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Paudel BB, Tan SF, Fox TE, Ung J, Golla U, Shaw JJP, Dunton W, Lee I, Fares WA, Patel S, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Feith DJ, Claxton D, Janes KA, Loughran TP. Acute myeloid leukemia stratifies as 2 clinically relevant sphingolipidomic subtypes. Blood Adv 2024; 8:1137-1142. [PMID: 38170742 PMCID: PMC10909712 DOI: 10.1182/bloodadvances.2023010535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Todd E. Fox
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Microbiology/Immunology/Cancer Biology, University of Virginia, Charlottesville, VA
| | - Upendarrao Golla
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
| | - Jeremy J. P. Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Wendy Dunton
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Irene Lee
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX
| | - Wisam A. Fares
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Satyam Patel
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Aaron D. Viny
- Department of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Herbert Irving Comprehensive Cancer Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
| | - Brian M. Barth
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK
| | - Martin S. Tallman
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Myles Cabot
- Department of Biochemistry & Molecular Biology, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
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2
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Hu X, Logan JG, Kwon Y, Lima JAC, Jacobs DR, Duprez D, Brumback L, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Blackwell TW, Papanicolaou G, Mitchell GF, Rich SS, Rotter JI, Van Den Berg DJ, Chirinos JA, Hughes TM, Garrett-Bakelman FE, Manichaikul A. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. Sci Rep 2023; 13:17680. [PMID: 37848499 PMCID: PMC10582077 DOI: 10.1038/s41598-023-44806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
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Affiliation(s)
- Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jeongok G Logan
- School of Nursing, University of Virginia, Charlottesville, VA, USA
| | - Younghoon Kwon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joao A C Lima
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David R Jacobs
- Division of Epidemiology, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Duprez
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, USA
| | - Lyndia Brumback
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, NC, USA
| | - Russell P Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Thomas W Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David J Van Den Berg
- Department of Preventive Medicine and Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julio A Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy M Hughes
- Department of Internal Medicine - Section of Gerontology and Geriatric Medicine, and Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, Department of Medicine, University of Virginia, 1340 Jefferson Park Ave., Pinn hall 6054, Charlottesville, VA, 22908, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
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3
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Neelamraju Y, Gjini E, Chhangawala S, Fan H, He S, Jing CB, Nguyen AT, Prajapati S, Sheridan C, Houvras Y, Melnick A, Look AT, Garrett-Bakelman FE. Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome. Front Hematol 2023; 2:1235170. [PMID: 37937078 PMCID: PMC10629367 DOI: 10.3389/frhem.2023.1235170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Introduction Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (tet2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously, we reported a stable zebrafish line with a loss-of-function mutation in the tet2 gene. The tet2m/m-mutant zebrafish developed a pre-MDS state with kidney marrow dysplasia, but normal circulating blood counts by 11 months of age and accompanying anemia, signifying the onset of MDS, by 24 months of age. Methods In the current study, we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 and 15 months of age and conducted enhanced reduced representation of bisulfite sequencing (ERRBS) and bulk RNA-seq to measure changes in DNA methylation and gene expression of hematopoietic stem and progenitor cells (HSPCs). Results and discussion A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 months of age when compared with the wild type. Furthermore, hypermethylated genes were significantly enriched for targets of SUZ12 and the metal-response-element-binding transcription factor 2 (MTF2)-involved in the polycomb repressive complex 2 (PRC2). However, between 4 and 15 months of age, we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analyses identified upregulation of genes associated with mTORC1 signaling and interferon gamma and alpha responses in tet2m/m HSPCs at 4 months of age when compared with the wild type. Downregulated genes in HSPCs of tet2-mutant fish at 4 months of age were enriched for cell cycle regulation, heme metabolism, and interleukin 2 (IL2)/signal transducer and activator of transcription 5 (STAT5) signaling, possibly related to increased self-renewal and clonal advantage in HSPCs with tet2 loss of function. Finally, there was an overall inverse correlation between overall increased promoter methylation and gene expression.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Evisa Gjini
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Hao Fan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Ashley T. Nguyen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Subhash Prajapati
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Caroline Sheridan
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | | | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Francine E. Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, University of Virginia, Charlottesville, VA, United States
- University of Virginia Cancer Center, Charlottesville, VA, United States
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4
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Rapaport F, Seier K, Neelamraju Y, Hassane D, Baslan T, Gildea DT, Haddox S, Lee T, Murdock HM, Sheridan C, Thurmond A, Wang L, Carroll M, Cripe LD, Fernandez H, Mason CE, Paietta E, Roboz GJ, Sun Z, Tallman MS, Zhang Y, Gönen M, Levine R, Melnick AM, Kleppe M, Garrett-Bakelman FE. Correction: Integrative analysis identifies an older female-linked AML patient group with better risk in ECOG-ACRIN Cancer Research Group's clinical trial E3999. Blood Cancer J 2023; 13:103. [PMID: 37407550 PMCID: PMC10322919 DOI: 10.1038/s41408-023-00862-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Affiliation(s)
- Franck Rapaport
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA
| | - Kenneth Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Duane Hassane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel T Gildea
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Tak Lee
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - H Moses Murdock
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Caroline Sheridan
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexis Thurmond
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Ling Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Larry D Cripe
- Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Hugo Fernandez
- Department of Malignant Hematology & Cellular Therapy, Moffitt Cancer Center, Tampa, FL, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, USA
| | | | - Gail J Roboz
- Weill Cornell Medicine and The New York Presbyterian Hospital, New York, NY, USA
| | - Zhuoxin Sun
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Maria Kleppe
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, University of Virginia, Charlottesville, VA, USA.
- University of Virginia Cancer Center, Charlottesville, VA, USA.
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5
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Paudel BB, Tan SF, Fox TE, Ung J, Shaw J, Dunton W, Lee I, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Claxton D, Feith DJ, Janes KA, Loughran TP. Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes. bioRxiv 2023:2023.04.13.536805. [PMID: 37131653 PMCID: PMC10153188 DOI: 10.1101/2023.04.13.536805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the sphingolipid family of bioactive molecules in 213 primary AML samples and 30 common human AML cell lines. Using an integrative approach, we identify two distinct sphingolipid subtypes in AML characterized by a reciprocal abundance of hexosylceramide (Hex) and sphingomyelin (SM) species. The two Hex-SM clusters organize diverse samples more robustly than known AML driver mutations and are coupled to latent transcriptional states. Using transcriptomic data, we develop a machine-learning classifier to infer the Hex-SM status of AML cases in TCGA and BeatAML clinical repositories. The analyses show that the sphingolipid subtype with deficient Hex and abundant SM is enriched for leukemic stemness transcriptional programs and comprises an unappreciated high-risk subgroup with poor clinical outcomes. Our sphingolipid-focused examination of AML identifies patients least likely to benefit from standard of care and raises the possibility that sphingolipidomic interventions could switch the subtype of AML patients who otherwise lack targetable alternatives.
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Affiliation(s)
- B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Todd E. Fox
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, VA
| | - Jeremy Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Wendy Dunton
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Irene Lee
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Aaron D. Viny
- Departments of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
| | - Brian M. Barth
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD
| | - Martin S. Tallman
- Northwestern University Feinberg School of Medicine Robert H. Lurie Comprehensive Cancer Center Chicago, IL
| | - Myles Cabot
- Department of Biochemistry & Molecular Biology, Brody School of Medicine, and the East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - David Claxton
- Penn State Cancer Institute, Hershey, PA
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
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6
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Wang Z, Neelamraju Y, Meydan C, Dunham N, Gandara J, Lee T, Prajapati S, Rapaport F, Sheridan C, Zumbo P, Becker M, Bullinger L, Carroll M, D’Andrea R, Dillon R, Levine R, Mason CE, Melnick A, Neuberg D, Bekiranov S, Zang C, Garrett-Bakelman FE. Abstract 3155: Gene expression profiles reveal distinct regulatory activities of transcription factors GATA1 and TAL1 upon AML relapse. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
The purpose of this study is to identify key regulatory pathways that potentially drive abnormal gene expression program in relapsed Acute Myeloid Leukemia (AML) patients, by integrative computational analyses on multi-omics molecular profiles. Relapsed AML remains a clinical challenge. Epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML. However, what specific transcriptional programs and potential regulatory mechanisms contribute to disease relapse are not yet well understood. To characterize the global transcriptional landscapes in relapsed AML, we integrated genomics data from two cohorts of matched diagnosis and relapse patient specimens. We identified 5,416 differentially expressed genes (DEGs) between diagnosis and relapse in Cohort I. Unsupervised clustering yielded three distinct DEG groups: group A, B and C genes that were predominantly (88%) down-regulated, divergently regulated, or predominantly (65%) up-regulated, respectively, upon relapse. The expression pattern of all DEGs separated the patients into two clusters, most robustly by Group B genes. Interestingly, the majority of DEGs did not associate with changes in gene promoter methylation. Similar patterns were observed in Cohort II. We used Binding Analysis for Regulation of Transcription (BART) to identify transcriptional regulators (TRs) that potentially regulated the DEGs not associated with DNA methylation changes, and assessed the differential expression of identified TRs during disease progression. PU.1 was identified as a potential TR for Group A genes and was down-regulated upon relapse. GATA1 and TAL1 were identified as regulating Group B genes and were up-regulated in patient cluster1 and down-regulated in cluster2, consistent with the expression pattern of Group B genes. RBBP5 was a top predicted TR for Group C genes and was up-regulated upon relapse. We next validated the potential functionality of those predicted factors. In NSG mice transplanted with a human AML specimen, TAL1 and GATA1 were downregulated in AML cells collected four weeks after chemotherapy treatment, and were inferred as TRs for the down-regulated genes, similar to the patient data. PU.1 was inferred as regulating the up-regulated genes. Furthermore, we found that the level of differential expression of TAL1, GATA1, and PU.1 in each patient specimen associated with the correlation of DEG profiles between the patient specimen and TR perturbation in human-derived hematopoietic cell lines. Our results support the possibility that in some AML patients, TRs with roles in hematopoiesis and leukemia might contribute to disease relapse. Further mechanistic studies deciphering the molecular and phenotypic events facilitated by these TRs will yield significant insight into disease biology and possible therapeutic targeting approaches in relapsed AML.
