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Yao X, Xing M, Ooi WF, Tan P, Teh BT. Epigenomic Consequences of Coding and Noncoding Driver Mutations. Trends Cancer 2016; 2:585-605. [PMID: 28741489 DOI: 10.1016/j.trecan.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022]
Abstract
Chromatin alterations are integral to the pathogenic process of cancer, as demonstrated by recent discoveries of frequent mutations in chromatin-modifier genes and aberrant DNA methylation states in different cancer types. Progress is being made on elucidating how chromatin alterations, and how proteins catalyzing these alterations, mechanistically contribute to tissue-specific tumorigenesis. In parallel, technologies enabling the genome-wide profiling of histone modifications have revealed the existence of noncoding driver genetic alterations in cancer. In this review, we survey the current knowledge of coding and noncoding cancer drivers, and discuss their impact on the chromatin landscape. Translational implications of these findings for novel cancer therapies are also presented.
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Affiliation(s)
- Xiaosai Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Manjie Xing
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore.
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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302
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Hlady RA, Roy S, Dutta S, Datta K, Opavsky R. Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma. PLoS Genet 2016; 12:e1006334. [PMID: 27690235 PMCID: PMC5045215 DOI: 10.1371/journal.pgen.1006334] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/31/2016] [Indexed: 12/29/2022] Open
Abstract
DNA methyltransferase 3A (DNMT3A) is an enzyme involved in DNA methylation that is frequently mutated in human hematologic malignancies. We have previously shown that inactivation of Dnmt3a in hematopoietic cells results in chronic lymphocytic leukemia in mice. Here we show that 12% of Dnmt3a-deficient mice develop CD8+ mature peripheral T cell lymphomas (PTCL) and 29% of mice are affected by both diseases. 10% of Dnmt3a+/- mice develop lymphomas, suggesting that Dnmt3a is a haploinsufficient tumor suppressor in PTCL. DNA methylation was deregulated genome-wide with 10-fold more hypo- than hypermethylated promoters and enhancers, demonstrating that hypomethylation is a major event in the development of PTCL. Hypomethylated promoters were enriched for binding sites of transcription factors AML1, NF-κB and OCT1, implying the transcription factors potential involvement in Dnmt3a-associated methylation. Whereas 71 hypomethylated genes showed an increased expression in PTCL, only 3 hypermethylated genes were silenced, suggesting that cancer-specific hypomethylation has broader effects on the transcriptome of cancer cells than hypermethylation. Interestingly, transcriptomes of Dnmt3a+/- and Dnmt3aΔ/Δ lymphomas were largely conserved and significantly overlapped with those of human tumors. Importantly, we observed downregulation of tumor suppressor p53 in Dnmt3a+/- and Dnmt3aΔ/Δ lymphomas as well as in pre-tumor thymocytes from 9 months old but not 6 weeks old Dnmt3a+/- tumor-free mice, suggesting that p53 downregulation is chronologically an intermediate event in tumorigenesis. Decrease in p53 is likely an important event in tumorigenesis because its overexpression inhibited proliferation in mouse PTCL cell lines, suggesting that low levels of p53 are important for tumor maintenance. Altogether, our data link the haploinsufficient tumor suppressor function of Dnmt3a in the prevention of mouse mature CD8+ PTCL indirectly to a bona fide tumor suppressor of T cell malignancies p53. Global deregulation of cytosine methylation is an epigenetic hallmark of hematologic malignancies that may promote tumorigenesis by silencing tumor suppressor genes, upregulating oncogenes, and inducing genomic instability. DNA methyltransferase 3a (DNMT3A) is one of the three catalytically active enzymes responsible for cytosine methylation and one of the most frequently mutated genes in myeloid and T cell malignancies. Its role in malignant hematopoiesis, however, remains poorly understood. Here we show that Dnmt3a is a haploinsufficient tumor suppressor in the prevention of peripheral T cell lymphomas in mice. Our molecular studies identified a large number of genes deregulated in the absence of Dnmt3a that may be putative drivers of oncogenesis. We also show that downregulation of the tumor suppressor p53 is an important event in the development of mouse T cell lymphomas. Thus, this study establishes a novel mouse model to elucidate how epigenetic deregulation of transcription contributes to the pathogenesis of T cell lymphomas.
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Affiliation(s)
- Staci L. Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - G. Michael Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ryan A. Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sohini Roy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Samikshan Dutta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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303
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Possible role of intragenic DNA hypermethylation in gene silencing of the tumor suppressor gene NR4A3 in acute myeloid leukemia. Leuk Res 2016; 50:85-94. [PMID: 27697661 DOI: 10.1016/j.leukres.2016.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 08/09/2016] [Accepted: 09/26/2016] [Indexed: 12/29/2022]
Abstract
Expression of the tumor suppressor gene NR4A3 is silenced in the blasts of acute myeloid leukemia (AML), irrespective of the karyotype. Although the transcriptional reactivation of NR4A3 is considered to have a broad-spectrum anti-leukemic effect, the therapeutic modalities targeting this gene have been hindered by our minimal understanding of the transcriptional mechanisms regulating its expression, particularly in human AML. Here we show the role of intragenic DNA hypermethylation in reducing the expression of NR4A3 in AML. Bisulfite sequencing analysis revealed that CpG sites at the intragenic region encompassing exon 3 of NR4A3, but not the promoter region, are hypermethylated in AML cell lines and primary AML cells. A DNA methyltransferase inhibitor restored the expression of NR4A3 following a reduction in DNA methylation levels at intragenic CpG sites. The in silico data revealed an enrichment of H3K4me1 and H2A.Z at exon 3 of NR4A3 in human non-malignant cells but that was excluded specifically in leukemia cells with CpG hypermethylation. This suggests that exon 3 represents a functional regulatory element involved in the transcriptional regulation of NR4A3. Our findings improve the current understanding of the mechanism underlying NR4A3 silencing and facilitate the development of NR4A3-targeted therapy.
