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Chen X, Guo Y, Zhao T, Lu J, Fang J, Wang Y, Wang GG, Song J. Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction. Nat Commun 2024; 15:6217. [PMID: 39043678 PMCID: PMC11266573 DOI: 10.1038/s41467-024-50526-3] [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: 09/15/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
Isoform 1 of DNA methyltransferase DNMT3A (DNMT3A1) specifically recognizes nucleosome monoubiquitylated at histone H2A lysine-119 (H2AK119ub1) for establishment of DNA methylation. Mis-regulation of this process may cause aberrant DNA methylation and pathogenesis. However, the molecular basis underlying DNMT3A1-nucleosome interaction remains elusive. Here we report the cryo-EM structure of DNMT3A1's ubiquitin-dependent recruitment (UDR) fragment complexed with H2AK119ub1-modified nucleosome. DNMT3A1 UDR occupies an extensive nucleosome surface, involving the H2A-H2B acidic patch, a surface groove formed by H2A and H3, nucleosomal DNA, and H2AK119ub1. The DNMT3A1 UDR's interaction with H2AK119ub1 affects the functionality of DNMT3A1 in cells in a context-dependent manner. Our structural and biochemical analysis also reveals competition between DNMT3A1 and JARID2, a cofactor of polycomb repression complex 2 (PRC2), for nucleosome binding, suggesting the interplay between different epigenetic pathways. Together, this study reports a molecular basis for H2AK119ub1-dependent DNMT3A1-nucleosome association, with important implications in DNMT3A1-mediated DNA methylation in development.
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Affiliation(s)
- Xinyi Chen
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ting Zhao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
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2
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Jafari PA, Bagheri R, Lavasani S, Goudarzi S. DNMT3A-R882: a mutation with many paradoxes. Ann Hematol 2024:10.1007/s00277-024-05874-x. [PMID: 38969930 DOI: 10.1007/s00277-024-05874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Understanding the underlying mechanism of acute myeloid leukemia (AML) has led to the discovery of novel biomarkers to help predict, treat and monitor leukemia. DNA (cytosine-5)-methyltransferase 3 A (DNMT3A) is considered a prognostic and therapeutic epigenetic target in AML patients with a hotspot mutation of R882. R882 mutation is associated with impaired differentiation of Hematopoietic stem cells in the bone marrow and disease progression. The prevalence of R882 mutation varied in different ethnicities and countries, and similarly, its prognostic impact differed among numerous studies. Nevertheless, the co-occurrence of mutations in R882 with NPM1 and FLT3 has been reported more frequently and is associated with a worse prognosis. These studies also suggest diverse results regarding bone marrow transplantation response as a treatment, while chemoresistance is reached as a conclusive outcome These findings highlight the crucial need for an in-depth discussion on the significance of the R882 mutation in AML patients. Understanding its impact on leukemic transformation, prognosis, and treatment is vital for advancing clinical implications.
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Affiliation(s)
| | - Ramin Bagheri
- Mashhad University of Medical Sciences, Mashhad, Iran
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Rogers JH, Rosen A, Reyes JM, Ketkar S, Conneely SE, Gupta R, Yang L, Miller MB, Medrano G, Aguilar R, Uchenda N, Goodell MA, Rau RE. Dose-dependent effects of Dnmt3a in an inducible murine model of Kras G12D-driven leukemia. Exp Hematol 2024; 135:104248. [PMID: 38834136 DOI: 10.1016/j.exphem.2024.104248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/06/2024]
Abstract
DNMT3A mutations are frequently found in clonal hematopoiesis and a variety of hematologic malignancies, including acute myeloid leukemia. An assortment of mouse models have been engineered to explore the tumorigenic potential and malignant lineage bias due to loss of function of DNMT3A in consort with commonly comutated genes in myeloid malignancies, such as Flt3, Nras, Kras, and c-Kit. We employed several tamoxifen-inducible Cre-ERT2 murine model systems to study the effects of constitutively active KrasG12D-driven myeloid leukemia (Kras) development together with heterozygous (3aHet) or homozygous Dnmt3a deletion (3aKO). Due to the rapid generation of diverse nonhematologic tumors appearing after tamoxifen induction, we employed a transplantation model. With pretransplant tamoxifen induction, most Kras mice died quickly of T-cell malignancies regardless of Dnmt3a status. Using posttransplant induction, we observed a dose-dependent effect of DNMT3A depletion that skewed the leukemic phenotype toward a myeloid lineage. Specifically, 64% of 3aKO/Kras mice had exclusively myeloid disease compared with 36% of 3aHet/Kras and only 13% of Kras mice. Here, 3aKO combined with Kras led to increased disease burden, multiorgan infiltration, and faster disease progression. DOT1L inhibition exerted profound antileukemic effects in malignant 3aKO/Kras cells, but not malignant cells with Kras mutation alone, consistent with the known sensitivity of DNMT3A-mutant leukemia to DOT1L inhibition. RNAseq from malignant myeloid cells revealed that biallelic Dnmt3a deletion was associated with loss of cell-cycle regulation, MYC activation, and TNF⍺ signaling. Overall, we developed a robust model system for mechanistic and preclinical investigations of acute myeloid leukemia with DNMT3A and Ras-pathway lesions.
