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Koschmann C, Al-Holou WN, Alonso MM, Anastas J, Bandopadhayay P, Barron T, Becher O, Cartaxo R, Castro MG, Chung C, Clausen M, Dang D, Doherty R, Duchatel R, Dun M, Filbin M, Franson A, Galban S, Garcia Moure M, Garton H, Gowda P, Marques JG, Hawkins C, Heath A, Hulleman E, Ji S, Jones C, Kilburn L, Kline C, Koldobskiy MA, Lim D, Lowenstein PR, Lu QR, Lum J, Mack S, Magge S, Marini B, Martin D, Marupudi N, Messinger D, Mody R, Morgan M, Mota M, Muraszko K, Mueller S, Natarajan SK, Nazarian J, Niculcea M, Nuechterlein N, Okada H, Opipari V, Pai MP, Pal S, Peterson E, Phoenix T, Prensner JR, Pun M, Raju GP, Reitman ZJ, Resnick A, Rogawski D, Saratsis A, Sbergio SG, Souweidane M, Stafford JM, Tzaridis T, Venkataraman S, Vittorio O, Wadden J, Wahl D, Wechsler-Reya RJ, Yadav VN, Zhang X, Zhang Q, Venneti S. A road map for the treatment of pediatric diffuse midline glioma. Cancer Cell 2024; 42:1-5. [PMID: 38039965 PMCID: PMC11067690 DOI: 10.1016/j.ccell.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/04/2023] [Accepted: 11/04/2023] [Indexed: 12/03/2023]
Abstract
Recent clinical trials for H3K27-altered diffuse midline gliomas (DMGs) have shown much promise. We present a consensus roadmap and identify three major barriers: (1) refinement of experimental models to include immune and brain-specific components; (2) collaboration among researchers, clinicians, and industry to integrate patient-derived data through sharing, transparency, and regulatory considerations; and (3) streamlining clinical efforts including biopsy, CNS-drug delivery, endpoint determination, and response monitoring. We highlight the importance of comprehensive collaboration to advance the understanding, diagnostics, and therapeutics for DMGs.
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Affiliation(s)
| | | | | | | | | | - Tara Barron
- Stanford University, Stanford, CA 94305, USA
| | - Oren Becher
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | - Chan Chung
- Daegu Gyeongbuk Institute of Science & Technology, Daegu, South Korea
| | | | - Derek Dang
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ryan Duchatel
- University of Newcastle, Callaghan, NSW 2308, Australia
| | - Matthew Dun
- University of Newcastle, Callaghan, NSW 2308, Australia
| | | | | | | | | | - Hugh Garton
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Allison Heath
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Sunjong Ji
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Chris Jones
- Division of Molecular Pathology, Institute for Cancer Research, London SM2 5NG, UK
| | | | - Cassie Kline
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Daniel Lim
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Q Richard Lu
- Cincinnati Children's Hospital Medical Center, and University of Cincinnati, Cincinnati, OH 45229, USA
| | - Joanna Lum
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Suresh Magge
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Donna Martin
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Rajen Mody
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mateus Mota
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Sabine Mueller
- University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of Zurich, Zurich, Switzerland
| | | | - Javad Nazarian
- Children's National, Washington, DC 20010, USA; University of Zurich, Zurich, Switzerland
| | | | - Nicholas Nuechterlein
- University of Michigan, Ann Arbor, MI 48109, USA; National Institutes of Health, Bethesda, MD, USA
| | - Hideho Okada
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | - Timothy Phoenix
- Cincinnati Children's Hospital Medical Center, and University of Cincinnati, Cincinnati, OH 45229, USA
| | | | - Matthew Pun
- University of Michigan, Ann Arbor, MI 48109, USA
| | - G Praveen Raju
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Adam Resnick
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | | | | | - Mark Souweidane
- Weill Cornell Medicine, New York Presbyterian and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James M Stafford
- Weill Cornell Medicine, New York Presbyterian and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Theophilos Tzaridis
- Herbert Irving Comprehensive Cancer Center and Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Orazio Vittorio
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Jack Wadden
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Wahl
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Xu Zhang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Qiang Zhang
- University of Michigan, Ann Arbor, MI 48109, USA
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Tetens AR, Martin AM, Arnold A, Novak OV, Idrizi A, Tryggvadottir R, Craig-Schwartz J, Liapodimitri A, Lunsford K, Barbato MI, Eberhart CG, Resnick AC, Raabe EH, Koldobskiy MA. DNA methylation landscapes in DIPG reveal methylome variability that can be modified pharmacologically. Neurooncol Adv 2024; 6:vdae023. [PMID: 38468866 PMCID: PMC10926944 DOI: 10.1093/noajnl/vdae023] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Background Diffuse intrinsic pontine glioma (DIPG) is a uniformly lethal brainstem tumor of childhood, driven by histone H3 K27M mutation and resultant epigenetic dysregulation. Epigenomic analyses of DIPG have shown global loss of repressive chromatin marks accompanied by DNA hypomethylation. However, studies providing a static view of the epigenome do not adequately capture the regulatory underpinnings of DIPG cellular heterogeneity and plasticity. Methods To address this, we performed whole-genome bisulfite sequencing on a large panel of primary DIPG specimens and applied a novel framework for analysis of DNA methylation