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304
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Expression of immunoproteasome genes is regulated by cell-intrinsic and -extrinsic factors in human cancers. Sci Rep 2016; 6:34019. [PMID: 27659694 PMCID: PMC5034284 DOI: 10.1038/srep34019] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/06/2016] [Indexed: 01/07/2023] Open
Abstract
Based on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas, we report that expression of constitutive proteasome (CP) genes (PSMB5, PSMB6, PSMB7) and immunoproteasome (IP) genes (PSMB8, PSMB9, PSMB10) is increased in most cancer types. In breast cancer, expression of IP genes was determined by the abundance of tumor infiltrating lymphocytes and high expression of IP genes was associated with longer survival. In contrast, IP upregulation in acute myeloid leukemia (AML) was a cell-intrinsic feature that was not associated with longer survival. Expression of IP genes in AML was IFN-independent, correlated with the methylation status of IP genes, and was particularly high in AML with an M5 phenotype and/or MLL rearrangement. Notably, PSMB8 inhibition led to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. Co-clustering analysis revealed that genes correlated with IP subunits in non-M5 AMLs were primarily implicated in immune processes. However, in M5 AML, IP genes were primarily co-regulated with genes involved in cell metabolism and proliferation, mitochondrial activity and stress responses. We conclude that M5 AML cells can upregulate IP genes in a cell-intrinsic manner in order to resist cell stress.
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305
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Abstract
Understanding the molecular pathogenesis of peripheral T cell lymphomas (PTCLs) has lagged behind that of B cell lymphomas due to disease rarity. However, novel approaches are gradually clarifying these mechanisms, and gene profiling has identified specific signaling pathways governing PTCL cell survival and growth. For example, genetic alterations have been discovered, including signal transducer and activator of transcription (STAT)3 and STAT5b mutations in several PTCLs, disease-specific ras homolog family member A (RHOA) mutations in angioimmunoblastic T cell lymphoma (AITL), and recurrent translocations at the dual specificity phosphatase 22 (DUSP22) locus in anaplastic lymphoma receptor tyrosine kinase (ALK)-negative anaplastic large cell lymphomas (ALCLs). Intriguingly, some PTCL-relevant mutations are seen in apparently normal blood cells as well as tumor cells, while others are confined to tumor cells. These data have dramatically changed our understanding of PTCL origins: once considered to originate from mature T lymphocytes, some PTCLs are now believed to emerge from immature hematopoietic progenitor cells.
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Affiliation(s)
- Mamiko Sakata-Yanagimoto
- Department of Hematology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
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306
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Ho C, Kluk MJ. Molecular Pathology: Predictive, Prognostic, and Diagnostic Markers in Lymphoid Neoplasms. Surg Pathol Clin 2016; 9:489-521. [PMID: 27523974 DOI: 10.1016/j.path.2016.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lymphoid neoplasms show great diversity in morphology, immunophenotypic profile, and postulated cells of origin, which also reflects the variety of genetic alterations within this group of tumors. This review discusses many of the currently known genetic alterations in selected mature B-cell and T-cell lymphoid neoplasms, and their significance as diagnostic, prognostic, and therapeutic markers. Given the rapidly increasing number of genetic alterations that have been described in this group of tumors, and that the clinical significance of many is still being studied, this is not an entirely exhaustive review of all of the genetic alterations that have been reported.
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Affiliation(s)
- Caleb Ho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Michael J Kluk
- Department of Pathology, Weill Cornell Medical College, 525 East 68th Street, Mailbox #79, F-540, New York, NY 10065, USA.
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307
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Kyono Y, Subramani A, Ramadoss P, Hollenberg AN, Bonett RM, Denver RJ. Liganded Thyroid Hormone Receptors Transactivate the DNA Methyltransferase 3a Gene in Mouse Neuronal Cells. Endocrinology 2016; 157:3647-57. [PMID: 27387481 PMCID: PMC5007891 DOI: 10.1210/en.2015-1529] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Thyroid hormone (T3) is essential for proper neurological development. The hormone, bound to its receptors, regulates gene transcription in part by modulating posttranslational modifications of histones. Methylation of DNA, which is established by the de novo DNA methyltransferase (DNMT)3a and DNMT3b, and maintained by DNMT1 is another epigenetic modification influencing gene transcription. The expression of Dnmt3a, but not other Dnmt genes, increases in mouse brain in parallel with the postnatal rise in plasma [T3]. We found that treatment of the mouse neuroblastoma cell line Neuro2a[TRβ1] with T3 caused rapid induction of Dnmt3a mRNA, which was resistant to protein synthesis inhibition, supporting that it is a direct T3-response gene. Injection of T3 into postnatal day 6 mice increased Dnmt3a mRNA in the brain by 1 hour. Analysis of two chromatin immunoprecipitation-sequencing datasets, and targeted analyses using chromatin immunoprecipitation, transfection-reporter assays, and in vitro DNA binding identified 2 functional T3-response elements (TREs) at the mouse Dnmt3a locus located +30.3 and +49.3 kb from the transcription start site. Thyroid hormone receptors associated with both of these regions in mouse brain chromatin, but with only 1 (+30.3 kb) in Neuro2a[TRβ1] cells. Deletion of the +30.3-kb TRE using CRISPR/Cas9 genome editing eliminated or strongly reduced the Dnmt3a mRNA response to T3. Bioinformatics analysis showed that both TREs are highly conserved among eutherian mammals. Thyroid regulation of Dnmt3a may be an evolutionarily conserved mechanism for modulating global changes in DNA methylation during postnatal neurological development.
