1
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Luo F, Li B, Li J, Li Y. Simultaneous blastic plasmacytoid dendritic cell neoplasm and myelofibrosis: A case report. Oncol Lett 2024; 27:220. [PMID: 38586204 PMCID: PMC10996017 DOI: 10.3892/ol.2024.14354] [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: 08/02/2023] [Accepted: 12/05/2023] [Indexed: 04/09/2024] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an extremely rare and aggressive tumor with an unknown pathogenesis. Myelofibrosis (MF) is a type of myeloproliferative neoplasm. MF can be secondary to several hematological malignancies, including chronic myeloid leukemia, myelodysplastic syndrome and hairy cell leukemia. In the present report, a rare case of BPDCN secondary to MF is described. A 70-year-old male patient developed a large purplish-red rash with recurrent symptoms. BPDCN was confirmed by immunohistochemistry of a biopsy specimen and flow cytometry of bone marrow cells. Bone marrow histopathology revealed MF. Next-generation sequencing of peripheral blood revealed mutations in the Tet methylcytosine dioxygenase 2 and NRAS proto-oncogene GTPase genes. The patient underwent one cycle of chemoimmunotherapy, but the condition progressed, an infection developed and the patient eventually died. The present case suggests that BPDCN can occur in conjunction with MF and that the prognosis of such patients is poor. Pathological examination and genetic testing aided in the diagnosis and treatment. This case emphasizes the need to raise awareness of BPDCN among clinicians and to be alert to the potential for fatal infection in patients with BPDCN combined with MF following myelosuppression triggered during chemotherapy.
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Affiliation(s)
- Fuyi Luo
- Graduate School, Hebei North University, Zhangjiakou, Hebei 075000, P.R. China
- Department of Hematology, Hebei General Hospital, Shijiazhuang, Hebei 050000, P.R. China
| | - Bingjie Li
- Department of Pathology, Hebei General Hospital, Shijiazhuang, Hebei 050000, P.R. China
| | - Jing Li
- Department of Hematology, Hebei Province Hospital of Chinese Medicine, Shijiazhuang, Hebei 050000, P.R. China
| | - Yan Li
- Department of Hematology, Hebei General Hospital, Shijiazhuang, Hebei 050000, P.R. China
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2
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Katebi A, Chen X, Ramirez D, Li S, Lu M. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. NPJ Syst Biol Appl 2024; 10:38. [PMID: 38594351 PMCID: PMC11003984 DOI: 10.1038/s41540-024-00366-0] [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: 10/16/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sources, including gene expression and ATAC-seq datasets, curated gene regulatory interaction databases, and mathematical modeling to establish models of context-specific core gene regulatory networks (GRNs) for a mechanistic understanding of tumorigenesis of AML with IDH mutations. The approach adopts a new optimization procedure to identify the top network according to its accuracy in capturing gene expression states and its flexibility to allow sufficient control of state transitions. From GRN modeling, we identify key regulators associated with the function of IDH mutations, such as DNA methyltransferase DNMT1, and network destabilizers, such as E2F1. The constructed core regulatory network and outcomes of in-silico network perturbations are supported by survival data from AML patients. We expect that the combined bioinformatics and systems-biology modeling approach will be generally applicable to elucidate the gene regulation of disease progression.
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Affiliation(s)
- Ataur Katebi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Xiaowen Chen
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Daniel Ramirez
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA.
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3
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Dennis E, Murach M, Blackburn CM, Marshall M, Root K, Pattarabanjird T, Deroissart J, Erickson LD, Binder CJ, Bekiranov S, McNamara CA. Loss of TET2 increases B-1 cell number and IgM production while limiting CDR3 diversity. Front Immunol 2024; 15:1380641. [PMID: 38601144 PMCID: PMC11004297 DOI: 10.3389/fimmu.2024.1380641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Recent studies have demonstrated a role for Ten-Eleven Translocation-2 (TET2), an epigenetic modulator, in regulating germinal center formation and plasma cell differentiation in B-2 cells, yet the role of TET2 in regulating B-1 cells is largely unknown. Here, B-1 cell subset numbers, IgM production, and gene expression were analyzed in mice with global knockout of TET2 compared to wildtype (WT) controls. Results revealed that TET2-KO mice had elevated numbers of B-1a and B-1b cells in their primary niche, the peritoneal cavity, as well as in the bone marrow (B-1a) and spleen (B-1b). Consistent with this finding, circulating IgM, but not IgG, was elevated in TET2-KO mice compared to WT. Analysis of bulk RNASeq of sort purified peritoneal B-1a and B-1b cells revealed reduced expression of heavy and light chain immunoglobulin genes, predominantly in B-1a cells from TET2-KO mice compared to WT controls. As expected, the expression of IgM transcripts was the most abundant isotype in B-1 cells. Yet, only in B-1a cells there was a significant increase in the proportion of IgM transcripts in TET2-KO mice compared to WT. Analysis of the CDR3 of the BCR revealed an increased abundance of replicated CDR3 sequences in B-1 cells from TET2-KO mice, which was more clearly pronounced in B-1a compared to B-1b cells. V-D-J usage and circos plot analysis of V-J combinations showed enhanced usage of VH11 and VH12 pairings. Taken together, our study is the first to demonstrate that global loss of TET2 increases B-1 cell number and IgM production and reduces CDR3 diversity, which could impact many biological processes and disease states that are regulated by IgM.
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Affiliation(s)
- Emily Dennis
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
| | - Maria Murach
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Cassidy M.R. Blackburn
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Melissa Marshall
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Katherine Root
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Tanyaporn Pattarabanjird
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Justine Deroissart
- Department for Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Loren D. Erickson
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
| | - Christoph J. Binder
- Department for Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Stefan Bekiranov
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Coleen A. McNamara
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, United States
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4
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Pan X, Chang Y, Ruan G, Zhou S, Jiang H, Jiang Q, Huang X, Zhao XS. TET2 mutations contribute to adverse prognosis in acute myeloid leukemia (AML): results from a comprehensive analysis of 502 AML cases and the Beat AML public database. Clin Exp Med 2024; 24:35. [PMID: 38349460 PMCID: PMC10864580 DOI: 10.1007/s10238-024-01297-0] [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: 09/29/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
Despite the high incidence of tet methylcytosine dioxygenase 2 (TET2) mutations in acute myeloid leukemia (AML), the prognostic implications of these mutations in three AML risk groups based on the 2022 ELN AML risk classification are still unclear. A total of 502 consecutive de novo AML patients who had next-generation sequencing data available between March 2011 and July 2021 at the Peking University Institute of Hematology were enrolled in this study. Univariate and multivariate Cox regression analyses were performed to explore the prognostic impact of TET2 mutations in the above cohort and the Beat AML cohort. Of the 502 total AML patients, 76 (15.1%) carried TET2 mutations. Multivariate analysis revealed TET2 mutations as independent risk factor for overall survival (OS) in both the total AML cohort (OR = 1.649, p = 0.009) and in the 2022 ELN intermediate-risk cohort (HR = 1.967, p = 0.05). Analysis of RNA-seq data from the Beat AML study revealed 1042 differentially expressed genes (DEGs) between the TET2-mutant and TET2 wild-type groups. The results of enrichment analysis indicated the DEGs to be notably enriched in categories related to the PI3K-Akt signaling pathway. Collectively, our findings indicate that mutations in TET2 are prognostically disadvantageous in AML patients. Assessment of TET2 mutational status contributes to the stratification of intermediate-risk AML patients. Multiple genes and pathways of potential therapeutic relevance may be differentially modulated by TET2 mutations in AML.
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Affiliation(s)
- Xin'an Pan
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Yingjun Chang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Guorui Ruan
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Songhai Zhou
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Hao Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Qian Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
| | - Xiaojun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China
- Peking-Tsinghua Center for Life Sciences, Beijing, 100044, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, 2019RU029, Beijing, China
| | - Xiao-Su Zhao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 Xizhimen South Street, Beijing, 100044, China.
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, 2019RU029, Beijing, China.
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5
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Ghasemi B, Ahmadi J, Zaker F, Tabatabaei T, Kiani-Zadeh M, Kazemi A. Lower Levels of TET2 Gene Expression, with a Higher Level of TET2 Promoter Methylation in Patients with AML; Evidence for the Role of Aberrant Methylation in AML Pathogenesis. Indian J Hematol Blood Transfus 2024; 40:52-60. [PMID: 38312186 PMCID: PMC10831019 DOI: 10.1007/s12288-023-01673-y] [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: 01/25/2023] [Accepted: 05/24/2023] [Indexed: 02/06/2024] Open
Abstract
DNA methylation is a key epigenetic mechanism that is dysregulated in leukemia and plays a significant role in leukemogenesis. Ten-eleven translocation 2 (TET2) is one of the most frequently mutated genes among the DNA methylation regulators in hematologic malignancies, indicating its tumor-suppressor function. In this study, we investigated the expression and methylation status of TET2 in patients with AML. Quantitative RT-PCR was used to evaluate TET2 expression in peripheral blood mononuclear cells (PBMCs) from 51 newly diagnosed AML patients and 50 healthy controls. The methylation-sensitive high-resolution melting (MS-HRM) method was used in 45 patients with AML and 15 healthy controls to evaluate the promoter methylation of TET2. TET2 expression was significantly downregulated (P < 0.0001) in patients with AML compared to that in healthy controls. Furthermore, the methylation level of the TET2 promoter was significantly different between patients and controls. Aberrant methylation of the TET2 promoter was observed in 53.3% of the patients. Interestingly, a negative (- 0.3138) and significant (P = 0.0358) correlation between TET2 methylation and expression was found. The survival of patients with downregulated TET2 was poorer than that of other patients. TET2 gene expression was significantly downregulated while the promoter methylation was higher in patients, indicating that TET2 may be a tumor suppressor gene and a prognostic factor in AML and that transcriptional silencing of the TET2 gene may play a role in AML pathogenesis. Since epigenetic mechanisms are reversible, abnormal TET2 methylation could become a therapeutic target in the future.