Citation Format: Zhenjia Wang, Yaseswini Neelamraju, Cem Meydan, Nicholas Dunham, Jorge Gandara, Tak Lee, Subhash Prajapati, Franck Rapaport, Caroline Sheridan, Paul Zumbo, Michael Becker, Lars Bullinger, Martin Carroll, Richard D’Andrea, Richard Dillon, Ross Levine, Christopher E. Mason, Ari Melnick, Donna Neuberg, Stefan Bekiranov, Chongzhi Zang, Francine E. Garrett-Bakelman. Gene expression profiles reveal distinct regulatory activities of transcription factors GATA1 and TAL1 upon AML relapse [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3155.
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Affiliation(s)
| | | | | | | | | | - Tak Lee
- 2Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | - Richard D’Andrea
- 7University of South Australia and SA Pathology, Adelaide, Australia
| | | | - Ross Levine
- 3Memorial Sloan Kettering Cancer Center, New York, NY
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7
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Ung J, Tan SF, Fox TE, Shaw JJP, Vass LR, Costa-Pinheiro P, Garrett-Bakelman FE, Keng MK, Sharma A, Claxton DF, Levine RL, Tallman MS, Cabot MC, Kester M, Feith DJ, Loughran TP. Harnessing the power of sphingolipids: Prospects for acute myeloid leukemia. Blood Rev 2022; 55:100950. [PMID: 35487785 PMCID: PMC9475810 DOI: 10.1016/j.blre.2022.100950] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive, heterogenous malignancy characterized by clonal expansion of bone marrow-derived myeloid progenitor cells. While our current understanding of the molecular and genomic landscape of AML has evolved dramatically and opened avenues for molecularly targeted therapeutics to improve upon standard intensive induction chemotherapy, curative treatments are elusive, particularly in older patients. Responses to current AML treatments are transient and incomplete, necessitating the development of novel treatment strategies to improve outcomes. To this end, harnessing the power of bioactive sphingolipids to treat cancer shows great promise. Sphingolipids are involved in many hallmarks of cancer of paramount importance in AML. Leukemic blast survival is influenced by cellular levels of ceramide, a bona fide pro-death molecule, and its conversion to signaling molecules such as sphingosine-1-phosphate and glycosphingolipids. Preclinical studies demonstrate the efficacy of therapeutics that target dysregulated sphingolipid metabolism as well as their combinatorial synergy with clinically-relevant therapeutics. Thus, increased understanding of sphingolipid dysregulation may be exploited to improve AML patient care and outcomes. This review summarizes the current knowledge of dysregulated sphingolipid metabolism in AML, evaluates how pro-survival sphingolipids promote AML pathogenesis, and discusses the therapeutic potential of targeting these dysregulated sphingolipid pathways.
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Affiliation(s)
- Johnson Ung
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Su-Fern Tan
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Todd E Fox
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Jeremy J P Shaw
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Experimental Pathology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Luke R Vass
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Experimental Pathology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Pedro Costa-Pinheiro
- Cancer Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Francine E Garrett-Bakelman
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Michael K Keng
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Arati Sharma
- Penn State Cancer Institute, Hershey, PA, United States of America
| | - David F Claxton
- Penn State Cancer Institute, Hershey, PA, United States of America
| | - Ross L Levine
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Martin S Tallman
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Myles C Cabot
- Department of Biochemistry and Molecular Biology, East Carolina University, Brody School of Medicine, Greenville, NC, United States of America; East Carolina Diabetes and Obesity Institute, East Carolina University, Brody School of Medicine, Greenville, NC, United States of America
| | - Mark Kester
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - David J Feith
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Thomas P Loughran
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America.
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8
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Barreyro L, Sampson AM, Ishikawa C, Hueneman KM, Choi K, Pujato MA, Chutipongtanate S, Wyder M, Haffey WD, O'Brien E, Wunderlich M, Ramesh V, Kolb EM, Meydan C, Neelamraju Y, Bolanos LC, Christie S, Smith MA, Niederkorn M, Muto T, Kesari S, Garrett-Bakelman FE, Bartholdy B, Will B, Weirauch MT, Mulloy JC, Gul Z, Medlin S, Kovall RA, Melnick AM, Perentesis JP, Greis KD, Nurmemmedov E, Seibel WL, Starczynowski DT. Blocking UBE2N abrogates oncogenic immune signaling in acute myeloid leukemia. Sci Transl Med 2022; 14:eabb7695. [PMID: 35263148 DOI: 10.1126/scitranslmed.abb7695] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Dysregulation of innate immune signaling pathways is implicated in various hematologic malignancies. However, these pathways have not been systematically examined in acute myeloid leukemia (AML). We report that AML hematopoietic stem and progenitor cells (HSPCs) exhibit a high frequency of dysregulated innate immune-related and inflammatory pathways, referred to as oncogenic immune signaling states. Through gene expression analyses and functional studies in human AML cell lines and patient-derived samples, we found that the ubiquitin-conjugating enzyme UBE2N is required for leukemic cell function in vitro and in vivo by maintaining oncogenic immune signaling states. It is known that the enzyme function of UBE2N can be inhibited by interfering with thioester formation between ubiquitin and the active site. We performed in silico structure-based and cellular-based screens and identified two related small-molecule inhibitors UC-764864/65 that targeted UBE2N at its active site. Using these small-molecule inhibitors as chemical probes, we further revealed the therapeutic efficacy of interfering with UBE2N function. This resulted in the blocking of ubiquitination of innate immune- and inflammatory-related substrates in human AML cell lines. Inhibition of UBE2N function disrupted oncogenic immune signaling by promoting cell death of leukemic HSPCs while sparing normal HSPCs in vitro. Moreover, baseline oncogenic immune signaling states in leukemic cells derived from discrete subsets of patients with AML exhibited a selective dependency on UBE2N function in vitro and in vivo. Our study reveals that interfering with UBE2N abrogates leukemic HSPC function and underscores the dependency of AML cells on UBE2N-dependent oncogenic immune signaling states.