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Affiliation(s)
- Yasuhiro Kyono
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Arasakumar Subramani
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Preeti Ramadoss
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Anthony N Hollenberg
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Ronald M Bonett
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Robert J Denver
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
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308
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Upchurch GM, Haney SL, Opavsky R. Aberrant Promoter Hypomethylation in CLL: Does It Matter for Disease Development? Front Oncol 2016; 6:182. [PMID: 27563627 PMCID: PMC4980682 DOI: 10.3389/fonc.2016.00182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Over the last 30 years, studies of aberrant DNA methylation in hematologic malignancies have been dominated by the primary focus of understanding promoter hypermethylation. These efforts not only resulted in a better understanding of the basis of epigenetic silencing of tumor suppressor genes but also resulted in approval of hypomethylating agents for the treatment of several malignancies, such as myelodysplastic syndrome and acute myeloid leukemia. Recent advances in global methylation profiling coupled with the use of mouse models suggest that aberrant promoter hypomethylation is also a frequent event in hematologic malignancies, particularly in chronic lymphocytic leukemia (CLL). Promoter hypomethylation affects gene expression and, therefore, may play an important role in disease pathogenesis. Here, we review recent findings and discuss the potential involvement of aberrant promoter hypomethylation in CLL.
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Affiliation(s)
- Garland Michael Upchurch
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, NE , USA
| | - Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center , Omaha, NE , USA
| | - Rene Opavsky
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA; Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE, USA
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309
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Abstract
Enhancer elements function as the logic gates of the genetic regulatory circuitry. One of their most important functions is the integration of extracellular signals with intracellular cell fate information to generate cell type-specific transcriptional responses. Mutations occurring in cancer often misregulate enhancers that normally control the signal-dependent expression of growth-related genes. This misregulation can result from trans-acting mechanisms, such as activation of the transcription factors or epigenetic regulators that control enhancer activity, or can be caused in cis by direct mutations that alter the activity of the enhancer or its target gene specificity. These processes can generate tumour type-specific super-enhancers and establish a 'locked' gene regulatory state that drives the uncontrolled proliferation of cancer cells. Here, we review the role of enhancers in cancer, and their potential as therapeutic targets.
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Affiliation(s)
- Inderpreet Sur
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
- Genome-Scale Biology Program, University of Helsinki, Biomedicum, PO Box 63, Helsinki 00014, Finland
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310
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miR-449a inhibits colorectal cancer progression by targeting SATB2. Oncotarget 2016; 8:100975-100988. [PMID: 29254139 PMCID: PMC5731849 DOI: 10.18632/oncotarget.10900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/06/2016] [Indexed: 12/16/2022] Open
Abstract
miR-449a has been reported to act as a tumor suppressor in several cancers, however, it is controversial whether it inhibits tumor growth in colorectal cancer. The mechanisms underlying its expression and functions in colorectal cancers are still largely unknown. SATB2 is a sensitive and specific marker for CRC diagnosis. However, the mechanisms by which the expression and functions of SATB2 are regulated still remain to be clarified. We investigated the expression and functional significance of miR-449a and SATB2 and the mechanisms of their dysregulation in human CRC cells. miR-449a overexpression or SATB2 depletion inhibited tumor growth and promoted apoptosis in colorectal tumor cells in vitro and in xenograft mouse model, partially by downregulating SATB2. Expression of miR-449a was increased epigenetically via knocking down their targets, particularly SATB2. miR-449a was downregulated and STAB2 expression was upregulated in human CRCs. Their expressions were significantly associated with overall survival of CRC patients. Our findings demonstrate the existence of a miR-449a-SATB2 negative feedback loop that maintains low levels of miR-449a as well as high level of SATB2, thereby promoting CRC development.
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311
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Abstract
Mammalian embryonic development is a tightly regulated process that, from a single zygote, produces a large number of cell types with hugely divergent functions. Distinct cellular differentiation programmes are facilitated by tight transcriptional and epigenetic regulation. However, the contribution of epigenetic regulation to tissue homeostasis after the completion of development is less well understood. In this Review, we explore the effects of epigenetic dysregulation on adult stem cell function. We conclude that, depending on the tissue type and the epigenetic regulator affected, the consequences range from negligible to stem cell malfunction and disruption of tissue homeostasis, which may predispose to diseases such as cancer.
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312
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Lu R, Wang P, Parton T, Zhou Y, Chrysovergis K, Rockowitz S, Chen WY, Abdel-Wahab O, Wade PA, Zheng D, Wang GG. Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development. Cancer Cell 2016; 30:92-107. [PMID: 27344947 PMCID: PMC4945461 DOI: 10.1016/j.ccell.2016.05.008] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 03/03/2016] [Accepted: 05/19/2016] [Indexed: 12/19/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) is frequently mutated in hematological cancers; however, the underlying oncogenic mechanism remains elusive. Here, we report that the DNMT3A mutational hotspot at Arg882 (DNMT3A(R882H)) cooperates with NRAS mutation to transform hematopoietic stem/progenitor cells and induce acute leukemia development. Mechanistically, DNMT3A(R882H) directly binds to and potentiates transactivation of stemness genes critical for leukemogenicity including Meis1, Mn1, and Hoxa gene cluster. DNMT3A(R882H) induces focal epigenetic alterations, including CpG hypomethylation and concurrent gain of active histone modifications, at cis-regulatory elements such as enhancers to facilitate gene transcription. CRISPR/Cas9-mediated ablation of a putative Meis1 enhancer carrying DNMT3A(R882H)-induced DNA hypomethylation impairs Meis1 expression. Importantly, DNMT3A(R882H)-induced gene-expression programs can be repressed through Dot1l inhibition, providing an attractive therapeutic strategy for DNMT3A-mutated leukemias.
