18 results on '"Vasanthakumar A"'
Search Results
2. DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID
- Author
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Aparna Vasanthakumar, Nyasha Chambwe, Lucy A. Godley, F. Nina Papavasiliou, Jennifer Ishii, Rita Shaknovich, Olivier Elemento, Bao Q. Vuong, Matthias Kormaksson, David Redmond, Ari Melnick, Jayanta Chaudhuri, Matt Teater, and Pilar M. Dominguez
- Subjects
Somatic hypermutation ,Biology ,Lymphocyte Activation ,Article ,General Biochemistry, Genetics and Molecular Biology ,Epigenesis, Genetic ,Cytosine ,Mice ,Cell Movement ,Cytidine Deaminase ,Activation-induced (cytidine) deaminase ,Animals ,Humans ,Epigenetics ,lcsh:QH301-705.5 ,Conserved Sequence ,Cell Proliferation ,Mice, Knockout ,Genetics ,B-Lymphocytes ,Mice, Inbred BALB C ,Germinal center ,Cell Differentiation ,Cytidine deaminase ,DNA Methylation ,Germinal Center ,Molecular biology ,DNA demethylation ,lcsh:Biology (General) ,DNA methylation ,biology.protein ,Reprogramming - Abstract
SummaryChanges in DNA methylation are required for the formation of germinal centers (GCs), but the mechanisms of such changes are poorly understood. Activation-induced cytidine deaminase (AID) has been recently implicated in DNA demethylation through its deaminase activity coupled with DNA repair. We investigated the epigenetic function of AID in vivo in germinal center B cells (GCBs) isolated from wild-type (WT) and AID-deficient (Aicda−/−) mice. We determined that the transit of B cells through the GC is associated with marked locus-specific loss of methylation and increased methylation diversity, both of which are lost in Aicda−/− animals. Differentially methylated cytosines (DMCs) between GCBs and naive B cells (NBs) are enriched in genes that are targeted for somatic hypermutation (SHM) by AID, and these genes form networks required for B cell development and proliferation. Finally, we observed significant conservation of AID-dependent epigenetic reprogramming between mouse and human B cells.
- Published
- 2015
3. The TNF Receptor Superfamily-NF-κB Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues
- Author
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Peggy P Teh, Najoua Lalaoui, Maria Fernanda Pascutti, Yang Liao, Vanessa L. Bryant, Jessica C Tempany, Taco W. Kuijpers, Axel Kallies, Philip D. Hodgkin, Paul Tuijnenburg, Lisa A. Mielke, Martijn A. Nolte, Renee Gloury, Gordon K. Smyth, Alexandra L. Garnham, Anna E. Oja, Eloy Cuadrado, Tom Sidwell, Wei Shi, Ajithkumar Vasanthakumar, John Silke, Other departments, AII - Infectious diseases, Graduate School, AII - Amsterdam institute for Infection and Immunity, Paediatric Infectious Diseases / Rheumatology / Immunology, and Landsteiner Laboratory
- Subjects
0301 basic medicine ,Cell Survival ,Lymphoid Tissue ,Cellular differentiation ,Transcription Factor RelA ,Biology ,T-Lymphocytes, Regulatory ,General Biochemistry, Genetics and Molecular Biology ,Receptors, Tumor Necrosis Factor ,TNFRSF signaling ,03 medical and health sciences ,Mice ,0302 clinical medicine ,RAR-related orphan receptor gamma ,IRF4 ,Animals ,Homeostasis ,Humans ,RORγt+ Treg cells ,Transcription factor ,lcsh:QH301-705.5 ,effector Treg cells ,tissue Treg cells ,NF-kappa B ,FOXP3 ,Cell Differentiation ,Nuclear Receptor Subfamily 1, Group F, Member 3 ,Intestines ,030104 developmental biology ,lcsh:Biology (General) ,Interferon Regulatory Factors ,Cancer research ,Tumor necrosis factor alpha ,Signal transduction ,NF-κB/RelA ,TCR ,030215 immunology ,Interferon regulatory factors ,Signal Transduction - Abstract
