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Gioulbasani M, Äijö T, Valenzuela JE, Bettes JB, Tsagaratou A. TET proteins regulate Drosha expression and impact microRNAs in iNKT cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605991. [PMID: 39131272 PMCID: PMC11312547 DOI: 10.1101/2024.07.31.605991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
DNA demethylases TET2 and TET3 play a fundamental role in thymic invariant natural killer T (iNKT) cell differentiation by mediating DNA demethylation of genes encoding for lineage specifying factors. Paradoxically, differential gene expression analysis revealed that significant number of genes were upregulated upon TET2 and TET3 loss in iNKT cells. This unexpected finding could be potentially explained if loss of TET proteins was reducing the expression of proteins that suppress gene expression. In this study, we discover that TET2 and TET3 synergistically regulate Drosha expression, by generating 5hmC across the gene body and by impacting chromatin accessibility. As DROSHA is involved in microRNA biogenesis, we proceed to investigate the impact of TET2/3 loss on microRNAs in iNKT cells. We report that among the downregulated microRNAs are members of the Let-7 family that downregulate in vivo the expression of the iNKT cell lineage specifying factor PLZF. Our data link TET proteins with microRNA expression and reveal an additional layer of TET mediated regulation of gene expression.
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Affiliation(s)
- Marianthi Gioulbasani
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jair E. Valenzuela
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC, USA
| | - Julia Buquera Bettes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Ren L, Chang YF, Jiang SH, Li XH, Cheng HP. DNA methylation modification in Idiopathic pulmonary fibrosis. Front Cell Dev Biol 2024; 12:1416325. [PMID: 38915445 PMCID: PMC11194555 DOI: 10.3389/fcell.2024.1416325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and irreversible interstitial lung disease with a prognosis worse than lung cancer. It is a fatal lung disease with largely unknown etiology and pathogenesis, and no effective therapeutic drugs render its treatment largely unsuccessful. With continuous in-depth research efforts, the epigenetic mechanisms in IPF pathogenesis have been further discovered and concerned. As a widely studied mechanism of epigenetic modification, DNA methylation is primarily facilitated by DNA methyltransferases (DNMTs), resulting in the addition of a methyl group to the fifth carbon position of the cytosine base, leading to the formation of 5-methylcytosine (5-mC). Dysregulation of DNA methylation is intricately associated with the advancement of respiratory disorders. Recently, the role of DNA methylation in IPF pathogenesis has also received considerable attention. DNA methylation patterns include methylation modification and demethylation modification and regulate a range of essential biological functions through gene expression regulation. The Ten-Eleven-Translocation (TET) family of DNA dioxygenases is crucial in facilitating active DNA demethylation through the enzymatic conversion of the modified genomic base 5-mC to 5-hydroxymethylcytosine (5-hmC). TET2, a member of TET proteins, is involved in lung inflammation, and its protein expression is downregulated in the lungs and alveolar epithelial type II cells of IPF patients. This review summarizes the current knowledge of pathologic features and DNA methylation mechanisms of pulmonary fibrosis, focusing on the critical roles of abnormal DNA methylation patterns, DNMTs, and TET proteins in impacting IPF pathogenesis. Researching DNA methylation will enchance comprehension of the fundamental mechanisms involved in IPF pathology and provide novel diagnostic biomarkers and therapeutic targets for pulmonary fibrosis based on the studies involving epigenetic mechanisms.
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Affiliation(s)
- Lu Ren
- Clinical Nursing Teaching and Research Section, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Fen Chang
- Medicine School, Zhengzhou University of Industrial Technology, Zhengzhou, China
| | - Shi-He Jiang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Hong Li
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hai-Peng Cheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
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Zhang X, Gao X, Liu Z, Shao F, Yu D, Zhao M, Qin X, Wang S. Microbiota regulates the TET1-mediated DNA hydroxymethylation program in innate lymphoid cell differentiation. Nat Commun 2024; 15:4792. [PMID: 38839760 PMCID: PMC11153590 DOI: 10.1038/s41467-024-48794-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Innate lymphoid cell precursors (ILCPs) develop into distinct subsets of innate lymphoid cells (ILCs) with specific functions. The epigenetic program underlying the differentiation of ILCPs into ILC subsets remains poorly understood. Here, we reveal the genome-wide distribution and dynamics of the DNA methylation and hydroxymethylation in ILC subsets and their respective precursors. Additionally, we find that the DNA hydroxymethyltransferase TET1 suppresses ILC1 but not ILC2 or ILC3 differentiation. TET1 deficiency promotes ILC1 differentiation by inhibiting TGF-β signaling. Throughout ILCP differentiation at postnatal stage, gut microbiota contributes to the downregulation of TET1 level. Microbiota decreases the level of cholic acid in the gut, impairs TET1 expression and suppresses DNA hydroxymethylation, ultimately resulting in an expansion of ILC1s. In adult mice, TET1 suppresses the hyperactivation of ILC1s to maintain intestinal homeostasis. Our findings provide insights into the microbiota-mediated epigenetic programming of ILCs, which links microbiota-DNA methylation crosstalk to ILC differentiation.
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Affiliation(s)
- Xusheng Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xintong Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhen Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fei Shao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dou Yu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Min Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiwen Qin
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Shuo Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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4
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Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
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Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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Theofilatos D, Ho T, Waitt G, Äijö T, Schiapparelli LM, Soderblom EJ, Tsagaratou A. Deciphering the TET3 interactome in primary thymic developing T cells. iScience 2024; 27:109782. [PMID: 38711449 PMCID: PMC11070343 DOI: 10.1016/j.isci.2024.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
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Affiliation(s)
- Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tricia Ho
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Shao J, Xu Y, Olsen RJ, Kasparian S, Sun K, Mathur S, Zhang J, He C, Chen SH, Bernicker EH, Li Z. 5-Hydroxymethylcytosine in Cell-Free DNA Predicts Immunotherapy Response in Lung Cancer. Cells 2024; 13:715. [PMID: 38667328 PMCID: PMC11049556 DOI: 10.3390/cells13080715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) drastically improve therapeutic outcomes for lung cancer, but accurately predicting individual patient responses to ICIs remains a challenge. We performed the genome-wide profiling of 5-hydroxymethylcytosine (5hmC) in 85 plasma cell-free DNA (cfDNA) samples from lung cancer patients and developed a 5hmC signature that was significantly associated with progression-free survival (PFS). We built a 5hmC predictive model to quantify the 5hmC level and validated the model in the validation, test, and control sets. Low weighted predictive scores (wp-scores) were significantly associated with a longer PFS compared to high wp-scores in the validation [median 7.6 versus 1.8 months; p = 0.0012; hazard ratio (HR) 0.12; 95% confidence interval (CI), 0.03-0.54] and test (median 14.9 versus 3.3 months; p = 0.00074; HR 0.10; 95% CI, 0.02-0.50) sets. Objective response rates in patients with a low or high wp-score were 75.0% (95% CI, 42.8-94.5%) versus 0.0% (95% CI, 0.0-60.2%) in the validation set (p = 0.019) and 80.0% (95% CI, 44.4-97.5%) versus 0.0% (95% CI, 0.0-36.9%) in the test set (p = 0.0011). The wp-scores were also significantly associated with PFS in patients receiving single-agent ICI treatment (p < 0.05). In addition, the 5hmC predictive signature demonstrated superior predictive capability to tumor programmed death-ligand 1 and specificity to ICI treatment response prediction. Moreover, we identified novel 5hmC-associated genes and signaling pathways integral to ICI treatment response in lung cancer. This study provides proof-of-concept evidence that the cfDNA 5hmC signature is a robust biomarker for predicting ICI treatment response in lung cancer.