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MESH Headings
- Animals
- Arginine/genetics
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA Methyltransferase 3A
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genes, ras
- Homeodomain Proteins/genetics
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Methyltransferases/antagonists & inhibitors
- Mice
- Mutation
- Myeloid Ecotropic Viral Integration Site 1 Protein
- Neoplasm Proteins/genetics
- Neoplasms, Experimental
- Promoter Regions, Genetic
- Stem Cells/cytology
- Stem Cells/pathology
- Tumor Cells, Cultured
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Affiliation(s)
- Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ping Wang
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Trevor Parton
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yang Zhou
- Department of Pathology and Laboratory Medicine, McAllister Heart Institute, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Kaliopi Chrysovergis
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
| | - Shira Rockowitz
- Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Paul A Wade
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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313
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Chisholm RH, Lorenzi T, Clairambault J. Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation. Biochim Biophys Acta Gen Subj 2016; 1860:2627-45. [PMID: 27339473 DOI: 10.1016/j.bbagen.2016.06.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/25/2016] [Accepted: 06/05/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level. SCOPE OF REVIEW We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies. MAJOR CONCLUSIONS Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies. GENERAL SIGNIFICANCE Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Rebecca H Chisholm
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Tommaso Lorenzi
- School of Mathematics and Statistics, University of St Andrews, North Haugh, KY16 9SS, St Andrews, Scotland, United Kingdom. http://www.tommasolorenzi.com
| | - Jean Clairambault
- INRIA Paris, MAMBA team, 2, rue Simone Iff, CS 42112, 75589 Paris Cedex 12, France; Sorbonne Universités, UPMC Univ. Paris 6, UMR 7598, Laboratoire Jacques-Louis Lions, Boîte courrier 187, 4 Place Jussieu, 75252 Paris Cedex 05, France.
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314
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Yang L, Rodriguez B, Mayle A, Park HJ, Lin X, Luo M, Jeong M, Curry CV, Kim SB, Ruau D, Zhang X, Zhou T, Zhou M, Rebel VI, Challen GA, Gottgens B, Lee JS, Rau R, Li W, Goodell MA. DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias. Cancer Cell 2016; 29:922-934. [PMID: 27300438 PMCID: PMC4908977 DOI: 10.1016/j.ccell.2016.05.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 02/29/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
DNMT3A, the gene encoding the de novo DNA methyltransferase 3A, is among the most frequently mutated genes in hematologic malignancies. However, the mechanisms through which DNMT3A normally suppresses malignancy development are unknown. Here, we show that DNMT3A loss synergizes with the FLT3 internal tandem duplication in a dose-influenced fashion to generate rapid lethal lymphoid or myeloid leukemias similar to their human counterparts. Loss of DNMT3A leads to reduced DNA methylation, predominantly at hematopoietic enhancer regions in both mouse and human samples. Myeloid and lymphoid diseases arise from transformed murine hematopoietic stem cells. Broadly, our findings support a role for DNMT3A as a guardian of the epigenetic state at enhancer regions, critical for inhibition of leukemic transformation.
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Affiliation(s)
- Liubin Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin Rodriguez
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allison Mayle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hyun Jung Park
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xueqiu Lin
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Bioinformatics, School of Life sciences and Technology, Tongji University, Shanghai 20092, China
| | - Min Luo
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Choladda V. Curry
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sang-Bae Kim
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - David Ruau
- Wellcome Trust/MRC Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Xiaotian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ting Zhou
- Greehey Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | - Vivienne I. Rebel
- Greehey Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Grant A. Challen
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | - Ju-Seog Lee
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Rachel Rau
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Margaret A. Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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315
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Siraj AK, Masoodi T, Bu R, Beg S, Al-Sobhi SS, Al-Dayel F, Al-Dawish M, Alkuraya FS, Al-Kuraya KS. Genomic Profiling of Thyroid Cancer Reveals a Role for Thyroglobulin in Metastasis. Am J Hum Genet 2016; 98:1170-1180. [PMID: 27236916 DOI: 10.1016/j.ajhg.2016.04.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/26/2016] [Indexed: 01/30/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) has a wide geographic variation in incidence; it is most common in Saudi Arabia, where it is only second to breast cancer as the most common cancer among females. Genomic profiling of PTC from Saudi Arabia has not been attempted previously. We performed whole-exome sequencing of 101 PTC samples and the corresponding genomic DNA to identify genes with recurrent somatic mutations, then sequenced these genes by using a next-generation gene-panel approach in an additional 785 samples. In addition to BRAF, N-RAS, and H-RAS, which have previously been shown to be recurrently mutated in PTC, our analysis highlights additional genes, including thyroglobulin (TG), which harbored somatic mutations in 3% of the entire cohort. Surprisingly, although TG mutations were not exclusive to mutations in the RAS-MAP kinase pathway, their presence was associated with a significantly worse clinical outcome, which suggests a pathogenic role beyond driving initial oncogenesis. Analysis of metastatic PTC tissue revealed significant enrichment for TG mutations (p < 0.001), including events of apparent clonal expansion. Our results suggest a previously unknown role of TG somatic mutations in the pathogenesis of PTC and its malignant evolution.