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Affiliation(s)
- Jason H Rogers
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Allison Rosen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Jaime M Reyes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Shannon E Conneely
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Rohit Gupta
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX; Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Luibin Yang
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Matthew B Miller
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Geraldo Medrano
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Rogelio Aguilar
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Nneka Uchenda
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Margaret A Goodell
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Rachel E Rau
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics and the Ben Towne Center for Childhood Cancer Research, Seattle Children's Hospital, University of Washington, Seattle, WA..
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4
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Usart M, Stetka J, Luque Paz D, Hansen N, Kimmerlin Q, Almeida Fonseca T, Lock M, Kubovcakova L, Karjalainen R, Hao-Shen H, Börsch A, El Taher A, Schulz J, Leroux JC, Dirnhofer S, Skoda RC. Loss of Dnmt3a increases self-renewal and resistance to pegIFN-α in JAK2-V617F-positive myeloproliferative neoplasms. Blood 2024; 143:2490-2503. [PMID: 38493481 PMCID: PMC11208296 DOI: 10.1182/blood.2023020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024] Open
Abstract
ABSTRACT Pegylated interferon alfa (pegIFN-α) can induce molecular remissions in patients with JAK2-V617F-positive myeloproliferative neoplasms (MPNs) by targeting long-term hematopoietic stem cells (LT-HSCs). Additional somatic mutations in genes regulating LT-HSC self-renewal, such as DNMT3A, have been reported to have poorer responses to pegIFN-α. We investigated whether DNMT3A loss leads to alterations in JAK2-V617F LT-HSC functions conferring resistance to pegIFN-α treatment in a mouse model of MPN and in hematopoietic progenitors from patients with MPN. Long-term treatment with pegIFN-α normalized blood parameters and reduced splenomegaly and JAK2-V617F chimerism in single-mutant JAK2-V617F (VF) mice. However, pegIFN-α in VF;Dnmt3aΔ/Δ (VF;DmΔ/Δ) mice worsened splenomegaly and failed to reduce JAK2-V617F chimerism. Furthermore, LT-HSCs from VF;DmΔ/Δ mice compared with VF were less prone to accumulate DNA damage and exit dormancy upon pegIFN-α treatment. RNA sequencing showed that IFN-α induced stronger upregulation of inflammatory pathways in LT-HSCs from VF;DmΔ/Δ than from VF mice, indicating that the resistance of VF;DmΔ/Δ LT-HSC was not due to failure in IFN-α signaling. Transplantations of bone marrow from pegIFN-α-treated VF;DmΔ/Δ mice gave rise to more aggressive disease in secondary and tertiary recipients. Liquid cultures of hematopoietic progenitors from patients with MPN with JAK2-V617F and DNMT3A mutation showed increased percentages of JAK2-V617F-positive colonies upon IFN-α exposure, whereas in patients with JAK2-V617F alone, the percentages of JAK2-V617F-positive colonies decreased or remained unchanged. PegIFN-α combined with 5-azacytidine only partially overcame resistance in VF;DmΔ/Δ mice. However, this combination strongly decreased the JAK2-mutant allele burden in mice carrying VF mutation only, showing potential to inflict substantial damage preferentially to the JAK2-mutant clone.