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Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Yitian Xu
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Saro Kasparian
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Kai Sun
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Sunil Mathur
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Jun Zhang
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Shu-Hsia Chen
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Eric H. Bernicker
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
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Cui W, Luo C, Zhou L, Yu T, Meng Y, Yu Q, Lei Z, Wang Y, Peng L, Luo Q, Tang D, Sun R, Yu L. Roles of RNA m 5C modification patterns in prognosis and tumor microenvironment infiltration of diffuse large B-cell lymphoma. Am J Cancer Res 2024; 14:1768-1783. [PMID: 38726285 PMCID: PMC11076244 DOI: 10.62347/nxdr1826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/10/2024] [Indexed: 05/12/2024] Open
Abstract
Genetic and epigenetic aberrations display an essential role in the initiation and progression of diffuse large B-cell lymphoma (DLBCL). 5-methylcytosine (m5C), a common RNA modification, regulates various cellular processes and contributes to tumorigenesis and cancer progression. However, m5C alterations in DLBCL remain unclear. Our research constructed an m5C prognostic model utilizing GEO data sets, which can efficiently predict the prognosis of patients with DLBCL, and verified the m5C prognostic model genes by immunohistochemistry analysis. This model was constructed using unsupervised consensus clustering analyses, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Based on the expression of m5C genes in the model, patients with DLBCL could be effectively divided into groups with significant survival time differences. The m5C risk-score signature demonstrated a highly significant independent prognostic value. Results from tumor microenvironment analyses revealed that m5C genes altered the infiltration of eosinophils, Tregs, and M2 macrophages. Additionally, they regulated T cell activation by modulating the expression of CTLA4, PDL1, B2M, CD8A, ICOS, and other relevant immune checkpoint expressions. In conclusion, our study presents a robust m5C prognostic model that effectively predicts prognosis in DLBCL. This model may offer a new approach for prognostic stratification and potential therapeutic interventions for patients with DLBCL.
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Affiliation(s)
- Wenting Cui
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
- Department of Hematology, The First People’s Hospital of JiujiangJiujiang, Jiangxi, China
| | - Cancan Luo
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Lili Zhou
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Tiantian Yu
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Yongsheng Meng
- Department of Tumor Biobank, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuan, Shanxi, China
| | - Qianqian Yu
- Department of Tumor Biobank, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuan, Shanxi, China
| | - Zhixiang Lei
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Ya Wang
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Lijuan Peng
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Qingqing Luo
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Duozhuang Tang
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuan, Shanxi, China
| | - Li Yu
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Key Laboratory of Hematology of Jiangxi ProvinceNanchang, Jiangxi, China
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8
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Pushpakumar S, Singh M, Sen U, Tyagi N, Tyagi SC. The role of the mitochondrial trans-sulfuration in cerebro-cardio renal dysfunction during trisomy down syndrome. Mol Cell Biochem 2024; 479:825-829. [PMID: 37198322 DOI: 10.1007/s11010-023-04761-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
One in 700 children is born with the down syndrome (DS). In DS, there is an extra copy of X chromosome 21 (trisomy). Interestingly, the chromosome 21 also contains an extra copy of the cystathionine beta synthase (CBS) gene. The CBS activity is known to contribute in mitochondrial sulfur metabolism via trans-sulfuration pathway. We hypothesize that due to an extra copy of the CBS gene there is hyper trans-sulfuration in DS. We believe that understanding the mechanism of hyper trans-sulfuration during DS will be important in improving the quality of DS patients and towards developing new treatment strategies. We know that folic acid "1-carbon" metabolism (FOCM) cycle transfers the "1-carbon" methyl group to DNA (H3K4) via conversion of s-adenosyl methionine (SAM) to s-adenosyl homocysteine (SAH) by DNMTs (the gene writers). The demethylation reaction is carried out by ten-eleven translocation methylcytosine dioxygenases (TETs; the gene erasers) through epigenetics thus turning the genes off/on and opening the chromatin by altering the acetylation/HDAC ratio. The S-adenosyl homocysteine hydrolase (SAHH) hydrolyzes SAH to homocysteine (Hcy) and adenosine. The Hcy is converted to cystathionine, cysteine and hydrogen sulfide (H2S) via CBS/cystathioneγ lyase (CSE)/3-mercaptopyruvate sulfurtransferase (3MST) pathways. Adenosine by deaminase is converted to inosine and then to uric acid. All these molecules remain high in DS patients. H2S is a potent inhibitor of mitochondrial complexes I-IV, and regulated by UCP1. Therefore, decreased UCP1 levels and ATP production can ensue in DS subjects. Interestingly, children born with DS show elevated levels of CBS/CSE/3MST/Superoxide dismutase (SOD)/cystathionine/cysteine/H2S. We opine that increased levels of epigenetic gene writers (DNMTs) and decreased in gene erasers (TETs) activity cause folic acid exhaustion, leading to an increase in trans-sulphuration by CBS/CSE/3MST/SOD pathways. Thus, it is important to determine whether SIRT3 (inhibitor of HDAC3) can decrease the trans-sulfuration activity in DS patients. Since there is an increase in H3K4 and HDAC3 via epigenetics in DS, we propose that sirtuin-3 (Sirt3) may decrease H3K4 and HDAC3 and hence may be able to decrease the trans-sulfuration in DS. It would be worth to determine whether the lactobacillus, a folic acid producing probiotic, mitigates hyper-trans-sulphuration pathway in DS subjects. Further, as we know that in DS patients the folic acid is exhausted due to increase in CBS, Hcy and re-methylation. In this context, we suggest that folic acid producing probiotics such as lactobacillus might be able to improve re-methylation process and hence may help decrease the trans-sulfuration pathway in the DS patients.
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Affiliation(s)
- Sathnur Pushpakumar
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA
| | - Mahavir Singh
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA.