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316
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Wiedmeier JE, Kato C, Zhang Z, Lee H, Dunlap J, Nutt E, Rattray R, McKay S, Eide C, Press R, Mori M, Druker B, Dao KH. Clonal hematopoiesis as determined by the HUMARA assay is a marker for acquired mutations in epigenetic regulators in older women. Exp Hematol 2016; 44:857-865.e5. [PMID: 27235757 DOI: 10.1016/j.exphem.2016.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 01/07/2023]
Abstract
Recent large cohort studies revealed that healthy older individuals harbor somatic mutations that increase their risk for hematologic malignancy and all-cause cardiovascular deaths. The majority of these mutations are in chromatin and epigenetic regulatory genes (CERGs). CERGs play a key role in regulation of DNA methylation (DNMT3A and TET2) and histone function (ASXL1) and in clonal proliferation of hematopoietic stem cells. We hypothesize that older women manifesting clonal hematopoiesis, defined here as a functional phenomenon in which a hematopoietic stem cell has acquired a survival and proliferative advantage, harbor a higher frequency of somatic mutations in CERGs. The human androgen receptor gene (HUMARA) assay was used in our study to detect the presence of nonrandom X inactivation in women, a marker for clonal hematopoiesis. In our pilot study, we tested 127 blood samples from women ≥65 years old without a history of invasive cancer or hematologic malignancies. Applying stringent qualitative criteria, we found that 26% displayed clonal hematopoiesis; 52.8% displayed polyclonal hematopoiesis; and 21.3% had indeterminate patterns (too close to call by qualitative assessment). Using Illumina MiSeq next-generation sequencing, we identified somatic mutations in CERGs in 15.2% of subjects displaying clonal hematopoiesis (three ASXL1 and two DNMT3A mutations with an average variant allele frequency of 15.7%, range: 6.3%-23.3%). In a more limited sequencing analysis, we evaluated the frequency of ASXL1 mutations by Sanger sequencing and found mutations in 9.7% of the clonal samples and 0% of the polyclonal samples. By comparing several recent studies (with some caveats as described), we determined the fold enrichment of detecting CERG mutations by using the HUMARA assay as a functional screen for clonal hematopoiesis. We conclude that a functional assay of clonal hematopoiesis is enriching for older women with somatic mutations in CERGs, particularly for ASXL1 and TET2 mutations and less so for DNMT3A mutations.
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Affiliation(s)
- Julia Erin Wiedmeier
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Catherine Kato
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Zhenzhen Zhang
- School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Hyunjung Lee
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Jennifer Dunlap
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Eric Nutt
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Rogan Rattray
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Sarah McKay
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Christopher Eide
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA; Howard Hughes Medical Institute, Portland, OR, USA
| | - Richard Press
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Motomi Mori
- School of Public Health, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Brian Druker
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA; Howard Hughes Medical Institute, Portland, OR, USA
| | - Kim-Hien Dao
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA.
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317
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Yuan XQ, Peng L, Zeng WJ, Jiang BY, Li GC, Chen XP. DNMT3A R882 Mutations Predict a Poor Prognosis in AML: A Meta-Analysis From 4474 Patients. Medicine (Baltimore) 2016; 95:e3519. [PMID: 27149454 PMCID: PMC4863771 DOI: 10.1097/md.0000000000003519] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3 alpha (DNMT3A) mutations were widely believed to be independently associated with inferior prognosis in acute myeloid leukemia (AML) patients. As dominant missense alterations in DNMT3A mutations, R882 mutations cause the focal hypomethylation phenotype. However, there remains debate on the influence of R882 mutations on AML prognosis. Thus, this meta-analysis aimed at further illustrating the prognostic power of DNMT3A R882 mutations in AML patients.Eligible studies were identified from 5 databases containing PubMed, Embase, Web of Science, Clinical Trials, and the Cochrane Library (up to October 25, 2015). Effects (hazard ratios [HRs] with 95% confidence interval [CI]) of relapse-free survival (RFS) and overall survival (OS) were pooled to estimate the prognostic power of mutant DNMT3A R882 in overall patients and subgroups of AML patients.Eight competent studies with 4474 AML patients including 694 with DNMT3A R882 mutations were included. AML patients with DNMT3A R882 mutations showed significant shorter RFS (HR = 1.40, 95% CI = 1.24-1.59, P < 0.001) and OS (HR = 1.47, 95% CI = 1.17-1.86, P = 0.001) in the overall population. DNMT3A R882 mutations predicted worse RFS and OS among the subgroups of patients under age 60 (RFS: HR = 1.44, 95% CI = 1.25-1.66, P < 0.001; OS: HR = 1.48, 95% CI = 1.15-1.90, P = 0.002), over age 60 (RFS: HR = 2.03, 95% CI = 1.40-2.93, P < 0.001; OS: HR = 1.85, 95% CI = 1.36-2.53, P < 0.001), cytogenetically normal (CN)-AML (RFS: HR = 1.52, 95% CI = 1.26-1.83, P < 0.001; OS: HR = 1.67, 95% CI = 1.16-2.41, P = 0.006), and non-CN-AML (RFS: HR = 1.96, 95% CI = 1.20-3.21, P = 0.006; OS: HR = 2.51, 95% CI = 1.52-4.15, P = 0.0038).DNMT3A R882 mutations possessed significant unfavorable prognostic influence on RFS and OS in AML patients.
