzaC and AzadC exposure on the acute myeloid leukemia cell line MOLM-13. We found that while AzaC and AzadC share many effects on the cellular level, including decreased global DNA methylation, increased formation of DNA double-strand breaks, transcriptional downregulation of important oncogenes and similar changes on the proteome level, AzaC failed in contrast to AzadC to induce apoptosis efficiently in MOLM-13. The only cellular marker that correlated with this clear phenotypical outcome was the level of hydroxy-methyl-dC, an additional epigenetic mark that is placed by TET enzymes and repressed in cancer cells. Whereas AzadC increased hmdC substantially in MOLM-13, AzaC treatment did not result in any increase at all. This suggests that hmdC levels in cancer cells should be monitored as a response toward AzaC and AzadC and considered as a biomarker to judge whether AzaC or AzadC treatment leads to cell death in leukemic cells.
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Affiliation(s)
- Tina Aumer
- Department of Chemistry, Institute for Chemical Epigenetics, Ludwig-Maximilians-Universität München, Würmtalstr. 201, 81375, Munich, Germany
| | - Constanze B Gremmelmaier
- Faculty of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Leander S Runtsch
- Department of Chemistry, Institute for Chemical Epigenetics, Ludwig-Maximilians-Universität München, Würmtalstr. 201, 81375, Munich, Germany
| | - Johannes C Pforr
- Faculty of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - G Nur Yeşiltaç
- Institut Für Pharmazeutische Chemie, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Stefanie Kaiser
- Institut Für Pharmazeutische Chemie, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Franziska R Traube
- Department of Chemistry, Institute for Chemical Epigenetics, Ludwig-Maximilians-Universität München, Würmtalstr. 201, 81375, Munich, Germany.
- Faculty of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany.
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9
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Chen R, Ishak CA, De Carvalho DD. Endogenous Retroelements and the Viral Mimicry Response in Cancer Therapy and Cellular Homeostasis. Cancer Discov 2021; 11:2707-2725. [PMID: 34649957 DOI: 10.1158/2159-8290.cd-21-0506] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/14/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
Features of the cancer epigenome distinguish cancers from their respective cell of origin and establish therapeutic vulnerabilities that can be exploited through pharmacologic inhibition of DNA- or histone-modifying enzymes. Epigenetic therapies converge with cancer immunotherapies through "viral mimicry," a cellular state of active antiviral response triggered by endogenous nucleic acids often derived from aberrantly transcribed endogenous retrotransposons. This review describes the initial characterization and expansion of viral mimicry-inducing approaches as well as features that "prime" cancers for viral mimicry induction. Increased understanding of viral mimicry in therapeutic contexts suggests potential physiologic roles in cellular homeostasis. SIGNIFICANCE: Recent literature establishes elevated cytosolic double strand RNA (dsRNA) levels as a cancer-specific therapeutic vulnerability that can be elevated by viral mimicry-inducing therapies beyond tolerable thresholds to induce antiviral signaling and increase dependence on dsRNA stress responses mediated by ADAR1. Improved understanding of viral mimicry signaling and tolerance mechanisms reveals synergistic treatment combinations with epigenetic therapies that include inhibition of BCL2, ADAR1, and immune checkpoint blockade. Further characterization of viral mimicry tolerance may identify contexts that maximize efficacy of conventional cancer therapies.
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Affiliation(s)
- Raymond Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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10
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Ueda K, Steidl U. Epigenetic Achilles' heel of AML. NATURE CANCER 2021; 2:481-483. [PMID: 35122022 DOI: 10.1038/s43018-021-00212-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Koki Ueda
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University, Fukushima, Japan
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine (Oncology), Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY, USA.
- Blood Cancer Institute, Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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11
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Scheller M, Ludwig AK, Göllner S, Rohde C, Krämer S, Stäble S, Janssen M, Müller JA, He L, Bäumer N, Arnold C, Gerß J, Schönung M, Thiede C, Niederwieser C, Niederwieser D, Serve H, Berdel WE, Thiem U, Hemmerling I, Leuschner F, Plass C, Schlesner M, Zaugg J, Milsom MD, Trumpp A, Pabst C, Lipka DB, Müller-Tidow C. Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response. NATURE CANCER 2021; 2:527-544. [PMID: 35122024 DOI: 10.1038/s43018-021-00213-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/19/2021] [Indexed: 02/04/2023]
Abstract
Somatic mutations in DNA methyltransferase 3A (DNMT3A) are among the most frequent alterations in clonal hematopoiesis (CH) and acute myeloid leukemia (AML), with a hotspot in exon 23 at arginine 882 (DNMT3AR882). Here, we demonstrate that DNMT3AR882H-dependent CH and AML cells are specifically susceptible to the hypomethylating agent azacytidine (AZA). Addition of AZA to chemotherapy prolonged AML survival solely in individuals with DNMT3AR882 mutations, suggesting its potential as a predictive marker for AZA response. AML and CH mouse models confirmed AZA susceptibility specifically in DNMT3AR882H-expressing cells. Hematopoietic stem cells (HSCs) and progenitor cells expressing DNMT3AR882H exhibited cell autonomous viral mimicry response as a result of focal DNA hypomethylation at retrotransposon sequences. Administration of AZA boosted hypomethylation of retrotransposons specifically in DNMT3AR882H-expressing cells and maintained elevated levels of canonical interferon-stimulated genes (ISGs), thus leading to suppressed protein translation and increased apoptosis.
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Affiliation(s)
- Marina Scheller
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.
| | - Anne Kathrin Ludwig
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Stefanie Göllner
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Rohde
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Stephen Krämer
- Bioinformatics and Omics Data Analytics Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Sina Stäble
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Maike Janssen
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - James-Arne Müller
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lixiazi He
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nicole Bäumer
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Christian Arnold
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim Gerß
- Institute of Biostatistics and Clinical Research, WWU Münster, Münster, Germany
| | - Maximilian Schönung
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Christian Thiede
- Department of Medicine, University Hospital Dresden, Dresden, Germany
| | - Christian Niederwieser
- Interdisziplinäre Klinik und Poliklinik für Stammzelltransplantation, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | - Hubert Serve
- Department of Medicine II, University of Frankfurt, Frankfurt, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Ulrich Thiem
- Geriatrics and Gerontology, University of Hamburg, Hamburg, Germany
| | - Inga Hemmerling
- Department of Medicine, Cardiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Florian Leuschner
- Department of Medicine, Cardiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Judith Zaugg
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michael D Milsom
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Caroline Pabst
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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12
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Low Plasma Citrate Levels and Specific Transcriptional Signatures Associated with Quiescence of CD34 + Progenitors Predict Azacitidine Therapy Failure in MDS/AML Patients. Cancers (Basel) 2021; 13:cancers13092161. [PMID: 33946220 PMCID: PMC8125503 DOI: 10.3390/cancers13092161] [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: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Epigenetic drugs, such as azacitidine (AZA), hold promise in the treatment of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), however, the mechanisms predicting the patients’ response to AZA is not completely understood. Quiescence of hematopoietic CD34+ progenitors has been proposed as a predictive factor for AZA therapy failure in MDS/AML patients, but the interplay between CD34+ cell cycle status and their metabolic signature in a predisposition to AZA (non)responsiveness remains unclear. Our data on patients with MDS or AML with myelodysplasia-related changes (AML-MRC) suggest that AZA-responders have actively cycling CD34+ cells poised for erythro-myeloid differentiation, with high metabolic activity controlling histone acetylation. Conversely, the patients who progressed early on AZA therapy revealed quiescence signature of their CD34+ cells, with signs of reduced metabolically-controlled acetylation of histones needed for transcription-permissive chromatin configuration. Our study delineates plasma citrate levels and CD34+ cells’ transcriptional signatures associated with cycling status and metabolic characteristics as factors predicting the response to AZA monotherapy in MDS/AML-MRC patients. Abstract To better understand the molecular basis of resistance to azacitidine (AZA) therapy in myelodysplastic syndromes (MDS) and acute myeloid leukemia with myelodysplasia-related changes (AML-MRC), we performed RNA sequencing on pre-treatment CD34+ hematopoietic stem/progenitor cells (HSPCs) isolated from 25 MDS/AML-MRC patients of the discovery cohort (10 AZA responders (RD), six stable disease, nine progressive disease (PD) during AZA therapy) and from eight controls. Eleven MDS/AML-MRC samples were also available for analysis of selected metabolites, along with 17 additional samples from an independent validation cohort. Except for two patients, the others did not carry isocitrate dehydrogenase (IDH)1/2 mutations. Transcriptional landscapes of the patients’ HSPCs were comparable to those published previously, including decreased signatures of active cell cycling and DNA damage response in PD compared to RD and controls. In addition, PD-derived HSPCs revealed repressed markers of the tricarboxylic acid cycle, with IDH2 among the top 50 downregulated genes in PD compared to RD. Decreased citrate plasma levels, downregulated expression of the (ATP)-citrate lyase and other transcriptional/metabolic networks indicate metabolism-driven histone modifications in PD HSPCs. Observed histone deacetylation is consistent with transcription-nonpermissive chromatin configuration and quiescence of PD HSPCs. This study highlights the complexity of the molecular network underlying response/resistance to hypomethylating agents.