- School of Medicine, University of Louisville, Louisville, Kentucky, USA.
| | | | - N Tyagi
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA
| | - Suresh C Tyagi
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA
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9
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Zhu D, Zeng S, Su C, Li J, Xuan Y, Lin Y, Xu E, Fan Q. The interaction between DNA methylation and tumor immune microenvironment: from the laboratory to clinical applications. Clin Epigenetics 2024; 16:24. [PMID: 38331927 PMCID: PMC10854038 DOI: 10.1186/s13148-024-01633-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
DNA methylation is a pivotal epigenetic modification that affects gene expression. Tumor immune microenvironment (TIME) comprises diverse immune cells and stromal components, creating a complex landscape that can either promote or inhibit tumor progression. In the TIME, DNA methylation has been shown to play a critical role in influencing immune cell function and tumor immune evasion. DNA methylation regulates immune cell differentiation, immune responses, and TIME composition Targeting DNA methylation in TIME offers various potential avenues for enhancing immune cytotoxicity and reducing immunosuppression. Recent studies have demonstrated that modification of DNA methylation patterns can promote immune cell infiltration and function. However, challenges persist in understanding the precise mechanisms underlying DNA methylation in the TIME, developing selective epigenetic therapies, and effectively integrating these therapies with other antitumor strategies. In conclusion, DNA methylation of both tumor cells and immune cells interacts with the TIME, and thus affects clinical efficacy. The regulation of DNA methylation within the TIME holds significant promise for the advancement of tumor immunotherapy. Addressing these challenges is crucial for harnessing the full potential of epigenetic interventions to enhance antitumor immune responses and improve patient outcomes.
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Affiliation(s)
- Daoqi Zhu
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, No.111 Liuhua Road, Guangzhou, 510010, China
| | - Siying Zeng
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China
| | - Chao Su
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China
| | - Jingjun Li
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yiwen Xuan
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, No.111 Liuhua Road, Guangzhou, 510010, China
| | - Yongkai Lin
- Department of Endocrinology, The First Affiliated Hospital, Traditional Chinese Medicine University of Guangzhou, Guangzhou, 510405, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, No.111 Liuhua Road, Guangzhou, 510010, China.
| | - Qin Fan
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China.
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10
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Guler GD, Ning Y, Coruh C, Mognol GP, Phillips T, Nabiyouni M, Hazen K, Scott A, Volkmuth W, Levy S. Plasma cell-free DNA hydroxymethylation profiling reveals anti-PD-1 treatment response and resistance biology in non-small cell lung cancer. J Immunother Cancer 2024; 12:e008028. [PMID: 38212123 PMCID: PMC10806554 DOI: 10.1136/jitc-2023-008028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Treatment with immune checkpoint inhibitors (ICIs) targeting programmed death-1 (PD-1) can yield durable antitumor responses, yet not all patients respond to ICIs. Current approaches to select patients who may benefit from anti-PD-1 treatment are insufficient. 5-hydroxymethylation (5hmC) analysis of plasma-derived cell-free DNA (cfDNA) presents a novel non-invasive approach for identification of therapy response biomarkers which can tackle challenges associated with tumor biopsies such as tumor heterogeneity and serial sample collection. METHODS 151 blood samples were collected from 31 patients with non-small cell lung cancer (NSCLC) before therapy started and at multiple time points while on therapy. Blood samples were processed to obtain plasma-derived cfDNA, followed by enrichment of 5hmC-containing cfDNA fragments through biotinylation via a two-step chemistry and binding to streptavidin coated beads. 5hmC-enriched cfDNA and whole genome libraries were prepared in parallel and sequenced to obtain whole hydroxymethylome and whole genome plasma profiles, respectively. RESULTS Comparison of on-treatment time point to matched pretreatment samples from same patients revealed that anti-PD-1 treatment induced distinct changes in plasma cfDNA 5hmC profiles of responding patients, as judged by Response evaluation criteria in solid tumors, relative to non-responders. In responders, 5hmC accumulated over genes involved in immune activation such as inteferon (IFN)-γ and IFN-α response, inflammatory response and tumor necrosis factor (TNF)-α signaling, whereas in non-responders 5hmC increased over epithelial to mesenchymal transition genes. Molecular response to anti-PD-1 treatment, as measured by 5hmC changes in plasma cfDNA profiles were observed early on, starting with the first cycle of treatment. Comparison of pretreatment plasma samples revealed that anti-PD-1 treatment response and resistance associated genes can be captured by 5hmC profiling of plasma-derived cfDNA. Furthermore, 5hmC profiling of pretreatment plasma samples was able to distinguish responders from non-responders using T cell-inflamed gene expression profile, which was previously identified by tissue RNA analysis. CONCLUSIONS These results demonstrate that 5hmC profiling can identify response and resistance associated biological pathways in plasma-derived cfDNA, offering a novel approach for non-invasive prediction and monitoring of immunotherapy response in NSCLC.
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Affiliation(s)
| | - Yuhong Ning
- ClearNote Health Inc, San Diego, California, USA
| | - Ceyda Coruh
- ClearNote Health Inc, San Diego, California, USA
| | | | | | | | - Kyle Hazen
- ClearNote Health Inc, San Diego, California, USA
| | - Aaron Scott
- ClearNote Health Inc, San Diego, California, USA
| | | | - Samuel Levy
- ClearNote Health Inc, San Diego, California, USA
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11
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Tigu AB, Bancos A. The Role of Epigenetic Modifier Mutations in Peripheral T-Cell Lymphomas. Curr Issues Mol Biol 2023; 45:8974-8988. [PMID: 37998740 PMCID: PMC10670124 DOI: 10.3390/cimb45110563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are a group of diseases with a low incidence, high degree of heterogeneity, and a dismal prognosis in most cases. Because of the low incidence of these diseases, there have been few therapeutic novelties developed over time. Nevertheless, this fact is changing presently as epigenetic modifiers have been shown to be recurrently mutated in some types of PTCLs, especially in the cases of PTCLs not otherwise specified (PTCL-NOS), T follicular helper (TFH), and angioimmunoblastic T-cell lymphoma (AITL). These have brought about more insight into PTCL biology, especially in the case of PTCLs arising from TFH lymphocytes. From a biological perspective, it has been observed that ten-eleven translocators (TET2) mutated T lymphocytes tend to polarize to TFH, while Tregs lose their inhibitory properties. IDH2 R172 was shown to have inhibitory effects on TET2, mimicking the effects of TET2 mutations, as well as having effects on histone methylation. DNA methyltransferase 3A (DNMT3A) loss-of-function, although it was shown to have opposite effects to TET2 from an inflammatory perspective, was also shown to increase the number of T lymphocyte progenitors. Aside from bringing about more knowledge of PTCL biology, these mutations were shown to increase the sensitivity of PTCLs to certain epigenetic therapies, like hypomethylating agents (HMAs) and histone deacetylase inhibitors (HDACis). Thus, to answer the question from the title of this review: We found the Achilles heel, but only for one of the Achilles.
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Affiliation(s)
- Adrian-Bogdan Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Academy of Romanian Scientists, Ilfov 3, 050044 Bucharest, Romania
| | - Anamaria Bancos
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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12
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Carty SA. Biological insights into the role of TET2 in T cell lymphomas. Front Oncol 2023; 13:1199108. [PMID: 37841428 PMCID: PMC10570544 DOI: 10.3389/fonc.2023.1199108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Peripheral T cell lymphomas (PTCL) are a heterogenous group of mature T cell lymphomas with an overall poor prognosis. Understanding the molecular heterogeneity in PTCL subtypes may lead to improved understanding of the underlying biological mechanisms driving these diseases. Mutations in the epigenetic regulator TET2 are among the most frequent mutations identified in PTCL, with the highest frequency in angioimmunoblastic T cell lymphomas and other nodal T follicular helper (TFH) lymphomas. This review dissects the role of TET2 in nodal TFH cell lymphomas with a focus on emerging biological insights into the molecular mechanism promoting lymphomagenesis and the potential for epigenetic therapies to improve clinical outcomes.