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Affiliation(s)
- Laura Barreyro
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Avery M Sampson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chiharu Ishikawa
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathleen M Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mario A Pujato
- Center for Autoimmune Genetics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Somchai Chutipongtanate
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.,Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Michael Wyder
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Wendy D Haffey
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Eric O'Brien
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vighnesh Ramesh
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ellen M Kolb
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Lyndsey C Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Susanne Christie
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Molly A Smith
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Madeline Niederkorn
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Tomoya Muto
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Santosh Kesari
- Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Department of Medicine, University of Virginia, Charlottesville, VA, USA.,Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA.,University of Virginia Cancer Center, Charlottesville, VA, USA
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genetics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Zartash Gul
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen Medlin
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ari M Melnick
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
| | - John P Perentesis
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Elmar Nurmemmedov
- Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - William L Seibel
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
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9
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Prajapati SC, Dunham N, Fan H, Garrett-Bakelman FE. Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13. Biotechniques 2022; 72:81-84. [PMID: 35119307 PMCID: PMC9413368 DOI: 10.2144/btn-2021-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Acute myeloid leukemia patients with FMS-like tyrosine kinase 3–internal tandem duplications and mixed lineage leukemia–protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these abnormalities and is used in CRISPR experiments to identify disease drivers. However, experimental observations may be biased or inconclusive in the absence of experimentally validated positive control genes. We validated sgRNAs for knockdown of TP53 for cell proliferation and for DCK knockdown and CDA upregulation for cytarabine resistance control genes in MOLM-13 cells. We have provided a detailed CRISPR protocol applicable to both gene knockdown or activation experiments and downstream leukemic phenotype analyses. Inclusion of these controls in CRISPR experiments will enhance the capacity to identify novel myeloid leukemia drivers in MOLM-13 cells. CRISPR-Cas9 knockdown and upregulation approaches were used for changing the expression of control genes TP53, DCK, and CDA in the acute myeloid leukemia cell line MOLM-13. Lentivirus transduced cells were selected (sorted for green fluorescent protein positive cells or selected by antibiotic treatment), and knockdown or upregulation of genes in the stable cells was confirmed by real-time quantitative PCR and western blot analyses. EdU incorporation assay was used to measure cell proliferation. Colorimetric proliferation/survival assay and flow cytometric cell counting were used to measure cell growth and survival. Results from the experimental and control groups were compared using Student's t-test.
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Affiliation(s)
- Subhash C Prajapati
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicholas Dunham
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Hao Fan
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,University of Virginia Cancer Center, Charlottesville, VA 22903, USA
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10
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Batra RN, Lifshitz A, Vidakovic AT, Chin SF, Sati-Batra A, Sammut SJ, Provenzano E, Ali HR, Dariush A, Bruna A, Murphy L, Purushotham A, Ellis I, Green A, Garrett-Bakelman FE, Mason C, Melnick A, Aparicio SAJR, Rueda OM, Tanay A, Caldas C. DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation. Nat Commun 2021; 12:5406. [PMID: 34518533 PMCID: PMC8437946 DOI: 10.1038/s41467-021-25661-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/18/2021] [Indexed: 11/08/2022] Open
Abstract
DNA methylation is aberrant in cancer, but the dynamics, regulatory role and clinical implications of such epigenetic changes are still poorly understood. Here, reduced representation bisulfite sequencing (RRBS) profiles of 1538 breast tumors and 244 normal breast tissues from the METABRIC cohort are reported, facilitating detailed analysis of DNA methylation within a rich context of genomic, transcriptional, and clinical data. Tumor methylation from immune and stromal signatures are deconvoluted leading to the discovery of a tumor replication-linked clock with genome-wide methylation loss in non-CpG island sites. Unexpectedly, methylation in most tumor CpG islands follows two replication-independent processes of gain (MG) or loss (ML) that we term epigenomic instability. Epigenomic instability is correlated with tumor grade and stage, TP53 mutations and poorer prognosis. After controlling for these global trans-acting trends, as well as for X-linked dosage compensation effects, cis-specific methylation and expression correlations are uncovered at hundreds of promoters and over a thousand distal elements. Some of these targeted known tumor suppressors and oncogenes. In conclusion, this study demonstrates that global epigenetic instability can erode cancer methylomes and expose them to localized methylation aberrations in-cis resulting in transcriptional changes seen in tumors.
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Affiliation(s)
- Rajbir Nath Batra
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics, and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ankita Sati-Batra
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Elena Provenzano
- Cancer Research UK Cambridge Centre, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - H Raza Ali
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ali Dariush
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Leigh Murphy
- Research Institute in Oncology and Hematology, Winnipeg, Manitoba, Canada
| | - Arnie Purushotham
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Ian Ellis
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Andrew Green
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Francine E Garrett-Bakelman
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Chris Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Samuel A J R Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Centre, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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11
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Olson TL, Cheon H, Xing JC, Olson KC, Paila U, Hamele CE, Neelamraju Y, Shemo BC, Schmachtenberg M, Sundararaman SK, Toro MF, Keller CA, Farber EA, Onengut-Gumuscu S, Garrett-Bakelman FE, Hardison RC, Feith DJ, Ratan A, Loughran TP. Frequent somatic TET2 mutations in chronic NK-LGL leukemia with distinct patterns of cytopenias. Blood 2021; 138:662-673. [PMID: 33786584 PMCID: PMC8394905 DOI: 10.1182/blood.2020005831] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 03/30/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic natural killer large granular lymphocyte (NK-LGL) leukemia, also referred to as chronic lymphoproliferative disorder of NK cells, is a rare disorder defined by prolonged expansion of clonal NK cells. Similar prevalence of STAT3 mutations in chronic T-LGL and NK-LGL leukemia is suggestive of common pathogenesis. We undertook whole-genome sequencing to identify mutations unique to NK-LGL leukemia. The results were analyzed to develop a resequencing panel that was applied to 58 patients. Phosphatidylinositol 3-kinase pathway gene mutations (PIK3CD/PIK3AP1) and TNFAIP3 mutations were seen in 5% and 10% of patients, respectively. TET2 was exceptional in that mutations were present in 16 (28%) of 58 patient samples, with evidence that TET2 mutations can be dominant and exclusive to the NK compartment. Reduced-representation bisulfite sequencing revealed that methylation patterns were significantly altered in TET2 mutant samples. The promoter of TET2 and that of PTPRD, a negative regulator of STAT3, were found to be methylated in additional cohort samples, largely confined to the TET2 mutant group. Mutations in STAT3 were observed in 19 (33%) of 58 patient samples, 7 of which had concurrent TET2 mutations. Thrombocytopenia and resistance to immunosuppressive agents were uniquely observed in those patients with only TET2 mutation (Games-Howell post hoc test, P = .0074; Fisher's exact test, P = .00466). Patients with STAT3 mutation, inclusive of those with TET2 comutation, had lower hematocrit, hemoglobin, and absolute neutrophil count compared with STAT3 wild-type patients (Welch's t test, P ≤ .015). We present the discovery of TET2 mutations in chronic NK-LGL leukemia and evidence that it identifies a unique molecular subtype.
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Affiliation(s)
- Thomas L Olson
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - HeeJin Cheon
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Medical Scientist Training Program, University of Virginia School of Medicine, Charlottesville, VA
| | - Jeffrey C Xing
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Medical Scientist Training Program, University of Virginia School of Medicine, Charlottesville, VA
| | - Kristine C Olson
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Umadevi Paila
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
| | - Cait E Hamele
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
| | - Bryna C Shemo
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Matt Schmachtenberg
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Shriram K Sundararaman
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Mariella F Toro
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA; and
| | - Emily A Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
| | | | - Francine E Garrett-Bakelman
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA; and
| | - David J Feith
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Thomas P Loughran
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
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12
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Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR. An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Front Cell Dev Biol 2021; 9:630067. [PMID: 33816475 PMCID: PMC8017264 DOI: 10.3389/fcell.2021.630067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 01/02/2023] Open
Abstract
Cell fate decisions during development are governed by multi-factorial regulatory mechanisms including chromatin remodeling, DNA methylation, binding of transcription factors to specific loci, RNA transcription and protein synthesis. However, the mechanisms by which such regulatory “dimensions” coordinate cell fate decisions are currently poorly understood. Here we quantified the multi-dimensional molecular changes that occur in mouse embryonic stem cells (mESCs) upon depletion of Estrogen related receptor beta (Esrrb), a key pluripotency regulator. Comparative analyses of expression changes subsequent to depletion of Esrrb or Nanog, indicated that a system of interlocked feed-forward loops involving both factors, plays a central part in regulating the timing of mESC fate decisions. Taken together, our meta-analyses support a hierarchical model in which pluripotency is maintained by an Oct4-Sox2 regulatory module, while the timing of differentiation is regulated by a Nanog-Esrrb module.