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13
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Saliba AN, John AJ, Kaufmann SH. Resistance to venetoclax and hypomethylating agents in acute myeloid leukemia. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:125-142. [PMID: 33796823 PMCID: PMC8011583 DOI: 10.20517/cdr.2020.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite the success of the combination of venetoclax with the hypomethylating agents (HMA) decitabine or azacitidine in inducing remission in older, previously untreated patients with acute myeloid leukemia (AML), resistance - primary or secondary - still constitutes a significant roadblock in the quest to prolong the duration of response. Here we review the proposed and proven mechanisms of resistance to venetoclax monotherapy, HMA monotherapy, and the doublet of venetoclax and HMA for the treatment of AML. We approach the mechanisms of resistance to HMAs and venetoclax in the light of the agents' mechanisms of action. We briefly describe potential therapeutic strategies to circumvent resistance to this promising combination, including alternative scheduling or the addition of other agents to the HMA and venetoclax backbone. Understanding the mechanisms of action and evolving resistance in AML remains a priority in order to maximize the benefit from novel drugs and combinations, identify new therapeutic targets, define potential prognostic markers, and avoid treatment failure.
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Affiliation(s)
- Antoine N Saliba
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - August J John
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Scott H Kaufmann
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
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14
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Lai J, Fu Y, Tian S, Huang S, Luo X, Lin L, Zhang X, Wang H, Lin Z, Zhao H, Lin S, Zhao J, Xu S, Li D, Cai S, Dong L, Qian J, Liang J, Li Q, Zhang Y, Fan J, Balderas R, Chen Q. Zebularine elevates STING expression and enhances cGAMP cancer immunotherapy in mice. Mol Ther 2021; 29:1758-1771. [PMID: 33571681 DOI: 10.1016/j.ymthe.2021.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 12/02/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
DNA methylation abnormality is closely related to tumor occurrence and development. Chemical inhibitors targeting DNA methyltransferase (DNMTis) have been used in treating cancer. However, the impact of DNMTis on antitumor immunity has not been well elucidated. In this study, we show that zebularine (a demethylating agent) treatment of cancer cells led to increased levels of interferon response in a cyclic guanosine monophosphate-AMP (cGAMP) synthase (cGAS)- and stimulator of interferon genes (STING)-dependent manner. This treatment also specifically sensitized the cGAS-STING pathway in response to DNA stimulation. Incorporation of zebularine into genomic DNA caused demethylation and elevated expression of a group of genes, including STING. Without causing DNA damage, zebularine led to accumulation of DNA species in the cytoplasm of treated cells. In syngeneic tumor models, administration of zebularine alone reduced tumor burden and extended mice survival. This effect synergized with cGAMP and immune checkpoint blockade therapy. The efficacy of zebularine was abolished in nude mice and in cGAS-/- or STING-/- mice, indicating its dependency on host immunity. Analysis of tumor cells indicates upregulation of interferon-stimulated genes (ISGs) following zebularine administration. Zebularine promoted infiltration of CD8 T cells and natural killer (NK) cells into tumor and therefore suppressed tumor growth. This study unveils the role of zebularine in sensitizing the cGAS-STING pathway to promote anti-tumor immunity and provides the foundation for further therapeutic development.
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Affiliation(s)
- Junzhong Lai
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China; The Cancer Center, Union Hospital, Fujian Medical University, Fuzhou, Fujian Province 350117, China
| | - Yajuan Fu
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Shuoran Tian
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Shanlu Huang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Xuan Luo
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Lili Lin
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Xing Zhang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Hanze Wang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Zhang Lin
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Heng Zhao
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Shujin Lin
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Junhong Zhao
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Shan Xu
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Daliang Li
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Shaoli Cai
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Luna Dong
- BD Biosciences Shanghai, New Bund World Trade Center III, Building B, No. 11, Lane 221, Dongyu Road, Pudong New District, Shanghai 200126, China
| | - Jing Qian
- BD Biosciences Shanghai, New Bund World Trade Center III, Building B, No. 11, Lane 221, Dongyu Road, Pudong New District, Shanghai 200126, China
| | - Jiadi Liang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Qiumei Li
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Yong Zhang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | - Jiqiang Fan
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China
| | | | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou, Fujian Province 350117, China; Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, Fujian 350117, China.
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15
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He Y, Xu L, Feng J, Wu K, Zhao Y, Huang H. HDAC Inhibitor LBH589 Suppresses the Proliferation but Enhances the Antileukemic Effect of Human γδT Cells. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:623-630. [PMID: 33005729 PMCID: PMC7515977 DOI: 10.1016/j.omto.2020.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
γδT cells have potent effects on hematological malignancies, and their functions can be regulated by anti-tumor agents. Histone deacetylase inhibitors (HDACis) not only have antileukemic activity on leukemia but also affect immune cells during therapeutic application. In this in vitro study, we showed that LBH589, a pan-HDACi, impaired the proliferation of human γδT cells, as well as their proportions in peripheral blood mononuclear cells (PBMCs). At the specific concentration, LBH589 induced significant antileukemic activity of γδT cells against the HL-60 cells and Kasumi cells in a dose-dependent manner. However, the expression levels of activating receptor and molecules, as well as interferon-γ (IFN-γ) expression on γδT cells, were not affected by LBH589. After treatment with LBH589 for indicated times, extracellular-regulated protein kinase (ERK), Akt, and c-Jun N-terminal kinase (JNK) signaling pathways in γδT cells were not activated. In contrast, a stronger expression of Notch was observed and sustained for 72 h. Inhibition of Notch signaling by FLI-06, the γ-secretase inhibitor, significantly reversed the enhanced antileukemic ability of γδT cells induced by LBH589. For the first time, our investigations demonstrate that LBH589 can inhibit proliferation of γδT cells but facilitate their antileukemic effects via activation of Notch signaling.
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Affiliation(s)
- Ying He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
- Zhejiang Provincial People’s Hospital, 158 Shangtang Road, Hangzhou, Zhejiang 310014, China
- Institute of Hematology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Lin Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
- Institute of Hematology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Jingjing Feng
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
- Institute of Hematology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Kangni Wu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
- Institute of Hematology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Yanmin Zhao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
- Institute of Hematology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
- Corresponding author: Yanmin Zhao, Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China.
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
- Institute of Hematology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
- Corresponding author: He Huang, Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China.
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16
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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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17
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Ohtani H, Ørskov AD, Helbo AS, Gillberg L, Liu M, Zhou W, Ungerstedt J, Hellström-Lindberg E, Sun W, Liang G, Jones PA, Grønbæk K. Activation of a Subset of Evolutionarily Young Transposable Elements and Innate Immunity Are Linked to Clinical Responses to 5-Azacytidine. Cancer Res 2020; 80:2441-2450. [PMID: 32245794 DOI: 10.1158/0008-5472.can-19-1696] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/06/2019] [Accepted: 03/24/2020] [Indexed: 12/19/2022]
Abstract
The DNA methyltransferase inhibitors (DNMTi) 5-azacytidine and 5-aza-2-deoxycytidine have been approved for the treatment of different types of hematologic malignancies. However, only about 50% of patients respond to treatment. Therefore, a more comprehensive understanding of the molecular changes in patients treated with DNMTi is needed. Here, we examined gene expression profiles in a total of 150 RNA samples from two adult cohorts and one pediatric cohort with hematologic cancers taken before, during, and after treatment with 5-azacytidine (40 patients; 15 nonresponders, 25 responders). Using each patient as their own control, malignant cells showed preferential activation of a subset of evolutionarily young transposable elements (TE), including endogenous retroviral long terminal repeats (LTR), short and long interspersed nuclear elements (SINE and LINE), and the type I IFN pathway in responders, all independent of disease classification. Transfection of eight upregulated LTRs into recipient human cells in culture showed robust and heterogenous activation of six genes in the type I IFN pathway. These results, obtained in diverse hematologic disease entities, show that common targets (TE) activated by the same drug (5-azacytidine) elicit an immune response, which may be important for patient's responses to DNMTi. SIGNIFICANCE: Activation of specific classes of evolutionarily young transposable elements can lead to activation of the innate immune system.
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Affiliation(s)
| | - Andreas D Ørskov
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra S Helbo
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Linn Gillberg
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Minmin Liu
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Wanding Zhou
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Johanna Ungerstedt
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Weili Sun
- Department of Pediatrics, Pediatric Hematology Oncology, City of Hope National Medical Center, Duarte, California
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan.
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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18
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Dahn ML, Cruickshank BM, Jackson AJ, Dean C, Holloway RW, Hall SR, Coyle KM, Maillet H, Waisman DM, Goralski KB, Giacomantonio CA, Weaver ICG, Marcato P. Decitabine Response in Breast Cancer Requires Efficient Drug Processing and Is Not Limited by Multidrug Resistance. Mol Cancer Ther 2020; 19:1110-1122. [PMID: 32156786 DOI: 10.1158/1535-7163.mct-19-0745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/30/2020] [Accepted: 03/05/2020] [Indexed: 11/16/2022]
Abstract
Dysregulation of DNA methylation is an established feature of breast cancers. DNA demethylating therapies like decitabine are proposed for the treatment of triple-negative breast cancers (TNBC) and indicators of response need to be identified. For this purpose, we characterized the effects of decitabine in a panel of 10 breast cancer cell lines and observed a range of sensitivity to decitabine that was not subtype specific. Knockdown of potential key effectors demonstrated the requirement of deoxycytidine kinase (DCK) for decitabine response in breast cancer cells. In treatment-naïve breast tumors, DCK was higher in TNBCs, and DCK levels were sustained or increased post chemotherapy treatment. This suggests that limited DCK levels will not be a barrier to response in patients with TNBC treated with decitabine as a second-line treatment or in a clinical trial. Methylome analysis revealed that genome-wide, region-specific, tumor suppressor gene-specific methylation, and decitabine-induced demethylation did not predict response to decitabine. Gene set enrichment analysis of transcriptome data demonstrated that decitabine induced genes within apoptosis, cell cycle, stress, and immune pathways. Induced genes included those characterized by the viral mimicry response; however, knockdown of key effectors of the pathway did not affect decitabine sensitivity suggesting that breast cancer growth suppression by decitabine is independent of viral mimicry. Finally, taxol-resistant breast cancer cells expressing high levels of multidrug resistance transporter ABCB1 remained sensitive to decitabine, suggesting that the drug could be used as second-line treatment for chemoresistant patients.