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Affiliation(s)
- Shannon A. Carty
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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13
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Wen H, Ji T, Lin L, Cheng N, Zhu K, Cao L. High Expression of Ten Eleven Translocation 1 Is Associated with Poor Prognosis in Hepatocellular Carcinoma. Mediators Inflamm 2023; 2023:2664370. [PMID: 37181808 PMCID: PMC10175022 DOI: 10.1155/2023/2664370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/03/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Background DNA methylation patterns have been found to be distinct between tumor and normal patients. However, the effect of DNA demethylation enzymes, ten eleven translocation (TET) proteins, has not been comprehensively characterized in liver cancer. In this research, we sought to unravel the linkage of TET proteins with prognosis, immune characteristics and biological pathways in hepatocellular carcinoma (HCC). Materials and Methods Four independent datasets with gene expression data and clinical data of HCC samples were downloaded from public databases. CIBERSORT, single sample Gene Set Enrichment Analysis (ssGSEA), MCP-counter, and TIMER were implemented to evaluate immune cell infiltration. limma was employed to screen differentially expressed genes (DEGs) between two groups. The demethylation-related risk model was established by using univariate Cox regression analysis, the least absolute shrinkage and selection operator (LASSO), and stepwise Akaike information criterion (stepAIC). Results TET1 was significantly higher expressed in tumor samples than that in normal samples. HCC patients with advanced stages (III+IV) and grades (G3+G4) had higher TET1 expression compared to early stages (I+II) and grades (G1+G2). HCC samples with high TET1 expression had worse prognosis than that with low expression. High and low TET1 expression groups had distinct immune cell infiltration and response to immunotherapy and chemotherapy. We identified 90 DEGs related to DNA demethylation in high vs. low TET1 expression groups. Furthermore, we established a risk model based on 90 DEGs containing seven key prognostic genes (SERPINH1, CDC20, HACD2, SPHK1, UGT2B15, SLC1A5, and CYP2C9) with effectiveness and robustness in predicting HCC prognosis. Conclusions Our study suggested TET1 as a potential indicator in HCC progression. TET1 was closely involved in immune infiltration and activation of oncogenic pathways. The DNA demethylation-related risk model was potential to be applied for predicting HCC prognosis in clinics.
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Affiliation(s)
- Haopeng Wen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Tengfei Ji
- Department of Hepatobiliary Surgery, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), Guangzhou 510000, China
| | - Liteng Lin
- Department of Minimally Invasive Interventional Radiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Nan Cheng
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Kangshun Zhu
- Department of Minimally Invasive Interventional Radiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Liangqi Cao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
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14
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Donzel M, Trecourt A, Balme B, Harou O, Mauduit C, Bachy E, Guesquières H, Fontaine J, Ortonne N, Perier-Muzet M, Dalle S, Traverse-Glehen A. Deciphering the spectrum of cutaneous lymphomas expressing TFH markers. Sci Rep 2023; 13:6500. [PMID: 37081015 PMCID: PMC10119163 DOI: 10.1038/s41598-023-33031-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
T-follicular helper (TFH) markers are expressed in the microenvironnement of marginal zone B-cell lymphoma (MZL), and in lymphomas arising from TFH-cells, sometimes making the differential diagnosis difficult. In the skin, the "TFH-spectrum" is poorly defined, going from primary cutaneous lymphoproliferative disorder with small/medium CD4+ T-cells (SMLPD) to cutaneous localizations of systemic angioimmunoblastic T-cell lymphoma (cAITL), and may pass through intermediate forms (primary cutaneous T-follicular helper derived lymphoma, not otherwise specified (PCTFHL,NOS)). We retrospectively analyzed 20 MZL, 13 SMLPD, 5 PCTFHL, and 11 cAITL clinically, histologically, and molecularly, to define tools to differentiate them. Characteristics that might favor the diagnosis of MZL over SMLPD are: multiple skin nodules (p < 0.001), nodular architecture (p < 0.01), residual germinal centers with follicular dendritic cell network (p < 0.001), monotypic plasma cells (p < 0.001), and few staining with PD1 (p = 0.016) or CXCL13 (p = 0.03). PCTFHL and cAITL presented as multiple (p < 0.01) lesions, in older patients (p < 0.01), with systemic symptoms and/or biological alterations (p < 0.01). Immunophenotypic loss of T-cell markers (p < 0.001), BCL6 (p = 0.023) and/or CD10 staining (p = 0.08), and a higher proliferative index (≥ 30%, p = 0.039) favoured these diagnoses over SMLPD. Pathogenic variants were observed by genomic sequencing in 47% of MZL (TNFAIP3 (32%), EP300 (21%), NOTCH2 (16%), KMT2D (16%), CARD11 (10.5%)), 8% of SMLPD (TET2), 40% of PCTFHL (SOCS1 (20%), ARID1A (20%)) and 64% of cAITL (TET2 (63.6%), RHOA (36.4%), NOTCH1 (9%)). This study characterizes the various clinical and histological features between cutaneous lymphomas expressing TFH markers and highlights the value of the interest of screening for genomic mutations in difficult cases.
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Affiliation(s)
- Marie Donzel
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France.
| | - Alexis Trecourt
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France
| | - Brigitte Balme
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France
| | - Olivier Harou
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France
| | - Claire Mauduit
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France
| | - Emmanuel Bachy
- Hospices Civils de Lyon, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, CLB, UCBL, Université Lyon 1, Lyon, France
- Hospices Civils de Lyon, Service d'Hématologie, Hôpital Lyon Sud, Lyon, France
| | - Hervé Guesquières
- Hospices Civils de Lyon, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, CLB, UCBL, Université Lyon 1, Lyon, France
- Hospices Civils de Lyon, Service d'Hématologie, Hôpital Lyon Sud, Lyon, France
| | - Juliette Fontaine
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France
| | - Nicolas Ortonne
- Biological Immunology, APHP Henri Mondor Hospital, Paris Est Creteil University (UPEC) and INSERM U955 Team Ortonne (NFL), Créteil, France
- Department of Dermatology, APHP Henri Mondor Hospital, Créteil, France
| | - Marie Perier-Muzet
- Hospices Civils de Lyon, Service de Dermatologie, Hôpital Lyon Sud, Lyon, France
| | - Stéphane Dalle
- Hospices Civils de Lyon, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, CLB, UCBL, Université Lyon 1, Lyon, France
- Hospices Civils de Lyon, Service de Dermatologie, Hôpital Lyon Sud, Lyon, France
| | - Alexandra Traverse-Glehen
- Institut de Pathologie multisites, Hospices Civils de Lyon, Hôpital Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Lyon, Pierre-Bénite, France
- Hospices Civils de Lyon, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, CLB, UCBL, Université Lyon 1, Lyon, France
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15
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Xia M, Yan R, Wang W, Kong A, Zhang M, Miao Z, Ge W, Wan B, Xu X. The Tet2–Upf1 complex modulates mRNA stability under stress conditions. Front Genet 2023; 14:1158954. [PMID: 37091805 PMCID: PMC10117899 DOI: 10.3389/fgene.2023.1158954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Introduction: Environmental stress promotes epigenetic alterations that impact gene expression and subsequently participate in the pathological processes of the disorder. Among epigenetic regulations, ten–eleven Translocation (Tet) enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA and RNA and function as critical players in the pathogenesis of diseases. Our previous results showed that chronic stress increases the expression of cytoplasmic Tet2 in the hippocampus of mice exposed to chronic mild stress (CMS). Whether the cytoplasmic Tet2 alters RNA 5hmC modification in chronic stress-related processes remains largely unknown.Methods: To explore the role of cytoplasmic Tet2 under CMS conditions, we established CMS mice model and detected the expression of RNA 5hmC by dot blot. We verified the interaction of Tet2 and its interacting protein by co-immunoprecipitation combined with mass spectrometry and screened downstream target genes by cluster analysis of Tet2 and upstream frameshift 1 (Upf1) interacting RNA. The expression of protein was detected by Western blot and the expression of the screened target genes was detected by qRT-PCR.Results: In this study, we found that increased cytoplasmic Tet2 expression under CMS conditions leads to increase in total RNA 5hmC modification. Tet2 interacted with the key non-sense-mediated mRNA decay (NMD) factor Upf1, regulated the stability of stress-related genes such as Unc5b mRNA, and might thereby affect neurodevelopment.Discussion: In summary, this study revealed that Tet2-mediated RNA 5hmC modification is involved in stress-related mRNA stability regulation and may serve as a potential therapeutic target for chronic stress-related diseases such as depression.