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Affiliation(s)
- Ana Sevilla
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Departament de Biología Cellular, Fisiología i Immunología, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain
| | - Dimitri Papatsenko
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amin R Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Vasileva
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Richard D Unwin
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom.,Centre for Advanced Discovery and Experimental Therapeutics, Central Manchester University Hospitals NHS Foundation Trust, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Gary LeRoy
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Edward Y Chen
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Dung-Fang Lee
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benjamin Trinite
- Institut de Recerca de La Sida, IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute, Hospital Universitari Germans Trias I Pujol, Catalonia, Spain
| | - Ryan L Webb
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jie Su
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Julian Gingold
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Benjamin A Garcia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom
| | - Ben D MacArthur
- The Centre for Human Development, Stem Cells and Regeneration, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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13
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Rapaport F, Neelamraju Y, Baslan T, Hassane D, Gruszczynska A, Robert de Massy M, Farnoud N, Haddox S, Lee T, Medina-Martinez J, Sheridan C, Thurmond A, Becker M, Bekiranov S, Carroll M, Moses Murdock H, Valk PJM, Bullinger L, D'Andrea R, Lowe SW, Neuberg D, Levine RL, Melnick A, Garrett-Bakelman FE. Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia. Leukemia 2021; 35:2688-2692. [PMID: 33580203 PMCID: PMC8357838 DOI: 10.1038/s41375-021-01153-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 01/22/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Franck Rapaport
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Duane Hassane
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Agata Gruszczynska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Marc Robert de Massy
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noushin Farnoud
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Tak Lee
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Juan Medina-Martinez
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Sheridan
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Alexis Thurmond
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Michael Becker
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Heardly Moses Murdock
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany.,Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - Richard D'Andrea
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Donna Neuberg
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ross L Levine
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari Melnick
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA. .,Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA. .,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA. .,University of Virginia Cancer Center, Charlottesville, VA, USA.
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14
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Duy C, Li M, Teater M, Meydan C, Garrett-Bakelman FE, Lee TC, Chin CR, Durmaz C, Kawabata KC, Dhimolea E, Mitsiades CS, Doehner H, D'Andrea RJ, Becker MW, Paietta EM, Mason CE, Carroll M, Melnick AM. Chemotherapy Induces Senescence-Like Resilient Cells Capable of Initiating AML Recurrence. Cancer Discov 2021; 11:1542-1561. [PMID: 33500244 DOI: 10.1158/2159-8290.cd-20-1375] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/28/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
Patients with acute myeloid leukemia (AML) frequently relapse after chemotherapy, yet the mechanism by which AML reemerges is not fully understood. Herein, we show that primary AML cells enter a senescence-like phenotype following chemotherapy in vitro and in vivo. This is accompanied by induction of senescence/inflammatory and embryonic diapause transcriptional programs, with downregulation of MYC and leukemia stem cell genes. Single-cell RNA sequencing suggested depletion of leukemia stem cells in vitro and in vivo, and enrichment for subpopulations with distinct senescence-like cells. This senescence effect was transient and conferred superior colony-forming and engraftment potential. Entry into this senescence-like phenotype was dependent on ATR, and persistence of AML cells was severely impaired by ATR inhibitors. Altogether, we propose that AML relapse is facilitated by a senescence-like resilience phenotype that occurs regardless of their stem cell status. Upon recovery, these post-senescence AML cells give rise to relapsed AMLs with increased stem cell potential. SIGNIFICANCE: Despite entering complete remission after chemotherapy, relapse occurs in many patients with AML. Thus, there is an urgent need to understand the relapse mechanism in AML and the development of targeted treatments to improve outcome. Here, we identified a senescence-like resilience phenotype through which AML cells can survive and repopulate leukemia.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Cihangir Duy
- Cancer Signaling and Epigenetics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania. .,Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Meng Li
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Matt Teater
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Tak C Lee
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Ceyda Durmaz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Kimihito C Kawabata
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | | | - Ari M Melnick
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York.
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15
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Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, Mishra T, Lucotti S, Rana BK, Melnick AM, Zhang H, Matei I, Kelsen D, Yu K, Lyden DC, Taylor L, Bailey SM, Snyder MP, Garrett-Bakelman FE, Ossowski S, De Vlaminck I, Mason CE. Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. iScience 2020; 23:101844. [PMID: 33376973 PMCID: PMC7756145 DOI: 10.1016/j.isci.2020.101844] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsies based on cell-free DNA (cfDNA) or exosomes provide a noninvasive approach to monitor human health and disease but have not been utilized for astronauts. Here, we profile cfDNA characteristics, including fragment size, cellular deconvolution, and nucleosome positioning, in an astronaut during a year-long mission on the International Space Station, compared to his identical twin on Earth and healthy donors. We observed a significant increase in the proportion of cell-free mitochondrial DNA (cf-mtDNA) inflight, and analysis of post-flight exosomes in plasma revealed a 30-fold increase in circulating exosomes and patient-specific protein cargo (including brain-derived peptides) after the year-long mission. This longitudinal analysis of astronaut cfDNA during spaceflight and the exosome profiles highlights their utility for astronaut health monitoring, as well as cf-mtDNA levels as a potential biomarker for physiological stress or immune system responses related to microgravity, radiation exposure, and the other unique environmental conditions of spaceflight.
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Affiliation(s)
- Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Fanny A. Pelissier Vatter
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Michele Cioffi
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Varsha Rao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | | | - Philip Burnham
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Craig Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Chris Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Timothy Donahoe
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Brinda K. Rana
- Department of Psychiatry University of California, San Diego, La Jolla, CA, USA
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Haiying Zhang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David C. Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Lynn Taylor
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Susan M. Bailey
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- University of Virginia Cancer Center, Charlottesville, VA, USA
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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16
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Luxton JJ, McKenna MJ, Taylor LE, George KA, Zwart SR, Crucian BE, Drel VR, Garrett-Bakelman FE, Mackay MJ, Butler D, Foox J, Grigorev K, Bezdan D, Meydan C, Smith SM, Sharma K, Mason CE, Bailey SM. Temporal Telomere and DNA Damage Responses in the Space Radiation Environment. Cell Rep 2020; 33:108435. [PMID: 33242411 DOI: 10.1016/j.celrep.2020.108435] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023] Open
Abstract
Telomeres, repetitive terminal features of chromosomes essential for maintaining genome integrity, shorten with cell division, lifestyle factors and stresses, and environmental exposures, and so they provide a robust biomarker of health, aging, and age-related diseases. We assessed telomere length dynamics (changes over time) in three unrelated astronauts before, during, and after 1-year or 6-month missions aboard the International Space Station (ISS). Similar to our results for National Aeronautics and Space Administration's (NASA's) One-Year Mission twin astronaut (Garrett-Bakelman et al., 2019), significantly longer telomeres were observed during spaceflight for two 6-month mission astronauts. Furthermore, telomere length shortened rapidly after return to Earth for all three crewmembers and, overall, telomere length tended to be shorter after spaceflight than before spaceflight. Consistent with chronic exposure to the space radiation environment, signatures of persistent DNA damage responses were also detected, including mitochondrial and oxidative stress, inflammation, and telomeric and chromosomal aberrations, which together provide potential mechanistic insight into spaceflight-specific telomere elongation.
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Affiliation(s)
- Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Lynn E Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | | | - Viktor R Drel
- Center for Renal Precision Medicine, UT Health, San Antonio, TX, USA
| | - Francine E Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Medicine, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Matthew J Mackay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Kumar Sharma
- Center for Renal Precision Medicine, UT Health, San Antonio, TX, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA.
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17
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Abshiru NA, Sikora JW, Camarillo JM, Morris JA, Compton PD, Lee T, Neelamraju Y, Haddox S, Sheridan C, Carroll M, Cripe LD, Tallman MS, Paietta EM, Melnick AM, Thomas PM, Garrett-Bakelman FE, Kelleher NL. Targeted detection and quantitation of histone modifications from 1,000 cells. PLoS One 2020; 15:e0240829. [PMID: 33104722 PMCID: PMC7588077 DOI: 10.1371/journal.pone.0240829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/02/2020] [Indexed: 01/30/2023] Open
Abstract
Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.
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Affiliation(s)
- Nebiyu A. Abshiru
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jacek W. Sikora
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jeannie M. Camarillo
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Juliette A. Morris
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Philip D. Compton
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Tak Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Caroline Sheridan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Larry D. Cripe
- Indiana University/Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States of America
| | - Martin S. Tallman
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | | | - Ari M. Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Paul M. Thomas
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Francine E. Garrett-Bakelman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
- Division of Hematology/Medical Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
- * E-mail: (FEGB); (NLK)
| | - Neil L. Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
- * E-mail: (FEGB); (NLK)
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18
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Li M, Teater M, Meydan C, Garrett-Bakelman FE, Chin C, Carroll M, Melnick A, Duy C. Abstract 651: Chemotherapy induces a transient senescence-like state capable of initiating AML recurrence. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In acute myeloid leukemia (AML), chemotherapy is frequently followed by disease relapse, yet the mechanism by which AML reemerges is not fully understood. We hypothesized that chemotherapy-induced senescence (CIS) facilitates survival to genotoxic exposure, allowing AML cells to endure treatment in a transiently dormant state while retaining potential for leukemic repopulation.
Here we show that, following treatment with cytarabine (AraC), primary AML cells exhibit hallmark senescence features, including morphological changes, senescence-associated transcriptomic alterations, and senescence-associated-beta-galactosidase (SA-β-gal) activity. To quantify SA-β-gal activity, we used a fluorogenic substrate that enabled sensitive cytometric quantification of the senescence marker in viable cells. Mechanistically, we demonstrate that genotoxic stress following AraC treatment activated the ATR kinase, a key regulator of DNA damage response. Inhibition of ATR abrogated CIS in leukemia cells and induced cell death, indicating that CIS mediates stress survival.