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Affiliation(s)
- Bahare Ghasemi
- Present Address: Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Javad Ahmadi
- Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Farhad Zaker
- Present Address: Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Tahere Tabatabaei
- Present Address: Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Kiani-Zadeh
- Present Address: Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Kazemi
- Present Address: Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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6
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Signoretti C, Gupte SA. G6PD Orchestrates Genome-Wide DNA Methylation and Gene Expression in the Vascular Wall. Int J Mol Sci 2023; 24:16727. [PMID: 38069050 PMCID: PMC10706803 DOI: 10.3390/ijms242316727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Recent advances have revealed the importance of epigenetic modifications to gene regulation and transcriptional activity. DNA methylation, a determinant of genetic imprinting and the de novo silencing of genes genome-wide, is known to be controlled by DNA methyltransferases (DNMT) and demethylases (TET) under disease conditions. However, the mechanism(s)/factor(s) influencing the expression and activity of epigenetic writers and erasers, and thus DNA methylation, in healthy vascular tissue is incompletely understood. Based on our recent studies, we hypothesized that glucose-6-phosphate dehydrogenase (G6PD) is a modifier of DNMT and TET expression and activity and an enabler of gene expression. In the aorta of CRISPR-edited rats with the Mediterranean G6PD variant, we determined DNA methylation by whole-genome bisulfite sequencing, gene expression by RNA sequencing, and large artery stiffness by echocardiography. Here, we documented higher expression of Dnmt1, Dnmt3a, Tet2, and Tet3 in aortas from Mediterranean G6PDS188F variant (a loss-of-function single nucleotide polymorphism) rats than their wild-type littermates. Concomitantly, we identified 17,618 differentially methylated loci genome-wide (5787 hypermethylated loci, including down-regulated genes encoding inflammation- and vasoconstriction-causing proteins, and 11,827 hypomethylated loci, including up-regulated genes encoding smooth muscle cell differentiation- and fatty acid metabolism-promoting proteins) in aortas from G6PDS188F as compared to wild-type rats. Our results demonstrated that nitric oxide, which is generated in a G6PD-derived NADPH-dependent manner, increases TET and decreases DNMT activity. Further, we observed less large artery (aorta) stiffness in G6PDS188F as compared to wild-type rats. These results establish a noncanonical function of the wild-type G6PD and G6PDS188F variant in the regulation of DNA methylation and gene expression in healthy vascular tissue and reveal that the G6PDS188F variant contributes to reducing large artery stiffness.
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Affiliation(s)
| | - Sachin A. Gupte
- Department of Pharmacology, New York Medical College, Valhalla, NY 10595, USA;
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7
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Antwi SO, Heckman M, White L, Yan I, Sarangi V, Lauer KP, Reddy J, Ahmed F, Veliginti S, Mejías Febres ED, Hatia RI, Chang P, Izquierdo-Sanchez L, Boix L, Rojas A, Banales JM, Reig M, Stål P, Gómez MR, Singal AG, Li D, Hassan MM, Roberts LR, Patel T. Metabolic liver cancer: associations of rare and common germline variants in one-carbon metabolism and DNA methylation genes. Hum Mol Genet 2023; 32:2646-2655. [PMID: 37369012 PMCID: PMC10407694 DOI: 10.1093/hmg/ddad099] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/29/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Animal studies implicate one-carbon metabolism and DNA methylation genes in hepatocellular carcinoma (HCC) development in the setting of metabolic perturbations. Using human samples, we investigated the associations between common and rare variants in these closely related biochemical pathways and risk for metabolic HCC development in a multicenter international study. We performed targeted exome sequencing of 64 genes among 556 metabolic HCC cases and 643 cancer-free controls with metabolic conditions. Multivariable logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for multiple comparisons. Gene-burden tests were used for rare variant associations. Analyses were performed in the overall sample and among non-Hispanic whites. The results show that among non-Hispanic whites, presence of rare functional variants in ABCC2 was associated with 7-fold higher risk of metabolic HCC (OR = 6.92, 95% CI: 2.38-20.15, P = 0.0004), and this association remained significant when analyses were restricted to functional rare variants observed in ≥2 participants (cases 3.2% versus controls 0.0%, P = 1.02 × 10-5). In the overall multiethnic sample, presence of rare functional variants in ABCC2 was nominally associated with metabolic HCC (OR = 3.60, 95% CI: 1.52-8.58, P = 0.004), with similar nominal association when analyses were restricted to functional rare variants observed in ≥2 participants (cases 2.9% versus controls 0.2%, P = 0.006). A common variant in PNPLA3 (rs738409[G]) was associated with higher HCC risk in the overall sample (P = 6.36 × 10-6) and in non-Hispanic whites (P = 0.0002). Our findings indicate that rare functional variants in ABCC2 are associated with susceptibility to metabolic HCC in non-Hispanic whites. PNPLA3-rs738409 is also associated with metabolic HCC risk.
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Affiliation(s)
- Samuel O Antwi
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Michael Heckman
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Launia White
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Irene Yan
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Vivekananda Sarangi
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Kimberly P Lauer
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Joseph Reddy
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, Florida, USA
| | - Fowsiyo Ahmed
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Swathi Veliginti
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Rikita I Hatia
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ping Chang
- Department of Gastrointestinal Medical Oncology, The MD Anderson Cancer Center, Houston, TX, USA
| | - Laura Izquierdo-Sanchez
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, San Sebastian, Spain
| | - Loreto Boix
- BCLC Group, Liver Unit, ICMDM, IDIBAPS, Hospital Clinic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Angela Rojas
- SeLiver Group, UCM Digestive Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, Seville, Spain
- Hepatic and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, San Sebastian, Spain
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Maria Reig
- BCLC Group, Liver Unit, ICMDM, IDIBAPS, Hospital Clinic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Per Stål
- Department of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Manuel Romero Gómez
- SeLiver Group, UCM Digestive Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, Seville, Spain
- Hepatic and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
| | - Amit G Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The MD Anderson Cancer Center, Houston, TX, USA
| | - Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tushar Patel
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
- Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA
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8
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Katebi A, Chen X, Li S, Lu M. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.29.551111. [PMID: 37577526 PMCID: PMC10418072 DOI: 10.1101/2023.07.29.551111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sources, including gene expression and ATAC-seq datasets, curated gene regulatory interaction databases, and mathematical modeling to establish models of context-specific core gene regulatory networks (GRNs) for a mechanistic understanding of tumorigenesis of AML with IDH mutations. The approach adopts a novel optimization procedure to identify the optimal network according to its accuracy in capturing gene expression states and its flexibility to allow sufficient control of state transitions. From GRN modeling, we identify key regulators associated with the function of IDH mutations, such as DNA methyltransferase DNMT1, and network destabilizers, such as E2F1. The constructed core regulatory network and outcomes of in-silico network perturbations are supported by survival data from AML patients. We expect that the combined bioinformatics and systems-biology modeling approach will be generally applicable to elucidate the gene regulation of disease progression.
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Affiliation(s)
- Ataur Katebi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Xiaowen Chen
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
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9
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Bramlett C, Eerdeng J, Jiang D, Lee Y, Garcia I, Vergel-Rodriguez M, Condie P, Nogalska A, Lu R. RNA splicing factor Rbm25 underlies heterogeneous preleukemic clonal expansion in mice. Blood 2023; 141:2961-2972. [PMID: 36947858 PMCID: PMC10315624 DOI: 10.1182/blood.2023019620] [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: 01/04/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
Clonal expansion sets the stage for cancer genesis by allowing for the accumulation of molecular alterations. Although genetic mutations such as Tet2 that induce clonal expansion and malignancy have been identified, these mutations are also frequently found in healthy individuals. Here, we tracked preleukemic clonal expansion using genetic barcoding in an inducible Tet2 knockout mouse model and found that only a small fraction of hematopoietic stem cells (HSCs) expanded excessively upon Tet2 knockout. These overexpanded HSCs expressed significantly lower levels of genes associated with leukemia and RNA splicing than nonoverexpanded Tet2 knockout HSCs. Knocking down Rbm25, an identified RNA splicing factor, accelerated the expansion of Tet2-knockout hematopoietic cells in vitro and in vivo. Our data suggest that mutations of an epigenetic factor Tet2 induce variability in the expression of an RNA splicing factor Rbm25, which subsequently drives heterogeneous preleukemic clonal expansion. This heterogeneous clonal expansion could contribute to the variable disease risks across individuals.
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Affiliation(s)
- Charles Bramlett
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jiya Eerdeng
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Du Jiang
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Yeachan Lee
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Ivon Garcia
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Mary Vergel-Rodriguez
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Patrick Condie
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Anna Nogalska
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Rong Lu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
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10
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Kwon SS, Cho YK, Hahn S, Oh J, Won D, Shin S, Kang JM, Ahn JG, Lee ST, Choi JR. Genetic diagnosis of inborn errors of immunity using clinical exome sequencing. Front Immunol 2023; 14:1178582. [PMID: 37325673 PMCID: PMC10264570 DOI: 10.3389/fimmu.2023.1178582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Inborn errors of immunity (IEI) include a variety of heterogeneous genetic disorders in which defects in the immune system lead to an increased susceptibility to infections and other complications. Accurate, prompt diagnosis of IEI is crucial for treatment plan and prognostication. In this study, clinical utility of clinical exome sequencing (CES) for diagnosis of IEI was evaluated. For 37 Korean patients with suspected symptoms, signs, or laboratory abnormalities associated with IEI, CES that covers 4,894 genes including genes related to IEI was performed. Their clinical diagnosis, clinical characteristics, family history of infection, and laboratory results, as well as detected variants, were reviewed. With CES, genetic diagnosis of IEI was made in 15 out of 37 patients (40.5%). Seventeen pathogenic variants were detected from IEI-related genes, BTK, UNC13D, STAT3, IL2RG, IL10RA, NRAS, SH2D1A, GATA2, TET2, PRF1, and UBA1, of which four variants were previously unreported. Among them, somatic causative variants were identified from GATA2, TET2, and UBA1. In addition, we identified two patients incidentally diagnosed IEI by CES, which was performed to diagnose other diseases of patients with unrecognized IEI. Taken together, these results demonstrate the utility of CES for the diagnosis of IEI, which contributes to accurate diagnosis and proper treatments.
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Affiliation(s)
- Soon Sung Kwon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Youn Keong Cho
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seungmin Hahn
- Department of Pediatric Hemato-oncology, Yonsei Cancer Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jiyoung Oh
- Division of Clinical Genetics, Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Man Kang
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Gyun Ahn
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome, Seoul, Republic of Korea
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11
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Jing CB, Prutsch N, He S, Zimmerman MW, Landesman Y, Look AT. Synthetic lethal targeting of TET2-mutant haematopoietic stem and progenitor cells by XPO1 inhibitors. Br J Haematol 2023; 201:489-501. [PMID: 36746437 PMCID: PMC10121884 DOI: 10.1111/bjh.18667] [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: 10/15/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
TET2 inactivating mutations serve as initiating genetic lesions in the transformation of haematopoietic stem and progenitor cells (HSPCs). In this study, we analysed known drugs in zebrafish embryos for their ability to selectively kill tet2-mutant HSPCs in vivo. We found that the exportin 1 (XPO1) inhibitors, selinexor and eltanexor, selectively kill tet2-mutant HSPCs. In serial replating colony assays, these small molecules were selectively active in killing murine Tet2-deficient Lineage-, Sca1+, Kit+ (LSK) cells, and also TET2-inactivated human acute myeloid leukaemia (AML) cells. Selective killing of TET2-mutant HSPCs and human AML cells by these inhibitors was due to increased levels of apoptosis, without evidence of DNA damage based on increased γH2AX expression. The finding that TET2 loss renders HSPCs and AML cells selectively susceptible to cell death induced by XPO1 inhibitors provides preclinical evidence of the selective activity of these drugs, justifying further clinical studies of these small molecules for the treatment of TET2-mutant haematopoietic malignancies, and to suppress clonal expansion in age-related TET2-mutant clonal haematopoiesis.