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Affiliation(s)
- Meiling Xia
- Departments of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Rui Yan
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Wenjuan Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Anqi Kong
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Meng Zhang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Zhigang Miao
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Wei Ge
- Institute of Neuroscience, Soochow University, Suzhou, China
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Wei Ge, ; Bo Wan, ; Xingshun Xu,
| | - Bo Wan
- Institute of Neuroscience, Soochow University, Suzhou, China
- *Correspondence: Wei Ge, ; Bo Wan, ; Xingshun Xu,
| | - Xingshun Xu
- Departments of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
- *Correspondence: Wei Ge, ; Bo Wan, ; Xingshun Xu,
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16
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Jin M, Ji J, Chen X, Zhou Y, Wang D, Liu A. The emerging role of TET enzymes in the immune microenvironment at the maternal-fetal interface during decidualization and early pregnancy. Front Immunol 2023; 13:1066599. [PMID: 36685517 PMCID: PMC9850229 DOI: 10.3389/fimmu.2022.1066599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
A dysregulated immune microenvironment at the maternal-fetal interface in early pregnancy may lead to early pregnancy loss, fetal growth restriction, and preeclampsia. However, major questions about how epigenetic modifications regulate the immune microenvironment during the decidualization process and embryo implantation remain unanswered. DNA methylation, the main epigenetic mechanism involved in the endometrial cycle, is crucial for specific transcriptional networks associated with endometrial stromal cell (ESC) proliferation, hormone response, decidualization, and embryo implantation. Ten-eleven translocation (TET) enzymes, responsible for catalyzing the conversion of 5-methylcytosine to 5-hydroxymethylcyosine, 5-formylytosine, and 5-carboxylcyosine to achieve the DNA demethylation process, appear to play a critical role in decidualization and embryo implantation. Here, we provide a comprehensive view of their structural similarities and the common mechanism of regulation in the microenvironment at the maternal-fetal interface during decidualization and early pregnancy. We also discuss their physiological role in the decidual immune microenvironment. Finally, we propose a key hypothesis regarding TET enzymes at the maternal-fetal interface between decidual immune cells and ESCs. Future work is needed to elucidate their functional role and examine therapeutic strategies targeting these enzymes in pregnancy-related disease preclinical models, which would be of great value for future implications in disease diagnosis or treatment.
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Affiliation(s)
- Mengmeng Jin
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Jianxiong Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xi Chen
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Ying Zhou
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Dimin Wang
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China,*Correspondence: Aixia Liu, ; Dimin Wang,
| | - Aixia Liu
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China,Department of Reproductive Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China,*Correspondence: Aixia Liu, ; Dimin Wang,
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17
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Tsagaratou A. TET Proteins in the Spotlight: Emerging Concepts of Epigenetic Regulation in T Cell Biology. Immunohorizons 2023; 7:106-115. [PMID: 36645853 PMCID: PMC10152628 DOI: 10.4049/immunohorizons.2200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that oxidize 5-methylcytosine to form 5-hydroxymethylcytosine and downstream oxidized modified cytosines. In the past decade, intensive research established that TET-mediated DNA demethylation is critical for immune cell development and function. In this study, we discuss major advances regarding the role of TET proteins in regulating gene expression in the context of T cell lineage specification, function, and proliferation. Then, we focus on open questions in the field. We discuss recent findings regarding the diverse roles of TET proteins in other systems, and we ask how these findings might relate to T cell biology. Finally, we ask how this tremendous progress on understanding the multifaceted roles of TET proteins in shaping T cell identity and function can be translated to improve outcomes of human disease, such as hematological malignancies and immune response to cancer.
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Affiliation(s)
- Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC
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18
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López-Nevado M, Ortiz-Martín J, Serrano C, Pérez-Saez MA, López-Lorenzo JL, Gil-Etayo FJ, Rodríguez-Frías E, Cabrera-Marante O, Morales-Pérez P, Rodríguez-Pinilla MS, Manso R, Salgado-Sánchez RN, Cerdá-Montagud A, Quesada-Espinosa JF, Gómez-Rodríguez MJ, Paz-Artal E, Muñoz-Calleja C, Arranz-Sáez R, Allende LM. Novel Germline TET2 Mutations in Two Unrelated Patients with Autoimmune Lymphoproliferative Syndrome-Like Phenotype and Hematologic Malignancy. J Clin Immunol 2023; 43:165-180. [PMID: 36066697 DOI: 10.1007/s10875-022-01361-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
Somatic mutations in the ten-eleven translocation methylcytosine dioxygenase 2 gene (TET2) have been associated to hematologic malignancies. More recently, biallelic, and monoallelic germline mutations conferring susceptibility to lymphoid and myeloid cancer have been described. We report two unrelated autoimmune lymphoproliferative syndrome-like patients who presented with T-cell lymphoma associated with novel germline biallelic or monoallelic mutations in the TET2 gene. Both patients presented a history of chronic lymphoproliferation with lymphadenopathies and splenomegaly, cytopenias, and immune dysregulation. We identified the first compound heterozygous patient for TET2 mutations (P1) and the first ALPS-like patient with a monoallelic TET2 mutation (P2). P1 had the most severe form of autosomal recessive disease due to TET2 loss of function resulting in absent TET2 expression and profound increase in DNA methylation. Additionally, the immunophenotype showed some alterations in innate and adaptive immune system as inverted myeloid/plasmacytoid dendritic cells ratio, elevated terminally differentiated effector memory CD8 + T-cells re-expressing CD45RA, regulatory T-cells, and Th2 circulating follicular T-cells. Double-negative T-cells, vitamin B12, and IL-10 were elevated according to the ALPS-like suspicion. Interestingly, the healthy P1's brother carried a TET2 mutation and presented some markers of immune dysregulation. P2 showed elevated vitamin B12, hypergammaglobulinemia, and decreased HDL levels. Therefore, novel molecular defects in TET2 confirm and expand both clinical and immunological phenotype, contributing to a better knowledge of the bridge between cancer and immunity.