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Affiliation(s)
- Xiao-Qing Yuan
- From the Department of Clinical Pharmacology, Xiangya Hospital; Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics (X-QY, W-JZ, X-PC); Cancer Research Institute, Central South University; Key Laboratory of Carcinogenesis, National Health and Family Planning Commission; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha (LP, B-YJ, G-CL); and Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, P.R. China (X-PC)
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318
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Hlady RA, Suresh A, Pirruccello SJ, Shukla V, Lu R, Costinean S, Rizzino A, Karpf AR, Joshi S, Swanson P, Opavsky R. Promoter Hypomethylation and Expression Is Conserved in Mouse Chronic Lymphocytic Leukemia Induced by Decreased or Inactivated Dnmt3a. Cell Rep 2016; 15:1190-201. [PMID: 27134162 DOI: 10.1016/j.celrep.2016.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/18/2016] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
DNA methyltransferase 3a (DNMT3A) catalyzes the formation of 5-methyl-cytosine in mammalian genomic DNA, and it is frequently mutated in human hematologic malignancies. Bi-allelic loss of Dnmt3a in mice results in leukemia and lymphoma, including chronic lymphocytic leukemia (CLL). Here, we investigate whether mono-allelic loss of Dnmt3a is sufficient to induce disease. We show that, by 16 months of age, 65% of Dnmt3a(+/-) mice develop a CLL-like disease, and 15% of mice develop non-malignant myeloproliferation. Genome-wide methylation analysis reveals that reduced Dnmt3a levels induce promoter hypomethylation at similar loci in Dnmt3a(+/-) and Dnmt3a(Δ/Δ) CLL, suggesting that promoters are particularly sensitive to Dnmt3a levels. Gene expression analysis identified 26 hypomethylated and overexpressed genes common to both Dnmt3a(+/-) and Dnmt3a(Δ/Δ) CLL as putative oncogenic drivers. Our data provide evidence that Dnmt3a is a haplo-insufficient tumor suppressor in CLL and highlights the importance of deregulated molecular events in disease pathogenesis.
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Affiliation(s)
- Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - G Michael Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Abhinav Suresh
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Samuel J Pirruccello
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vipul Shukla
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Runqing Lu
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Stefan Costinean
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Adam R Karpf
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shantaram Joshi
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Patrick Swanson
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68102, USA
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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319
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Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies. Blood 2016; 128:e1-9. [PMID: 27121471 DOI: 10.1182/blood-2015-11-683334] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers.
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320
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Bronzini I, Aresu L, Paganin M, Marchioretto L, Comazzi S, Cian F, Riondato F, Marconato L, Martini V, Te Kronnie G. DNA methylation and targeted sequencing of methyltransferases family genes in canine acute myeloid leukaemia, modelling human myeloid leukaemia. Vet Comp Oncol 2016; 15:910-918. [PMID: 27098563 DOI: 10.1111/vco.12231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 03/11/2016] [Indexed: 01/13/2023]
Abstract
Tumours shows aberrant DNA methylation patterns, being hypermethylated or hypomethylated compared with normal tissues. In human acute myeloid leukaemia (hAML) mutations in DNA methyltransferase (DNMT3A) are associated to a more aggressive tumour behaviour. As AML is lethal in dogs, we defined global DNA methylation content, and screened the C-terminal domain of DNMT3 family of genes for sequence variants in 39 canine acute myeloid leukaemia (cAML) cases. A heterogeneous pattern of DNA methylation was found among cAML samples, with subsets of cases being hypermethylated or hypomethylated compared with healthy controls; four recurrent single nucleotide variations (SNVs) were found in DNMT3L gene. Although SNVs were not directly correlated to whole genome DNA methylation levels, all hypomethylated cAML cases were homozygous for the deleterious mutation at p.Arg222Trp. This study contributes to understand genetic modifications of cAML, leading up to studies that will elucidate the role of methylome alterations in the pathogenesis of AML in dogs.
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Affiliation(s)
- I Bronzini
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - L Aresu
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - M Paganin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - L Marchioretto
- Department of Cellular Biotechnology and Hematology, Sapienza University of Rome, Rome, Italy
| | - S Comazzi
- Department of Veterinary Science and Public Health, University of Milan, Milano, Italy
| | - F Cian
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - F Riondato
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - L Marconato
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - V Martini
- Department of Veterinary Science and Public Health, University of Milan, Milano, Italy
| | - G Te Kronnie
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
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321
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Yan B, Ng C, Moshi G, Ban K, Lee PL, Seah E, Chiu L, Koay ESC, Liu TC, Ng CH, Chng WJ, Koh LP. Myelodysplastic features in a patient with germline CEBPA-mutant acute myeloid leukaemia. J Clin Pathol 2016; 69:652-4. [PMID: 27010436 DOI: 10.1136/jclinpath-2016-203672] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/07/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Christopher Ng
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Grace Moshi
- Department of Laboratory Medicine, Haematology Division, National University Health System, Singapore, Singapore
| | - Kenneth Ban
- Department of Biochemistry, National University of Singapore, Singapore, Singapore Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Peak-Ling Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Elaine Seah
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Evelyn S C Koay
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Te-Chih Liu
- Department of Laboratory Medicine, Haematology Division, National University Health System, Singapore, Singapore
| | - Chin Hin Ng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore Cancer Science Institute, National University of Singapore, Singapore, Singapore Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Liang Piu Koh
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
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322
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Lukashevich OV, Cherepanova NA, Jurkovska RZ, Jeltsch A, Gromova ES. Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity. BMC BIOCHEMISTRY 2016; 17:7. [PMID: 27001594 PMCID: PMC4802922 DOI: 10.1186/s12858-016-0064-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood. RESULTS Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202. CONCLUSIONS We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.