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Affiliation(s)
- Chang-Bin Jing
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - Nicole Prutsch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | | | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Division of Pediatric Hematology/Oncology Boston Children’s Hospital, Boston, Massachusetts
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12
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Tang X, Wang Z, Wang J, Cui S, Xu R, Wang Y. Functions and regulatory mechanisms of resting hematopoietic stem cells: a promising targeted therapeutic strategy. Stem Cell Res Ther 2023; 14:73. [PMID: 37038215 PMCID: PMC10088186 DOI: 10.1186/s13287-023-03316-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/29/2023] [Indexed: 04/12/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are the common and essential precursors of all blood cells, including immune cells, and they are responsible for the lifelong maintenance and damage repair of blood tissue homeostasis. The vast majority (> 95%) of HSCs are in a resting state under physiological conditions and are only activated to play a functional role under stress conditions. This resting state affects their long-term survival and is also closely related to the lifelong maintenance of hematopoietic function; however, abnormal changes may also be an important factor leading to the decline of immune function in the body and the occurrence of diseases in various systems. While the importance of resting HSCs has attracted increasing research attention, our current understanding of this topic remains insufficient, and the direction of clinical targeted treatments is unclear. Here, we describe the functions of HSCs, analyze the regulatory mechanisms that affect their resting state, and discuss the relationship between resting HSCs and different diseases, with a view to providing guidance for the future clinical implementation of related targeted treatments.
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Affiliation(s)
- Xinyu Tang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhenzhen Wang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan, 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan, China
- Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jingyi Wang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan, 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan, China
- Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Siyuan Cui
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan, 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan, China
- Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruirong Xu
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan, 250014, China.
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan, China.
- Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
| | - Yan Wang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan, 250014, China.
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan, China.
- Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
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13
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Jensen JL, Easaw S, Anderson T, Varma Y, Zhang J, Jensen BC, Coombs CC. Clonal Hematopoiesis and the Heart: a Toxic Relationship. Curr Oncol Rep 2023; 25:455-463. [PMID: 36920637 PMCID: PMC10015145 DOI: 10.1007/s11912-023-01398-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2023] [Indexed: 03/16/2023]
Abstract
PURPOSE OF REVIEW Clonal hematopoiesis (CH) refers to the expansion of hematopoietic stem cell clones and their cellular progeny due to somatic mutations, mosaic chromosomal alterations (mCAs), or copy number variants which naturally accumulate with age. CH has been linked to increased risk of blood cancers, but CH has also been linked to adverse cardiovascular outcomes. RECENT FINDINGS A combination of clinical outcome studies and mouse models have offered strong evidence that CH mutations either correlate with or cause atherosclerosis, diabetes mellitus, chronic kidney disease, heart failure, pulmonary hypertension, aortic aneurysm, myocardial infarction, stroke, aortic stenosis, poor outcomes following transcatheter aortic valve replacement (TAVR) or orthotopic heart transplant, death or need of renal replacement therapy secondary to cardiogenic shock, death from cardiovascular causes at large, and enhance anthracycline cardiac toxicity. Mechanistically, some adverse outcomes are caused by macrophage secretion of IL-1β and IL-6, neutrophil invasion of injured myocardium, and T-cell skewing towards inflammatory phenotypes. CH mutations lead to harmful inflammation and arterial wall invasion by bone marrow-derived cells resulting in poor cardiovascular health and outcomes. Blockade of IL-1β or JAK2 signaling are potential avenues for preventing CH-caused cardiovascular morbidity and mortality.
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Affiliation(s)
- Jeffrey L Jensen
- Department of Medicine, Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Saumya Easaw
- Carolinas Hospitalist Group, Atrium Health, Charlotte, NC, USA
| | - Travis Anderson
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yash Varma
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jiandong Zhang
- Department of Medicine, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brian C Jensen
- Department of Medicine, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catherine C Coombs
- Department of Medicine, Division of Hematology and Oncology, University of California, 101 The City Dr S, Irvine, Orange, CA, 92868-3201, USA.
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14
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Signoretti C, Gupte SA. Studies in CRISPR-generated Mediterranean G6PD variant rats reveal G6PD orchestrates genome-wide DNA methylation and gene expression in vascular wall. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531429. [PMID: 36945640 PMCID: PMC10028921 DOI: 10.1101/2023.03.06.531429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Background Recent advances have revealed the importance of epigenetic modifications to gene regulation and transcriptional activity. DNA methylation, a determinant of genetic imprinting and de novo silencing of genes genome-wide, is known to be controlled by DNA methyltransferases (DNMT) and demethylases (TET) under disease conditions. However, the mechanism(s)/factor(s) influencing the expression and activity of DNMTs and TETs, and thus DNA methylation, in healthy vascular tissue is incompletely understood. Based on our recent studies, we hypothesized that glucose-6-phosphate dehydrogenase (G6PD) is a modifier of DNMT and TET expression and activity and an enabler of gene expression. Methods In aorta of CRISPR-edited rats with the Mediterranean G6PD variant we determined DNA methylation by whole-genome bisulfite sequencing, gene expression by RNA sequencing, and large artery stiffness by echocardiography. Results Here, we documented higher expression of Dnmt3a, Tet2, and Tet3 in aortas from Mediterranean G6PDS188F variant (a loss-of-function single nucleotide polymorphism) rats than their wild-type littermates. Concomitantly, we identified 17,618 differentially methylated loci genome-wide (5,787 hypermethylated loci, including down-regulated genes encoding inflammation- and vasoconstriction-causing proteins, and 11,827 hypomethylated loci, including up-regulated genes encoding smooth muscle cell differentiation- and fatty acid metabolism-promoting proteins) in aorta from G6PDS188F as compared to wild-type rats. Further, we observed less large artery (aorta) stiffness in G6PDS188F as compared to wild-type rats. Conclusions These results establish a noncanonical function of the wild-type G6PD and G6PDS188F variant in the regulation of DNA methylation and gene expression in healthy vascular tissue and reveals G6PDS188F variant contributes to reduce large artery stiffness.
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Affiliation(s)
| | - Sachin A. Gupte
- Department of Pharmacology, New York Medical College, Valhalla, NY, USA, 10595
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15
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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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16
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Targeted Epigenetic Interventions in Cancer with an Emphasis on Pediatric Malignancies. Biomolecules 2022; 13:biom13010061. [PMID: 36671446 PMCID: PMC9855367 DOI: 10.3390/biom13010061] [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: 11/26/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past two decades, novel hallmarks of cancer have been described, including the altered epigenetic landscape of malignant diseases. In addition to the methylation and hyd-roxymethylation of DNA, numerous novel forms of histone modifications and nucleosome remodeling have been discovered, giving rise to a wide variety of targeted therapeutic interventions. DNA hypomethylating drugs, histone deacetylase inhibitors and agents targeting histone methylation machinery are of distinguished clinical significance. The major focus of this review is placed on targeted epigenetic interventions in the most common pediatric malignancies, including acute leukemias, brain and kidney tumors, neuroblastoma and soft tissue sarcomas. Upcoming novel challenges include specificity and potential undesirable side effects. Different epigenetic patterns of pediatric and adult cancers should be noted. Biological significance of epigenetic alterations highly depends on the tissue microenvironment and widespread interactions. An individualized treatment approach requires detailed genetic, epigenetic and metabolomic evaluation of cancer. Advances in molecular technologies and clinical translation may contribute to the development of novel pediatric anticancer treatment strategies, aiming for improved survival and better patient quality of life.
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17
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Wang Y, Liu Y, Qu S, Liang W, Sun L, Ci D, Ren Z, Fan LM, Qian W. Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2374-2384. [PMID: 36178606 DOI: 10.1111/jipb.13376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N) availability is a major limiting factor for plant growth and agricultural productivity. Although the gene regulation network in response to N starvation has been extensively studied, it remains unknown whether N starvation has an impact on the activity of transposable elements (TEs). Here, we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions. Through genetic screening of idm1-14 suppressors, we cloned GLU1, which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway. We found that glutamate synthase 1 (GLU1) and its functional homologs GLU2 and glutamate transport 1 (GLT1) are redundantly required for TE silencing, suggesting that N metabolism can regulate TE activity. Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation. Genetic analysis indicated that N starvation-induced TE activation is also independent of other well-established epigenetic mechanisms, including histone methylation and heterochromatin decondensation. Our results provide new insights into the regulation of TE activity under stressful environments in planta.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shaofeng Qu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Dong Ci
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
| | - Zhitong Ren
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Liu-Min Fan
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
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18
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Al-Dabet MM, Shahzad K, Elwakiel A, Sulaj A, Kopf S, Bock F, Gadi I, Zimmermann S, Rana R, Krishnan S, Gupta D, Manoharan J, Fatima S, Nazir S, Schwab C, Baber R, Scholz M, Geffers R, Mertens PR, Nawroth PP, Griffin JH, Keller M, Dockendorff C, Kohli S, Isermann B. Reversal of the renal hyperglycemic memory in diabetic kidney disease by targeting sustained tubular p21 expression. Nat Commun 2022; 13:5062. [PMID: 36030260 PMCID: PMC9420151 DOI: 10.1038/s41467-022-32477-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 07/29/2022] [Indexed: 02/07/2023] Open
Abstract
A major obstacle in diabetes is the metabolic or hyperglycemic memory, which lacks specific therapies. Here we show that glucose-mediated changes in gene expression largely persist in diabetic kidney disease (DKD) despite reversing hyperglycemia. The senescence-associated cyclin-dependent kinase inhibitor p21 (Cdkn1a) was the top hit among genes persistently induced by hyperglycemia and was associated with induction of the p53-p21 pathway. Persistent p21 induction was confirmed in various animal models, human samples and in vitro models. Tubular and urinary p21-levels were associated with DKD severity and remained elevated despite improved blood glucose levels in humans. Mechanistically, sustained tubular p21 expression in DKD is linked to demethylation of its promoter and reduced DNMT1 expression. Two disease resolving agents, protease activated protein C (3K3A-aPC) and parmodulin-2, reversed sustained tubular p21 expression, tubular senescence, and DKD. Thus, p21-dependent tubular senescence is a pathway contributing to the hyperglycemic memory, which can be therapeutically targeted. Persistent diabetic complications despite controlled blood glucose levels, known as hyperglycemic memory, remain a poorly understood phenomenon in diabetic kidney disease. Here the authors identify senescence-associated gene p21 as a regulator of hyperglycemic memory, the suppression of which improves hyperglycemic memory and renal function.