After exiting the thymus, Foxp3(+) regulatory T (Treg) cells undergo further differentiation in the periphery, resulting in the generation of mature, fully suppressive effector (e) Treg cells in a process dependent on TCR signaling and the transcription factor IRF4. Here, we show that tumor necrosis factor receptor superfamily (TNFRSF) signaling plays a crucial role in the development and maintenance of eTreg cells. TNFRSF signaling activated the NF-kappa B transcription factor RelA, which was required to maintain eTreg cells in lymphoid and non-lymphoid tissues, including ROR gamma t(+) Treg cells in the small intestine. In response to TNFRSF signaling, RelA regulated basic cellular processes, including cell survival and proliferation, but was dispensable for IRF4 expression or DNAbinding, indicating that both pathways operated independently. Importantly, mutations in the RelA binding partner NF-kappa B1 compromised eTreg cells in humans, suggesting that the TNFRSF-NF-kappa B axis was required in a non-redundant manner to maintain eTreg cells in mice and humans
- Published
- 2017
4. TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma
- Author
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Aparna Vasanthakumar, Nanduri R. Prabhakar, Susan L. Cohn, Sanchari Bhattacharyya, Amit Verma, Roland H. Wenger, Jozef Madzo, Lucy A. Godley, Jayasri Nanduri, Tushar D. Bhagat, Yiting Yu, Christopher J. Mariani, and Ali Ekrem Yesilkanal
- Subjects
Biology ,Response Elements ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,Mixed Function Oxygenases ,Cytosine ,Neuroblastoma ,Downregulation and upregulation ,Cell Line, Tumor ,Proto-Oncogene Proteins ,Gene expression ,medicine ,Humans ,Epigenetics ,lcsh:QH301-705.5 ,Gene ,Regulation of gene expression ,Hypoxia (medical) ,DNA Methylation ,Hypoxia-Inducible Factor 1, alpha Subunit ,Molecular biology ,Cell Hypoxia ,Up-Regulation ,DNA-Binding Proteins ,Gene Expression Regulation, Neoplastic ,DNA demethylation ,lcsh:Biology (General) ,DNA methylation ,5-Methylcytosine ,medicine.symptom - Abstract
SUMMARY The ten-eleven-translocation 5-methylcytosine dioxygenase (TET) family of enzymes catalyzes the conversion of 5-methylcytosine (5-mC) to 5-hydroxyme-thylcytosine (5-hmC), a modified cytosine base that facilitates gene expression. Cells respond to hypoxia by inducing a transcriptional program regulated in part by oxygen-dependent dioxygenases that require Fe(II) and α-ketoglutarate. Given that the TET enzymes also require these cofactors, we hypothesized that the TETs regulate the hypoxia-induced transcriptional program. Here, we demonstrate that hypoxia increases global 5-hmC levels, with accumulation of 5-hmC density at canonical hypoxia response genes. A subset of 5-hmC gains colocalize with hypoxia response elements facilitating DNA demethylation and HIF binding. Hypoxia results in transcriptional activation of TET1, and full induction of hypoxia-responsive genes and global 5-hmC increases require TET1. Finally, we show that 5-hmC increases and TET1 upregulation in hypoxia are HIF-1 dependent. These findings establish TET1-mediated 5-hmC changes as an important epigenetic component of the hypoxic response.