We next analyzed the gene expression profiles of the minor residual fraction of chemotherapy-surviving cells ex vivo and in patients after chemotherapy. We found that leukemia stem cell (LSC) gene signatures were largely depleted in chemotherapy-surviving cells. However, we did find that the CIS signature was positively enriched. To recapitulate relapse of disease, we established an AML relapse model using primary human specimens engrafted in NSG mice. Treatment of AML-engrafted NSG mice with a physiologically relevant regimen of AraC reduced leukemic burden to a small residual leukemia fraction 8 days after therapeutic initiation. This reduction in leukemic burden was reversed to full blown leukemia present at day 29. Gene expression analysis of purified human AML cells at nadir (day 8) showed significant enrichment for senescence signatures. This enrichment was reduced by day 29 post-treatment, as expression was partially reversed to untreated levels. While we did not observe an enrichment of LSC signatures at nadir, we found an enrichment of LSC gene signatures in 60% of xenografted AML cases after overt recurrence of disease, suggesting partial reversal of the senescence phenotype and recovery of the LSC phenotype. We observed a similar pattern, when we performed RNA-seq analysis in matched AML specimens from patients at diagnosis vs relapse. To examine if LSCs might be present in the CIS cell population, we performed scRNA-seq in primary AML before and after chemotherapy. Although chemotherapy killed a majority of AML cells, we did not find an enrichment of LSCs on single cell level compared to untreated control cells in most AML specimens. Instead, we found increased expression of the CIS gene signature. Next, to test if CIS cells possess self-renewal capability, we sorted for SA-β-gal+ cells after AraC exposure and seeded them in CFC assays. We found colony-forming potential of CIS cells, suggesting a capacity to repopulate leukemia. To confirm that leukemia can be initiated from CIS AML in vivo, we transplanted sorted CIS AML cells into NSG mice and found that these cells successfully repopulated leukemia.
Altogether, we propose a mechanism of AML relapse whereby AML cells survive chemotherapy via acquisition of a transient senescent-like state.
Citation Format: Meng Li, Matt Teater, Cem Meydan, Francine E. Garrett-Bakelman, Christopher Chin, Martin Carroll, Ari Melnick, Cihangir Duy. Chemotherapy induces a transient senescence-like state capable of initiating AML recurrence [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 651.
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Affiliation(s)
- Meng Li
- 1Weill Cornell Medicine, New York, NY
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19
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Martin GH, Roy N, Chakraborty S, Desrichard A, Chung SS, Woolthuis CM, Hu W, Berezniuk I, Garrett-Bakelman FE, Hamann J, Devlin SM, Chan TA, Park CY. CD97 is a critical regulator of acute myeloid leukemia stem cell function. J Exp Med 2019; 216:2362-2377. [PMID: 31371381 PMCID: PMC6781010 DOI: 10.1084/jem.20190598] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/20/2019] [Accepted: 06/27/2019] [Indexed: 12/15/2022] Open
Abstract
Despite significant efforts to improve therapies for acute myeloid leukemia (AML), clinical outcomes remain poor. Understanding the mechanisms that regulate the development and maintenance of leukemic stem cells (LSCs) is important to reveal new therapeutic opportunities. We have identified CD97, a member of the adhesion class of G protein-coupled receptors (GPCRs), as a frequently up-regulated antigen on AML blasts that is a critical regulator of blast function. High levels of CD97 correlate with poor prognosis, and silencing of CD97 reduces disease aggressiveness in vivo. These phenotypes are due to CD97's ability to promote proliferation, survival, and the maintenance of the undifferentiated state in leukemic blasts. Collectively, our data credential CD97 as a promising therapeutic target on LSCs in AML.
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Affiliation(s)
- Gaëlle H Martin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Pathology, New York University School of Medicine, New York, NY
| | - Nainita Roy
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Sohini Chakraborty
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Alexis Desrichard
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stephen S Chung
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carolien M Woolthuis
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Iryna Berezniuk
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology/Oncology, University of Virginia, Charlottesville, VA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA.,Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY
| | - Jörg Hamann
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Sean M Devlin
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher Y Park
- Department of Pathology, New York University School of Medicine, New York, NY
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20
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Duy C, Teater M, Garrett-Bakelman FE, Lee TC, Meydan C, Glass JL, Li M, Hellmuth JC, Mohammad HP, Smitheman KN, Shih AH, Abdel-Wahab O, Tallman MS, Guzman ML, Muench D, Grimes HL, Roboz GJ, Kruger RG, Creasy CL, Paietta EM, Levine RL, Carroll M, Melnick AM. Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML. Cancer Discov 2019; 9:872-889. [PMID: 31076479 DOI: 10.1158/2159-8290.cd-19-0106] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/17/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
Abstract
Disruption of epigenetic regulation is a hallmark of acute myeloid leukemia (AML), but epigenetic therapy is complicated by the complexity of the epigenome. Herein, we developed a long-term primary AML ex vivo platform to determine whether targeting different epigenetic layers with 5-azacytidine and LSD1 inhibitors would yield improved efficacy. This combination was most effective in TET2 mut AML, where it extinguished leukemia stem cells and particularly induced genes with both LSD1-bound enhancers and cytosine-methylated promoters. Functional studies indicated that derepression of genes such as GATA2 contributes to drug efficacy. Mechanistically, combination therapy increased enhancer-promoter looping and chromatin-activating marks at the GATA2 locus. CRISPRi of the LSD1-bound enhancer in patient-derived TET2 mut AML was associated with dampening of therapeutic GATA2 induction. TET2 knockdown in human hematopoietic stem/progenitor cells induced loss of enhancer 5-hydroxymethylation and facilitated LSD1-mediated enhancer inactivation. Our data provide a basis for rational targeting of cooperating aberrant promoter and enhancer epigenetic marks driven by mutant epigenetic modifiers. SIGNIFICANCE: Somatic mutations of genes encoding epigenetic modifiers are a hallmark of AML and potentially disrupt many components of the epigenome. Our study targets two different epigenetic layers at promoters and enhancers that cooperate to aberrant gene silencing, downstream of the actions of a mutant epigenetic regulator.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Cihangir Duy
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.
| | - Matt Teater
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Tak C Lee
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Jacob L Glass
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meng Li
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | | | | | - Alan H Shih
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Monica L Guzman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - David Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Gail J Roboz
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | | | | | | | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin Carroll
- Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Ari M Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York. .,Department of Pharmacology, Weill Cornell Medicine, New York, New York
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21
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Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science 2019; 364:364/6436/eaau8650. [PMID: 30975860 DOI: 10.1126/science.aau8650] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.
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Affiliation(s)
- Francine E Garrett-Bakelman
- Weill Cornell Medicine, New York, NY, USA.,University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Ruben C Gur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ling Lin
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Jad Nasrini
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Lynn Taylor
- Colorado State University, Fort Collins, CO, USA
| | | | | | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sara Ahadi
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aditya Ambati
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Songjie Chen
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Marisa Covington
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | - Brian E Crucian
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | - David F Dinges
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | - Ryan P Hillary
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Peng Jiang
- Northwestern University, Evanston, IL, USA
| | | | | | | | | | | | | | | | - Tyler M Moore
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Hemal H Patel
- University of California, San Diego, La Jolla, CA, USA
| | | | - Varsha Rao
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rintaro Saito
- University of California, San Diego, La Jolla, CA, USA
| | - Denis N Salins
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Michael B Stenger
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | | | | | | | - Jing Zhang
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | - John B Charles
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
| | - Craig E Kundrot
- Space Life and Physical Sciences Division, NASA Headquarters, Washington, DC, USA.
| | - Graham B I Scott
- National Space Biomedical Research Institute, Baylor College of Medicine, Houston, TX, USA.
| | | | - Mathias Basner
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | | | | | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | | | - Brinda K Rana
- University of California, San Diego, La Jolla, CA, USA.
| | - Scott M Smith
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
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22
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Chung SS, Eng WS, Hu W, Khalaj M, Garrett-Bakelman FE, Tavakkoli M, Levine RL, Carroll M, Klimek VM, Melnick AM, Park CY. CD99 is a therapeutic target on disease stem cells in myeloid malignancies. Sci Transl Med 2018; 9:9/374/eaaj2025. [PMID: 28123069 DOI: 10.1126/scitranslmed.aaj2025] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 09/12/2016] [Accepted: 11/22/2016] [Indexed: 12/16/2022]
Abstract
Acute myeloid leukemia (AML) and the myelodysplastic syndromes (MDS) are initiated and sustained by self-renewing malignant stem cells; thus, eradication of AML and MDS stem cells is required for cure. We identified CD99 as a cell surface protein frequently overexpressed on AML and MDS stem cells. Expression of CD99 allows for prospective separation of leukemic stem cells (LSCs) from functionally normal hematopoietic stem cells in AML, and high CD99 expression on AML blasts enriches for functional LSCs as demonstrated by limiting dilution xenotransplant studies. Monoclonal antibodies (mAbs) targeting CD99 induce the death of AML and MDS cells in a SARC family kinase-dependent manner in the absence of immune effector cells or complement, and anti-CD99 mAbs exhibit antileukemic activity in AML xenografts. These data establish CD99 as a marker of AML and MDS stem cells, as well as a promising therapeutic target in these disorders.