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Affiliation(s)
- Marta López-Nevado
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
| | | | - Cristina Serrano
- Immunology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - María A Pérez-Saez
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - José L López-Lorenzo
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Francisco J Gil-Etayo
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Edgar Rodríguez-Frías
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Oscar Cabrera-Marante
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Pablo Morales-Pérez
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Rebeca Manso
- Pathology Department, Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | | | - Ana Cerdá-Montagud
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Juan F Quesada-Espinosa
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - María J Gómez-Rodríguez
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
- School of Medicine, Complutense University of Madrid, Madrid, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Cecilia Muñoz-Calleja
- Immunology Department, University Hospital La Princesa, Madrid, Spain
- School of Medicine, University Autónoma de Madrid, Madrid, Spain
- Research Institute Hospital de La Princesa, Madrid, Spain
| | - Reyes Arranz-Sáez
- Hematology Department, University Hospital La Princesa, Madrid, Spain
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
- School of Medicine, Complutense University of Madrid, Madrid, Spain.
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19
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Characterization of global research hotspots and trends on ten-eleven translocation 2: visualization and bibliometric analysis. Am J Transl Res 2022; 14:8504-8522. [PMID: 36628244 PMCID: PMC9827328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/15/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND OBJECTIVE Ten-eleven translocation-2 (TET2) is member of the methylcytosine dioxygenase family and plays important roles in a variety of physiological and pathological processes; however, no bibliometric analysis has been performed to methodically evaluate the scientific research on TET2. Therefore, the aim of this study was to conduct a visual and scientometric analysis of TET2 research and to explore its current landscape, future direction, and research frontiers. METHODS Publications related to TET2 research were retrieved from the Web of Science Core Collection (WoSCC) from 2009 to 2021. Excel, CiteSpace, and VOSviewer were utilized to perform the bibliometric visualization analysis. RESULTS A total of 2384 articles were retrieved. The number of publications on TET2 has been steadily increasing from 2009 to 2021. The USA is the top contributor to the topic, with the largest number of publications. Harvard University and the Institut National de la Santé et de la Recherche Médicale were the leading institutions, while Levine RL of Memorial Sloan-Kettering Cancer Center is the most prolific and influential author. In TET2-related publications, the high-frequency keywords were: "tet2", "DNA methylation", "5-hrdroxymethylcytosine", "5-methylcytosine", "mutations", and "acute myeloid-leukemia". Based on keyword bursts, the emerging TET2 research hotspots include "inflammation", "gene expression", "landscape", and "clonal hematopoiesis". CONCLUSION Research on TET2 is constantly growing and evolving during the last decade. Here, we provide an objective and comprehensive analysis of the global status, research hotspots, and potential trends in the field of TET2 research by using a bibliometric approach. These results will assist researchers in mastering the knowledge structure and guiding the future research directions of TET2.
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20
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Chen HY, Almonte-Loya A, Lay FY, Hsu M, Johnson E, González-Avalos E, Yin J, Bruno RS, Ma Q, Ghoneim HE, Wozniak DJ, Harrison FE, Lio CWJ. Epigenetic remodeling by vitamin C potentiates plasma cell differentiation. eLife 2022; 11:73754. [PMID: 36069787 PMCID: PMC9451539 DOI: 10.7554/elife.73754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Ascorbate (vitamin C) is an essential micronutrient in humans. The severe chronic deficiency of ascorbate, termed scurvy, has long been associated with increased susceptibility to infections. How ascorbate affects the immune system at the cellular and molecular levels remained unclear. From a micronutrient analysis, we identified ascorbate as a potent enhancer for antibody response by facilitating the IL-21/STAT3-dependent plasma cell differentiation in mouse and human B cells. The effect of ascorbate is unique as other antioxidants failed to promote plasma cell differentiation. Ascorbate is especially critical during early B cell activation by poising the cells to plasma cell lineage without affecting the proximal IL-21/STAT3 signaling and the overall transcriptome. As a cofactor for epigenetic enzymes, ascorbate facilitates TET2/3-mediated DNA modification and demethylation of multiple elements at the Prdm1 locus. DNA demethylation augments STAT3 association at the Prdm1 promoter and a downstream enhancer, thus ensuring efficient gene expression and plasma cell differentiation. The results suggest that an adequate level of ascorbate is required for antibody response and highlight how micronutrients may regulate the activity of epigenetic enzymes to regulate gene expression. Our findings imply that epigenetic enzymes can function as sensors to gauge the availability of metabolites and influence cell fate decisions.
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Affiliation(s)
- Heng-Yi Chen
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Ana Almonte-Loya
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Fang-Yun Lay
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Michael Hsu
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Eric Johnson
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Edahí González-Avalos
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Jieyun Yin
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Richard S Bruno
- Human Nutrition Program, The Ohio State University, Columbus, OH, United States
| | - Qin Ma
- Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Fiona E Harrison
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
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21
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Äijö T, Theofilatos D, Cheng M, Smith MD, Xiong Y, Baldwin AS, Tsagaratou A. TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner. Front Immunol 2022; 13:940995. [PMID: 35990681 PMCID: PMC9389146 DOI: 10.3389/fimmu.2022.940995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
TET proteins mediate DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other oxidative derivatives. We have previously demonstrated a dynamic enrichment of 5hmC during T and invariant natural killer T cell lineage specification. Here, we investigate shared signatures in gene expression of Tet2/3 DKO CD4 single positive (SP) and iNKT cells in the thymus. We discover that TET proteins exert a fundamental role in regulating the expression of the lineage specifying factor Th-POK, which is encoded by Zbtb7b. We demonstrate that TET proteins mediate DNA demethylation - surrounding a proximal enhancer, critical for the intensity of Th-POK expression. In addition, TET proteins drive the DNA demethylation of site A at the Zbtb7b locus to facilitate GATA3 binding. GATA3 induces Th-POK expression in CD4 SP cells. Finally, by introducing a novel mouse model that lacks TET3 and expresses full length, catalytically inactive TET2, we establish a causal link between TET2 catalytic activity and lineage specification of both conventional and unconventional T cells.