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Affiliation(s)
- Marc Usart
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jan Stetka
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Biology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Damien Luque Paz
- University of Angers, Nantes Université, Centre Hospitalier Universitaire Angers, INSERM, Centre National de la Recherche Scientifique, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, Angers, France
| | - Nils Hansen
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Quentin Kimmerlin
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Tiago Almeida Fonseca
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Melissa Lock
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Lucia Kubovcakova
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Riikka Karjalainen
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hui Hao-Shen
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Anastasiya Börsch
- Department of Biomedicine, Bioinformatics, University of Basel and University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Athimed El Taher
- Department of Biomedicine, Bioinformatics, University of Basel and University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jessica Schulz
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Stefan Dirnhofer
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Radek C. Skoda
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
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5
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Patnaik MM, Tefferi A. Chronic myelomonocytic leukemia: 2024 update on diagnosis, risk stratification and management. Am J Hematol 2024; 99:1142-1165. [PMID: 38450850 PMCID: PMC11096042 DOI: 10.1002/ajh.27271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
DISEASE OVERVIEW Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic stem cell disorder with overlapping features of myelodysplastic syndromes and myeloproliferative neoplasms, characterized by prominent monocytosis and an inherent risk for leukemic transformation (~15%-20% over 3-5 years). DIAGNOSIS Newly revised diagnostic criteria include sustained (>3 months) peripheral blood (PB) monocytosis (≥0.5 × 109/L; monocytes ≥10% of leukocyte count), consistent bone marrow (BM) morphology, <20% BM or PB blasts (including promonocytes), and cytogenetic or molecular evidence of clonality. Cytogenetic abnormalities occur in ~30% of patients, while >95% harbor somatic mutations: TET2 (~60%), SRSF2 (~50%), ASXL1 (~40%), RAS pathway (~30%), and others. The presence of ASXL1 and DNMT3A mutations and absence of TET2 mutations negatively impact overall survival (ASXL1WT/TET2MT genotype being favorable). RISK STRATIFICATION Several risk models serve similar purposes in identifying high-risk patients that are considered for allogeneic stem cell transplant (ASCT) earlier than later. Risk factors in the Mayo Molecular Model (MMM) include presence of truncating ASXL1 mutations, absolute monocyte count >10 × 109/L, hemoglobin <10 g/dL, platelet count <100 × 109/L, and the presence of circulating immature myeloid cells; the resulting 4-tiered risk categorization includes high (≥3 risk factors), intermediate-2 (2 risk factors), intermediate-1 (1 risk factor), and low (no risk factors); the corresponding median survivals were 16, 31, 59, and 97 months. CMML is also classified as being "myeloproliferative (MP-CMML)" or "myelodysplastic (MD-CMML)," based on the presence or absence of leukocyte count of ≥13 × 109/L. TREATMENT ASCT is the only treatment modality that secures cure or long-term survival and is appropriate for MMM high/intermediate-2 risk disease. Drug therapy is currently not disease-modifying and includes hydroxyurea and hypomethylating agents; a recent phase-3 study (DACOTA) comparing hydroxyurea and decitabine, in high-risk MP-CMML, showed similar overall survival at 23.1 versus 18.4 months, respectively, despite response rates being higher for decitabine (56% vs. 31%). UNIQUE DISEASE ASSOCIATIONS These include systemic inflammatory autoimmune diseases, leukemia cutis and lysozyme-induced nephropathy; the latter requires close monitoring of renal function during leukocytosis and is a potential indication for cytoreductive therapy.