variability, permitting the derivation of comprehensive genome-wide DNA methylation potential energy landscapes that capture intrinsic epigenetic variation. Results We show that DIPG has a markedly disordered epigenome with increasingly stochastic DNA methylation at genes regulating pluripotency and developmental identity, potentially enabling cells to sample diverse transcriptional programs and differentiation states. The DIPG epigenetic landscape was responsive to treatment with the hypomethylating agent decitabine, which produced genome-wide demethylation and reduced the stochasticity of DNA methylation at active enhancers and bivalent promoters. Decitabine treatment elicited changes in gene expression, including upregulation of immune signaling such as the interferon response, STING, and MHC class I expression, and sensitized cells to the effects of histone deacetylase inhibition. Conclusions This study provides a resource for understanding the epigenetic instability that underlies DIPG heterogeneity. It suggests the application of epigenetic therapies to constrain the range of epigenetic states available to DIPG cells, as well as the use of decitabine in priming for immune-based therapies.
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Affiliation(s)
- Ashley R Tetens
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Allison M Martin
- Pediatric Hematology-Oncology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Antje Arnold
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Orlandi V Novak
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jordyn Craig-Schwartz
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Athanasia Liapodimitri
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kayleigh Lunsford
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael I Barbato
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles G Eberhart
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eric H Raabe
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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3
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Fang Y, Ji Z, Zhou W, Abante J, Koldobskiy MA, Ji H, Feinberg A. DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence. Nucleic Acids Res 2023; 51:2046-2065. [PMID: 36762477 PMCID: PMC10018346 DOI: 10.1093/nar/gkad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/20/2022] [Revised: 12/02/2022] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
Epigenetic information defines tissue identity and is largely inherited in development through DNA methylation. While studied mostly for mean differences, methylation also encodes stochastic change, defined as entropy in information theory. Analyzing allele-specific methylation in 49 human tissue sample datasets, we find that methylation entropy is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Then applying information theory to 42 mouse embryo methylation datasets, we find that the contribution of methylation entropy to time- and tissue-specific patterns of development is comparable to the contribution of methylation mean, and methylation entropy is associated with sequence and chromatin features conserved with human. Moreover, methylation entropy is directly related to gene expression variability in development, suggesting a role for epigenetic entropy in developmental plasticity.
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Affiliation(s)
- Yuqi Fang
- Center for Epigenetics, Johns Hopkins University, 855 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhicheng Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jordi Abante
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University, 855 N. Wolfe St., Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University, 855 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, 600 N Wolfe St, Baltimore, MD 21205, USA
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Ktena YP, Koldobskiy MA, Barbato MI, Fu HH, Luznik L, Llosa NJ, Haile A, Klein OR, Liu C, Gamper CJ, Cooke KR. Donor T cell DNMT3a regulates alloreactivity in mouse models of hematopoietic stem cell transplantation. J Clin Invest 2022; 132:e158047. [PMID: 35608905 PMCID: PMC9246380 DOI: 10.1172/jci158047] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
DNA methyltransferase 3a (DNMT3a) is an important part of the epigenetic machinery that stabilizes patterns of activated T cell responses. We hypothesized that donor T cell DNMT3a regulates alloreactivity after allogeneic blood and marrow transplantation (allo-BMT). T cell conditional Dnmt3a KO mice were used as donors in allo-BMT models. Mice receiving allo-BMT from KO donors developed severe acute graft-versus-host disease (aGVHD), with increases in inflammatory cytokine levels and organ histopathology scores. KO T cells migrated and proliferated in secondary lymphoid organs earlier and demonstrated an advantage in trafficking to the small intestine. Donor T cell subsets were purified after BMT for whole-genome bisulfite sequencing (WGBS) and RNA-Seq. KO T cells had global methylation similar to that of WT cells, with distinct, localized areas of hypomethylation. Using a highly sensitive computational method, we produced a comprehensive profile of the altered epigenome landscape. Hypomethylation corresponded with changes in gene expression in several pathways of T cell signaling and differentiation. Additionally, Dnmt3a-KO T cells resulted in superior graft-versus-tumor activity. Our findings demonstrate a critical role for DNMT3a in regulating T cell alloreactivity and reveal pathways that control T cell tolerance. These results also provide a platform for deciphering clinical data that associate donor DNMT3a mutations with increased GVHD, decreased relapse, and improved survival.