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Affiliation(s)
- Margaret L Dahn
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Ainsleigh J Jackson
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Cheryl Dean
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ryan W Holloway
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Steven R Hall
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Krysta M Coyle
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hillary Maillet
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David M Waisman
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kerry B Goralski
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.,College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Carman A Giacomantonio
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Surgery, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian C G Weaver
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Psychology and Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada.,Brain Repair Centre, Halifax, Nova Scotia, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada. .,Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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19
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Cahill KE, Karimi YH, Karrison TG, Jain N, Green M, Weiner H, Fulton N, Kadri S, Godley LA, Artz AS, Liu H, Thirman MJ, Le Beau MM, McNerney ME, Segal J, Larson RA, Stock W, Odenike O. A phase 1 study of azacitidine with high-dose cytarabine and mitoxantrone in high-risk acute myeloid leukemia. Blood Adv 2020; 4:599-606. [PMID: 32074275 PMCID: PMC7042987 DOI: 10.1182/bloodadvances.2019000795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022] Open
Abstract
In this phase 1 study, azacitidine (AZA) was given before high-dose cytarabine (HiDAC) and mitoxantrone (mito) based on the hypothesis that epigenetic priming with a hypomethylating agent before cytotoxic chemotherapy would improve response rates in patients with high-risk acute myeloid leukemia (AML), including relapsed/refractory disease. The primary objective was to establish the recommended phase 2 dose of AZA given before standard HiDAC/mito. In a dose escalation scheme, 46 patients (median age, 66 years) received AZA at 37.5, 50, or 75 mg/m2 subcutaneously or IV once daily on days 1 to 5 followed by HiDAC (3000 mg/m2) and mitoxantrone (30 mg/m2) once each on days 6 and 10 (the HiDAC/mito dose was reduced 33% in elderly subjects). Two dose-limiting toxicities occurred (both in the same patient): acute liver failure and kidney injury at the 50 mg/m2 dose. The 30-day induction death rate was 2.2% (1 of 46). The overall response rate, including complete remission and complete remission with incomplete count recovery, was 61% (28 of 46). Previously untreated patients aged ≥60 years with therapy-related AML and de novo AML were more likely to respond than untreated patients with AML progressing from an antecedent hematologic disorder (myelodysplastic syndrome and chronic myelomonocytic leukemia). Patients with favorable European Leukemia Network risk (P = .008), NPM1 mutations (P = .007), or IDH2 mutations (P = .03) were more likely to respond, and those with TP53 mutations (P = .03) were less likely to respond. The recommended phase 2 dose of AZA is 75 mg/m2 per day on days 1 to 5 followed by HiDAC (3000 mg/m2) and mitoxantrone (30 mg/m2) once each on days 6 and 10. This trial was registered at www.clinicaltrials.gov as #NCT01839240.
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Affiliation(s)
- Kirk E Cahill
- Department of Medicine, University of Chicago Medicine, Chicago, IL
| | - Yasmin H Karimi
- Department of Medicine, University of Chicago Medicine, Chicago, IL
| | - Theodore G Karrison
- Department of Public Health Sciences, University of Chicago, Chicago, IL; and
- Comprehensive Cancer Center
| | - Nitin Jain
- Section of Hematology/Oncology, Department of Medicine, and
| | - Margaret Green
- Section of Hematology/Oncology, Department of Medicine, and
| | - Howard Weiner
- Section of Hematology/Oncology, Department of Medicine, and
| | - Noreen Fulton
- Section of Hematology/Oncology, Department of Medicine, and
| | - Sabah Kadri
- Department of Pathology, University of Chicago Medicine, Chicago, IL
| | - Lucy A Godley
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Andrew S Artz
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Hongtao Liu
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Michael J Thirman
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Michelle M Le Beau
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Megan E McNerney
- Comprehensive Cancer Center
- Department of Pathology, University of Chicago Medicine, Chicago, IL
| | - Jeremy Segal
- Comprehensive Cancer Center
- Department of Pathology, University of Chicago Medicine, Chicago, IL
| | - Richard A Larson
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Wendy Stock
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
| | - Olatoyosi Odenike
- Comprehensive Cancer Center
- Section of Hematology/Oncology, Department of Medicine, and
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20
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Putative promoters within gene bodies control exon expression via TET1‐mediated H3K36 methylation. J Cell Physiol 2020; 235:6711-6724. [DOI: 10.1002/jcp.29566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/13/2020] [Indexed: 12/31/2022]
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21
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Mendez LM, Posey RR, Pandolfi PP. The Interplay Between the Genetic and Immune Landscapes of AML: Mechanisms and Implications for Risk Stratification and Therapy. Front Oncol 2019; 9:1162. [PMID: 31781488 PMCID: PMC6856667 DOI: 10.3389/fonc.2019.01162] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022] Open
Abstract
AML holds a unique place in the history of immunotherapy by virtue of being among the first malignancies in which durable remissions were achieved with "adoptive immunotherapy," now known as allogeneic stem cell transplantation. The successful deployment of unselected adoptive cell therapy established AML as a disease responsive to immunomodulation. Classification systems for AML have been refined and expanded over the years in an effort to capture the variability of this heterogeneous disease and risk-stratify patients. Current systems increasingly incorporate information about cytogenetic alterations and genetic mutations. The advent of next generation sequencing technology has enabled the comprehensive identification of recurrent genetic mutations, many with predictive power. Recurrent genetic mutations found in AML have been intensely studied from a cell intrinsic perspective leading to the genesis of multiple, recently approved targeted therapies including IDH1/2-mutant inhibitors and FLT3-ITD/-TKD inhibitors. However, there is a paucity of data on the effects of these targeted agents on the leukemia microenvironment, including the immune system. Recently, the phenomenal success of checkpoint inhibitors and CAR-T cells has re-ignited interest in understanding the mechanisms leading to immune dysregulation and suppression in leukemia, with the objective of harnessing the power of the immune system via novel immunotherapeutics. A paradigm has emerged that places crosstalk with the immune system at the crux of any effective therapy. Ongoing research will reveal how AML genetics inform the composition of the immune microenvironment paving the way for personalized immunotherapy.
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Affiliation(s)
- Lourdes M. Mendez
- Department of Medicine and Pathology, Cancer Research Institute, Beth Israel Deaconess Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Ryan R. Posey
- Department of Medicine and Pathology, Cancer Research Institute, Beth Israel Deaconess Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Pier Paolo Pandolfi
- Department of Medicine and Pathology, Cancer Research Institute, Beth Israel Deaconess Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
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22
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Oellerich T, Schneider C, Thomas D, Knecht KM, Buzovetsky O, Kaderali L, Schliemann C, Bohnenberger H, Angenendt L, Hartmann W, Wardelmann E, Rothenburger T, Mohr S, Scheich S, Comoglio F, Wilke A, Ströbel P, Serve H, Michaelis M, Ferreirós N, Geisslinger G, Xiong Y, Keppler OT, Cinatl J. Selective inactivation of hypomethylating agents by SAMHD1 provides a rationale for therapeutic stratification in AML. Nat Commun 2019; 10:3475. [PMID: 31375673 PMCID: PMC6677770 DOI: 10.1038/s41467-019-11413-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 07/08/2019] [Indexed: 02/08/2023] Open
Abstract
Hypomethylating agents decitabine and azacytidine are regarded as interchangeable in the treatment of acute myeloid leukemia (AML). However, their mechanisms of action remain incompletely understood, and predictive biomarkers for HMA efficacy are lacking. Here, we show that the bioactive metabolite decitabine triphosphate, but not azacytidine triphosphate, functions as activator and substrate of the triphosphohydrolase SAMHD1 and is subject to SAMHD1-mediated inactivation. Retrospective immunohistochemical analysis of bone marrow specimens from AML patients at diagnosis revealed that SAMHD1 expression in leukemic cells inversely correlates with clinical response to decitabine, but not to azacytidine. SAMHD1 ablation increases the antileukemic activity of decitabine in AML cell lines, primary leukemic blasts, and xenograft models. AML cells acquire resistance to decitabine partly by SAMHD1 up-regulation. Together, our data suggest that SAMHD1 is a biomarker for the stratified use of hypomethylating agents in AML patients and a potential target for the treatment of decitabine-resistant leukemia. In acute myeloid leukemia, hypomethylating agents decitabine and azacytidine are used interchangeably. Here, the authors show that the major metabolite of decitabine, but not azacytidine, is subject to SAMHD1 inactivation, highlighting SAMHD1 as a potential biomarker and therapeutic target
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Affiliation(s)
- Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,German Cancer Consortium/German Cancer Research Center, Heidelberg, 69120, Germany.,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, 60596, Germany
| | - Constanze Schneider
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, 60596, Germany.,Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany
| | - Dominique Thomas
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Olga Buzovetsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, 17475, Germany
| | | | | | - Linus Angenendt
- Department of Medicine A, University Hospital Münster, Münster, 48149, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute for Pathology, University Hospital Münster, Münster, 48149, Germany
| | - Eva Wardelmann
- Gerhard Domagk Institute for Pathology, University Hospital Münster, Münster, 48149, Germany
| | - Tamara Rothenburger
- Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany
| | - Sebastian Mohr
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Sebastian Scheich
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Federico Comoglio
- Department of Haematology, Cambridge Institute of Medical Research, Cambridge University, Cambridge, CB2 0XY, UK
| | - Anne Wilke
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center, Göttingen, 37075, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,German Cancer Consortium/German Cancer Research Center, Heidelberg, 69120, Germany.,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, 60596, Germany
| | - Martin Michaelis
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Nerea Ferreirós
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Gerd Geisslinger
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Translational Medicine and Pharmacology (TMP), Frankfurt, 60596, Germany
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Oliver T Keppler
- Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany. .,Max von Pettenkofer Institute, Virology, Faculty of Medicine, LMU München, Munich, 80336, Germany.
| | - Jindrich Cinatl
- Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany.