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Affiliation(s)
- Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew D. Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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22
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The Multiple Myeloma Landscape: Epigenetics and Non-Coding RNAs. Cancers (Basel) 2022; 14:cancers14102348. [PMID: 35625953 PMCID: PMC9139326 DOI: 10.3390/cancers14102348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Recent findings in multiple myeloma have led to therapies which have improved patient life quality and expectancy. However, frequent relapse and drug resistance emphasize the need for more efficient therapeutic approaches. The discovery of non-coding RNAs as key actors in multiple myeloma has broadened the molecular landscape of this disease, together with classical epigenetic factors such as methylation and acetylation. microRNAs and long non-coding RNAs comprise the majority of the described non-coding RNAs dysregulated in multiple myeloma, while circular RNAs are recently emerging as promising molecular targets. This review provides a comprehensive overview of the most recent knowledge on this topic and suggests new therapeutic strategies. Abstract Despite advances in available treatments, multiple myeloma (MM) remains an incurable disease and represents a challenge in oncohematology. New insights into epigenetic factors contributing to MM development and progression have improved the knowledge surrounding its molecular basis. Beyond classical epigenetic factors, including methylation and acetylation, recent genome analyses have unveiled the importance of non-coding RNAs in MM pathogenesis. Non-coding RNAs have become of interest, as their dysregulation opens the door to new therapeutic approaches. The discovery, in the past years, of molecular techniques, such as CRISPR-Cas, has led to innovative therapies with potential benefits to achieve a better outcome for MM patients. This review summarizes the current knowledge on epigenetics and non-coding RNAs in MM pathogenesis.
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23
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Waheed SO, Varghese A, Chaturvedi SS, Karabencheva-Christova TG, Christov CZ. How Human TET2 Enzyme Catalyzes the Oxidation of Unnatural Cytosine Modifications in Double-Stranded DNA. ACS Catal 2022; 12:5327-5344. [PMID: 36339349 PMCID: PMC9629818 DOI: 10.1021/acscatal.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylation of cytosine bases is strongly linked to gene expression, imprinting, aging, and carcinogenesis. The Ten-eleven translocation (TET) family of enzymes, which are Fe(II)/2-oxoglutarate (2OG)-dependent enzymes, employ Fe(IV)=O species to dealkylate the lesioned bases to an unmodified cytosine. Recently, it has been shown that the TET2 enzyme can catalyze promiscuously DNA substrates containing unnatural alkylated cytosine. Such unnatural substrates of TET can be used as direct probes for measuring the TET activity or capturing TET from cellular samples. Herein, we studied the catalytic mechanisms during the oxidation of the unnatural C5-position modifications (5-ethylcytosine (5eC), 5-vinylcytosine (5vC) and 5-ethynylcytosine (5eyC)) and the demethylation of N4-methylated lesions (4-methylcytosine (4mC) and 4,4-dimethylcytosine(4dmC)) of the cytosine base by the TET2 enzyme using molecular dynamics (MD) and combined quantum mechanics and molecular mechanics (QM/MM) computational approaches. The results reveal that the chemical nature of the alkylation of the double-stranded (ds) DNA substrates induces distinct changes in the interactions in the binding site, the second coordination sphere, and long-range correlated motions of the ES complexes. The rate-determining hydrogen atom transfer (HAT) is faster in N4-methyl substituent substrates than in the C5-alkylations. Importantly, the calculations show the preference of hydroxylation over desaturation in both 5eC and 5vC substrates. The studies elucidate the post-hydroxylation rearrangements of the hydroxylated intermediates of 5eyC and 5vC to ketene and 5-formylmethylcytosine (5fmC), respectively, and hydrolysis of hemiaminal intermediate of 4mC to formaldehyde and unmodified cytosine proceed exclusively in aqueous solution outside of the enzyme environment. Overall, the studies show that the chemical nature of the unnatural alkylated cytosine substrates exercises distinct effects on the binding interactions, reaction mechanism, and dynamics of TET2.
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Affiliation(s)
- Sodiq O. Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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24
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Gerecke C, Egea Rodrigues C, Homann T, Kleuser B. The Role of Ten-Eleven Translocation Proteins in Inflammation. Front Immunol 2022; 13:861351. [PMID: 35386689 PMCID: PMC8977485 DOI: 10.3389/fimmu.2022.861351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Ten-eleven translocation proteins (TET1-3) are dioxygenases that oxidize 5-methyldeoxycytosine, thus taking part in passive and active demethylation. TETs have shown to be involved in immune cell development, affecting from self-renewal of stem cells and lineage commitment to terminal differentiation. In fact, dysfunction of TET proteins have been vastly associated with both myeloid and lymphoid leukemias. Recently, there has been accumulating evidence suggesting that TETs regulate immune cell function during innate and adaptive immune responses, thereby modulating inflammation. In this work, we pursue to review the current and recent evidence on the mechanistic aspects by which TETs regulate immune cell maturation and function. We will also discuss the complex interplay of TET expression and activity by several factors to modulate a multitude of inflammatory processes. Thus, modulating TET enzymes could be a novel pharmacological approach to target inflammation-related diseases and myeloid and lymphoid leukemias, when their activity is dysregulated.
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Affiliation(s)
- Christian Gerecke
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Caue Egea Rodrigues
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Thomas Homann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Burkhard Kleuser
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
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25
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Role of Myeloid Tet Methylcytosine Dioxygenase 2 in Pulmonary and Peritoneal Inflammation Induced by Lipopolysaccharide and Peritonitis Induced by Escherichia coli. Cells 2021; 11:cells11010082. [PMID: 35011643 PMCID: PMC8750455 DOI: 10.3390/cells11010082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/15/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Tet methylcytosine dioxygenase 2 (Tet2) mediates demethylation of DNA. We here sought to determine the expression and function of Tet2 in macrophages upon exposure to lipopolysaccharide (LPS), and in the host response to LPS induced lung and peritoneal inflammation, and during Escherichia (E.) coli induced peritonitis. LPS induced Tet2 expression in mouse macrophages and human monocytes in vitro, as well as in human alveolar macrophages after bronchial instillation in vivo. Bone marrow-derived macrophages from myeloid Tet2 deficient (Tet2fl/flLysMCre) mice displayed enhanced production of IL-1β, IL-6 and CXCL1 upon stimulation with several Toll-like receptor agonists; similar results were obtained with LPS stimulated alveolar and peritoneal macrophages. Histone deacetylation was involved in the effect of Tet2 on IL-6 production, whilst methylation at the Il6 promoter was not altered by Tet2 deficiency. Tet2fl/flLysMCre mice showed higher IL-6 and TNF levels in bronchoalveolar and peritoneal lavage fluid after intranasal and intraperitoneal LPS administration, respectively, whilst other inflammatory responses were unaltered. E. coli induced stronger production of IL-1β and IL-6 by Tet2 deficient peritoneal macrophages but not in peritoneal lavage fluid of Tet2fl/flLysMCre mice after in vivo intraperitoneal infection. Tet2fl/flLysMCre mice displayed enhanced bacterial growth during E. coli peritonitis, which was associated with a reduced capacity of Tet2fl/flLysMCre peritoneal macrophages to inhibit the growth of E. coli in vitro. Collectively, these data suggest that Tet2 is involved in the regulation of macrophage functions triggered by LPS and during E. coli infection.