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Affiliation(s)
- Yiouli P. Ktena
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Michael A. Koldobskiy
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Michael I. Barbato
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Han-Hsuan Fu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Leo Luznik
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicolas J. Llosa
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Azeb Haile
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Orly R. Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Christopher J. Gamper
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Kenneth R. Cooke
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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5
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Christodoulou I, Ho WJ, Marple A, Ravich JW, Tam A, Rahnama R, Fearnow A, Rietberg C, Yanik S, Solomou EE, Varadhan R, Koldobskiy MA, Bonifant CL. Engineering CAR-NK cells to secrete IL-15 sustains their anti-AML functionality but is associated with systemic toxicities. J Immunother Cancer 2021; 9:jitc-2021-003894. [PMID: 34896980 PMCID: PMC8655609 DOI: 10.1136/jitc-2021-003894] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [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] [Accepted: 11/14/2021] [Indexed: 01/15/2023] Open
Abstract
Background The prognosis of patients with recurrent/refractory acute myelogenous leukemia (AML) remains poor and cell-based immunotherapies hold promise to improve outcomes. Natural Killer (NK) cells can elicit an antileukemic response via a repertoire of activating receptors that bind AML surface ligands. NK-cell adoptive transfer is safe but thus far has shown limited anti-AML efficacy. Here, we aimed to overcome this limitation by engineering NK cells to express chimeric antigen receptors (CARs) to boost their anti-AML activity and interleukin (IL)-15 to enhance their persistence. Methods We characterized in detail NK-cell populations expressing a panel of AML (CD123)-specific CARs and/or IL-15 in vitro and in AML xenograft models. Results CARs with 2B4.ζ or 4-1BB.ζ signaling domains demonstrated greater cell surface expression and endowed NK cells with improved anti-AML activity in vitro. Initial in vivo testing revealed that only 2B4.ζ Chimeric Antigen Receptor (CAR)-NK cells had improved anti-AML activity in comparison to untransduced (UTD) and 4-1BB.ζ CAR-NK cells. However, the benefit was transient due to limited CAR-NK-cell persistence. Transgenic expression of secretory interleukin (sIL)-15 in 2B4.ζ CAR and UTD NK cells improved their effector function in the setting of chronic antigen simulation in vitro. Multiparameter flow analysis after chronic antigen exposure identified the expansion of unique NK-cell subsets. 2B4.ζ/sIL-15 CAR and sIL-15 NK cells maintained an overall activated NK-cell phenotype. This was confirmed by transcriptomic analysis, which revealed a highly proliferative and activated signature in these NK-cell groups. In vivo, 2B4.ζ/sIL-15 CAR-NK cells had potent anti-AML activity in one model, while 2B4.ζ/sIL-15 CAR and sIL-15 NK cells induced lethal toxicity in a second model. Conclusion Transgenic expression of CD123-CARs and sIL-15 enabled NK cells to function in the setting of chronic antigen exposure but was associated with systemic toxicities. Thus, our study provides the impetus to explore inducible and controllable expression systems to provide cytokine signals to AML-specific CAR-NK cells before embarking on early-phase clinical testing.