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Affiliation(s)
- Moh'd Mohanad Al-Dabet
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany.,Department of Medical Laboratories, Faculty of Health Sciences, American University of Madaba (AUM), Amman, Jordan
| | - Khurrum Shahzad
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany.,Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Ahmed Elwakiel
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Alba Sulaj
- Internal Medicine I and Clinical Chemistry, German Diabetes Center (DZD), University of Heidelberg, Heidelberg, Germany
| | - Stefan Kopf
- Internal Medicine I and Clinical Chemistry, German Diabetes Center (DZD), University of Heidelberg, Heidelberg, Germany
| | - Fabian Bock
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ihsan Gadi
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Silke Zimmermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Rajiv Rana
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Shruthi Krishnan
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Dheerendra Gupta
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Jayakumar Manoharan
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Sameen Fatima
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Sumra Nazir
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany
| | - Constantin Schwab
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Ronny Baber
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany.,Leipzig Medical Biobank, Leipzig University, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Rene Mertens
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, Magdeburg, Germany
| | - Peter P Nawroth
- Internal Medicine I and Clinical Chemistry, German Diabetes Center (DZD), University of Heidelberg, Heidelberg, Germany
| | - John H Griffin
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Maria Keller
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany.,Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Shrey Kohli
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany.
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Germany.
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19
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Travaglini S, Gurnari C, Antonelli S, Silvestrini G, Noguera NI, Ottone T, Voso MT. The Anti-Leukemia Effect of Ascorbic Acid: From the Pro-Oxidant Potential to the Epigenetic Role in Acute Myeloid Leukemia. Front Cell Dev Biol 2022; 10:930205. [PMID: 35938170 PMCID: PMC9352950 DOI: 10.3389/fcell.2022.930205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Data derived from high-throughput sequencing technologies have allowed a deeper understanding of the molecular landscape of Acute Myeloid Leukemia (AML), paving the way for the development of novel therapeutic options, with a higher efficacy and a lower toxicity than conventional chemotherapy. In the antileukemia drug development scenario, ascorbic acid, a natural compound also known as Vitamin C, has emerged for its potential anti-proliferative and pro-apoptotic activities on leukemic cells. However, the role of ascorbic acid (vitamin C) in the treatment of AML has been debated for decades. Mechanistic insight into its role in many biological processes and, especially, in epigenetic regulation has provided the rationale for the use of this agent as a novel anti-leukemia therapy in AML. Acting as a co-factor for 2-oxoglutarate-dependent dioxygenases (2-OGDDs), ascorbic acid is involved in the epigenetic regulations through the control of TET (ten-eleven translocation) enzymes, epigenetic master regulators with a critical role in aberrant hematopoiesis and leukemogenesis. In line with this discovery, great interest has been emerging for the clinical testing of this drug targeting leukemia epigenome. Besides its role in epigenetics, ascorbic acid is also a pivotal regulator of many physiological processes in human, particularly in the antioxidant cellular response, being able to scavenge reactive oxygen species (ROS) to prevent DNA damage and other effects involved in cancer transformation. Thus, for this wide spectrum of biological activities, ascorbic acid possesses some pharmacologic properties attractive for anti-leukemia therapy. The present review outlines the evidence and mechanism of ascorbic acid in leukemogenesis and its therapeutic potential in AML. With the growing evidence derived from the literature on situations in which the use of ascorbate may be beneficial in vitro and in vivo, we will finally discuss how these insights could be included into the rational design of future clinical trials.
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Affiliation(s)
- S. Travaglini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - C. Gurnari
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - S. Antonelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - G. Silvestrini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - N. I. Noguera
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - T. Ottone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - M. T. Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
- *Correspondence: M. T. Voso,
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20
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Florez MA, Tran BT, Wathan TK, DeGregori J, Pietras EM, King KY. Clonal hematopoiesis: Mutation-specific adaptation to environmental change. Cell Stem Cell 2022; 29:882-904. [PMID: 35659875 PMCID: PMC9202417 DOI: 10.1016/j.stem.2022.05.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) describes a widespread expansion of genetically variant hematopoietic cells that increases exponentially with age and is associated with increased risks of cancers, cardiovascular disease, and other maladies. Here, we discuss how environmental contexts associated with CHIP, such as old age, infections, chemotherapy, or cigarette smoking, alter tissue microenvironments to facilitate the selection and expansion of specific CHIP mutant clones. Further, we consider major remaining gaps in knowledge, including intrinsic effects, clone size thresholds, and factors affecting clonal competition, that will determine future application of this field in transplant and preventive medicine.
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Affiliation(s)
- Marcus A Florez
- Medical Scientist Training Program and Program in Translational Biology and Molecular Medicine, Graduate School of Biomedical Sciences, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA
| | - Brandon T Tran
- Graduate School of Biomedical Sciences, Program in Cancer and Cell Biology, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA
| | - Trisha K Wathan
- Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric M Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine Y King
- Medical Scientist Training Program and Program in Translational Biology and Molecular Medicine, Graduate School of Biomedical Sciences, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Program in Cancer and Cell Biology, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA.
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21
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Muñoz-Urbano M, Quintero-González DC, Vasquez G. T cell metabolism and possible therapeutic targets in systemic lupus erythematosus: a narrative review. Immunopharmacol Immunotoxicol 2022; 44:457-470. [PMID: 35352607 DOI: 10.1080/08923973.2022.2055568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the immunopathogenesis of systemic lupus erythematosus (SLE), there is a dysregulation of specific immune cells, including T cells. The metabolic reprogramming in T cells causes different effects. Metabolic programs are critical checkpoints in immune responses and are involved in the etiology of autoimmune disease. For instance, resting lymphocytes generate energy through oxidative phosphorylation (OXPHOS) and fatty acid oxidation (FAO), whereas activated lymphocytes rapidly shift to the glycolytic pathway. Specifically, mitochondrial dysfunction, oxidative stress, abnormal metabolism (including glucose, lipid, and amino acid metabolism), and mTOR signaling are hallmarks of T lymphocyte metabolic dysfunction in SLE. Herein it is summarized how metabolic defects contribute to T cell responses in SLE, and some epigenetic alterations involved in the disease. Finally, it is shown how metabolic defects could be modified therapeutically.
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Affiliation(s)
| | | | - Gloria Vasquez
- Rheumatology Section, Universidad de Antioquia, Medellín, Colombia.,Grupo de Inmunología Celular e Inmunogenética, Universidad de Antioquia, Medellín, Colombia
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22
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Hajishengallis G, Li X, Divaris K, Chavakis T. Maladaptive trained immunity and clonal hematopoiesis as potential mechanistic links between periodontitis and inflammatory comorbidities. Periodontol 2000 2022; 89:215-230. [PMID: 35244943 DOI: 10.1111/prd.12421] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Periodontitis is bidirectionally associated with systemic inflammatory disorders. The prevalence and severity of this oral disease and linked comorbidities increases with aging. Here, we review two newly emerged concepts, trained innate immunity (TII) and clonal hematopoiesis of indeterminate potential (CHIP), which together support a potential hypothesis on how periodontitis affects and is affected by comorbidities and why the susceptibility to periodontitis and comorbidities increases with aging. Given that chronic diseases are largely triggered by the action of inflammatory immune cells, modulation of their bone marrow precursors, the hematopoietic stem and progenitor cells (HSPCs), may affect multiple disorders that emerge as comorbidities. Such alterations in HSPCs can be mediated by TII and/or CHIP, two non-mutually exclusive processes sharing a bias for enhanced myelopoiesis and production of innate immune cells with heightened proinflammatory potential. TII is a state of elevated immune responsiveness based on innate immune (epigenetic) memory. Systemic inflammation can initiate TII in the bone marrow via sustained rewiring of HSPCs, which thereby display a skewing toward the myeloid lineage, resulting in generation of hyper-reactive or "trained" myeloid cells. CHIP arises from aging-related somatic mutations in HSPCs, which confer a survival and proliferation advantage to the mutant HSPCs and give rise to an outsized fraction of hyper-inflammatory mutant myeloid cells in the circulation and tissues. This review discusses emerging evidence that supports the notion that TII and CHIP may underlie a causal and age-related association between periodontitis and comorbidities. A holistic mechanistic understanding of the periodontitis-systemic disease connection may offer novel diagnostic and therapeutic targets for treating inflammatory comorbidities.
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Affiliation(s)
- George Hajishengallis
- Department of Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaofei Li
- Department of Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimon Divaris
- Division of Pediatrics and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
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23
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Besaratinia A, Caceres A, Tommasi S. DNA Hydroxymethylation in Smoking-Associated Cancers. Int J Mol Sci 2022; 23:2657. [PMID: 35269796 PMCID: PMC8910185 DOI: 10.3390/ijms23052657] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/01/2023] Open
Abstract
5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (A.C.); (S.T.)
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24
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Udono H, Nishida M. Pharmacological effects on anaplerotic pathways alters the metabolic landscape in the tumor microenvironment, causing unpredictable, sustained antitumor immunity. Int Immunol 2021; 34:133-140. [PMID: 34491338 DOI: 10.1093/intimm/dxab067] [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: 08/06/2021] [Accepted: 09/06/2021] [Indexed: 11/14/2022] Open
Abstract
To achieve sustained antitumor immunity, tumor-infiltrating effector CD8 T lymphocytes (CD8 TILs) must be able to produce cytokines, including IFNγ and proliferate robustly within the local tumor tissue upon antigen recognition. IFNγ production by CD8 TILs depends on glycolysis, whereas their proliferation additionally requires oxidative phosphorylation (OxPhos). The level of OxPhos, and hence the oxygen consumption rate, depends on mitochondrial biogenesis and requires the loading of metabolic precursors into the tricarboxylic acid cycle to keep it functioning. This is referred to as anaplerosis. Recent advances in the field of immuno-metabolism have shown the impact of pharmacological agents on anaplerotic pathways, resulting in metabolic downregulation in tumor cells; in contrast, the agents trigger sustained antitumor immunity by upregulating both glycolysis and OxPhos in CD8 TILs. The opposing effects of pharmacological inhibition (and/or activation) on anaplerosis in tumor cells and CD8 TILs are unpredictable. Careful dissection of the underlying mechanism might confer important knowledge, helping us to step into a new era for cancer immunotherapy.