- Published
- 2014
5. The TNF Receptor Superfamily-NF-κB Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues
- Author
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Vasanthakumar, Ajithkumar, primary, Liao, Yang, additional, Teh, Peggy, additional, Pascutti, Maria F., additional, Oja, Anna E., additional, Garnham, Alexandra L., additional, Gloury, Renee, additional, Tempany, Jessica C., additional, Sidwell, Tom, additional, Cuadrado, Eloy, additional, Tuijnenburg, Paul, additional, Kuijpers, Taco W., additional, Lalaoui, Najoua, additional, Mielke, Lisa A., additional, Bryant, Vanessa L., additional, Hodgkin, Philip D., additional, Silke, John, additional, Smyth, Gordon K., additional, Nolte, Martijn A., additional, Shi, Wei, additional, and Kallies, Axel, additional
- Published
- 2017
- Full Text
- View/download PDF
6. DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID
- Author
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Dominguez, Pilar M., primary, Teater, Matt, additional, Chambwe, Nyasha, additional, Kormaksson, Matthias, additional, Redmond, David, additional, Ishii, Jennifer, additional, Vuong, Bao, additional, Chaudhuri, Jayanta, additional, Melnick, Ari, additional, Vasanthakumar, Aparna, additional, Godley, Lucy A., additional, Papavasiliou, F. Nina, additional, Elemento, Olivier, additional, and Shaknovich, Rita, additional
- Published
- 2015
- Full Text
- View/download PDF
7. DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia
- Author
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Rampal, Raajit, primary, Alkalin, Altuna, additional, Madzo, Jozef, additional, Vasanthakumar, Aparna, additional, Pronier, Elodie, additional, Patel, Jay, additional, Li, Yushan, additional, Ahn, Jihae, additional, Abdel-Wahab, Omar, additional, Shih, Alan, additional, Lu, Chao, additional, Ward, Patrick S., additional, Tsai, Jennifer J., additional, Hricik, Todd, additional, Tosello, Valeria, additional, Tallman, Jacob E., additional, Zhao, Xinyang, additional, Daniels, Danette, additional, Dai, Qing, additional, Ciminio, Luisa, additional, Aifantis, Iannis, additional, He, Chuan, additional, Fuks, Francois, additional, Tallman, Martin S., additional, Ferrando, Adolfo, additional, Nimer, Stephen, additional, Paietta, Elisabeth, additional, Thompson, Craig B., additional, Licht, Jonathan D., additional, Mason, Christopher E., additional, Godley, Lucy A., additional, Melnick, Ari, additional, Figueroa, Maria E., additional, and Levine, Ross L., additional
- Published
- 2014
- Full Text
- View/download PDF
8. TET1-Mediated Hydroxymethylation Facilitates Hypoxic Gene Induction in Neuroblastoma
- Author
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Mariani, Christopher J., primary, Vasanthakumar, Aparna, additional, Madzo, Jozef, additional, Yesilkanal, Ali, additional, Bhagat, Tushar, additional, Yu, Yiting, additional, Bhattacharyya, Sanchari, additional, Wenger, Roland H., additional, Cohn, Susan L., additional, Nanduri, Jayasri, additional, Verma, Amit, additional, Prabhakar, Nanduri R., additional, and Godley, Lucy A., additional
- Published
- 2014
- Full Text
- View/download PDF
9. Hydroxymethylation at Gene Regulatory Regions Directs Stem/Early Progenitor Cell Commitment during Erythropoiesis
- Author
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Madzo, Jozef, primary, Liu, Hui, additional, Rodriguez, Alexis, additional, Vasanthakumar, Aparna, additional, Sundaravel, Sriram, additional, Caces, Donne Bennett D., additional, Looney, Timothy J., additional, Zhang, Li, additional, Lepore, Janet B., additional, Macrae, Trisha, additional, Duszynski, Robert, additional, Shih, Alan H., additional, Song, Chun-Xiao, additional, Yu, Miao, additional, Yu, Yiting, additional, Grossman, Robert, additional, Raumann, Brigitte, additional, Verma, Amit, additional, He, Chuan, additional, Levine, Ross L., additional, Lavelle, Don, additional, Lahn, Bruce T., additional, Wickrema, Amittha, additional, and Godley, Lucy A., additional
- Published
- 2014
- Full Text
- View/download PDF
10. DNA Hydroxymethylation Profiling Reveals that WT1Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia
- Author
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Rampal, Raajit, Alkalin, Altuna, Madzo, Jozef, Vasanthakumar, Aparna, Pronier, Elodie, Patel, Jay, Li, Yushan, Ahn, Jihae, Abdel-Wahab, Omar, Shih, Alan, Lu, Chao, Ward, Patrick S., Tsai, Jennifer J., Hricik, Todd, Tosello, Valeria, Tallman, Jacob E., Zhao, Xinyang, Daniels, Danette, Dai, Qing, Ciminio, Luisa, Aifantis, Iannis, He, Chuan, Fuks, Francois, Tallman, Martin S., Ferrando, Adolfo, Nimer, Stephen, Paietta, Elisabeth, Thompson, Craig B., Licht, Jonathan D., Mason, Christopher E., Godley, Lucy A., Melnick, Ari, Figueroa, Maria E., and Levine, Ross L.