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Affiliation(s)
- Ilias Christodoulou
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Internal Medicine, University of Patras School of Health Sciences, Patras, Western Greece, Greece
| | - Won Jin Ho
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Marple
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonas W Ravich
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ada Tam
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruyan Rahnama
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam Fearnow
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Cambrynne Rietberg
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Sean Yanik
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Elena E Solomou
- Department of Internal Medicine, University of Patras School of Health Sciences, Patras, Western Greece, Greece
| | - Ravi Varadhan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Koldobskiy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Challice L Bonifant
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA .,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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6
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Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou W, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji H, Goutsias J, Feinberg AP. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nat Biomed Eng 2021; 5:360-376. [PMID: 33859388 PMCID: PMC8370714 DOI: 10.1038/s41551-021-00703-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/31/2019] [Accepted: 02/18/2021] [Indexed: 02/02/2023]
Abstract
In cancer, linking epigenetic alterations to drivers of transformation has been difficult, in part because DNA methylation analyses must capture epigenetic variability, which is central to tumour heterogeneity and tumour plasticity. Here, by conducting a comprehensive analysis, based on information theory, of differences in methylation stochasticity in samples from patients with paediatric acute lymphoblastic leukaemia (ALL), we show that ALL epigenomes are stochastic and marked by increased methylation entropy at specific regulatory regions and genes. By integrating DNA methylation and single-cell gene-expression data, we arrived at a relationship between methylation entropy and gene-expression variability, and found that epigenetic changes in ALL converge on a shared set of genes that overlap with genetic drivers involved in chromosomal translocations across the disease spectrum. Our findings suggest that an epigenetically driven gene-regulation network, with UHRF1 (ubiquitin-like with PHD and RING finger domains 1) as a central node, links genetic drivers and epigenetic mediators in ALL.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka A Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Challice L Bonifant
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick A Brown
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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7
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Rao F, Cha J, Xu J, Xu R, Vandiver MS, Tyagi R, Tokhunts R, Koldobskiy MA, Fu C, Barrow R, Wu M, Fiedler D, Barrow JC, Snyder SH. Inositol Pyrophosphates Mediate the DNA-PK/ATM-p53 Cell Death Pathway by Regulating CK2 Phosphorylation of Tti1/Tel2. Mol Cell 2020; 79:702. [PMID: 32822581 DOI: 10.1016/j.molcel.2020.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Park TS, Zimmerlin L, Evans-Moses R, Thomas J, Huo JS, Kanherkar R, He A, Ruzgar N, Grebe R, Bhutto I, Barbato M, Koldobskiy MA, Lutty G, Zambidis ET. Vascular progenitors generated from tankyrase inhibitor-regulated naïve diabetic human iPSC potentiate efficient revascularization of ischemic retina. Nat Commun 2020; 11:1195. [PMID: 32139672 PMCID: PMC7058090 DOI: 10.1038/s41467-020-14764-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 06/20/2019] [Accepted: 01/28/2020] [Indexed: 01/15/2023] Open
Abstract
Here, we report that the functionality of vascular progenitors (VP) generated from normal and disease-primed conventional human induced pluripotent stem cells (hiPSC) can be significantly improved by reversion to a tankyrase inhibitor-regulated human naïve epiblast-like pluripotent state. Naïve diabetic vascular progenitors (N-DVP) differentiated from patient-specific naïve diabetic hiPSC (N-DhiPSC) possessed higher vascular functionality, maintained greater genomic stability, harbored decreased lineage-primed gene expression, and were more efficient in migrating to and re-vascularizing the deep neural layers of the ischemic retina than isogenic diabetic vascular progenitors (DVP). These findings suggest that reprogramming to a stable naïve human pluripotent stem cell state may effectively erase dysfunctional epigenetic donor cell memory or disease-associated aberrations in patient-specific hiPSC. More broadly, tankyrase inhibitor-regulated naïve hiPSC (N-hiPSC) represent a class of human stem cells with high epigenetic plasticity, improved multi-lineage functionality, and potentially high impact for regenerative medicine.