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Affiliation(s)
- Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Mikako Nishida
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
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25
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Glutamine metabolism regulates endothelial to hematopoietic transition and hematopoietic lineage specification. Sci Rep 2021; 11:17589. [PMID: 34475502 PMCID: PMC8413451 DOI: 10.1038/s41598-021-97194-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/20/2021] [Indexed: 12/16/2022] Open
Abstract
During hematopoietic development, definitive hematopoietic cells are derived from hemogenic endothelial (HE) cells through a process known as endothelial to hematopoietic transition (EHT). During EHT, transitioning cells proliferate and undergo progressive changes in gene expression culminating in the new cell identity with corresponding changes in function, phenotype and morphology. However, the metabolic pathways fueling this transition remain unclear. We show here that glutamine is a crucial regulator of EHT and a rate limiting metabolite in the hematopoietic differentiation of HE cells. Intriguingly, different hematopoietic lineages require distinct derivatives of glutamine. While both derivatives, α-ketoglutarate and nucleotides, are required for early erythroid differentiation of HE during glutamine deprivation, lymphoid differentiation relies on α-ketoglutarate alone. Furthermore, treatment of HE cells with α-ketoglutarate in glutamine-free conditions pushes their differentiation towards lymphoid lineages both in vitro and in vivo, following transplantation into NSG mice. Thus, we report an essential role for glutamine metabolism during EHT, regulating both the emergence and the specification of hematopoietic cells through its various derivatives.
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26
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Iwata S, Tanaka Y. Therapeutic perspectives on the metabolism of lymphocytes in patients with rheumatoid arthritis and systemic lupus erythematosus. Expert Rev Clin Immunol 2021; 17:1121-1130. [PMID: 34351835 DOI: 10.1080/1744666x.2021.1964957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The activation of autoreactive T- and B-cells and production of autoantibodies by B cells are involved in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Recently, the concept of 'immunometabolism' has attracted significant attention. Immune cells produce large amounts of energy in the form of ATP and biosynthesize biological components such as nucleic acids and lipids via metabolic reprogramming to activate, differentiate, and exert their functions. AREAS COVERED While the mechanisms underlying the metabolism of CD4+ T cells in SLE have been extensively studied, the metabolic changes underlying B cell activation, differentiation, and function remain unclear. Drugs targeting mTOR and AMPK, such as sirolimus, rapamycin, and metformin, have shown some efficacy and tolerability in clinical trials on patients with SLE, but have not led to breakthroughs. In this review, we summarize the current knowledge on the immunometabolic mechanisms involved in SLE and RA and discuss the potential novel therapeutic drugs. EXPERT OPINION The intensity of activation of different immune cells and their metabolic kinetics vary in different autoimmune diseases; thus, understanding the disease- and cell-specific metabolic mechanisms may help in the development of clinically effective immunometabolism-targeting drugs.
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Affiliation(s)
- Shigeru Iwata
- The First Department of Internal Medicine, Assistant Professor, University of Occupational and Environmental Health, Japan, School of Medicine, Kitakyushu, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, Professor and Chairman, Deputy Director, University of Occupational and Environmental Health, Japan, the University Hospital, School of Medicine, Kitakyushu, Japan
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27
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Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
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28
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Kitagawa A, Jacob C, Jordan A, Waddell I, McMurtry IF, Gupte SA. Inhibition of Glucose-6-Phosphate Dehydrogenase Activity Attenuates Right Ventricle Pressure and Hypertrophy Elicited by VEGFR Inhibitor + Hypoxia. J Pharmacol Exp Ther 2021; 377:284-292. [PMID: 33758056 PMCID: PMC11047074 DOI: 10.1124/jpet.120.000166] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Pulmonary hypertension (PH) is a disease of hyperplasia of pulmonary vascular cells. The pentose phosphate pathway (PPP)-a fundamental glucose metabolism pathway-is vital for cell growth. Because treatment of PH is inadequate, our goal was to determine whether inhibition of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the PPP, prevents maladaptive gene expression that promotes smooth muscle cell (SMC) growth, reduces pulmonary artery remodeling, and normalizes hemodynamics in experimental models of PH. PH was induced in mice by exposure to 10% oxygen (Hx) or weekly injection of vascular endothelial growth factor receptor blocker [Sugen5416 (SU); 20 mg kg-1] during exposure to hypoxia (Hx + SU). A novel G6PD inhibitor (N-[(3β,5α)-17-oxoandrostan-3-yl]sulfamide; 1.5 mg kg-1) was injected daily during exposure to Hx. We measured right ventricle (RV) pressure and left ventricle pressure-volume relationships and gene expression in lungs of normoxic, Hx, and Hx + SU and G6PD inhibitor-treated mice. RV systolic and end-diastolic pressures were higher in Hx and Hx + SU than normoxic control mice. Hx and Hx + SU decreased expression of epigenetic modifiers (writers and erasers), increased hypomethylation of the DNA, and induced aberrant gene expression in lungs. G6PD inhibition decreased maladaptive expression of genes and SMC growth, reduced pulmonary vascular remodeling, and decreased right ventricle pressures compared with untreated PH groups. Pharmacologic inhibition of G6PD activity, by normalizing activity of epigenetic modifiers and DNA methylation, efficaciously reduces RV pressure overload in Hx and Hx + SU mice and preclinical models of PH and appears to be a safe pharmacotherapeutic strategy. SIGNIFICANCE STATEMENT: The results of this study demonstrated that inhibition of a metabolic enzyme efficaciously reduces pulmonary hypertension. For the first time, this study shows that a novel inhibitor of glucose-6-phosphate dehydrogenase, the rate-limiting enzyme in the fundamental pentose phosphate pathway, modulates DNA methylation and alleviates pulmonary artery remodeling and dilates pulmonary artery to reduce pulmonary hypertension.
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Affiliation(s)
- Atsushi Kitagawa
- Department of Pharmacology, New York Medical College, Valhalla, New York (A.K., C.J., S.A.G.); Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom (A.J., I.W.); and Departments of Pharmacology and Internal Medicine and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama (I.F.M.)
| | - Christina Jacob
- Department of Pharmacology, New York Medical College, Valhalla, New York (A.K., C.J., S.A.G.); Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom (A.J., I.W.); and Departments of Pharmacology and Internal Medicine and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama (I.F.M.)
| | - Allan Jordan
- Department of Pharmacology, New York Medical College, Valhalla, New York (A.K., C.J., S.A.G.); Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom (A.J., I.W.); and Departments of Pharmacology and Internal Medicine and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama (I.F.M.)
| | - Ian Waddell
- Department of Pharmacology, New York Medical College, Valhalla, New York (A.K., C.J., S.A.G.); Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom (A.J., I.W.); and Departments of Pharmacology and Internal Medicine and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama (I.F.M.)
| | - Ivan F McMurtry
- Department of Pharmacology, New York Medical College, Valhalla, New York (A.K., C.J., S.A.G.); Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom (A.J., I.W.); and Departments of Pharmacology and Internal Medicine and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama (I.F.M.)
| | - Sachin A Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York (A.K., C.J., S.A.G.); Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom (A.J., I.W.); and Departments of Pharmacology and Internal Medicine and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama (I.F.M.)
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Nintedanib targets KIT D816V neoplastic cells derived from induced pluripotent stem cells of systemic mastocytosis. Blood 2021; 137:2070-2084. [PMID: 33512435 DOI: 10.1182/blood.2019004509] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/08/2020] [Indexed: 01/10/2023] Open
Abstract
The KIT D816V mutation is found in >80% of patients with systemic mastocytosis (SM) and is key to neoplastic mast cell (MC) expansion and accumulation in affected organs. Therefore, KIT D816V represents a prime therapeutic target for SM. Here, we generated a panel of patient-specific KIT D816V induced pluripotent stem cells (iPSCs) from patients with aggressive SM and mast cell leukemia to develop a patient-specific SM disease model for mechanistic and drug-discovery studies. KIT D816V iPSCs differentiated into neoplastic hematopoietic progenitor cells and MCs with patient-specific phenotypic features, thereby reflecting the heterogeneity of the disease. CRISPR/Cas9n-engineered KIT D816V human embryonic stem cells (ESCs), when differentiated into hematopoietic cells, recapitulated the phenotype observed for KIT D816V iPSC hematopoiesis. KIT D816V causes constitutive activation of the KIT tyrosine kinase receptor, and we exploited our iPSCs and ESCs to investigate new tyrosine kinase inhibitors targeting KIT D816V. Our study identified nintedanib, a US Food and Drug Administration-approved angiokinase inhibitor that targets vascular endothelial growth factor receptor, platelet-derived growth factor receptor, and fibroblast growth factor receptor, as a novel KIT D816V inhibitor. Nintedanib selectively reduced the viability of iPSC-derived KIT D816V hematopoietic progenitor cells and MCs in the nanomolar range. Nintedanib was also active on primary samples of KIT D816V SM patients. Molecular docking studies show that nintedanib binds to the adenosine triphosphate binding pocket of inactive KIT D816V. Our results suggest nintedanib as a new drug candidate for KIT D816V-targeted therapy of advanced SM.
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Epigenetics in a Spectrum of Myeloid Diseases and Its Exploitation for Therapy. Cancers (Basel) 2021; 13:cancers13071746. [PMID: 33917538 PMCID: PMC8038780 DOI: 10.3390/cancers13071746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The genome is stored in the limited space of the nucleus in a highly condensed form. The regulation of this packaging contributes to determining the accessibility of genes and is important for cell function. Genes affecting the genome’s packaging are frequently mutated in bone marrow cells that give rise to the different types of blood cells. Here, we first discuss the molecular functions of these genes and their role in blood generation under healthy conditions. Then, we describe how their mutations relate to a subset of diseases including blood cancers. Finally, we provide an overview of the current efforts of using and developing drugs targeting these and related genes. Abstract Mutations in genes encoding chromatin regulators are early events contributing to developing asymptomatic clonal hematopoiesis of indeterminate potential and its frequent progression to myeloid diseases with increasing severity. We focus on the subset of myeloid diseases encompassing myelodysplastic syndromes and their transformation to secondary acute myeloid leukemia. We introduce the major concepts of chromatin regulation that provide the basis of epigenetic regulation. In greater detail, we discuss those chromatin regulators that are frequently mutated in myelodysplastic syndromes. We discuss their role in the epigenetic regulation of normal hematopoiesis and the consequence of their mutation. Finally, we provide an update on the drugs interfering with chromatin regulation approved or in development for myelodysplastic syndromes and acute myeloid leukemia.