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Affiliation(s)
- Stephen S Chung
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - William S Eng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mona Khalaj
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Francine E Garrett-Bakelman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell School of Medicine, New York, NY 10065, USA
| | - Montreh Tavakkoli
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Virginia M Klimek
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell School of Medicine, New York, NY 10065, USA
| | - Christopher Y Park
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Departments of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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23
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Kunimoto H, Meydan C, Nazir A, Whitfield J, Shank K, Rapaport F, Maher R, Pronier E, Meyer SC, Garrett-Bakelman FE, Tallman M, Melnick A, Levine RL, Shih AH. Cooperative Epigenetic Remodeling by TET2 Loss and NRAS Mutation Drives Myeloid Transformation and MEK Inhibitor Sensitivity. Cancer Cell 2018; 33:44-59.e8. [PMID: 29275866 PMCID: PMC5760367 DOI: 10.1016/j.ccell.2017.11.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/02/2017] [Accepted: 11/17/2017] [Indexed: 12/11/2022]
Abstract
Mutations in epigenetic modifiers and signaling factors often co-occur in myeloid malignancies, including TET2 and NRAS mutations. Concurrent Tet2 loss and NrasG12D expression in hematopoietic cells induced myeloid transformation, with a fully penetrant, lethal chronic myelomonocytic leukemia (CMML), which was serially transplantable. Tet2 loss and Nras mutation cooperatively led to decrease in negative regulators of mitogen-activated protein kinase (MAPK) activation, including Spry2, thereby causing synergistic activation of MAPK signaling by epigenetic silencing. Tet2/Nras double-mutant leukemia showed preferential sensitivity to MAPK kinase (MEK) inhibition in both mouse model and patient samples. These data provide insights into how epigenetic and signaling mutations cooperate in myeloid transformation and provide a rationale for mechanism-based therapy in CMML patients with these high-risk genetic lesions.
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Affiliation(s)
- Hiroyoshi Kunimoto
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cem Meydan
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Abbas Nazir
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Justin Whitfield
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Franck Rapaport
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rebecca Maher
- University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Elodie Pronier
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sara C Meyer
- Division of Hematology, University Hospital Basel, 4031 Basel, Switzerland; Department of Biomedicine, University Hospital Basel, 4031 Basel, Switzerland
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medical College, New York, NY 10065, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Martin Tallman
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ari Melnick
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medical College, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Alan H Shih
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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24
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Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME. Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Cancer Discov 2017; 7:868-883. [PMID: 28408400 DOI: 10.1158/2159-8290.cd-16-1032] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 04/07/2017] [Indexed: 11/16/2022]
Abstract
We performed cytosine methylation sequencing on genetically diverse patients with acute myeloid leukemia (AML) and found leukemic DNA methylation patterning is primarily driven by nonpromoter regulatory elements and CpG shores. Enhancers displayed stronger differential methylation than promoters, consisting predominantly of hypomethylation. AMLs with dominant hypermethylation featured greater epigenetic disruption of promoters, whereas those with dominant hypomethylation displayed greater disruption of distal and intronic regions. Mutations in IDH and DNMT3A had opposing and mutually exclusive effects on the epigenome. Notably, co-occurrence of both mutations resulted in epigenetic antagonism, with most CpGs affected by either mutation alone no longer affected in double-mutant AMLs. Importantly, this epigenetic antagonism precedes malignant transformation and can be observed in preleukemic LSK cells from Idh2R140Q or Dnmt3aR882H single-mutant and Idh2R140Q/Dnmt3aR882H double-mutant mice. Notably, IDH/DNMT3A double-mutant AMLs manifested upregulation of a RAS signaling signature and displayed unique sensitivity to MEK inhibition ex vivo as compared with AMLs with either single mutation.Significance: AML is biologically heterogeneous with subtypes characterized by specific genetic and epigenetic abnormalities. Comprehensive DNA methylation profiling revealed that differential methylation of nonpromoter regulatory elements is a driver of epigenetic identity, that gene mutations can be context-dependent, and that co-occurrence of mutations in epigenetic modifiers can result in epigenetic antagonism. Cancer Discov; 7(8); 868-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 783.
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Affiliation(s)
- Jacob L Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York
| | - Duane Hassane
- Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York
| | - Bas J Wouters
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.,Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Hiroyoshi Kunimoto
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roberto Avellino
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Francine E Garrett-Bakelman
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.,Department of Medicine, University of Virginia, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Olga A Guryanova
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shira Redlich
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cem Meydan
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Tingting Qin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mame Fall
- Epigenomics Core Facility, Weill Medical College of Cornell University, New York, New York
| | - Alicia Alonso
- Epigenomics Core Facility, Weill Medical College of Cornell University, New York, New York
| | - Monica L Guzman
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Craig B Thompson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Ari Melnick
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.
| | - Maria E Figueroa
- Department of Human Genetics and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.
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25
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Shih AH, Meydan C, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL. Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. Cancer Discov 2017; 7:494-505. [PMID: 28193779 DOI: 10.1158/2159-8290.cd-16-1049] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 11/16/2022]
Abstract
Genomic studies in acute myeloid leukemias (AML) have identified mutations that drive altered DNA methylation, including TET2 and IDH2 Here, we show that models of AML resulting from TET2 or IDH2 mutations combined with FLT3ITD mutations are sensitive to 5-azacytidine or to the IDH2 inhibitor AG-221, respectively. 5-azacytidine and AG-221 treatment induced an attenuation of aberrant DNA methylation and transcriptional output and resulted in a reduction in leukemic blasts consistent with antileukemic activity. These therapeutic benefits were associated with restoration of leukemic cell differentiation, and the normalization of hematopoiesis was derived from mutant cells. By contrast, combining AG-221 or 5-azacytidine with FLT3 inhibition resulted in a reduction in mutant allele burden, progressive recovery of normal hematopoiesis from non-mutant stem-progenitor cells, and reversal of dysregulated DNA methylation and transcriptional output. Together, our studies suggest combined targeting of signaling and epigenetic pathways can increase therapeutic response in AML.Significance: AMLs with mutations in TET2 or IDH2 are sensitive to epigenetic therapy through inhibition of DNA methyltransferase activity by 5-azacytidine or inhibition of mutant IDH2 through AG-221. These inhibitors induce a differentiation response and can be used to inform mechanism-based combination therapy. Cancer Discov; 7(5); 494-505. ©2017 AACR.See related commentary by Thomas and Majeti, p. 459See related article by Yen et al., p. 478This article is highlighted in the In This Issue feature, p. 443.
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Affiliation(s)
- Alan H Shih
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cem Meydan
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York.,Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Patrick S Ward
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abbas Nazir
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eytan M Stein
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristina Knapp
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | | | - Kim Straley
- Agios Pharmaceuticals, Cambridge, Massachusetts
| | | | - Christopher E Mason
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ari Melnick
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York.
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
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Garrett-Bakelman FE, Melnick AM. Mutant IDH: a targetable driver of leukemic phenotypes linking metabolism, epigenetics and transcriptional regulation. Epigenomics 2016; 8:945-57. [PMID: 27431380 DOI: 10.2217/epi-2016-0008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aberrant epigenomic programming is a hallmark of acute myeloid leukemia. This is partially due to somatic mutations that perturb cytosine methylation, histone post-translational modifications and transcription factors. Remarkably, mutations in the IDH1 and IDH2 genes perturb the epigenome through all three of these mechanisms. Mutant IDH enzymes produce high levels of the oncometabolite (R)-2-hydroxyglutarate that competitively inhibits dioxygenase enzymes that modify methylcytosine to hydroxymethylcytosine and histone tail methylation. The development of IDH mutant specific inhibitors may now enable the therapeutic reprogramming of both layers of the epigenome spontaneously to revert the malignant phenotype of these leukemias and improve clinical outcome for acute myeloid leukemia patients with IDH mutations.