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Affiliation(s)
- Tea Soon Park
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ludovic Zimmerlin
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca Evans-Moses
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Justin Thomas
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jeffrey S Huo
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Riya Kanherkar
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alice He
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nensi Ruzgar
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rhonda Grebe
- Wilmer Eye Institute, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Imran Bhutto
- Wilmer Eye Institute, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Barbato
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael A Koldobskiy
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gerard Lutty
- Wilmer Eye Institute, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Koldobskiy MA, Abante J, Jenkinson G, Pujadas E, Tetens A, Zhao F, Tryggvadottir R, Idrizi A, Reinisch A, Majeti R, Goutsias J, Feinberg AP. A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML. Epigenetics 2020; 15:841-858. [PMID: 32114880 DOI: 10.1080/15592294.2020.1734149] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/24/2022] Open
Abstract
Translocations of the KMT2A (MLL) gene define a biologically distinct and clinically aggressive subtype of acute myeloid leukaemia (AML), marked by a characteristic gene expression profile and few cooperating mutations. Although dysregulation of the epigenetic landscape in this leukaemia is particularly interesting given the low mutation frequency, its comprehensive analysis using whole genome bisulphite sequencing (WGBS) has not been previously performed. Here we investigated epigenetic dysregulation in nine MLL-rearranged (MLL-r) AML samples by comparing them to six normal myeloid controls, using a computational method that encapsulates mean DNA methylation measurements along with analyses of methylation stochasticity. We discovered a dramatically altered epigenetic profile in MLL-r AML, associated with genome-wide hypomethylation and a markedly increased DNA methylation entropy reflecting an increasingly disordered epigenome. Methylation discordance mapped to key genes and regulatory elements that included bivalent promoters and active enhancers. Genes associated with significant changes in methylation stochasticity recapitulated known MLL-r AML expression signatures, suggesting a role for the altered epigenetic landscape in the transcriptional programme initiated by MLL translocations. Accordingly, we established statistically significant associations between discordances in methylation stochasticity and gene expression in MLL-r AML, thus providing a link between the altered epigenetic landscape and the phenotype.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University , Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Whitaker Biomedical Engineering Institute, Johns Hopkins University , Baltimore, MD, USA.,Department of Health Science Research, Mayo Clinic , Rochester, MN, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai , New York, NY, USA
| | - Ashley Tetens
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Feifei Zhao
- Department of Medicine, Division of Hematology, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, CA, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Andreas Reinisch
- Department of Medicine, Division of Hematology, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, CA, USA.,Division of Hematology, Medical University of Graz , Graz, Austria
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, CA, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University , Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA
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10
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Jenkinson G, Abante J, Koldobskiy MA, Feinberg AP, Goutsias J. Ranking genomic features using an information-theoretic measure of epigenetic discordance. BMC Bioinformatics 2019; 20:175. [PMID: 30961526 PMCID: PMC6454630 DOI: 10.1186/s12859-019-2777-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/14/2018] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It is therefore crucial to know which genes, or other genomic features of interest, exhibit significant discordance in DNA methylation between two phenotypes. We have previously proposed an approach for ranking genes based on methylation discordance within their promoter regions, determined by centering a window of fixed size at their transcription start sites. However, we cannot use this method to identify statistically significant genomic features and handle features of variable length and with missing data. Results We present a new approach for computing the statistical significance of methylation discordance within genomic features of interest in single and multiple test/reference studies. We base the proposed method on a well-articulated hypothesis testing problem that produces p- and q-values for each genomic feature, which we then use to identify and rank features based on the statistical significance of their epigenetic dysregulation. We employ the information-theoretic concept of mutual information to derive a novel test statistic, which we can evaluate by computing Jensen-Shannon distances between the probability distributions of methylation in a test and a reference sample. We design the proposed methodology to simultaneously handle biological, statistical, and technical variability in the data, as well as variable feature lengths and missing data, thus enabling its wide-spread use on any list of genomic features. This is accomplished by estimating, from reference data, the null distribution of the test statistic as a function of feature length using generalized additive regression models. Differential assessment, using normal/cancer data from healthy fetal tissue and pediatric high-grade glioma patients, illustrates the potential of our approach to greatly facilitate the exploratory phases of clinically and biologically relevant methylation studies. Conclusions The proposed approach provides the first computational tool for statistically testing and ranking genomic features of interest based on observed DNA methylation discordance in comparative studies that accounts, in a rigorous manner, for biological, statistical, and technical variability in methylation data, as well as for variability in feature length and for missing data. Electronic supplementary material The online version of this article (10.1186/s12859-019-2777-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Garrett Jenkinson