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Iancu IV, Botezatu A, Plesa A, Huica I, Fudulu A, Albulescu A, Bostan M, Mihaila M, Grancea C, Manda DA, Dobrescu R, Vladoiu SV, Anton G, Badiu CV. Alterations of regulatory factors and DNA methylation pattern in thyroid cancer. Cancer Biomark 2021; 28:255-268. [PMID: 32390600 DOI: 10.3233/cbm-190871] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE DNA methylation plays an important role in thyroid oncogenesis. The aim of this study was to investigate the connection between global and local DNA methylation status and to establish the levels of important DNA methylation regulators (TET family and DNMT1) in thyroid tumours: follicular adenoma-FA, papillary thyroid carcinoma-PTC (classic papillary thyroid carcinoma-cPTC and papillary thyroid carcinoma follicular variant fvPTC). METHODS Global DNA methylation profile in thyroid tumours tissue (41 paired samples) was assessed by 5-methylcytosine and 5-hydroxymethylcytosine levels evaluation (ELISA), along with TETs and DNMT1 genes expression quantification. Also, it was investigated for the first time TET1 and TET2 promoter's methylation in thyroid tumours. BRAF V600E mutation and RET/PTC translocation testing were performed on all investigated samples. In vitro studies upon DNA methylation in K1 thyroid cancer cells were performed with demethylating agents (5-AzaC and vitamin C). RESULTS TET1 and TET2 displayed a significantly reduced gene expression level in PTC, while DNMT1 gene presented a high level of expression. PTC samples presented increased levels of 5-methylcytosine and low levels of 5-hydroxymethylcytosine. 5-methylcytosine levels were associated with TET1/TET2 expression levels. TET1 gene expression was significantly lower in patients positive for BRAF mutation and with RET/PTC rearrangement. TET2 gene was found hypermethylated in thyroid carcinoma patients overall, especially in PTC-follicular variant samples (p= 0.0002), where TET2 gene expression levels were significantly reduced (p= 0.0031). Furthermore, the data indicate for all thyroid cancer patients a good sensitivity (81.08%) and specificity (86.49%) regarding the use of TET1 (p< 0.0001), and TET2 (71.79%, 64.10%, p= 0.0001) hypermethylation as biomarkers for thyroid oncogenesis. CONCLUSIONS These results suggest that TET1/TET2 gene expression and methylation may serve as potential diagnostic tools for thyroid neoplasia. Our study showed that the methylation of TET1 increases in malignant thyroid tumours. fvPTC patients presented lower methylation levels compared to cPTC and could be a discriminatory factor between two cancer types and benign lesions. TET2 is a poorer discriminator between FA and fvPTC, but it can be useful for cPTC identification. K1-cells treated with demethylating agents showed a demethylation effect, especially upon TET2 gene. The cumulative effect of L-AA and 5-AzaC proved to have a potent combined demethylating effect on genes promoter's activation and could open new perspectives for thyroid cancer therapy.
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Affiliation(s)
- Iulia V Iancu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Anca Botezatu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Adriana Plesa
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Irina Huica
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Alina Fudulu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Adrian Albulescu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,National Institute for Chemical Pharmaceutical Research and Development, Bucharest, Romania
| | - Marinela Bostan
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Mirela Mihaila
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Camelia Grancea
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Dana Alice Manda
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Ruxandra Dobrescu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania.,"Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Susana Vilma Vladoiu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Gabriela Anton
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Corin Virgil Badiu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania.,"Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,"Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
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Gemović B, Perović V, Davidović R, Drljača T, Veljkovic N. Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies. PLoS One 2021; 16:e0244948. [PMID: 33395407 PMCID: PMC7781373 DOI: 10.1371/journal.pone.0244948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
For the last couple of decades, there has been a significant growth in sequencing data, leading to an extraordinary increase in the number of gene variants. This places a challenge on the bioinformatics research community to develop and improve computational tools for functional annotation of new variants. Genes coding for epigenetic regulators have important roles in cancer pathogenesis and mutations in these genes show great potential as clinical biomarkers, especially in hematologic malignancies. Therefore, we developed a model that specifically focuses on these genes, with an assumption that it would outperform general models in predicting the functional effects of amino acid substitutions. EpiMut is a standalone software that implements a sequence based alignment-free method. We applied a two-step approach for generating sequence based features, relying on the biophysical and biochemical indices of amino acids and the Fourier Transform as a sequence transformation method. For each gene in the dataset, the machine learning algorithm-Naïve Bayes was used for building a model for prediction of the neutral or disease-related status of variants. EpiMut outperformed state-of-the-art tools used for comparison, PolyPhen-2, SIFT and SNAP2. Additionally, EpiMut showed the highest performance on the subset of variants positioned outside conserved functional domains of analysed proteins, which represents an important group of cancer-related variants. These results imply that EpiMut can be applied as a first choice tool in research of the impact of gene variants in epigenetic regulators, especially in the light of the biomarker role in hematologic malignancies. EpiMut is freely available at https://www.vin.bg.ac.rs/180/tools/epimut.php.
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Affiliation(s)
- Branislava Gemović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- * E-mail:
| | - Vladimir Perović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Radoslav Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Tamara Drljača
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- Heliant d.o.o., Belgrade, Serbia
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Abstract
Myelodysplastic syndromes (MDS) are clonal hematological disorders arising from hematopoietic stem cells that have accumulated various genetic abnormalities. MDS are heterogeneous in nature but uniformly characterized by chronic and progressive cytopenia from ineffective hematopoiesis, dysplasia in single or multiple lineages, and transformation to acute leukemia in a subset of patients. The genomic landscape revealed by next-generation sequencing has provided a comprehensive picture of the molecular pathways involved in MDS pathogenesis. Recurrent mutational targets in MDS are the genes involved in RNA splicing, DNA methylation, histone modification, transcription, signal transduction, cohesin complex and DNA repair. Sequential acquisition of mutations in these sets of genes serves as a driver for the initiation, clonal evolution and progression of MDS. Based on these findings, novel agents targeting driver mutations of MDS are currently under development and expected to improve the clinical outcome of MDS in the coming decades.
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Affiliation(s)
- Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Japan
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Chebly A, Chouery E, Ropio J, Kourie HR, Beylot-Barry M, Merlio JP, Tomb R, Chevret E. Diagnosis and treatment of lymphomas in the era of epigenetics. Blood Rev 2020; 48:100782. [PMID: 33229141 DOI: 10.1016/j.blre.2020.100782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/05/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Lymphomas represent a heterogeneous group of cancers characterized by clonal lymphoproliferation. Over the past decades, frequent epigenetic dysregulations have been identified in hematologic malignancies including lymphomas. Many of these impairments occur in genes with established roles and well-known functions in the regulation and maintenance of the epigenome. In hematopoietic cells, these dysfunctions can result in abnormal DNA methylation, erroneous chromatin state and/or altered miRNA expression, affecting many different cellular functions. Nowadays, it is evident that epigenetic dysregulations in lymphoid neoplasms are mainly caused by genetic alterations in genes encoding for enzymes responsible for histone or chromatin modifications. We summarize herein the recent epigenetic modifiers findings in lymphomas. We focus also on the most commonly mutated epigenetic regulators and emphasize on actual epigenetic therapies.
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Affiliation(s)
- Alain Chebly
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Eliane Chouery
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Joana Ropio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Porto University, Institute of Biomedical Sciences of Abel Salazar, 4050-313 Porto, Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Institute of Molecular Pathology and Immunology (Ipatimup), Cancer Biology group, 4200-465 Porto, Portugal
| | - Hampig Raphael Kourie
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Hematology-Oncology Department, Beirut, Lebanon
| | - Marie Beylot-Barry
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Dermatology Department, 33000 Bordeaux, France
| | - Jean-Philippe Merlio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Tumor Bank and Tumor Biology Laboratory, 33600 Pessac, France
| | - Roland Tomb
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Dermatology Department, Beirut, Lebanon
| | - Edith Chevret
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France.
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Loss of Tet2 affects platelet function but not coagulation in mice. BLOOD SCIENCE 2020; 2:129-136. [PMID: 35400021 PMCID: PMC8974955 DOI: 10.1097/bs9.0000000000000055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/19/2020] [Indexed: 12/17/2022] Open
Abstract
Ten-eleven translocation 2 (TET2) functions as a methylcytosine dioxygenase that catalyzes the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. TET2 has been shown to be crucial for the maintenance and differentiation of hematopoietic stem cells, and its deletion and/or mutations results in the expansion of HSPCs, and leads to hematological malignancies. TET2 mutations were found in a variety of hematological disorders such as CMML (60%), MDS (30%), MPN (13%) and AML (20%). Interestingly, it was shown that CMML patients with TET2 mutation exhibited fewer platelets than CMML patients without TET2 mutation. However, the role and function of TET2 in platelet hemostasis and thrombogenesis is not well defined. Here in this study, using a genetically engineered Tet2 deletion mouse model, we found that the absence of Tet2 caused a decrease in the proportion of MEP cells and hyperploid megakaryocytes. Additionally, Tet2-deficient mice displayed impaired platelet activation and aggregation under stimulation of ADP and low concentrations of thrombin, although the modestly compromised platelet function and MEP differentiation in Tet2-deficient mice could be compensated without affecting blood coagulation function. Our study indicate that Tet2 deficiency leads to mild impairment of platelet function and thrombopoiesis in mice.
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DNA Methylation Dysfunction in Chronic Kidney Disease. Genes (Basel) 2020; 11:genes11070811. [PMID: 32708735 PMCID: PMC7397141 DOI: 10.3390/genes11070811] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023] Open
Abstract
Renal disease is the common denominator of a number of underlying disease conditions, whose prevalence has been dramatically increasing over the last two decades. Two aspects are particularly relevant to the subject of this review: (I) most cases are gathered under the umbrella of chronic kidney disease since they require—predictably for several lustrums—continuous clinical monitoring and treatment to slow down disease progression and prevent complications; (II) cardiovascular disease is a terrible burden in this population of patients, in that it claims many lives yearly, while only a scant minority reach the renal disease end stage. Why indeed a review on DNA methylation and renal disease? As we hope to convince you, the present evidence supports the role of the existence of various derangements of the epigenetic control of gene expression in renal disease, which hold the potential to improve our ability, in the future, to more effectively act toward disease progression, predict outcomes and offer novel therapeutic approaches.
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Siref A, McCormack C, Huang Q, Lim W, Alkan S. Diminished expression of 5hmc in Reed-Sternberg cells in classical Hodgkin lymphoma is a common epigenetic marker. Leuk Res 2020; 96:106408. [PMID: 32659407 DOI: 10.1016/j.leukres.2020.106408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/28/2020] [Accepted: 06/28/2020] [Indexed: 02/08/2023]
Abstract
Loss of the epigenetic marker 5-hydroxymethylcytosine (5hmC) has been demonstrated in a variety of neoplasms. Several recent studies have shown epigenetic alteration in Classical Hodgkin lymphoma (CHL), which may impact treatment. We demonstrate near universal depletion of 5hmC in the neoplastic Hodgkin Reed-Sternberg (H/RS) cells in all cases of CHL (49/49). We hypothesized that the addition of vitamin C-a cofactor for the ten-eleven translocation (TET) enzymes which oxidize 5-methylcytosine (5mC) to 5hmC - may replenish levels of 5hmC. The CHL cell line L428 was grown in optimal conditions and then subjected to vitamin C treatment, which demonstrated reduced cell viability as well as caspase activation and increased concentration of 5hmC. A more detailed understanding of the epigenetic landscape of CHL may help guide future therapies.