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Affiliation(s)
- Olga V Lukashevich
- Department of Chemistry, Moscow State University, 119991, Moscow, Russia
| | | | - Renata Z Jurkovska
- BioMedX Innovation Center, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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323
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DNA methylation in normal and malignant hematopoiesis. Int J Hematol 2016; 103:617-26. [PMID: 26943352 DOI: 10.1007/s12185-016-1957-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/08/2016] [Indexed: 01/08/2023]
Abstract
The study of DNA methylation has been a rapidly expanding field since its dawn in the 1960s. DNA methylation is an epigenetic modification that plays a crucial role in guiding the differentiation of stem cells to their destined lineage, and in maintaining tissue homeostasis. Moreover, aberrant DNA methylation has been well characterized as a significant contributing factor in the pathogenesis of a variety of cancers. Hematopoiesis is a process that is uniquely susceptible to epigenetic changes due to the small pool of actively cycling stem cells that give rise to the entire mature immune-hematopoietic system. Mutations in DNA methyltransferase enzymes have been shown to be initiating events in the development of hematological malignancies such as acute myeloid leukemia and, therefore, have become targets for improved diagnostics and therapy. The spatial and temporal regulation of DNA methylation in the hematopoietic developmental hierarchy is critical to hematopoietic homeostasis. An improved understanding of the roles that DNA methylation plays in normal and malignant hematopoiesis will have a significant impact on the future of regenerative stem cell therapy and clinical treatment of hematopoietic malignancies. This review aims to highlight current developments in the field and prioritize future research directions.
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Deynoux M, Sunter N, Hérault O, Mazurier F. Hypoxia and Hypoxia-Inducible Factors in Leukemias. Front Oncol 2016; 6:41. [PMID: 26955619 PMCID: PMC4767894 DOI: 10.3389/fonc.2016.00041] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/08/2016] [Indexed: 01/10/2023] Open
Abstract
Despite huge improvements in the treatment of leukemia, the percentage of patients suffering relapse still remains significant. Relapse most often results from a small number of leukemic stem cells (LSCs) within the bone marrow, which are able to self-renew, and therefore reestablish the full tumor. The marrow microenvironment contributes considerably in supporting the protection and development of leukemic cells. LSCs share specific niches with normal hematopoietic stem cells with the niche itself being composed of a variety of cell types, including mesenchymal stem/stromal cells, bone cells, immune cells, neuronal cells, and vascular cells. A hallmark of the hematopoietic niche is low oxygen partial pressure, indeed this hypoxia is necessary for the long-term maintenance of hematopoietic stem/progenitor cells. Hypoxia is a strong signal, principally maintained by members of the hypoxia-inducible factor (HIF) family. In solid tumors, it has been well established that hypoxia triggers intrinsic metabolic changes and microenvironmental modifications, such as the stimulation of angiogenesis, through activation of HIFs. As leukemia is not considered a “solid” tumor, the role of oxygen in the disease was presumed to be inconsequential and remained long overlooked. This view has now been revised since hypoxia has been shown to influence leukemic cell proliferation, differentiation, and resistance to chemotherapy. However, the role of HIF proteins remains controversial with HIFs being considered as either oncogenes or tumor suppressor genes, depending on the study and model. The purpose of this review is to highlight our knowledge of hypoxia and HIFs in leukemic development and therapeutic resistance and to discuss the recent hypoxia-based strategies proposed to eradicate leukemias.
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Affiliation(s)
- Margaux Deynoux
- Génétique, Immunothérapie, Chimie et Cancer (GICC) UMR 7292, CNRS, UFR de Médecine, Université François-Rabelais de Tours , Tours , France
| | - Nicola Sunter
- Génétique, Immunothérapie, Chimie et Cancer (GICC) UMR 7292, CNRS, UFR de Médecine, Université François-Rabelais de Tours , Tours , France
| | - Olivier Hérault
- Génétique, Immunothérapie, Chimie et Cancer (GICC) UMR 7292, CNRS, UFR de Médecine, Université François-Rabelais de Tours, Tours, France; Service d'Hématologie Biologique, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Frédéric Mazurier
- Génétique, Immunothérapie, Chimie et Cancer (GICC) UMR 7292, CNRS, UFR de Médecine, Université François-Rabelais de Tours , Tours , France
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325
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Hou HA, Tien HF. Mutations in epigenetic modifiers in acute myeloid leukemia and their clinical utility. Expert Rev Hematol 2016; 9:447-69. [DOI: 10.1586/17474086.2016.1144469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
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326
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327
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Abstract
Aberrant DNA methylation is a characteristic feature of cancer including blood malignancies. Mutations in the DNA methylation regulators DNMT3A, TET1/2 and IDH1/2 are recurrent in leukemia and lymphoma. Specific and distinct DNA methylation patterns characterize subtypes of AML and lymphoma. Regulatory regions such as promoter CpG islands, CpG shores and enhancers show changes in methylation during transformation. However, the reported poor correlation between changes in methylation and gene expression in many mouse models and human studies reflects the complexity in the precise molecular mechanism for why aberrant DNA methylation promotes malignancies. This review will summarize current concepts regarding the mechanisms behind aberrant DNA methylation in hematopoietic malignancy and discuss its importance in cancer prognosis, tumor heterogeneity and relapse.