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23
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Dimopoulos K, Grønbæk K. Epigenetic therapy in hematological cancers. APMIS 2019; 127:316-328. [DOI: 10.1111/apm.12906] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/22/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Konstantinos Dimopoulos
- Department of Hematology Rigshospitalet University Hospital Copenhagen Copenhagen Denmark
- Biotech Research and Innovation Centre (BRIC) Novo Nordisk Foundation Center for Stem Cell Biology DanStem Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Kirsten Grønbæk
- Department of Hematology Rigshospitalet University Hospital Copenhagen Copenhagen Denmark
- Biotech Research and Innovation Centre (BRIC) Novo Nordisk Foundation Center for Stem Cell Biology DanStem Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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24
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Stomper J, Lübbert M. Can we predict responsiveness to hypomethylating agents in AML? Semin Hematol 2019; 56:118-124. [PMID: 30926087 DOI: 10.1053/j.seminhematol.2019.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 11/11/2022]
Abstract
DNA-hypomethylating agents (HMAs) were developed as nonintensive treatment alternatives to standard chemotherapy in older, unfit patients with acute myeloid leukemia and myelodysplastic syndrome. Given their distinct effects on the methylome and transcriptome of malignant cells compared to cytarabine (Ara-C) and other cytotoxic drugs not inhibiting DNA methyltransferases, it is of great interest to define their specific clinical ``signature.'' Here, we present and discuss clinical, genetic, and epigenetic predictors of responsiveness to HMAs. Indeed, mounting evidence supports the notion that HMAs are not "just another kind of low-dose Ara-C." Not only patient factors (age, performance status, comorbidities, etc.), blast counts, and early platelet response, but also adverse genetics (monosomal karyotype and/or a TP53 mutation) have predictive potential. Given the surprising-and initially counterintuitive-responses observed in patients with the latter features, these are subject to mechanistic studies to elucidate their as yet unresolved interaction with HMAs. Finally, other potential biomarkers for HMA response such as elevated fetal hemoglobin might also contribute to overcome the present challenges in predicting responsiveness to HMAs.
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Affiliation(s)
- Julia Stomper
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; German Cancer Research Consortium (DKTK), Freiburg, Germany.
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25
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Cazaly E, Saad J, Wang W, Heckman C, Ollikainen M, Tang J. Making Sense of the Epigenome Using Data Integration Approaches. Front Pharmacol 2019; 10:126. [PMID: 30837884 PMCID: PMC6390500 DOI: 10.3389/fphar.2019.00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/31/2019] [Indexed: 12/19/2022] Open
Abstract
Epigenetic research involves examining the mitotically heritable processes that regulate gene expression, independent of changes in the DNA sequence. Recent technical advances such as whole-genome bisulfite sequencing and affordable epigenomic array-based technologies, allow researchers to measure epigenetic profiles of large cohorts at a genome-wide level, generating comprehensive high-dimensional datasets that may contain important information for disease development and treatment opportunities. The epigenomic profile for a certain disease is often a result of the complex interplay between multiple genetic and environmental factors, which poses an enormous challenge to visualize and interpret these data. Furthermore, due to the dynamic nature of the epigenome, it is critical to determine causal relationships from the many correlated associations. In this review we provide an overview of recent data analysis approaches to integrate various omics layers to understand epigenetic mechanisms of complex diseases, such as obesity and cancer. We discuss the following topics: (i) advantages and limitations of major epigenetic profiling techniques, (ii) resources for standardization, annotation and harmonization of epigenetic data, and (iii) statistical methods and machine learning methods for establishing data-driven hypotheses of key regulatory mechanisms. Finally, we discuss the future directions for data integration that shall facilitate the discovery of epigenetic-based biomarkers and therapies.
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Affiliation(s)
- Emma Cazaly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Joseph Saad
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Wenyu Wang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Caroline Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Mathematics and Statistics, University of Turku, Turku, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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26
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Chen B, Tang H, Chen X, Zhang G, Wang Y, Xie X, Liao N. Transcriptomic analyses identify key differentially expressed genes and clinical outcomes between triple-negative and non-triple-negative breast cancer. Cancer Manag Res 2018; 11:179-190. [PMID: 30613165 PMCID: PMC6306052 DOI: 10.2147/cmar.s187151] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose There are significant differences in the biological behavior between triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC). In the present study, we identify key differential genes and clinical outcomes between TNBC and non-TNBC. Materials and methods Transcriptomic analyses used GEO datasets (GSE76275), gene ontology, KEGG pathway analysis and cBioPortal. Quantitative RT-PCR analysis (qRT-PCR) was used to validate the differentially expressed genes. We used the KM Plotter Online Tool and 240 patients with TNBC tissue microarray to assay the prognostic value of HORMAD1. Results The upregulated differentially expressed genes were enriched in transcription factor activity, sequence-specific DNA binding and nucleic acid binding transcription factor activity. Only 16 genes were upregulated when further screened for fold change >4-fold change. HORMAD1 and SOX8 exhibited high frequencies of change of greater than 10% (HORMAD1 was close to 20%). qRT-PCR results indicated that HORMAD1 and SOX8 mRNA levels were significantly upregulated in TNBC samples. In KM Plotter Online Tool, high HORMAD1 was associated with worse outcome. In our tissue microarray (including 240 TNBC tissues), IHC analysis revealed that 29.7% (55/240) of the tumor samples exhibited high HORMAD1 expression and 70.3% (185/240) of the tumor samples exhibited low HORMAD1 expression levels. Meanwhile, high HORMAD1 group has a bad prognosis. Conclusion The status of transcriptional activation is an important difference between TNBC and non-TNBC. HORMAD1 is a key differential gene associated with poor outcome in TNBC. Epigenetic therapy and agents targeting cancer/testis antigens might potentially help to customize therapies of TNBC.
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Affiliation(s)
- Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,
| | - Xi Chen
- Department of Anatomy, Hengyang Medical College, University of South China, Hengyang, China
| | - Guochun Zhang
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
| | - Yulei Wang
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
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27
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Marchal C, de Dieuleveult M, Saint-Ruf C, Guinot N, Ferry L, Olalla Saad ST, Lazarini M, Defossez PA, Miotto B. Depletion of ZBTB38 potentiates the effects of DNA demethylating agents in cancer cells via CDKN1C mRNA up-regulation. Oncogenesis 2018; 7:82. [PMID: 30310057 PMCID: PMC6182000 DOI: 10.1038/s41389-018-0092-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022] Open
Abstract
DNA methyltransferase inhibitor (DNMTi) treatments have been used for patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), and have shown promising beneficial effects in some other types of cancers. Here, we demonstrate that the transcriptional repressor ZBTB38 is a critical regulator of the cellular response to DNMTi. Treatments with 5-azacytidine, or its derivatives decitabine and zebularine, lead to down-regulation of ZBTB38 protein expression in cancer cells, in parallel with cellular damage. The depletion of ZBTB38 by RNA interference enhances the toxicity of DNMTi in cell lines from leukemia and from various solid tumor types. Further we observed that inactivation of ZBTB38 causes the up-regulation of CDKN1C mRNA, a previously described indirect target of DNMTi. We show that CDKN1C is a key actor of DNMTi toxicity in cells lacking ZBTB38. Finally, in patients with MDS a high level of CDKN1C mRNA expression before treatment correlates with a better clinical response to a drug regimen combining 5-azacytidine and histone deacetylase inhibitors. Collectively, our results suggest that the ZBTB38 protein is a target of DNMTi and that its depletion potentiates the toxicity of DNMT inhibitors in cancer cells, providing new opportunities to enhance the response to DNMT inhibitor therapies in patients with MDS and other cancers.