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Affiliation(s)
- Andrew Siref
- Cedars-Sinai Medical Center, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., Room #4711, Los Angeles, CA 90048-1804, United States
| | - Colin McCormack
- Cedars-Sinai Medical Center, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., Room #4711, Los Angeles, CA 90048-1804, United States
| | - Qin Huang
- Cedars-Sinai Medical Center, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., Room #4711, Los Angeles, CA 90048-1804, United States
| | - Washington Lim
- Cedars-Sinai Medical Center, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., Room #4711, Los Angeles, CA 90048-1804, United States
| | - Serhan Alkan
- Cedars-Sinai Medical Center, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., Room #4711, Los Angeles, CA 90048-1804, United States.
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38
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Jing CB, Fu C, Prutsch N, Wang M, He S, Look AT. Synthetic lethal targeting of TET2-mutant hematopoietic stem and progenitor cells (HSPCs) with TOP1-targeted drugs and PARP1 inhibitors. Leukemia 2020; 34:2992-3006. [PMID: 32572188 DOI: 10.1038/s41375-020-0927-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 05/21/2020] [Accepted: 06/10/2020] [Indexed: 11/09/2022]
Abstract
Inactivating mutations in TET2 serve as an initiating genetic lesion in the transformation of hematopoietic stem and progenitor cells (HSPCs). Thus, effective therapy for this subset of patients would ideally include drugs that are selectively lethal in TET2-mutant HSPCs, at dosages that spare normal HSPCs. In this study, we tested 129 FDA-approved anticancer drugs in a tet2-deficient zebrafish model and showed that topoisomerase 1 (TOP1)-targeted drugs and PARP1 inhibitors selectively kill tet2-mutant HSPCs. We found that Tet2-deficient murine bone marrow progenitors and CRISPR-Cas9-induced TET2-mutant human AML cells were more sensitive to both classes of drugs compared with matched control cells. The mechanism underlying the selective killing of TET2-mutant blood cells by these drugs was due to aberrantly low levels of tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that is important for removing TOP1 cleavage complexes (TOP1cc). Low TDP1 levels yield sensitivity to TOP1-targeted drugs or PARP1 inhibitors and an inability to remove TOP1 cleavage complexes, leading to DNA double-strand breaks and cell death. The finding that TET2 mutations render HSPCs uniquely vulnerable to disruption of TOP1 and PARP1 activity may therefore represent a unique opportunity to use relatively low dosages of these drugs for the "precision therapy" of TET2-mutant myeloid malignancies.
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Affiliation(s)
- Chang-Bin Jing
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cong Fu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nicole Prutsch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Meng Wang
- Department of Dermatology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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A genomics-informed computational biology platform prospectively predicts treatment responses in AML and MDS patients. Blood Adv 2020; 3:1837-1847. [PMID: 31208955 DOI: 10.1182/bloodadvances.2018028316] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/12/2019] [Indexed: 12/14/2022] Open
Abstract
Patients with myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML) are generally older and have more comorbidities. Therefore, identifying personalized treatment options for each patient early and accurately is essential. To address this, we developed a computational biology modeling (CBM) and digital drug simulation platform that relies on somatic gene mutations and gene CNVs found in malignant cells of individual patients. Drug treatment simulations based on unique patient-specific disease networks were used to generate treatment predictions. To evaluate the accuracy of the genomics-informed computational platform, we conducted a pilot prospective clinical study (NCT02435550) enrolling confirmed MDS and AML patients. Blinded to the empirically prescribed treatment regimen for each patient, genomic data from 50 evaluable patients were analyzed by CBM to predict patient-specific treatment responses. CBM accurately predicted treatment responses in 55 of 61 (90%) simulations, with 33 of 61 true positives, 22 of 61 true negatives, 3 of 61 false positives, and 3 of 61 false negatives, resulting in a sensitivity of 94%, a specificity of 88%, and an accuracy of 90%. Laboratory validation further confirmed the accuracy of CBM-predicted activated protein networks in 17 of 19 (89%) samples from 11 patients. Somatic mutations in the TET2, IDH1/2, ASXL1, and EZH2 genes were discovered to be highly informative of MDS response to hypomethylating agents. In sum, analyses of patient cancer genomics using the CBM platform can be used to predict precision treatment responses in MDS and AML patients.
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40
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Allocco JB, Alegre ML. Exploiting immunometabolism and T cell function for solid organ transplantation. Cell Immunol 2020; 351:104068. [PMID: 32139072 PMCID: PMC7150626 DOI: 10.1016/j.cellimm.2020.104068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/25/2022]
Abstract
Cellular metabolism is central to T cell function and proliferation, with most of the research to date focusing on cancer and autoimmunity. Cellular metabolism is associated with a host of physiological phenomena, from epigenetic changes, to cellular function and fate. For the purpose of this review, we will discuss the metabolism of T cells relating to their differentiation and function. We will cover a variety of metabolic processes, ranging from glycolysis to amino acid metabolism. Understanding how T cell metabolism informs T cell function may be useful to understand alloimmune responses and design novel therapies to improve graft outcome.
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Affiliation(s)
- Jennifer B Allocco
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL 60637, United States
| | - Maria-Luisa Alegre
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL 60637, United States.
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41
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Invariant phenotype and molecular association of biallelic TET2 mutant myeloid neoplasia. Blood Adv 2020; 3:339-349. [PMID: 30709865 DOI: 10.1182/bloodadvances.2018024216] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/12/2018] [Indexed: 12/29/2022] Open
Abstract
Somatic TET2 mutations (TET2 MT) are frequent in myeloid neoplasia (MN), particularly chronic myelomonocytic leukemia (CMML). TET2 MT includes mostly loss-of-function/hypomorphic hits. Impaired TET2 activity skews differentiation of hematopoietic stem cells toward proliferating myeloid precursors. This study was prompted by the observation of frequent biallelic TET2 gene inactivations (biTET2 i ) in CMML. We speculated that biTET2 i might be associated with distinct clinicohematological features. We analyzed TET2 MT in 1045 patients with MN. Of 82 biTET2 i cases, 66 were biTET2 MT, 13 were hemizygous TET2 MT, and 3 were homozygous TET2 MT (uniparental disomy); the remaining patients (denoted biTET2 - hereafter) were either monoallelic TET2 MT (n = 96) or wild-type TET2 (n = 823). Truncation mutations were found in 83% of biTET2 i vs 65% of biTET2 - cases (P = .02). TET2 hits were founder lesions in 72% of biTET2 i vs 38% of biTET2 - cases (P < .0001). In biTET2 i , significantly concurrent hits included SRSF2 MT (33%; P < .0001) and KRAS/NRAS MT (16%; P = .03) as compared with biTET2 - When the first TET2 hit was ancestral in biTET2 i , the most common subsequent hits affected a second TET2 MT, followed by SRSF2 MT, ASXL1 MT, RAS MT, and DNMT3A MT BiTET2 i patients without any monocytosis showed an absence of SRSF2 MT BiTET2 i patients were older and had monocytosis, CMML, normal karyotypes, and lower-risk disease compared with biTET2 - patients. Hence, while a second TET2 hit occurred frequently, biTET2 i did not portend faster progression but rather determined monocytic differentiation, consistent with its prevalence in CMML. Additionally, biTET2 i showed lower odds of cytopenias and marrow blasts (≥5%) and higher odds of myeloid dysplasia and marrow hypercellularity. Thus, biTET2 i might represent an auxiliary assessment tool in MN.
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Wang J, He N, Wang R, Tian T, Han F, Zhong C, Zhang C, Hua M, Ji C, Ma D. Analysis of TET2 and EZH2 gene functions in chromosome instability in acute myeloid leukemia. Sci Rep 2020; 10:2706. [PMID: 32066746 PMCID: PMC7026035 DOI: 10.1038/s41598-020-59365-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/23/2020] [Indexed: 11/09/2022] Open
Abstract
TET2 and EZH2 play important roles in the epigenetic regulation in many cancers. However, their specific roles in acute myeloid leukemia (AML) pathogenesis remain unknown. Here, the expression, methylation or mutation of EZH2 and TET2 was determined and further correlated with the levels of the chromosome instability (CIN) genes MAD2 and CDC20. We down-regulated EZH2 and TET2 in AML cell lines and assessed the effect on CIN using fluorescence in situ hybridization (FISH). Our results showed that TET2, EZH2, MAD2 and CDC20 were aberrantly expressed in AML patients. The expression level of MAD2 or CDC20 was positively correlated with that of TET2 or EZH2. Hypermethylation of the TET2 gene down-regulated its transcription. Down-regulation of EZH2 or TET2 expression inhibited apoptosis, affected MAD2 and CDC20 expression, and promoted CIN in AML cells. Decitabine treatment restored TET2 methylation and EZH2 transcription and ameliorated CIN in AML. Therefore, TET2 and EZH2 play a tumor-inhibiting role in AML that affects CIN via MAD2 and CDC20.
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Affiliation(s)
- Jingyi Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China.,Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, P.R. China
| | - Na He
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Ruiqing Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Tian Tian
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fengjiao Han
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Chaoqin Zhong
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Chen Zhang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Mingqiang Hua
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, P.R. China.
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T cell metabolism: new insights in systemic lupus erythematosus pathogenesis and therapy. Nat Rev Rheumatol 2020; 16:100-112. [PMID: 31949287 DOI: 10.1038/s41584-019-0356-x] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/12/2022]
Abstract
T cell subsets are critically involved in the development of systemic autoimmunity and organ inflammation in systemic lupus erythematosus (SLE). Each T cell subset function (such as effector, helper, memory or regulatory function) is dictated by distinct metabolic pathways requiring the availability of specific nutrients and intracellular enzymes. The activity of these enzymes or nutrient transporters influences the differentiation and function of T cells in autoimmune responses. Data are increasingly emerging on how metabolic processes control the function of various T cell subsets and how these metabolic processes are altered in SLE. Specifically, aberrant glycolysis, glutaminolysis, fatty acid and glycosphingolipid metabolism, mitochondrial hyperpolarization, oxidative stress and mTOR signalling underwrite the known function of T cell subsets in patients with SLE. A number of medications that are used in the care of patients with SLE affect cell metabolism, and the development of novel therapeutic approaches to control the activity of metabolic enzymes in T cell subsets represents a promising endeavour in the search for effective treatment of systemic autoimmune diseases.