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Affiliation(s)
- Francine E Garrett-Bakelman
- Division of Hematology/Medical Oncology, Department of Medicine, Weill Cornell Medicine, 413 East 69th Street, BRB 14th floor, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology/Medical Oncology, Department of Medicine, Weill Cornell Medicine, 413 East 69th Street, BRB 14th floor, New York, NY, USA
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27
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Li S, Garrett-Bakelman FE, Chung SS, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Connon J, Sanders MA, Valk PJ, Bullinger L, Luger S, Becker MW, Lewis ID, To LB, D’Andrea RJ, Grimwade D, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Carroll M, Park CY, Neuberg DS, Levine RL, Melnick AM, Mason CE. Abstract LB-073: Epigenome evolution in relapsed acute myeloid leukemia. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute myeloid leukemia (AML) is a predominantly fatal hematopoietic malignancy with high inter-patient and intra-patient genetic and epigenetic heterogeneity. The prognosis of relapsed AML remains dismal, yet the epigenetic basis of relapse is still unclear. Here we investigated whether and how the epigenome evolution impacts AML progression with biological and clinical relevance.
Methods: We obtained clinical annotation and AML specimens from 138 patients with paired diagnosis and relapsed samples. We used normal bone marrow (NBM) as epigenetic/transcriptomic controls and patients’ matched germline DNA as genetic controls. We then performed DNA methylation sequencing (ERRBS), RNA-seq, and Exome-seq. For one patient with 5 serial time points, we performed whole genome sequencing (WGS), ERRBS, and single cell RNA-seq. We measured the epigenetic allele burden using a compositional entropy-based approach (Methclone) and methylation heterogeneity using epipolymorphism.
Results: We found that diagnosis stage epigenetic allele burden (ΔS < -90) was linked to an inferior clinical outcome (p = 0.0064, log-rank test of relapse-free survival). The higher significance in promoter regions implies the functional impact of epigenetic dynamics. Promoter epiallele shift was associated with more differential expression events (p = 3.8 × 10−6, Wilcoxon signed-rank test) and promoter epiallele diversity is significantly associated with single cell resolution transcriptional heterogeneity (p < 2.2 × 10−16, ANOVA test). The global methylation heterogeneity is decreased from diagnosis to relapse, indicating a selective impact of chemotherapy on epigenetic variability (p = 0.0056, paired Wilcoxon test).
We investigated epigenetic allele burden progression from diagnosis to relapse by classifying patients into three clusters using K-means clustering: those with 1) decreased, 2) stable, or 3) increased abundance of epiallele burden. No association was seen between epigenetic clusters and patterns of genetic evolution, and the genetic abundance is higher in Cluster 3 than Cluster 1 (p = 0.048, Wilcoxon test), indicating divergent paths of genetic and epigenetic evolution. We next examined differential expression in the epigenetic cluster samples at diagnosis compared to NBM. Cluster 1 specific genes were enriched for cell cycle processes, while Cluster 3 genes were enriched for immune responses (p < 0.001, gene ontology hypergeometric tests). Integrating WGS and ERRBS data showed that epiallele burden is more dynamic than somatic mutations; a significant increase in epiallele burden preceded a major increase of somatic mutational abundance.
Summary: Our results indicate that epigenetic dynamics may provide leukemia cells greater evolutionary fitness via transcriptional adaptation and is associated with clinical outcome. This provides an alternative mechanism of AML resilience during progression and a potential predictor of relapse.
Citation Format: Sheng Li, Francine E. Garrett-Bakelman, Stephen S. Chung, Todd Hricik, Franck Rapaport, Jay Patel, Richard Dillon, Priyanka Vijay, Anna L. Brown, Alexander E. Perl, Joy Connon, Mathijs A. Sanders, Peter J.M. Valk, Lars Bullinger, Selina Luger, Michael W. Becker, Ian D. Lewis, Luen Bik To, Richard J. D’Andrea, David Grimwade, Ruud Delwel, Bob Löwenberg, Hartmut Döhner, Konstanze Döhner, Monica L. Guzman, Duane C. Hassane, Gail J. Roboz, Martin Carroll, Christopher Y. Park, Donna S. Neuberg, Ross L. Levine, Ari M. Melnick, Christopher E. Mason. Epigenome evolution in relapsed acute myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-073.
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Affiliation(s)
- Sheng Li
- 1Weill Cornell Medical College, New York, NY
| | | | | | - Todd Hricik
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jay Patel
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Anna L. Brown
- 4SA Pathology, University of South Australia, and Royal Adelaide Hospital, Adelaide, Australia
| | | | - Joy Connon
- 5University of Pennsylvania, Philadelphia, PA
| | | | | | | | | | | | - Ian D. Lewis
- 9SA Pathology, University of South Australia, Royal Adelaide Hospital, and University of Adelaide, Adelaide, Australia
| | - Luen Bik To
- 4SA Pathology, University of South Australia, and Royal Adelaide Hospital, Adelaide, Australia
| | - Richard J. D’Andrea
- 4SA Pathology, University of South Australia, and Royal Adelaide Hospital, Adelaide, Australia
| | | | - Ruud Delwel
- 6Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bob Löwenberg
- 6Erasmus University Medical Center, Rotterdam, Netherlands
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Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJM, D'Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nat Med 2016; 22:792-9. [PMID: 27322744 PMCID: PMC4938719 DOI: 10.1038/nm.4125] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022]
Abstract
Genetic heterogeneity contributes to clinical outcome and progression of most tumors. Yet, little is known regarding allelic diversity for epigenetic compartments and almost no data exists for acute myeloid leukemia (AML). Here we examined epigenetic heterogeneity as assessed by cytosine methylation within defined genomic loci with four CpGs (epigenetic alleles), somatic mutations and transcriptomes of AML patient samples at serial time points. We observe that epigenetic allele burden is linked to inferior outcome and varies considerably during disease progression. Epigenetic and genetic allelic burden and patterning follow different patterns and kinetics during disease progression. We observed a subset of AMLs with high epiallele and low somatic mutation burden at diagnosis, a subset with high somatic mutation and lower epiallele burdens at diagnosis, and a subset with a mixed profile, suggesting distinct modes of tumor heterogeneity. Genes linked to promoter-associated epiallele shifts during tumor progression display increased single-cell transcriptional variance and differential expression, suggesting functional impact on gene regulation. Thus, genetic and epigenetic heterogeneity can occur with distinct kinetics, each likely able to impact biological and clinical features of tumors.
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Affiliation(s)
- Sheng Li
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Francine E Garrett-Bakelman
- Division of Hematology-Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Stephen S Chung
- Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mathijs A Sanders
- Erasmus University Medical Center, Department of Hematology, Rotterdam, the Netherlands
| | - Todd Hricik
- Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Franck Rapaport
- Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jay Patel
- Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard Dillon
- Department of Medical and Molecular Genetics, King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Priyanka Vijay
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Anna L Brown
- Center for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Department of Hematology, SA Pathology and Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Alexander E Perl
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joy Cannon
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Selina Luger
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael Becker
- University of Rochester Medical Center, Rochester, New York, USA
| | - Ian D Lewis
- Center for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia.,Department of Hematology, SA Pathology and Royal Adelaide Hospital, Adelaide, South Australia, Australia.,School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Luen Bik To
- Department of Hematology, SA Pathology and Royal Adelaide Hospital, Adelaide, South Australia, Australia.,School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Ruud Delwel
- Erasmus University Medical Center, Department of Hematology, Rotterdam, the Netherlands
| | - Bob Löwenberg
- Erasmus University Medical Center, Department of Hematology, Rotterdam, the Netherlands
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Monica L Guzman
- Division of Hematology-Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Duane C Hassane
- Division of Hematology-Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Gail J Roboz
- Division of Hematology-Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - David Grimwade
- Department of Medical and Molecular Genetics, King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Peter J M Valk
- Erasmus University Medical Center, Department of Hematology, Rotterdam, the Netherlands
| | - Richard J D'Andrea
- Center for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Department of Hematology, SA Pathology and Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher Y Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ross Levine
- Leukemia Service, Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ari M Melnick
- Division of Hematology-Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.,The Feil Family Brain and Mind Research Institute, New York, New York, USA
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Guryanova OA, Lieu YK, Garrett-Bakelman FE, Spitzer B, Glass JL, Shank K, Martinez ABV, Rivera SA, Durham BH, Rapaport F, Keller MD, Pandey S, Bastian L, Tovbin D, Weinstein AR, Teruya-Feldstein J, Abdel-Wahab O, Santini V, Mason CE, Melnick AM, Mukherjee S, Levine RL. Dnmt3a regulates myeloproliferation and liver-specific expansion of hematopoietic stem and progenitor cells. Leukemia 2015; 30:1133-42. [PMID: 26710888 PMCID: PMC4856586 DOI: 10.1038/leu.2015.358] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 12/22/2022]
Abstract
DNMT3A mutations are observed in myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), and acute myeloid leukemia (AML). Transplantation studies have elucidated an important role for Dnmt3a in stem cell self-renewal and in myeloid differentiation. Here we investigated the impact of conditional hematopoietic Dnmt3a loss on disease phenotype in primary mice. Mx1-Cre-mediated Dnmt3a ablation led to the development of a lethal, fully penetrant myeloproliferative neoplasm with myelodysplasia (MDS/MPN) characterized by peripheral cytopenias and by marked, progressive hepatomegaly. We detected expanded stem/progenitor populations in the liver of Dnmt3a-ablated mice. The MDS/MPN induced by Dnmt3a ablation was transplantable, including the marked hepatomegaly. Homing studies showed that Dnmt3a-deleted bone marrow cells preferentially migrated to the liver. Gene expression and DNA methylation analyses of progenitor cell populations identified differential regulation of hematopoietic regulatory pathways, including fetal liver hematopoiesis transcriptional programs. These data demonstrate that Dnmt3a ablation in the hematopoietic system leads to myeloid transformation in vivo, with cell autonomous aberrant tissue tropism and marked extramedullary hematopoiesis (EMH) with liver involvement. Hence, in addition to the established role of Dnmt3a in regulating self-renewal, Dnmt3a regulates tissue tropism and limits myeloid progenitor expansion in vivo.