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Affiliation(s)
- Maria Guillamot
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Luisa Cimmino
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
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328
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Cole CB, Verdoni AM, Ketkar S, Leight ER, Russler-Germain DA, Lamprecht TL, Demeter RT, Magrini V, Ley TJ. PML-RARA requires DNA methyltransferase 3A to initiate acute promyelocytic leukemia. J Clin Invest 2015; 126:85-98. [PMID: 26595813 DOI: 10.1172/jci82897] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 10/14/2015] [Indexed: 12/27/2022] Open
Abstract
The DNA methyltransferases DNMT3A and DNMT3B are primarily responsible for de novo methylation of specific cytosine residues in CpG dinucleotides during mammalian development. While loss-of-function mutations in DNMT3A are highly recurrent in acute myeloid leukemia (AML), DNMT3A mutations are almost never found in AML patients with translocations that create oncogenic fusion genes such as PML-RARA, RUNX1-RUNX1T1, and MLL-AF9. Here, we explored how DNMT3A is involved in the function of these fusion genes. We used retroviral vectors to express PML-RARA, RUNX1-RUNX1T1, or MLL-AF9 in bone marrow cells derived from WT or DNMT3A-deficient mice. Additionally, we examined the phenotypes of hematopoietic cells from Ctsg-PML-RARA mice, which express PML-RARA in early hematopoietic progenitors and myeloid precursors, with or without DNMT3A. We determined that the methyltransferase activity of DNMT3A, but not DNMT3B, is required for aberrant PML-RARA-driven self-renewal ex vivo and that DNMT3A is dispensable for RUNX1-RUNX1T1- and MLL-AF9-driven self-renewal. Furthermore, both the PML-RARA-driven competitive transplantation advantage and development of acute promyelocytic leukemia (APL) required DNMT3A. Together, these findings suggest that PML-RARA requires DNMT3A to initiate APL in mice.
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329
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Ko M, An J, Rao A. DNA methylation and hydroxymethylation in hematologic differentiation and transformation. Curr Opin Cell Biol 2015; 37:91-101. [PMID: 26595486 DOI: 10.1016/j.ceb.2015.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 10/21/2015] [Accepted: 10/26/2015] [Indexed: 01/09/2023]
Abstract
Maintenance of the balance of DNA methylation and demethylation is fundamental for normal cellular development and function. Members of the Ten-Eleven-Translocation (TET) family proteins are Fe(II)-dependent and 2-oxoglutarate-dependent dioxygenases that catalyze sequential oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and subsequent oxidized derivatives in DNA. In addition to their roles as intermediates in DNA demethylation, these oxidized methylcytosines are novel epigenetic modifications of DNA. DNA methylation and hydroxymethylation profiles are markedly disrupted in a wide range of cancers but how these changes are related to the pathogenesis of cancers is still ambiguous. In this review, we discuss the current understanding of TET protein functions in normal and malignant hematopoietic development and the ongoing questions to be resolved.
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Affiliation(s)
- Myunggon Ko
- School of Life Sciences, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulju-gun, Ulsan 689-798, Republic of Korea.
| | - Jungeun An
- Center for Genomic Integrity, Institute for Basic Science (IBS), UNIST-gil 50, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
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330
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Brazel AJ, Vernimmen D. The complexity of epigenetic diseases. J Pathol 2015; 238:333-44. [PMID: 26419725 PMCID: PMC4982038 DOI: 10.1002/path.4647] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/10/2015] [Accepted: 09/21/2015] [Indexed: 12/29/2022]
Abstract
Over the past 30 years, a plethora of pathogenic mutations affecting enhancer regions and epigenetic regulators have been identified. Coupled with more recent genome‐wide association studies (GWAS) and epigenome‐wide association studies (EWAS) implicating major roles for regulatory mutations in disease, it is clear that epigenetic mechanisms represent important biomarkers for disease development and perhaps even therapeutic targets. Here, we discuss the diversity of disease‐causing mutations in enhancers and epigenetic regulators, with a particular focus on cancer. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ailbhe Jane Brazel
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian, UK
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331
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Lim DA. Transcriptional and epigenetic insights from stem cells and developing tissues. Development 2015; 142:2549-53. [PMID: 26243867 DOI: 10.1242/dev.122424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In March 2015, over 200 scientists gathered in Steamboat Springs, Colorado, USA, for the Keystone Symposium 'Transcriptional and Epigenetic Influences on Stem Cell States' to discuss the molecular mechanisms of pluripotency, cell differentiation, cell reprogramming and transdifferentiation, among other topics. In this meeting, translational research on stem cells for disease modeling and therapy was also presented. This Meeting Review describes key themes and selected findings, providing a timely update on this fast-moving area of research.
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Affiliation(s)
- Daniel A Lim
- Department of Neurological Surgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco Veterans Affairs Medical Center, University of California, San Francisco, San Francisco, CA 94143, USA
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332
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Meldi KM, Figueroa ME. Cytosine modifications in myeloid malignancies. Pharmacol Ther 2015; 152:42-53. [DOI: 10.1016/j.pharmthera.2015.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/16/2023]
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333
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Revisiting the case for genetically engineered mouse models in human myelodysplastic syndrome research. Blood 2015; 126:1057-68. [PMID: 26077396 DOI: 10.1182/blood-2015-01-624239] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/01/2015] [Indexed: 01/11/2023] Open
Abstract
Much-needed attention has been given of late to diseases specifically associated with an expanding elderly population. Myelodysplastic syndrome (MDS), a hematopoietic stem cell-based blood disease, is one of these. The lack of clear understanding of the molecular mechanisms underlying the pathogenesis of this disease has hampered the development of efficacious therapies, especially in the presence of comorbidities. Mouse models could potentially provide new insights into this disease, although primary human MDS cells grow poorly in xenografted mice. This makes genetically engineered murine models a more attractive proposition, although this approach is not without complications. In particular, it is unclear if or how myelodysplasia (abnormal blood cell morphology), a key MDS feature in humans, presents in murine cells. Here, we evaluate the histopathologic features of wild-type mice and 23 mouse models with verified myelodysplasia. We find that certain features indicative of myelodysplasia in humans, such as Howell-Jolly bodies and low neutrophilic granularity, are commonplace in healthy mice, whereas other features are similarly abnormal in humans and mice. Quantitative hematopoietic parameters, such as blood cell counts, are required to distinguish between MDS and related diseases. We provide data that mouse models of MDS can be genetically engineered and faithfully recapitulate human disease.
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334
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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