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Jiang L, Luo Y, Zhu S, Wang L, Ma L, Zhang H, Shen C, Yang W, Ren Y, Zhou X, Mei C, Ye L, Xu W, Yang H, Lu C, Jin J, Tong H. Mutation status and burden can improve prognostic prediction of patients with lower-risk myelodysplastic syndromes. Cancer Sci 2019; 111:580-591. [PMID: 31804030 PMCID: PMC7004535 DOI: 10.1111/cas.14270] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 11/24/2019] [Accepted: 11/28/2019] [Indexed: 01/09/2023] Open
Abstract
Patients with lower‐risk myelodysplastic syndromes (LR‐MDS) as defined by the International Prognostic Scoring System (IPSS) have more favorable prognosis in general, but significant inter‐individual heterogeneity exists. In this study, we examined the molecular profile of 15 MDS‐relevant genes in 159 patients with LR‐MDS using next‐generation sequencing. In univariate COX regression, shorter overall survival (OS) was associated with mutation status of ASXL1 (P = .001), RUNX1 (P = .031), EZH2 (P = .049), TP53 (P = .016), SRSF2 (P = .046), JAK2 (P = .040), and IDH2 (P = .035). We also found significantly shorter OS in patients with an adjusted TET2 variant allele frequency (VAF) ≥18% versus those with either an adjusted TET2 VAF <18% or without TET2 mutations (median: 20.4 vs 47.8 months; P = .020; HR = 2.183, 95%CI: 1.129‐4.224). After adjustment for IPSS, shorter OS was associated with mutation status of ASXL1 (P < .001; HR = 4.306, 95% CI: 2.144‐8.650), TP53 (P = .004; HR = 4.863, 95% CI: 1.662‐14.230) and JAK2 (P = .002; HR = 5.466, 95%CI: 1.848‐16.169), as well as adjusted TET2 VAF ≥18% (P = .008; HR = 2.492, 95% CI: 1.273‐4.876). Also, OS was increasingly shorter as the number of mutational factors increased (P < .001). A novel prognostic scoring system incorporating the presence/absence of the four independent mutational factors into the IPSS further stratified LR‐MDS patients into three prognostically different groups (P < .001). The newly developed scoring system redefined 10.1% (16/159) of patients as a higher‐risk group, who could not be predicted by the currently prognostic models. In conclusion, integration of the IPSS with mutation status/burden of certain MDS‐relevant genes may improve the prognostication of patients with LR‐MDS and could help identify those with worse‐than‐expected prognosis for more aggressive treatment.
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Affiliation(s)
- Lingxu Jiang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingwan Luo
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuanghong Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liya Ma
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chuying Shen
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenli Yang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanling Ren
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinping Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Mei
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weilai Xu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyang Yang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenxi Lu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongyan Tong
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Myelodysplastic Syndromes Diagnosis and Therapy Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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45
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Epigenetic Abnormalities in Acute Myeloid Leukemia and Leukemia Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31338820 DOI: 10.1007/978-981-13-7342-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
Recently advances in cancer genomics revealed the unexpected high frequencies of epigenetic abnormalities in human acute myeloid leukemia (AML). Accumulating data suggest that these leukemia-associated epigenetic factors play critical roles in both normal hematopoietic stem cells (HSCs) and leukemia stem cells (LSCs). In turn, these abnormalities result in susceptibilities of LSC and related diseases to epigenetic inhibitors. In this chapter, we will focus on the mutations of epigenetic factors in AML, their functional roles and mechanisms in normal hematopoiesis and leukemia genesis, especially in LSC, and potential treatment opportunities specifically for AML with epigenetic dysregulations.
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46
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Akella NM, Ciraku L, Reginato MJ. Fueling the fire: emerging role of the hexosamine biosynthetic pathway in cancer. BMC Biol 2019; 17:52. [PMID: 31272438 PMCID: PMC6610925 DOI: 10.1186/s12915-019-0671-3] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Altered metabolism and deregulated cellular energetics are now considered a hallmark of all cancers. Glucose, glutamine, fatty acids, and amino acids are the primary drivers of tumor growth and act as substrates for the hexosamine biosynthetic pathway (HBP). The HBP culminates in the production of an amino sugar uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that, along with other charged nucleotide sugars, serves as the basis for biosynthesis of glycoproteins and other glycoconjugates. These nutrient-driven post-translational modifications are highly altered in cancer and regulate protein functions in various cancer-associated processes. In this review, we discuss recent progress in understanding the mechanistic relationship between the HBP and cancer.
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Affiliation(s)
- Neha M Akella
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Lorela Ciraku
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Mauricio J Reginato
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
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Schoeler K, Aufschnaiter A, Messner S, Derudder E, Herzog S, Villunger A, Rajewsky K, Labi V. TET enzymes control antibody production and shape the mutational landscape in germinal centre B cells. FEBS J 2019; 286:3566-3581. [PMID: 31120187 PMCID: PMC6851767 DOI: 10.1111/febs.14934] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022]
Abstract
Upon activation by antigen, B cells form germinal centres where they clonally expand and introduce affinity-enhancing mutations into their B-cell receptor genes. Somatic mutagenesis and class switch recombination (CSR) in germinal centre B cells are initiated by the activation-induced cytidine deaminase (AID). Upon germinal centre exit, B cells differentiate into antibody-secreting plasma cells. Germinal centre maintenance and terminal fate choice require transcriptional reprogramming that associates with a substantial reconfiguration of DNA methylation patterns. Here we examine the role of ten-eleven-translocation (TET) proteins, enzymes that facilitate DNA demethylation and promote a permissive chromatin state by oxidizing 5-methylcytosine, in antibody-mediated immunity. Using a conditional gene ablation strategy, we show that TET2 and TET3 guide the transition of germinal centre B cells to antibody-secreting plasma cells. Optimal AID expression requires TET function, and TET2 and TET3 double-deficient germinal centre B cells show defects in CSR. However, TET2/TET3 double-deficiency does not prevent the generation and selection of high-affinity germinal centre B cells. Rather, combined TET2 and TET3 loss-of-function in germinal centre B cells favours C-to-T and G-to-A transition mutagenesis, a finding that may be of significance for understanding the aetiology of B-cell lymphomas evolving in conditions of reduced TET function.
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Affiliation(s)
- Katia Schoeler
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Andreas Aufschnaiter
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Simon Messner
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Emmanuel Derudder
- Institute for Biomedical Aging Research, University of Innsbruck, Austria
| | - Sebastian Herzog
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Andreas Villunger
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Klaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany
| | - Verena Labi
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
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Abstract
Cancer can be identified as a chaotic cell state, which breaks the rules that govern growth and reproduction, with main characteristics such as uncontrolled division, invading other tissues, usurping resources, and eventually killing its host. It was once believed that cancer is caused by a progressive series of genetic aberrations, and certain mutations of genes, including oncogenes and tumor suppressor genes, have been identified as the cause of cancer. However, piling evidence suggests that epigenetic modifications working in concert with genetic mechanisms to regulate transcriptional activity are dysregulated in many diseases, including cancer. Cancer epigenetics explain a wide range of heritable changes in gene expression, which do not come from any alteration in DNA sequences. Aberrant DNA methylation, histone modifications, and expression of long non-coding RNAs (lncRNAs) are key epigenetic mechanisms associated with tumor initiation, cancer progression, and metastasis. Within the past decade, cancer epigenetics have enabled us to develop novel biomarkers and therapeutic target for many types of cancers. In this review, we will summarize the major epigenetic changes involved in cancer biology along with clinical and preclinical results developed as novel cancer therapeutics.
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Affiliation(s)
- Jong Woo Park
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jeung-Whan Han
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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49
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Johnson MO, Wolf MM, Madden MZ, Andrejeva G, Sugiura A, Contreras DC, Maseda D, Liberti MV, Paz K, Kishton RJ, Johnson ME, de Cubas AA, Wu P, Li G, Zhang Y, Newcomb DC, Wells AD, Restifo NP, Rathmell WK, Locasale JW, Davila ML, Blazar BR, Rathmell JC. Distinct Regulation of Th17 and Th1 Cell Differentiation by Glutaminase-Dependent Metabolism. Cell 2018; 175:1780-1795.e19. [PMID: 30392958 PMCID: PMC6361668 DOI: 10.1016/j.cell.2018.10.001] [Citation(s) in RCA: 416] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/16/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022]
Abstract
Activated T cells differentiate into functional subsets with distinct metabolic programs. Glutaminase (GLS) converts glutamine to glutamate to support the tricarboxylic acid cycle and redox and epigenetic reactions. Here, we identify a key role for GLS in T cell activation and specification. Though GLS deficiency diminished initial T cell activation and proliferation and impaired differentiation of Th17 cells, loss of GLS also increased Tbet to promote differentiation and effector function of CD4 Th1 and CD8 CTL cells. This was associated with altered chromatin accessibility and gene expression, including decreased PIK3IP1 in Th1 cells that sensitized to IL-2-mediated mTORC1 signaling. In vivo, GLS null T cells failed to drive Th17-inflammatory diseases, and Th1 cells had initially elevated function but exhausted over time. Transient GLS inhibition, however, led to increased Th1 and CTL T cell numbers. Glutamine metabolism thus has distinct roles to promote Th17 but constrain Th1 and CTL effector cell differentiation.
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Affiliation(s)
- Marc O. Johnson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Melissa M. Wolf
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew Z. Madden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gabriela Andrejeva
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ayaka Sugiura
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Diana C. Contreras
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Damian Maseda
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maria V. Liberti
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Katelyn Paz
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rigel J. Kishton
- Center for Cell-Based Therapy, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew E. Johnson
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aguirre A. de Cubas
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pingsheng Wu
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Gongbo Li
- Department of Blood and Marrow Transplantation and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Yongliang Zhang
- Department of Blood and Marrow Transplantation and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Dawn C. Newcomb
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Vanderbilt Center for Immunobiology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew D. Wells
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas P. Restifo
- Center for Cell-Based Therapy, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - W. Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Vanderbilt Center for Immunobiology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Marco L. Davila
- Department of Blood and Marrow Transplantation and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Bruce R. Blazar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Vanderbilt Center for Immunobiology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Lead Contact,Correspondence:
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50
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Ineffective erythropoiesis of TET2 deficiency. Blood 2018; 132:2320-2321. [PMID: 30498069 DOI: 10.1182/blood-2018-10-878645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies by Qu et al1 in this issue of Blood provide new mechanistic insight into the ineffective erythropoiesis of TET2 deficiency including selective colony-forming unit–erythroid (CFU-E) hyperproliferation, heightened expression of KIT and AXL, and the rescue by KIT and AXL inhibitors of faltered late stage erythropoiesis.
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