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Affiliation(s)
- Claire Marchal
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
| | - Maud de Dieuleveult
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Claude Saint-Ruf
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nadège Guinot
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Laure Ferry
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013, Paris, France
| | - Sara T Olalla Saad
- Hematology and Blood Transfusion Center-University of Campinas/Hemocentro-Unicamp, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, Brazil
| | - Mariana Lazarini
- Department of Biological Sciences, Federal University of São Paulo, Diadema, Brazil
| | - Pierre-Antoine Defossez
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013, Paris, France
| | - Benoit Miotto
- INSERM, U1016, Institut Cochin, Paris, France. .,CNRS, UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
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28
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Chen M, Nie J, Liu Y, Li X, Zhang Y, Brock MV, Feng K, Wu Z, Li X, Shi L, Li S, Guo M, Mei Q, Han W. Phase Ib/II study of safety and efficacy of low-dose decitabine-primed chemoimmunotherapy in patients with drug-resistant relapsed/refractory alimentary tract cancer. Int J Cancer 2018; 143:1530-1540. [PMID: 29663379 PMCID: PMC6099263 DOI: 10.1002/ijc.31531] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/19/2018] [Accepted: 03/29/2018] [Indexed: 12/15/2022]
Abstract
The pressing need for improved therapeutic outcomes provides a good rationale for identifying effective strategies for alimentary tract (AT) cancer treatment. The potential re-sensitivity property to chemo- and immunotherapy of low-dose decitabine has been evident both preclinically and in previous phase I trials. We conducted a phase Ib/II trial evaluating low-dose decitabine-primed chemoimmunotherapy in patients with drug-resistant relapsed/refractory (R/R) esophageal, gastric or colorectal cancers. Forty-five patients received either the 5-day decitabine treatment with subsequent readministration of the previously resistant chemotherapy (decitabine-primed chemotherapy, D-C cohort) or the aforementioned regimen followed by cytokine-induced killer cells therapy (D-C and cytokine-induced killer [CIK] cell treatment, D-C + CIK cohort) based on their treatment history. Grade 3 to 4 adverse events (AEs) were reported in 11 (24.4%) of 45 patients. All AEs were controllable, and no patient experienced a treatment-related death. The objective response rate (ORR) and disease control rate (DCR) were 24.44% and 82.22%, respectively, including two patients who achieved durable complete responses. Clinical response could be associated with treatment-free interval and initial surgical resection history. ORR and DCR reached 28% and 92%, respectively, in the D-C + CIK cohort. Consistently, the progression-free survival (PFS) of the D-C + CIK cohort compared favorably to the best PFS of the pre-resistant unprimed therapy (p = 0.0001). The toxicity and ORRs exhibited were non-significantly different between cancer types and treatment cohort. The safety and efficacy of decitabine-primed re-sensitization to chemoimmunotherapy is attractive and promising. These data warrant further large-scale evaluation of drug-resistant R/R AT cancer patients with advanced stage disease.
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MESH Headings
- Adenocarcinoma/drug therapy
- Adenocarcinoma/immunology
- Adenocarcinoma/secondary
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/immunology
- Carcinoma, Squamous Cell/secondary
- Cells, Cultured
- Cohort Studies
- Cytokine-Induced Killer Cells/drug effects
- Cytokine-Induced Killer Cells/immunology
- Cytokine-Induced Killer Cells/pathology
- Decitabine/therapeutic use
- Digestive System/drug effects
- Digestive System/immunology
- Digestive System/pathology
- Digestive System Neoplasms/drug therapy
- Digestive System Neoplasms/immunology
- Digestive System Neoplasms/pathology
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm
- Female
- Follow-Up Studies
- Humans
- Immunotherapy
- Lymphatic Metastasis
- Male
- Middle Aged
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/pathology
- Prognosis
- Salvage Therapy
- Survival Rate
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Affiliation(s)
- Meixia Chen
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Jing Nie
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Yang Liu
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Xiang Li
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Yan Zhang
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | | | - Kaichao Feng
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Zhiqiang Wu
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Xiaolei Li
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Lu Shi
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Suxia Li
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Mingzhou Guo
- Department of Gastroenterology and HepatologyChinese PLA General HospitalBeijingPeople's Republic of China
| | - Qian Mei
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Weidong Han
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
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29
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Yeon A, You S, Kim M, Gupta A, Park MH, Weisenberger DJ, Liang G, Kim J. Rewiring of cisplatin-resistant bladder cancer cells through epigenetic regulation of genes involved in amino acid metabolism. Theranostics 2018; 8:4520-4534. [PMID: 30214636 PMCID: PMC6134931 DOI: 10.7150/thno.25130] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/23/2018] [Indexed: 12/26/2022] Open
Abstract
Alterations in DNA methylation are important epigenetic markers in bladder cancer (BC). These epigenome modifications may drive the mechanisms of aggressive chemo-resistant BC. Clinicopathological biomarkers that indicate chemotherapeutic resistance are critical for better assessing treatment strategies for individual patients. Thus, in this study, we aimed to determine whether DNA methylation of certain metabolic enzymes is significantly altered in cisplatin-resistant BC cells. Methods: To characterize CpG methylation and nucleosome accessibility in cisplatin-resistant BC cells, the Illumina Infinium HM450 DNA methylation assay was performed. Perturbed gene expression was found to be associated with cisplatin resistance, and the biological roles of spermidine/spermine N1-acetyltransferase (SAT1) and argininosuccinate synthase 1 (ASS1) were further studied using qRT-PCR analysis and various cell biology assays, including western blot. Results:ASS1 and SAT1, genes for amino acid and polyamine metabolism catalysts, respectively, were found to be vastly hypermethylated, resulting in greatly downregulated expression. ASS1 expression is of particular interest because prior studies have demonstrated its potential association with BC stage and recurrence. In regard to chemoresistance, we found that aberrant expression or induced stimulation of SAT1 restored cisplatin sensitivity in the cell culture system. We also found that the addition of exogenous arginine deiminase through administration of ADI-PEG 20 (pegylated arginine deiminase) increased ASS1 expression and enhanced cisplatin's apoptotic effects. Conclusions: Our study demonstrates a novel mechanistic link between the epigenetic perturbation of SAT1 and ASS1 and cancer metabolism in cisplatin-resistant bladder cancer cells. These findings suggest potential utility of SAT1 and ASS1 as predictive biomarkers in re-sensitizing bladder cancer to chemotherapy and personalizing therapy.
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Affiliation(s)
- Austin Yeon
- Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Minhyung Kim
- Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amit Gupta
- Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Myung Hee Park
- National Institute of Dental and Craniofacial Research, National Institutes of Health Bethesda, MD, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, University of Southern California
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jayoung Kim
- Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Departments of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, University of California Los Angeles, CA, USA
- Department of Urology, Ga Cheon University College of Medicine, Incheon, Republic of Korea
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30
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Stahl M, DeVeaux M, Montesinos P, Itzykson R, Ritchie EK, Sekeres MA, Barnard J, Podoltsev NA, Brunner A, Komrokji RS, Bhatt VR, Al-Kali A, Cluzeau T, Santini V, Roboz GJ, Fenaux P, Litzow M, Fathi AT, Perreault S, Kim TK, Prebet T, Vey N, Verma V, Germing U, Bergua J, Serrano J, Gore SD, Zeidan AM. Performance of the Medical Research Council (MRC) and the Leukemia Research Foundation (LRF) score in predicting survival benefit with hypomethylating agent use in patients with relapsed or refractory acute myeloid leukemia. Leuk Lymphoma 2018; 60:246-249. [PMID: 29963936 DOI: 10.1080/10428194.2018.1468893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Maximilian Stahl
- a Department of Internal Medicine, Section of Hematology, Yale University School of Medicine , New Haven , CT, USA
| | - Michelle DeVeaux
- b Department of Biostatistics, Yale School of Public Health , New Haven , CT, USA
| | - Pau Montesinos
- c Department of Medicine , University of Valencia, Hospital Universitario y Politécnico La Fe , Valencia, CIBERONC, Instituto III , Madrid , Spain
| | - Raphaël Itzykson
- d Department of Hematology/Oncology, Saint-Louis Hospital, University of Paris 7 , France
| | - Ellen K Ritchie
- e Division of Hematology and Oncology, Weill Cornell Medicine and The New York Presbyterian Hospital , New York , NY , USA
| | | | - John Barnard
- f Leukemia Program Cleveland Clinic , Cleveland , OH , USA
| | - Nikolai A Podoltsev
- a Department of Internal Medicine, Section of Hematology, Yale University School of Medicine , New Haven , CT, USA
| | - Andrew Brunner
- g Massachusetts General Hospital Cancer Center Harvard Medical School , Boston , MA , USA
| | - Rami S Komrokji
- h Department of Malignant Hematology , Moffitt Cancer Center and Research Institute , Tampa , FL , USA
| | - Vijaya R Bhatt
- i Division of Hematology/Oncology, University of Nebraska Medical Center , Omaha , NE , USA
| | | | - Thomas Cluzeau
- k Cote d'Azur University, Nice Sophia Antipolis University, CHU of Nice , Nice , France
| | - Valeria Santini
- l Division of Hematology , University of Florence , Florence , Italy
| | - Gail J Roboz
- e Division of Hematology and Oncology, Weill Cornell Medicine and The New York Presbyterian Hospital , New York , NY , USA
| | - Pierre Fenaux
- d Department of Hematology/Oncology, Saint-Louis Hospital, University of Paris 7 , France
| | | | - Amir T Fathi
- g Massachusetts General Hospital Cancer Center Harvard Medical School , Boston , MA , USA
| | - Sarah Perreault
- m Department of Pharmacy , Yale New Haven Hospital , New Haven , CT , USA
| | - Tae Kon Kim
- a Department of Internal Medicine, Section of Hematology, Yale University School of Medicine , New Haven , CT, USA
| | - Thomas Prebet
- a Department of Internal Medicine, Section of Hematology, Yale University School of Medicine , New Haven , CT, USA
| | - Norbert Vey
- n Department of Hematology , Institut Paoli Calmettes , Marseille , France
| | - Vivek Verma
- i Division of Hematology/Oncology, University of Nebraska Medical Center , Omaha , NE , USA
| | - Ulrich Germing
- o Department of Hematology , Oncology and Clinical Immunology , Heinrich-Heine-University Duesseldorf , Duesseldorf , Germany
| | - Juan Bergua
- p Hospital San Pedro Alcántara , Cáceres , Spain
| | - Josefina Serrano
- q Division of Hematology/Oncology, University Hospital Reina Sofia , Cordoba , Spain
| | - Steven D Gore
- a Department of Internal Medicine, Section of Hematology, Yale University School of Medicine , New Haven , CT, USA
| | - Amer M Zeidan
- a Department of Internal Medicine, Section of Hematology, Yale University School of Medicine , New Haven , CT, USA
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31
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DNA Methyltransferase Inhibitors in Myeloid Cancer: Clonal Eradication or Clonal Differentiation? ACTA ACUST UNITED AC 2018; 23:277-285. [PMID: 28926428 DOI: 10.1097/ppo.0000000000000282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA methyltransferase inhibitors, so-called hypomethylating agents (HMAs), are the only drugs approved for the treatment of higher-risk myelodysplastic syndromes and are widely used in this context. However, it is still unclear why some patients respond to HMAs, whereas others do not. Recent sequencing efforts have identified molecular disease entities that may be specifically sensitive to these drugs, and many attempts are being made to clarify how HMAs affect the malignant clone during treatment. Here, we review the most recent data on the clinical effects of HMAs in myeloid malignancies.