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Currently with Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
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11
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Abstract
This year is the tenth anniversary of the publication in this journal of a model suggesting the existence of 'tumour progenitor genes'. These genes are epigenetically disrupted at the earliest stages of malignancies, even before mutations, and thus cause altered differentiation throughout tumour evolution. The past decade of discovery in cancer epigenetics has revealed a number of similarities between cancer genes and stem cell reprogramming genes, widespread mutations in epigenetic regulators, and the part played by chromatin structure in cellular plasticity in both development and cancer. In the light of these discoveries, we suggest here a framework for cancer epigenetics involving three types of genes: 'epigenetic mediators', corresponding to the tumour progenitor genes suggested earlier; 'epigenetic modifiers' of the mediators, which are frequently mutated in cancer; and 'epigenetic modulators' upstream of the modifiers, which are responsive to changes in the cellular environment and often linked to the nuclear architecture. We suggest that this classification is helpful in framing new diagnostic and therapeutic approaches to cancer.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe Street, Rangos 570, Baltimore, Maryland 21205, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe Street, Rangos 570, Baltimore, Maryland 21205, USA
| | - Anita Göndör
- Department of Microbiology, Tumour and Cell Biology, Nobels väg 16, Karolinska Institutet, S-171 77 Stockholm, Sweden
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13
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Kim S, Kim SF, Maag D, Maxwell MJ, Resnick AC, Juluri KR, Chakraborty A, Koldobskiy MA, Cha SH, Barrow R, Snowman AM, Snyder SH. Amino acid signaling to mTOR mediated by inositol polyphosphate multikinase. Cell Metab 2011; 13:215-21. [PMID: 21284988 PMCID: PMC3042716 DOI: 10.1016/j.cmet.2011.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/01/2010] [Accepted: 12/06/2010] [Indexed: 10/18/2022]
Abstract
mTOR complex 1 (mTORC1; mammalian target of rapamycin [mTOR] in complex with raptor) is a key regulator of protein synthesis and cell growth in response to nutrient amino acids. Here we report that inositol polyphosphate multikinase (IPMK), which possesses both inositol phosphate kinase and lipid kinase activities, regulates amino acid signaling to mTORC1. This regulation is independent of IPMK's catalytic function, instead reflecting its binding with mTOR and raptor, which maintains the mTOR-raptor association. Thus, IPMK appears to be a physiologic mTOR cofactor, serving as a determinant of mTORC1 stability and amino acid-induced mTOR signaling. Substances that block IPMK-mTORC1 binding may afford therapeutic benefit in nutrient amino acid-regulated conditions such as obesity and diabetes.
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Affiliation(s)
- Seyun Kim
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Yang ZQ, Kwok BHB, Lin S, Koldobskiy MA, Crews CM, Danishefsky SJ. Simplified synthetic TMC-95A/B analogues retain the potency of proteasome inhibitory activity. Chembiochem 2003; 4:508-13. [PMID: 12794861 PMCID: PMC2556569 DOI: 10.1002/cbic.200300560] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [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: 01/15/2003] [Indexed: 12/21/2022]
Abstract
The proteasome regulates diverse intracellular processes, including cell-cycle progression, antigen presentation, and inflammatory response. Selective inhibitors of the proteasome have great therapeutic potential for the treatment of cancer and inflammatory disorders. Natural cyclic peptides TMC-95A and B represent a new class of noncovalent, selective proteasome inhibitors. To explore the structure-activity relationship of this class of proteasome inhibitors, a series of TMC-95A/B analogues were prepared and analyzed. We found that the unique enamide functionality at the C8 position of TMC-95s can be replaced with a simple allylamide. The asymmetric center at C36 that distinguishes TMC-95A from TMC-95B but which necessitates a complicated separation of the two compounds can be eliminated. Therefore, these findings could lead to the development of more accessible simple analogues as potential therapeutic agents.
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Affiliation(s)
- Zhi-Qiang Yang
- Laboratory of Bioorganic Chemistry, Sloan Kettering Institute for Cancer Research, 1275 York Avenue, New York 10021 (USA), Fax: (+1) 212-772-8691
| | - Benjamin H. B. Kwok
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06520-8103 (USA)
| | - Songnian Lin
- Laboratory of Bioorganic Chemistry, Sloan Kettering Institute for Cancer Research, 1275 York Avenue, New York 10021 (USA), Fax: (+1) 212-772-8691
| | - Michael A. Koldobskiy
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06520-8103 (USA)
| | - Craig M. Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06520-8103 (USA)
- Department of Pharmacology, Yale University, New Haven, CT 06520 (USA)
- Department of Chemistry, Yale University, New Haven, CT 06520 (USA)
| | - Samuel J. Danishefsky
- Laboratory of Bioorganic Chemistry, Sloan Kettering Institute for Cancer Research, 1275 York Avenue, New York 10021 (USA), Fax: (+1) 212-772-8691
- Department of Chemistry, Havemeyer Hall, Columbia University, New York 10027 (USA)
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