- Abstract
Somatic mutations in IDH1/IDH2and TET2result in impaired TET2-mediated conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The observation that WT1inactivating mutations anticorrelate with TET2/IDH1/IDH2mutations in acute myeloid leukemia (AML) led us to hypothesize that WT1 mutations may impact TET2 function. WT1mutant AML patients have reduced 5hmC levels similar to TET2/IDH1/IDH2mutant AML. These mutations are characterized by convergent, site-specific alterations in DNA hydroxymethylation, which drive differential gene expression more than alterations in DNA promoter methylation. WT1 overexpression increases global levels of 5hmC, and WT1 silencing reduced 5hmC levels. WT1 physically interacts with TET2 and TET3, and WT1 loss of function results in a similar hematopoietic differentiation phenotype as observed with TET2 deficiency. These data provide a role for WT1 in regulating DNA hydroxymethylation and suggest that TET2 IDH1/IDH2and WT1mutations define an AML subtype defined by dysregulated DNA hydroxymethylation.
- Published
- 2014
- Full Text
- View/download PDF
11. Hydroxymethylation at Gene Regulatory Regions Directs Stem/Early Progenitor Cell Commitment during Erythropoiesis
- Author
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Aparna Vasanthakumar, Jozef Madzo, Alexis Rodriguez, Timothy J. Looney, Amit Verma, Chun-Xiao Song, Li Zhang, Miao Yu, Ross L. Levine, Amittha Wickrema, Alan H. Shih, Yiting Yu, Chuan He, Donne Bennett D. Caces, Trisha A. Macrae, Sriram Sundaravel, Lucy A. Godley, Don Lavelle, Brigitte Raumann, Robert Duszynski, Janet B. Lepore, Hui Liu, Robert L. Grossman, and Bruce T. Lahn
- Subjects
Cellular differentiation ,CD34 ,Antigens, CD34 ,Biology ,Regulatory Sequences, Nucleic Acid ,General Biochemistry, Genetics and Molecular Biology ,Article ,Dioxygenases ,Histones ,Cytosine ,Erythroid Cells ,Humans ,Erythropoiesis ,Progenitor cell ,lcsh:QH301-705.5 ,Cells, Cultured ,Hematopoietic stem cell differentiation ,Tet methylcytosine dioxygenase 2 ,DNA Methylation ,Molecular biology ,Cell biology ,Haematopoiesis ,lcsh:Biology (General) ,DNA methylation ,Mutation ,5-Methylcytosine ,Stem cell ,Transcription Factors - Abstract
SummaryHematopoietic stem cell differentiation involves the silencing of self-renewal genes and induction of a specific transcriptional program. Identification of multiple covalent cytosine modifications raises the question of how these derivatized bases influence stem cell commitment. Using a replicative primary human hematopoietic stem/progenitor cell differentiation system, we demonstrate dynamic changes of 5-hydroxymethylcytosine (5-hmC) during stem cell commitment and differentiation to the erythroid lineage. Genomic loci that maintain or gain 5-hmC density throughout erythroid differentiation contain binding sites for erythroid transcription factors and several factors not previously recognized as erythroid-specific factors. The functional importance of 5-hmC was demonstrated by impaired erythroid differentiation, with augmentation of myeloid potential, and disrupted 5-hmC patterning in leukemia patient-derived CD34+ stem/early progenitor cells with TET methylcytosine dioxygenase 2 (TET2) mutations. Thus, chemical conjugation and affinity purification of 5-hmC-enriched sequences followed by sequencing serve as resources for deciphering functional implications for gene expression during stem cell commitment and differentiation along a particular lineage.