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26
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Dai E, Zhu Z, Wahed S, Qu Z, Storkus WJ, Guo ZS. Epigenetic modulation of antitumor immunity for improved cancer immunotherapy. Mol Cancer 2021; 20:171. [PMID: 34930302 PMCID: PMC8691037 DOI: 10.1186/s12943-021-01464-x] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
Epigenetic mechanisms play vital roles not only in cancer initiation and progression, but also in the activation, differentiation and effector function(s) of immune cells. In this review, we summarize current literature related to epigenomic dynamics in immune cells impacting immune cell fate and functionality, and the immunogenicity of cancer cells. Some important immune-associated genes, such as granzyme B, IFN-γ, IL-2, IL-12, FoxP3 and STING, are regulated via epigenetic mechanisms in immune or/and cancer cells, as are immune checkpoint molecules (PD-1, CTLA-4, TIM-3, LAG-3, TIGIT) expressed by immune cells and tumor-associated stromal cells. Thus, therapeutic strategies implementing epigenetic modulating drugs are expected to significantly impact the tumor microenvironment (TME) by promoting transcriptional and metabolic reprogramming in local immune cell populations, resulting in inhibition of immunosuppressive cells (MDSCs and Treg) and the activation of anti-tumor T effector cells, professional antigen presenting cells (APC), as well as cancer cells which can serve as non-professional APC. In the latter instance, epigenetic modulating agents may coordinately promote tumor immunogenicity by inducing de novo expression of transcriptionally repressed tumor-associated antigens, increasing expression of neoantigens and MHC processing/presentation machinery, and activating tumor immunogenic cell death (ICD). ICD provides a rich source of immunogens for anti-tumor T cell cross-priming and sensitizing cancer cells to interventional immunotherapy. In this way, epigenetic modulators may be envisioned as effective components in combination immunotherapy approaches capable of mediating superior therapeutic efficacy.
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Affiliation(s)
- Enyong Dai
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhi Zhu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Surgical Oncology, China Medical University, Shenyang, China
| | - Shudipto Wahed
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Zhaoxia Qu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Walter J Storkus
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Departments of Dermatology, Immunology, Pathology and Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY, USA.
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27
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Joshi P, Vijaykumar A, Enkhmandakh B, Mina M, Shin DG, Bayarsaihan D. Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors. J Biochem 2021; 171:123-129. [PMID: 34676418 DOI: 10.1093/jb/mvab114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022] Open
Abstract
The dental pulp is critical for the production of odontoblasts to create reparative dentin. In recent years dental pulp has become a promising source of mesenchymal stem cells that are capable of differentiating into multiple cell types. To elucidate the transcriptional control mechanisms specifying the early phases of odontoblast differentiation, we analyzed the DNA demethylation pattern associated with 5-hydroxymethylcytosine (5hmC) in the primary murine dental pulp. 5hmC plays an important role in chromatin accessibility and transcriptional control by modeling a dynamic equilibrium between DNA methylation and demethylation. Our research revealed 5hmC enrichment along genes and non-coding regulatory regions associated with specific developmental pathways in the genome of mouse incisor and molar dental pulp. Although the overall distribution of 5hmC is similar, the intensity and location of the 5hmC peaks significantly differs between the incisor and molar pulp genome, indicating cell type-specific epigenetic variations. Our study suggests that the differential DNA demethylation pattern could account for the distinct regulatory mechanisms underlying the tooth-specific ontogenetic programs.
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Affiliation(s)
- Pujan Joshi
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269, USA
| | - Anushree Vijaykumar
- Department of Craniofacial Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Badam Enkhmandakh
- Center for Regenerative Medicine & Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Mina Mina
- Department of Craniofacial Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Dong-Guk Shin
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269, USA
| | - Dashzeveg Bayarsaihan
- Institute for System Genomics & Center for Regenerative Medicine & Skeletal Development, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
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Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
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29
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Li L, Feng T, Zhou W, Liu Y, Li H. miRNAs in decidual NK cells: regulators worthy of attention during pregnancy. Reprod Biol Endocrinol 2021; 19:150. [PMID: 34600537 PMCID: PMC8486626 DOI: 10.1186/s12958-021-00812-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022] Open
Abstract
The critical immune effectors, including T, B, and natural killer (NK) cells, dendritic cells, and macrophages participate in regulating immune responses during pregnancy. Among these immune cells, decidual NK (dNK) cells are involved in key placental development processes at the maternal-fetal interface, such as uterine spiral artery remodeling, trophoblast invasion, and decidualization. Mechanistically, dNK cells significantly influence pregnancy outcome by secreting cytokines, chemokines, and angiogenic mediators and by their interactions with trophoblasts and other decidual cells. MicroRNAs (miRNAs) are small non-coding RNA molecules that participate in the initiation and progression of human diseases. Although the functions of circulating miRNAs in pathological mechanism has been extensively studied, the regulatory roles of miRNAs in NK cells, especially in dNK cells, have been rarely reported. In this review, we analyze the effects of miRNA regulations of dNK cell functions on the immune system during gestation. We discuss aberrant expressions of certain miRNAs in dNK cells that may lead to pathological consequences, such as recurrent pregnancy loss (RPL). Interestingly, miRNA expression patterns are also different between dNK cells and peripheral NK (pNK) cells, and pNK cells in the first- and third-trimester of gestation. The dysregulation of miRNA plays a pivotal regulatory role in driving immune functions of dNK and pNK cells. Further understanding of the molecular mechanisms of miRNAs in dNK cells may provide new insights into the development of therapeutics to prevent pregnancy failure.
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Affiliation(s)
- Liman Li
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ting Feng
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Weijie Zhou
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yuan Liu
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hong Li
- Center of Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
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Sinclair AJ. Could Changing the DNA Methylation Landscape Promote the Destruction of Epstein-Barr Virus-Associated Cancers? Front Cell Infect Microbiol 2021; 11:695093. [PMID: 34123880 PMCID: PMC8194487 DOI: 10.3389/fcimb.2021.695093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
DNA methylation at CpG motifs provides an epigenetic route to regulate gene expression. In general, an inverse correlation between DNA hypermethylation at CpG motifs and gene expression is observed. Epstein Barr-virus (EBV) infects people and the EBV genome resides in the nucleus where either its replication cycle initiates or it enters a long-term latency state where the viral genome becomes hypermethylated at CpG motifs. Viral gene expression shows a largely inverse correlation with DNA hypermethylation. DNA methylation occurs through the action of DNA methyl transferase enzymes: writer DNA methyl transferases add methyl groups to specific regions of unmethylated DNA; maintenance DNA methyl transferases reproduce the pattern of DNA methylation during genome replication. The impact of DNA methylation is achieved through the association of various proteins specifically with methylated DNA and their influence on gene regulation. DNA methylation can be changed through altering DNA methyl transferase activity or through the action of enzymes that further modify methylated CpG motifs. Azacytidine prodrugs that are incorporated into CpG motifs during DNA replication are recognized by DNA methyl transferases and block their function resulting in hypomethylation of DNA. EBV-associated cancers have hypermethylated viral genomes and many carcinomas also have highly hypermethylated cellular genomes. Decitabine, a member of the azacytidine prodrug family, reactivates viral gene expression and promotes the recognition of lymphoma cells by virus-specific cytotoxic T-cells. For EBV-associated cancers, the impact of decitabine on the cellular genome and the prospect of combining decitabine with other therapeutic approaches is currently unknown but exciting.
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Affiliation(s)
- Alison J Sinclair
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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