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32
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Yu J, Qin B, Moyer AM, Nowsheen S, Liu T, Qin S, Zhuang Y, Liu D, Lu SW, Kalari KR, Visscher DW, Copland JA, McLaughlin SA, Moreno-Aspitia A, Northfelt DW, Gray RJ, Lou Z, Suman VJ, Weinshilboum R, Boughey JC, Goetz MP, Wang L. DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine. J Clin Invest 2018; 128:2376-2388. [PMID: 29708513 DOI: 10.1172/jci97924] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/13/2018] [Indexed: 01/22/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with poor prognosis that lacks targeted therapies, especially in patients with chemotherapy-resistant disease. Since DNA methylation-induced silencing of tumor suppressors is common in cancer, reversal of promoter DNA hypermethylation by 5-aza-2'-deoxycytidine (decitabine), an FDA-approved DNA methyltransferase (DNMT) inhibitor, has proven effective in treating hematological neoplasms. However, its antitumor effect varies in solid tumors, stressing the importance of identifying biomarkers predictive of therapeutic response. Here, we focused on the identification of biomarkers to select decitabine-sensitive TNBC through increasing our understanding of the mechanism of decitabine action. We showed that protein levels of DNMTs correlated with response to decitabine in patient-derived xenograft (PDX) organoids originating from chemotherapy-sensitive and -resistant TNBCs, suggesting DNMT levels as potential biomarkers of response. Furthermore, all 3 methytransferases, DNMT1, DNMT3A, and DNMT3B, were degraded following low-concentration, long-term decitabine treatment both in vitro and in vivo. The DNMT proteins could be ubiquitinated by the E3 ligase, TNF receptor-associated factor 6 (TRAF6), leading to lysosome-dependent protein degradation. Depletion of TRAF6 blocked decitabine-induced DNMT degradation, conferring resistance to decitabine. Our study suggests a potential mechanism of regulating DNMT protein degradation and DNMT levels as response biomarkers for DNMT inhibitors in TNBCs.
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Affiliation(s)
- Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Bo Qin
- Department of Molecular Pharmacology and Experimental Therapeutics.,Department of Oncology, and
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Somaira Nowsheen
- Department of Oncology, and.,Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine and the Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota, USA
| | - Tongzheng Liu
- Department of Oncology, and.,Jinan University Institute of Tumor Pharmacology, Guangzhou, China
| | - Sisi Qin
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Yongxian Zhuang
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Duan Liu
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Shijia W Lu
- Department of Molecular Pharmacology and Experimental Therapeutics.,Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel W Visscher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | | - Richard J Gray
- Department of Surgery, Mayo Clinic, Scottsdale, Arizona, USA
| | | | - Vera J Suman
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics.,Department of Oncology, and
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics
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33
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RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun 2018; 9:1163. [PMID: 29563491 PMCID: PMC5862959 DOI: 10.1038/s41467-018-03513-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 01/26/2018] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
The roles of RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) in lineage-associated chromatin organization and drug response/resistance are unclear. Here we demonstrate that the RCMTs, namely NSUN3 and DNMT2, directly bind hnRNPK, a conserved RNA-binding protein. hnRNPK interacts with the lineage-determining transcription factors (TFs), GATA1 and SPI1/PU.1, and with CDK9/P-TEFb to recruit RNA-polymerase-II at nascent RNA, leading to formation of 5-Azacitidine (5-AZA)-sensitive chromatin structure. In contrast, NSUN1 binds BRD4 and RNA-polymerase-II to form an active chromatin structure that is insensitive to 5-AZA, but hypersensitive to the BRD4 inhibitor JQ1 and to the downregulation of NSUN1 by siRNAs. Both 5-AZA-resistant leukaemia cell lines and clinically 5-AZA-resistant myelodysplastic syndrome and acute myeloid leukaemia specimens have a significant increase in RNA:m5C and NSUN1-/BRD4-associated active chromatin. This study reveals novel RNA:m5C/RCMT-mediated chromatin structures that modulate 5-AZA response/resistance in leukaemia cells, and hence provides a new insight into treatment of leukaemia. Resistance to chemotherapy is a serious issue that can be influenced by RNA epigenetics and chromatin structure. Here, the authors show in leukaemia cells that RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) mediate chromatin structures that can modulate 5-Azacitidine response and resistance.
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34
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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35
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Zeidler R, de Freitas Soares BL, Bader A, Giri S. Molecular epigenetic targets for liver diseases: current challenges and future prospects. Drug Discov Today 2017; 22:1620-1636. [DOI: 10.1016/j.drudis.2017.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 06/28/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
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36
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XPLN is modulated by HDAC inhibitors and negatively regulates SPARC expression by targeting mTORC2 in human lung fibroblasts. Pulm Pharmacol Ther 2017; 44:61-69. [DOI: 10.1016/j.pupt.2017.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/12/2017] [Indexed: 11/19/2022]
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37
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Sato T, Issa JPJ, Kropf P. DNA Hypomethylating Drugs in Cancer Therapy. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026948. [PMID: 28159832 DOI: 10.1101/cshperspect.a026948] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aberrant DNA methylation is a critically important modification in cancer cells, which, through promoter and enhancer DNA methylation changes, use this mechanism to activate oncogenes and silence of tumor-suppressor genes. Targeting DNA methylation in cancer using DNA hypomethylating drugs reprograms tumor cells to a more normal-like state by affecting multiple pathways, and also sensitizes these cells to chemotherapy and immunotherapy. The first generation hypomethylating drugs azacitidine and decitabine are routinely used for the treatment of myeloid leukemias and a next-generation drug (guadecitabine) is currently in clinical trials. This review will summarize preclinical and clinical data on DNA hypomethylating drugs as a cancer therapy.
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Affiliation(s)
- Takahiro Sato
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140.,Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania 19111
| | - Patricia Kropf
- Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania 19111
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38
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Stahl M, Zeidan AM. Hypomethylating agents in combination with histone deacetylase inhibitors in higher risk myelodysplastic syndromes: Is there a light at the end of the tunnel? Cancer 2017; 123:911-914. [PMID: 28094843 DOI: 10.1002/cncr.30532] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 01/29/2023]
Affiliation(s)
- Maximilian Stahl
- Section of Hematology, Department of Internal Medicine, Yale University and Yale Cancer Center, New Haven, Connecticut
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University and Yale Cancer Center, New Haven, Connecticut
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39
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Daneshpajooh M, Bacos K, Bysani M, Bagge A, Ottosson Laakso E, Vikman P, Eliasson L, Mulder H, Ling C. HDAC7 is overexpressed in human diabetic islets and impairs insulin secretion in rat islets and clonal beta cells. Diabetologia 2017; 60:116-125. [PMID: 27796421 PMCID: PMC6518079 DOI: 10.1007/s00125-016-4113-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/30/2016] [Indexed: 12/19/2022]
Abstract
AIMS/HYPOTHESIS Pancreatic beta cell dysfunction is a prerequisite for the development of type 2 diabetes. Histone deacetylases (HDACs) may affect pancreatic endocrine function and glucose homeostasis through alterations in gene regulation. Our aim was to investigate the role of HDAC7 in human and rat pancreatic islets and clonal INS-1 beta cells (INS-1 832/13). METHODS To explore the role of HDAC7 in pancreatic islets and clonal beta cells, we used RNA sequencing, mitochondrial functional analyses, microarray techniques, and HDAC inhibitors MC1568 and trichostatin A. RESULTS Using RNA sequencing, we found increased HDAC7 expression in human pancreatic islets from type 2 diabetic compared with non-diabetic donors. HDAC7 expression correlated negatively with insulin secretion in human islets. To mimic the situation in type 2 diabetic islets, we overexpressed Hdac7 in rat islets and clonal beta cells. In both, Hdac7 overexpression resulted in impaired glucose-stimulated insulin secretion. Furthermore, it reduced insulin content, mitochondrial respiration and cellular ATP levels in clonal beta cells. Overexpression of Hdac7 also led to changes in the genome-wide gene expression pattern, including increased expression of Tcf7l2 and decreased expression of gene sets regulating DNA replication and repair as well as nucleotide metabolism. In accordance, Hdac7 overexpression reduced the number of beta cells owing to enhanced apoptosis. Finally, we found that inhibiting HDAC7 activity with pharmacological inhibitors or small interfering RNA-mediated knockdown restored glucose-stimulated insulin secretion in beta cells that were overexpressing Hdac7. CONCLUSIONS/INTERPRETATION Taken together, these results indicate that increased HDAC7 levels caused beta cell dysfunction and may thereby contribute to defects seen in type 2 diabetic islets. Our study supports HDAC7 inhibitors as a therapeutic option for the treatment of type 2 diabetes.