- Full Text
- View/download PDF
12. Blimp1 Prevents Methylation of Foxp3and Loss of Regulatory T Cell Identity at Sites of Inflammation
- Author
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Garg, Garima, Muschaweckh, Andreas, Moreno, Helena, Vasanthakumar, Ajithkumar, Floess, Stefan, Lepennetier, Gildas, Oellinger, Rupert, Zhan, Yifan, Regen, Tommy, Hiltensperger, Michael, Peter, Christian, Aly, Lilian, Knier, Benjamin, Palam, Lakshmi Reddy, Kapur, Reuben, Kaplan, Mark H., Waisman, Ari, Rad, Roland, Schotta, Gunnar, Huehn, Jochen, Kallies, Axel, and Korn, Thomas
- Abstract
Foxp3+regulatory T (Treg) cells restrict immune pathology in inflamed tissues; however, an inflammatory environment presents a threat to Treg cell identity and function. Here, we establish a transcriptional signature of central nervous system (CNS) Treg cells that accumulate during experimental autoimmune encephalitis (EAE) and identify a pathway that maintains Treg cell function and identity during severe inflammation. This pathway is dependent on the transcriptional regulator Blimp1, which prevents downregulation of Foxp3 expression and “toxic” gain-of-function of Treg cells in the inflamed CNS. Blimp1 negatively regulates IL-6- and STAT3-dependent Dnmt3a expression and function restraining methylation of Treg cell-specific conserved non-coding sequence 2 (CNS2) in the Foxp3locus. Consequently, CNS2 is heavily methylated when Blimp1 is ablated, leading to a loss of Foxp3 expression and severe disease. These findings identify a Blimp1-dependent pathway that preserves Treg cell stability in inflamed non-lymphoid tissues.
- Published
- 2019
- Full Text
- View/download PDF
13. The TNF Receptor Superfamily-NF-κB Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues
- Author
-
Ajithkumar Vasanthakumar, Yang Liao, Peggy Teh, Maria F. Pascutti, Anna E. Oja, Alexandra L. Garnham, Renee Gloury, Jessica C. Tempany, Tom Sidwell, Eloy Cuadrado, Paul Tuijnenburg, Taco W. Kuijpers, Najoua Lalaoui, Lisa A. Mielke, Vanessa L. Bryant, Philip D. Hodgkin, John Silke, Gordon K. Smyth, Martijn A. Nolte, Wei Shi, and Axel Kallies
- Subjects
TNFRSF signaling ,effector Treg cells ,NF-κB/RelA ,TCR ,IRF4 ,tissue Treg cells ,RORγt+ Treg cells ,Biology (General) ,QH301-705.5 - Abstract
After exiting the thymus, Foxp3+ regulatory T (Treg) cells undergo further differentiation in the periphery, resulting in the generation of mature, fully suppressive effector (e)Treg cells in a process dependent on TCR signaling and the transcription factor IRF4. Here, we show that tumor necrosis factor receptor superfamily (TNFRSF) signaling plays a crucial role in the development and maintenance of eTreg cells. TNFRSF signaling activated the NF-κB transcription factor RelA, which was required to maintain eTreg cells in lymphoid and non-lymphoid tissues, including RORγt+ Treg cells in the small intestine. In response to TNFRSF signaling, RelA regulated basic cellular processes, including cell survival and proliferation, but was dispensable for IRF4 expression or DNA binding, indicating that both pathways operated independently. Importantly, mutations in the RelA binding partner NF-κB1 compromised eTreg cells in humans, suggesting that the TNFRSF-NF-κB axis was required in a non-redundant manner to maintain eTreg cells in mice and humans.