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Affiliation(s)
- O A Guryanova
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y K Lieu
- Department of Medicine, Irving Cancer Research Center, Columbia University, New York, NY, USA
| | | | - B Spitzer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J L Glass
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - K Shank
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A B V Martinez
- Hematology Unit, University of Florence, Florence, Italy
| | - S A Rivera
- Department of Medicine, Irving Cancer Research Center, Columbia University, New York, NY, USA
| | - B H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Rapaport
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M D Keller
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Pandey
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - L Bastian
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Tovbin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A R Weinstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Teruya-Feldstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - O Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - V Santini
- Hematology Unit, University of Florence, Florence, Italy
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - A M Melnick
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - S Mukherjee
- Department of Medicine, Irving Cancer Research Center, Columbia University, New York, NY, USA
| | - R L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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30
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Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM. Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. J Vis Exp 2015:e52246. [PMID: 25742437 PMCID: PMC4354670 DOI: 10.3791/52246] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the use of a restriction enzyme followed by bisulfite conversion. Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) increases the biologically relevant genomic loci covered and has been used to profile cytosine methylation in DNA from human, mouse and other organisms. ERRBS initiates with restriction enzyme digestion of DNA to generate low molecular weight fragments for use in library preparation. These fragments are subjected to standard library construction for next generation sequencing. Bisulfite conversion of unmethylated cytosines prior to the final amplification step allows for quantitative base resolution of cytosine methylation levels in covered genomic loci. The protocol can be completed within four days. Despite low complexity in the first three bases sequenced, ERRBS libraries yield high quality data when using a designated sequencing control lane. Mapping and bioinformatics analysis is then performed and yields data that can be easily integrated with a variety of genome-wide platforms. ERRBS can utilize small input material quantities making it feasible to process human clinical samples and applicable in a range of research applications. The video produced demonstrates critical steps of the ERRBS protocol.
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Affiliation(s)
| | | | | | | | - Doron Betel
- Department of Medicine, Weill Cornell Medical College; Institute for Computational Biomedicine, Weill Cornell Medical College
| | - Alicia Alonso
- Department of Medicine, Weill Cornell Medical College
| | | | | | - Ari M Melnick
- Department of Medicine, Weill Cornell Medical College
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31
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Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics 2013; 14 Suppl 5:S10. [PMID: 23735126 PMCID: PMC3622633 DOI: 10.1186/1471-2105-14-s5-s10] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional analysis of enriched or whole-genome bisulfate conversion sequencing data, even though such data are increasingly common. Here, we describe an open-source, optimized method for determining empirically based DMRs (eDMR) from high-throughput sequence data that is applicable to enriched whole-genome methylation profiling datasets, as well as other globally enriched epigenetic modification data. RESULTS Here we show that our bimodal distribution model and weighted cost function for optimized regional methylation analysis provides accurate boundaries of regions harboring significant epigenetic modifications. Our algorithm takes the spatial distribution of CpGs into account for the enrichment assay, allowing for optimization of the definition of empirical regions for differential methylation. Combined with the dependent adjustment for regional p-value combination and DMR annotation, we provide a method that may be applied to a variety of datasets for rapid DMR analysis. Our method classifies both the directionality of DMRs and their genome-wide distribution, and we have observed that shows clinical relevance through correct stratification of two Acute Myeloid Leukemia (AML) tumor sub-types. CONCLUSIONS Our weighted optimization algorithm eDMR for calling DMRs extends an established DMR R pipeline (methylKit) and provides a needed resource in epigenomics. Our method enables an accurate and scalable way of finding DMRs in high-throughput methylation sequencing experiments. eDMR is available for download at http://code.google.com/p/edmr/.
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Affiliation(s)
- Sheng Li
- Department of Physiology and Biophysics,Weill Cornell Medical College, 1305 York Ave., New York, NY 10065, USA
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Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 2012; 13:R87. [PMID: 23034086 PMCID: PMC3491415 DOI: 10.1186/gb-2012-13-10-r87] [Citation(s) in RCA: 1138] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 10/03/2012] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation,
cellular specification and cancer development. Here, we describe an R package, methylKit, that
rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and
hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample
quality visualization, differential methylation analysis and annotation features, thus automating
and simplifying many of the steps for discerning statistically significant bases or regions of DNA
methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically
significant regions of differential methylation and stratify tumor subtypes. methylKit is available
at http://code.google.com/p/methylkit.
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Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJM, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 2012; 8:e1002781. [PMID: 22737091 PMCID: PMC3380828 DOI: 10.1371/journal.pgen.1002781] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 05/04/2012] [Indexed: 11/18/2022] Open
Abstract
We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns. As compared to normal controls, we observed widespread hypermethylation in IDH mutant AMLs, preferentially targeting promoter regions and CpG islands neighboring the transcription start sites of genes. In contrast, AMLs harboring translocations affecting the MLL gene displayed extensive loss of methylation of an almost mutually exclusive set of CpGs, which instead affected introns and distal intergenic CpG islands and shores. When analyzed in conjunction with gene expression profiles, it became apparent that these specific patterns of DNA methylation result in differing roles in gene expression regulation. However, despite this subtype-specific DNA methylation patterning, a much smaller set of CpG sites are consistently affected in both AML subtypes. Most CpG sites in this common core of aberrantly methylated CpGs were hypermethylated in both AML subtypes. Therefore, aberrant DNA methylation patterns in AML do not occur in a stereotypical manner but rather are highly specific and associated with specific driving genetic lesions. Acute myeloid leukemias (AML) are a group of malignancies that originate in the bone marrow. While many different genetic lesions have been linked to the different forms of this disease, it is also clear that these genetic lesions are not always sufficient to cause AML. DNA methylation plays a role in gene expression regulation, and abnormal distribution of DNA methylation has been observed in many cancers, including AML. Here we demonstrate that changes in DNA methylation in AML are not uniform across all AML subtypes, but rather they display unique patterns, which are closely linked to the underlying genetic lesions of each of the different forms of AML. Furthermore, these unique patterns of DNA methylation have different impacts on gene expression regulation in each AML subtype.
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Affiliation(s)
- Altuna Akalin
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, United States of America
| | - Matthias Kormaksson
- Department of Public Health, Weill Cornell Medical College, New York, New York, United States of America
| | - Jennifer Busuttil
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, United States of America
| | - Lu Zhang
- Illumina, Hayward, California, United States of America
| | | | - Thomas A. Milne
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Yongsheng Huang
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Debabrata Biswas
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York, United States of America
| | - Jay L. Hess
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - C. David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York, United States of America
| | - Robert G. Roeder
- Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York, United States of America
| | - Peter J. M. Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bob Löwenberg
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hugo F. Fernandez
- Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Elisabeth Paietta
- Cancer Center, Montefiore Medical Center–North Division, Bronx, New York, United States of America
| | - Martin S. Tallman
- Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (CEM); (AM); (MEF)
| | - Ari Melnick
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, United States of America
- Department of Pharmacology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (CEM); (AM); (MEF)
| | - Maria E. Figueroa
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (CEM); (AM); (MEF)
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