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Affiliation(s)
- Mahboubeh Daneshpajooh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, 20502, Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, 20502, Malmö, Sweden
| | - Madhusudhan Bysani
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, 20502, Malmö, Sweden
| | - Annika Bagge
- Molecular Metabolism Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Emilia Ottosson Laakso
- Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Petter Vikman
- Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Lena Eliasson
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Hindrik Mulder
- Molecular Metabolism Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, 20502, Malmö, Sweden.
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Drusbosky L, Medina C, Martuscello R, Hawkins KE, Chang M, Lamba JK, Vali S, Kumar A, Singh NK, Abbasi T, Sekeres MA, Mallo M, Sole F, Bejar R, Cogle CR. Computational drug treatment simulations on projections of dysregulated protein networks derived from the myelodysplastic mutanome match clinical response in patients. Leuk Res 2017; 52:1-7. [DOI: 10.1016/j.leukres.2016.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 01/19/2023]
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41
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Targeting the histone methyltransferase G9a activates imprinted genes and improves survival of a mouse model of Prader-Willi syndrome. Nat Med 2016; 23:213-222. [PMID: 28024084 DOI: 10.1038/nm.4257] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
Prader-Willi syndrome (PWS) is an imprinting disorder caused by a deficiency of paternally expressed gene(s) in the 15q11-q13 chromosomal region. The regulation of imprinted gene expression in this region is coordinated by an imprinting center (PWS-IC). In individuals with PWS, genes responsible for PWS on the maternal chromosome are present, but repressed epigenetically, which provides an opportunity for the use of epigenetic therapy to restore expression from the maternal copies of PWS-associated genes. Through a high-content screen (HCS) of >9,000 small molecules, we discovered that UNC0638 and UNC0642-two selective inhibitors of euchromatic histone lysine N-methyltransferase-2 (EHMT2, also known as G9a)-activated the maternal (m) copy of candidate genes underlying PWS, including the SnoRNA cluster SNORD116, in cells from humans with PWS and also from a mouse model of PWS carrying a paternal (p) deletion from small nuclear ribonucleoprotein N (Snrpn (S)) to ubiquitin protein ligase E3A (Ube3a (U)) (mouse model referred to hereafter as m+/pΔS-U). Both UNC0642 and UNC0638 caused a selective reduction of the dimethylation of histone H3 lysine 9 (H3K9me2) at PWS-IC, without changing DNA methylation, when analyzed by bisulfite genomic sequencing. This indicates that histone modification is essential for the imprinting of candidate genes underlying PWS. UNC0642 displayed therapeutic effects in the PWS mouse model by improving the survival and the growth of m+/pΔS-U newborn pups. This study provides the first proof of principle for an epigenetics-based therapy for PWS.
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Pechalrieu D, Etievant C, Arimondo PB. DNA methyltransferase inhibitors in cancer: From pharmacology to translational studies. Biochem Pharmacol 2016; 129:1-13. [PMID: 27956110 DOI: 10.1016/j.bcp.2016.12.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
DNA methylation is a mammalian epigenetic mark that participates to define where and when genes are expressed, both in normal cells and in the context of diseases. Like other epigenetic marks, it is reversible and can be modulated by chemical agents. Because it plays an important role in cancer by silencing certain genes, such as tumour suppressor genes, it is a promising therapeutic target. Two compounds are already approved to treat haematological cancers, and many efforts have been carried out to discover new molecules that inhibit DNA methyltransferases, the enzymes responsible for DNA methylation. Here, we analyse the molecular mechanisms and cellular pharmacology of these inhibitors, pointing out the necessity for new pharmacological models and paradigms. The parameters of pharmacological responses need to be redefined: the aim is cellular reprogramming rather than general cytotoxicity. Thus, "epigenetic" rather than cytotoxic dosages are defined. Another issue is the delay of the response: cellular reprogramming can take several generations to produce observable phenotypes. Is this compatible with laboratory scale experiments? Finally, it is important to consider the specificity for cancer cells compared to normal cells and the appearance of resistance. We also discuss different techniques that are used and the selection of pharmacological models.
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Affiliation(s)
- Dany Pechalrieu
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Chantal Etievant
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Paola B Arimondo
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France.
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43
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Lübbert M, Ihorst G, Sander PN, Bogatyreva L, Becker H, Wijermans PW, Suciu S, Bissé E, Claus R. Elevated fetal haemoglobin is a predictor of better outcome in MDS/AML patients receiving 5-aza-2'-deoxycytidine (Decitabine). Br J Haematol 2016; 176:609-617. [PMID: 27905102 DOI: 10.1111/bjh.14463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/31/2016] [Indexed: 01/20/2023]
Abstract
Although azanucleoside DNA-hypomethylating agents (HMAs) are routinely used for the treatment of myelodysplastic syndrome/acute myeloid leukaemia (MDS/AML), very few outcome predictors have been established. Expression of the β-like globin gene locus is tightly regulated by DNA methylation, is HMA-sensitive in vitro, and fetal haemoglobin (HbF) expression is under study as a potential biomarker for response of MDS patients to azacitidine. We determined HbF expression in 16 MDS and 36 AML patients receiving decitabine (DAC). Pre-treatment HbF was already elevated (>1·0% of total haemoglobin) in 7/16 and 12/36 patients, and HbF was induced by DAC in 81%/54% of MDS/AML patients, respectively. Elevated pre-treatment HbF was associated with longer median overall survival (OS): 26·6 vs. 8·6 months for MDS (hazard ratio [HR] 8·56, 95% confidence interval [CI] 1·74-42·49, P = 0·008, with similarly longer progression-free and AML-free survival), and 10·0 vs. 2·9 months OS for AML (HR 3·01, 95% CI 1·26-7·22, P = 0·014). In a multivariate analysis, the prognostic value of HbF was retained. Time-dependent Cox models revealed that the prognostic value of treatment-induced HbF induction was inferior to that of pre-treatment HbF. In conclusion, we provide first evidence for in vivo HbF induction by DAC in MDS/AML, and demonstrate prognostic value of elevated pre-treatment HbF, warranting prospective, randomized studies.
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Affiliation(s)
- Michael Lübbert
- Division of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gabriele Ihorst
- Clinical Trials Unit, University of Freiburg Medical Centre, Freiburg, Germany
| | - Philipp N Sander
- Division of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ljudmila Bogatyreva
- Division of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Centre - University of Freiburg, Freiburg, Germany
| | - Heiko Becker
- Division of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | | | - Emmanuel Bissé
- Institute for Laboratory Diagnostics, University of Freiburg, Freiburg, Germany
| | - Rainer Claus
- Division of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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44
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Selli C, Dixon JM, Sims AH. Accurate prediction of response to endocrine therapy in breast cancer patients: current and future biomarkers. Breast Cancer Res 2016; 18:118. [PMID: 27903276 PMCID: PMC5131493 DOI: 10.1186/s13058-016-0779-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Approximately 70% of patients have breast cancers that are oestrogen receptor alpha positive (ER+) and are therefore candidates for endocrine treatment. Many of these patients relapse in the years during or following completion of adjuvant endocrine therapy. Thus, many ER+ cancers have primary resistance or develop resistance to endocrine therapy during treatment. Recent improvements in our understanding of how tumours evolve during treatment with endocrine agents have identified both changes in gene expression and mutational profiles, in the primary cancer as well as in circulating tumour cells. Analysing these changes has the potential to improve the prediction of which specific patients will respond to endocrine treatment. Serially profiled biopsies during treatment in the neoadjuvant setting offer promise for accurate and early prediction of response to both current and novel drugs and allow investigation of mechanisms of resistance. In addition, recent advances in monitoring tumour evolution through non-invasive (liquid) sampling of circulating tumour cells and cell-free tumour DNA may provide a method to detect resistant clones and allow implementation of personalized treatments for metastatic breast cancer patients. This review summarises current and future biomarkers and signatures for predicting response to endocrine treatment, and discusses the potential for using approved drugs and novel agents to improve outcomes. Increased prediction accuracy is likely to require sequential sampling, utilising preoperative or neoadjuvant treatment and/or liquid biopsies and an improved understanding of both the dynamics and heterogeneity of breast cancer.
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Affiliation(s)
- Cigdem Selli
- Applied Bioinformatics of Cancer, Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Edinburgh, EH4 2XR, UK.,Department of Pharmacology, Faculty of Pharmacy, Ege University, Izmir, 35050, Turkey
| | - J Michael Dixon
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, EH4 2XR, UK
| | - Andrew H Sims
- Applied Bioinformatics of Cancer, Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Edinburgh, EH4 2XR, UK.
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45
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Kottakis F, Nicolay BN, Roumane A, Karnik R, Gu H, Nagle JM, Boukhali M, Hayward MC, Li YY, Chen T, Liesa M, Hammerman PS, Wong KK, Hayes DN, Shirihai OS, Dyson NJ, Haas W, Meissner A, Bardeesy N. LKB1 loss links serine metabolism to DNA methylation and tumorigenesis. Nature 2016; 539:390-395. [PMID: 27799657 PMCID: PMC5988435 DOI: 10.1038/nature20132] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
Intermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that is central to oncogenic transformation downstream of the liver kinase B1 (LKB1, also known as STK11) tumour suppressor, an integrator of nutrient availability, metabolism and growth. By developing genetically engineered mouse models and primary pancreatic epithelial cells, and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation is fuelled by pronounced mTOR-dependent induction of the serine-glycine-one-carbon pathway coupled to S-adenosylmethionine generation. At the same time, DNA methyltransferases are upregulated, leading to elevation in DNA methylation with particular enrichment at retrotransposon elements associated with their transcriptional silencing. Correspondingly, LKB1 deficiency sensitizes cells and tumours to inhibition of serine biosynthesis and DNA methylation. Thus, we define a hypermetabolic state that incites changes in the epigenetic landscape to support tumorigenic growth of LKB1-mutant cells, while resulting in potential therapeutic vulnerabilities.