- Published
- 2017
- Full Text
- View/download PDF
14. Blimp1 Prevents Methylation of Foxp3 and Loss of Regulatory T Cell Identity at Sites of Inflammation
- Author
-
Garima Garg, Andreas Muschaweckh, Helena Moreno, Ajithkumar Vasanthakumar, Stefan Floess, Gildas Lepennetier, Rupert Oellinger, Yifan Zhan, Tommy Regen, Michael Hiltensperger, Christian Peter, Lilian Aly, Benjamin Knier, Lakshmi Reddy Palam, Reuben Kapur, Mark H. Kaplan, Ari Waisman, Roland Rad, Gunnar Schotta, Jochen Huehn, Axel Kallies, and Thomas Korn
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Summary: Foxp3+ regulatory T (Treg) cells restrict immune pathology in inflamed tissues; however, an inflammatory environment presents a threat to Treg cell identity and function. Here, we establish a transcriptional signature of central nervous system (CNS) Treg cells that accumulate during experimental autoimmune encephalitis (EAE) and identify a pathway that maintains Treg cell function and identity during severe inflammation. This pathway is dependent on the transcriptional regulator Blimp1, which prevents downregulation of Foxp3 expression and “toxic” gain-of-function of Treg cells in the inflamed CNS. Blimp1 negatively regulates IL-6- and STAT3-dependent Dnmt3a expression and function restraining methylation of Treg cell-specific conserved non-coding sequence 2 (CNS2) in the Foxp3 locus. Consequently, CNS2 is heavily methylated when Blimp1 is ablated, leading to a loss of Foxp3 expression and severe disease. These findings identify a Blimp1-dependent pathway that preserves Treg cell stability in inflamed non-lymphoid tissues. : An inflammatory environment threatens the stability of Foxp3+ Treg cells. Garg et al. show that by expressing the transcriptional regulator Blimp1, Treg cells resist the IL-6-driven loss of Foxp3 in inflamed tissues. Blimp1 prevents the methylation and reduced expression of Foxp3 through inhibition of the methyltransferase Dnmt3a. Keywords: regulatory T cells, Blimp1, CNS2, epigenetic regulation, CNS, inflammation, DNA methyltransferases, Foxp3, Interleukin-6
- Published
- 2019
- Full Text
- View/download PDF
15. DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID
- Author
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Pilar M. Dominguez, Matt Teater, Nyasha Chambwe, Matthias Kormaksson, David Redmond, Jennifer Ishii, Bao Vuong, Jayanta Chaudhuri, Ari Melnick, Aparna Vasanthakumar, Lucy A. Godley, F. Nina Papavasiliou, Olivier Elemento, and Rita Shaknovich
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Changes in DNA methylation are required for the formation of germinal centers (GCs), but the mechanisms of such changes are poorly understood. Activation-induced cytidine deaminase (AID) has been recently implicated in DNA demethylation through its deaminase activity coupled with DNA repair. We investigated the epigenetic function of AID in vivo in germinal center B cells (GCBs) isolated from wild-type (WT) and AID-deficient (Aicda−/−) mice. We determined that the transit of B cells through the GC is associated with marked locus-specific loss of methylation and increased methylation diversity, both of which are lost in Aicda−/− animals. Differentially methylated cytosines (DMCs) between GCBs and naive B cells (NBs) are enriched in genes that are targeted for somatic hypermutation (SHM) by AID, and these genes form networks required for B cell development and proliferation. Finally, we observed significant conservation of AID-dependent epigenetic reprogramming between mouse and human B cells.
- Published
- 2015
- Full Text
- View/download PDF
16. DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia
- Author
-
Raajit Rampal, Altuna Alkalin, Jozef Madzo, Aparna Vasanthakumar, Elodie Pronier, Jay Patel, Yushan Li, Jihae Ahn, Omar Abdel-Wahab, Alan Shih, Chao Lu, Patrick S. Ward, Jennifer J. Tsai, Todd Hricik, Valeria Tosello, Jacob E. Tallman, Xinyang Zhao, Danette Daniels, Qing Dai, Luisa Ciminio, Iannis Aifantis, Chuan He, Francois Fuks, Martin S. Tallman, Adolfo Ferrando, Stephen Nimer, Elisabeth Paietta, Craig B. Thompson, Jonathan D. Licht, Christopher E. Mason, Lucy A. Godley, Ari Melnick, Maria E. Figueroa, and Ross L. Levine
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Summary: Somatic mutations in IDH1/IDH2 and TET2 result in impaired TET2-mediated conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The observation that WT1 inactivating mutations anticorrelate with TET2/IDH1/IDH2 mutations in acute myeloid leukemia (AML) led us to hypothesize that WT1 mutations may impact TET2 function. WT1 mutant AML patients have reduced 5hmC levels similar to TET2/IDH1/IDH2 mutant AML. These mutations are characterized by convergent, site-specific alterations in DNA hydroxymethylation, which drive differential gene expression more than alterations in DNA promoter methylation. WT1 overexpression increases global levels of 5hmC, and WT1 silencing reduced 5hmC levels. WT1 physically interacts with TET2 and TET3, and WT1 loss of function results in a similar hematopoietic differentiation phenotype as observed with TET2 deficiency. These data provide a role for WT1 in regulating DNA hydroxymethylation and suggest that TET2 IDH1/IDH2 and WT1 mutations define an AML subtype defined by dysregulated DNA hydroxymethylation. : Mutational studies in patients with acute myeloid leukemia (AML) have identified recurrent mutations in TET2 and IDH1/IDH2, and these mutations result in a reduction in 5-hydroxymethylcytosine (5hmC) levels. Rampal et al. demonstrate that WT1 mutations anticorrelate with TET2 and IDH1/IDH2 mutations, and WT1 mutant AMLs have decreased 5hmC levels, consistent with reduced TET2 function.
- Published
- 2014
- Full Text
- View/download PDF
17. TET1-Mediated Hydroxymethylation Facilitates Hypoxic Gene Induction in Neuroblastoma
- Author
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Christopher J. Mariani, Aparna Vasanthakumar, Jozef Madzo, Ali Yesilkanal, Tushar Bhagat, Yiting Yu, Sanchari Bhattacharyya, Roland H. Wenger, Susan L. Cohn, Jayasri Nanduri, Amit Verma, Nanduri R. Prabhakar, and Lucy A. Godley
- Subjects
Biology (General) ,QH301-705.5 - Abstract
The ten-eleven-translocation 5-methylcytosine dioxygenase (TET) family of enzymes catalyzes the conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), a modified cytosine base that facilitates gene expression. Cells respond to hypoxia by inducing a transcriptional program regulated in part by oxygen-dependent dioxygenases that require Fe(II) and α-ketoglutarate. Given that the TET enzymes also require these cofactors, we hypothesized that the TETs regulate the hypoxia-induced transcriptional program. Here, we demonstrate that hypoxia increases global 5-hmC levels, with accumulation of 5-hmC density at canonical hypoxia response genes. A subset of 5-hmC gains colocalize with hypoxia response elements facilitating DNA demethylation and HIF binding. Hypoxia results in transcriptional activation of TET1, and full induction of hypoxia-responsive genes and global 5-hmC increases require TET1. Finally, we show that 5-hmC increases and TET1 upregulation in hypoxia are HIF-1 dependent. These findings establish TET1-mediated 5-hmC changes as an important epigenetic component of the hypoxic response.
- Published
- 2014
- Full Text
- View/download PDF
18. Hydroxymethylation at Gene Regulatory Regions Directs Stem/Early Progenitor Cell Commitment during Erythropoiesis
- Author
-
Jozef Madzo, Hui Liu, Alexis Rodriguez, Aparna Vasanthakumar, Sriram Sundaravel, Donne Bennett D. Caces, Timothy J. Looney, Li Zhang, Janet B. Lepore, Trisha Macrae, Robert Duszynski, Alan H. Shih, Chun-Xiao Song, Miao Yu, Yiting Yu, Robert Grossman, Brigitte Raumann, Amit Verma, Chuan He, Ross L. Levine, Don Lavelle, Bruce T. Lahn, Amittha Wickrema, and Lucy A. Godley
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Hematopoietic stem cell differentiation involves the silencing of self-renewal genes and induction of a specific transcriptional program. Identification of multiple covalent cytosine modifications raises the question of how these derivatized bases influence stem cell commitment. Using a replicative primary human hematopoietic stem/progenitor cell differentiation system, we demonstrate dynamic changes of 5-hydroxymethylcytosine (5-hmC) during stem cell commitment and differentiation to the erythroid lineage. Genomic loci that maintain or gain 5-hmC density throughout erythroid differentiation contain binding sites for erythroid transcription factors and several factors not previously recognized as erythroid-specific factors. The functional importance of 5-hmC was demonstrated by impaired erythroid differentiation, with augmentation of myeloid potential, and disrupted 5-hmC patterning in leukemia patient-derived CD34+ stem/early progenitor cells with TET methylcytosine dioxygenase 2 (TET2) mutations. Thus, chemical conjugation and affinity purification of 5-hmC-enriched sequences followed by sequencing serve as resources for deciphering functional implications for gene expression during stem cell commitment and differentiation along a particular lineage.
- Published
- 2014
- Full Text
- View/download PDF
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