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Affiliation(s)
- Filippos Kottakis
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Brandon N. Nicolay
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Ahlima Roumane
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Rahul Karnik
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Julia M. Nagle
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Myriam Boukhali
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | | | - Yvonne Y. Li
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ting Chen
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Marc Liesa
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Peter S. Hammerman
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kwok Kin Wong
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - D. Neil Hayes
- UNC, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Orian S. Shirihai
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Nicholas J. Dyson
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Wilhelm Haas
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nabeel Bardeesy
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
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46
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Beck A, Eberherr C, Hagemann M, Cairo S, Häberle B, Vokuhl C, von Schweinitz D, Kappler R. Connectivity map identifies HDAC inhibition as a treatment option of high-risk hepatoblastoma. Cancer Biol Ther 2016; 17:1168-1176. [PMID: 27635950 DOI: 10.1080/15384047.2016.1235664] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Hepatoblastoma (HB) is the most common liver tumor of childhood, usually occurring in children under the age of 3 y. The prognosis of patients presenting with distant metastasis, vascular invasion and advanced tumor stages remains poor and children that do survive often face severe late effects from the aggressive chemotherapy regimen. To identify potential new therapeutics for high risk HB we used a 1,000-gene expression signature as input for a Connectivity Map (CMap) analysis, which predicted histone deacetylase (HDAC) inhibitors as a promising therapy option. Subsequent expression analysis of primary HB and HB cell lines revealed a general overexpression of HDAC1 and HDAC2, which has been suggested to be predictive for the efficacy of HDAC inhibition. Accordingly, treatment of HB cells with the HDAC inhibitors SAHA and MC1568 resulted in a potent reduction of cell viability, induction of apoptosis, reactivation of epigenetically suppressed tumor suppressor genes, and the reversion of the 16-gene HB classifier toward the more favorable expression signature. Most importantly, the combination of HDAC inhibitors and cisplatin - a major chemotherapeutic agent of HB treatment - revealed a strong synergistic effect, even at significantly reduced doses of cisplatin. Our findings suggest that HDAC inhibitors skew HB cells toward a more favorable prognostic phenotype through changes in gene expression, thus indicating a targeted molecular mechanism that seems to enhance the anti-proliferative effects of conventional chemotherapy. Thus, adding HDAC inhibitors to the treatment regimen of high risk HB could potentially improve outcomes and reduce severe late effects.
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Affiliation(s)
- Alexander Beck
- a Department of Pediatric Surgery, Dr. von Hauner Children's Hospital , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Corinna Eberherr
- a Department of Pediatric Surgery, Dr. von Hauner Children's Hospital , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Michaela Hagemann
- a Department of Pediatric Surgery, Dr. von Hauner Children's Hospital , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Stefano Cairo
- b XenTech , 4 rue Pierre Fontaine , Evry , France.,c University of Ferrara, LTTA Center, Department of Morphology , Surgery and Experimental Medicine, Via Fossato di Mortara , Ferrara , Italy
| | - Beate Häberle
- a Department of Pediatric Surgery, Dr. von Hauner Children's Hospital , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Christian Vokuhl
- d Institute of Paidopathology, Pediatric Tumor Registry, Christian-Albrechts-University Kiel , Kiel , Germany
| | - Dietrich von Schweinitz
- a Department of Pediatric Surgery, Dr. von Hauner Children's Hospital , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Roland Kappler
- a Department of Pediatric Surgery, Dr. von Hauner Children's Hospital , Ludwig-Maximilians-University Munich , Munich , Germany
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47
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Glenthøj A, Ørskov AD, Hansen JW, Hadrup SR, O'Connell C, Grønbæk K. Immune Mechanisms in Myelodysplastic Syndrome. Int J Mol Sci 2016; 17:ijms17060944. [PMID: 27314337 PMCID: PMC4926477 DOI: 10.3390/ijms17060944] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 12/12/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a spectrum of diseases, characterized by debilitating cytopenias and a propensity of developing acute myeloid leukemia. Comprehensive sequencing efforts have revealed a range of mutations characteristic, but not specific, of MDS. Epidemiologically, autoimmune diseases are common in patients with MDS, fueling hypotheses of common etiological mechanisms. Both innate and adaptive immune pathways are overly active in the hematopoietic niche of MDS. Although supportive care, growth factors, and hypomethylating agents are the mainstay of MDS treatment, some patients—especially younger low-risk patients with HLA-DR15 tissue type—demonstrate impressive response rates after immunosuppressive therapy. This is in contrast to higher-risk MDS patients, where several immune activating treatments, such as immune checkpoint inhibitors, are in the pipeline. Thus, the dual role of immune mechanisms in MDS is challenging, and rigorous translational studies are needed to establish the value of immune manipulation as a treatment of MDS.
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Affiliation(s)
- Andreas Glenthøj
- Epi-/Genome Laboratory, Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark.
| | - Andreas Due Ørskov
- Epi-/Genome Laboratory, Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark.
| | - Jakob Werner Hansen
- Epi-/Genome Laboratory, Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark.
| | - Sine Reker Hadrup
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Frederiksberg 1870, Denmark.
| | - Casey O'Connell
- Jane Anne Nohl Division of Hematology, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA.
- Stand up to Cancer Epigenetics Dream Team, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
| | - Kirsten Grønbæk
- Epi-/Genome Laboratory, Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark.
- Stand up to Cancer Epigenetics Dream Team, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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48
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Mechanistic insight into the aberrant silencing of the keratin 13 gene in oral squamous cell carcinoma cells. J Oral Biosci 2016. [DOI: 10.1016/j.job.2016.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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49
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Bell JSK, Kagey JD, Barwick BG, Dwivedi B, McCabe MT, Kowalski J, Vertino PM. Factors affecting the persistence of drug-induced reprogramming of the cancer methylome. Epigenetics 2016; 11:273-87. [PMID: 27082926 DOI: 10.1080/15592294.2016.1158364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aberrant DNA methylation is a critical feature of cancer. Epigenetic therapy seeks to reverse these changes to restore normal gene expression. DNA demethylating agents, including 5-aza-2'-deoxycytidine (DAC), are currently used to treat certain leukemias, and can sensitize solid tumors to chemotherapy and immunotherapy. However, it has been difficult to pin the clinical efficacy of these agents to specific demethylation events, and the factors that contribute to the durability of response remain largely unknown. Here we examined the genome-wide kinetics of DAC-induced DNA demethylation and subsequent remethylation after drug withdrawal in breast cancer cells. We find that CpGs differ in both their susceptibility to demethylation and propensity for remethylation after drug removal. DAC-induced demethylation was most apparent at CpGs with higher initial methylation levels and further from CpG islands. Once demethylated, such sites exhibited varied remethylation potentials. The most rapidly remethylating CpGs regained >75% of their starting methylation within a month of drug withdrawal. These sites had higher pretreatment methylation levels, were enriched in gene bodies, marked by H3K36me3, and tended to be methylated in normal breast cells. In contrast, a more resistant class of CpG sites failed to regain even 20% of their initial methylation after 3 months. These sites had lower pretreatment methylation levels, were within or near CpG islands, marked by H3K79me2 or H3K4me2/3, and were overrepresented in sites that become aberrantly hypermethylated in breast cancers. Thus, whereas DAC-induced demethylation affects both endogenous and aberrantly methylated sites, tumor-specific hypermethylation is more slowly regained, even as normal methylation promptly recovers. Taken together, these data suggest that the durability of DAC response is linked to its selective ability to stably reset at least a portion of the cancer methylome.
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Affiliation(s)
- Joshua S K Bell
- a Graduate Program in Genetics and Molecular Biology , Emory University , Atlanta , GA , USA
| | - Jacob D Kagey
- a Graduate Program in Genetics and Molecular Biology , Emory University , Atlanta , GA , USA
| | - Benjamin G Barwick
- a Graduate Program in Genetics and Molecular Biology , Emory University , Atlanta , GA , USA
| | - Bhakti Dwivedi
- b Winship Cancer Institute , Emory University , Atlanta , GA , USA
| | - Michael T McCabe
- c Department of Radiation Oncology , Emory University , Atlanta , GA , USA
| | - Jeanne Kowalski
- b Winship Cancer Institute , Emory University , Atlanta , GA , USA.,d Department of Biostatistics and Bioinformatics , Emory University , Atlanta , GA , USA
| | - Paula M Vertino
- b Winship Cancer Institute , Emory University , Atlanta , GA , USA.,c Department of Radiation Oncology , Emory University , Atlanta , GA , USA
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50
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Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Nat Commun 2016; 7:10767. [PMID: 26908133 PMCID: PMC4770084 DOI: 10.1038/ncomms10767] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/19/2016] [Indexed: 12/18/2022] Open
Abstract
The cytidine analogues azacytidine and 5-aza-2'-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In this study, we address this question in chronic myelomonocytic leukaemia. We describe a comprehensive analysis of the mutational landscape of these tumours, combining whole-exome and whole-genome sequencing. We identify an average of 14±5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of three mutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect.
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