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Affiliation(s)
- Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ayalew Tefferi
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Jing Q, Zhou C, Zhang J, Zhang P, Wu Y, Zhou J, Tong X, Li Y, Du J, Wang Y. Role of reactive oxygen species in myelodysplastic syndromes. Cell Mol Biol Lett 2024; 29:53. [PMID: 38616283 PMCID: PMC11017617 DOI: 10.1186/s11658-024-00570-0] [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: 11/09/2023] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
Reactive oxygen species (ROS) serve as typical metabolic byproducts of aerobic life and play a pivotal role in redox reactions and signal transduction pathways. Contingent upon their concentration, ROS production not only initiates or stimulates tumorigenesis but also causes oxidative stress (OS) and triggers cellular apoptosis. Mounting literature supports the view that ROS are closely interwoven with the pathogenesis of a cluster of diseases, particularly those involving cell proliferation and differentiation, such as myelodysplastic syndromes (MDS) and chronic/acute myeloid leukemia (CML/AML). OS caused by excessive ROS at physiological levels is likely to affect the functions of hematopoietic stem cells, such as cell growth and self-renewal, which may contribute to defective hematopoiesis. We review herein the eminent role of ROS in the hematological niche and their profound influence on the progress of MDS. We also highlight that targeting ROS is a practical and reliable tactic for MDS therapy.
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Affiliation(s)
- Qiangan Jing
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- HEALTH BioMed Research & Development Center, Health BioMed Co., Ltd, Ningbo, 315803, Zhejiang, China
| | - Chaoting Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Junyu Zhang
- Department of Hematology, Lishui Central Hospital, Lishui, 323000, Zhejiang, China
| | - Ping Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yunyi Wu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Junyu Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Xiangmin Tong
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, 310006, Zhejiang, China
| | - Yanchun Li
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, 310006, Zhejiang, China.
| | - Jing Du
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.
| | - Ying Wang
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, 310006, Zhejiang, China.
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7
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Lu J, Guo Y, Yin J, Chen J, Wang Y, Wang GG, Song J. Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat Commun 2024; 15:3111. [PMID: 38600075 PMCID: PMC11006857 DOI: 10.1038/s41467-024-47398-y] [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: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.
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Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
| | - Jianbin Chen
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.
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8
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Demirkiran N, Aydin B, Pehlivan M, Yuce Z, Sercan HO. Study of the effect of sFRP1 protein on molecules involved in the regulation of DNA methylation in CML cell line. Med Oncol 2024; 41:109. [PMID: 38592567 DOI: 10.1007/s12032-024-02336-2] [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: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
Wnt-signaling pathway plays a crucial role in the pathogenesis and progression of Chronic Myeloid Leukemia (CML). sFRP1 is involved in the suppression of the Wnt-signaling pathway and has been shown to be epigenetically silenced by promoter hypermethylation during CML progression. DNMT3A plays a crucial role in promoter hypermethylation and is responsible for establishing methylation patterns. We aimed to analyze the relationship between sFRP1 expression and DNMT3A, TET1, TET2 and TET3 proteins that are responsible for maintaining cellular methylation patterns; along with miRNAs miR144-3p and miR-767-5p that are known to be associated with these proteins. CML cell lines K562 and K562S which stably expresses sFRP1, were used to compare the changes in miR144-3p and miR-767-5p expression. DNMT3A, TET1, TET2 and TET3 protein levels were analyzed by Western blot. In K562S cells the expression of miR-144-3p and miR-767-5p were decreased along with DNMT3A and TET1 protein levels. On the contrary, TET2 protein was increased. Our results support other reports involving sFRP1 and methylation dynamics; as well as opening new avenues of exploration. Our data supports the conclusion that re-expression of sFRP1 protein alters the expression of factors that play important roles in the overall methylation patterns in the leukemic cell line K562.
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Affiliation(s)
- Nazli Demirkiran
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey
| | - Bengusu Aydin
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey
| | - Melek Pehlivan
- Department of Medical Laboratory Techniques, Izmir Katip Celebi University, Vocational School of Health Services, Izmir, Turkey
| | - Zeynep Yuce
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey
| | - H Ogun Sercan
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey.
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9
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Xu S, Yuan Z, Jiang C, Chen W, Li Q, Chen T. DNMT3A Cooperates with YAP/TAZ to Drive Gallbladder Cancer Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308531. [PMID: 38380551 PMCID: PMC11040361 DOI: 10.1002/advs.202308531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Gallbladder cancer (GBC) is an extremely lethal malignancy with aggressive behaviors, including liver or distant metastasis; however, the underlying mechanisms driving the metastasis of GBC remain poorly understood. In this study, it is found that DNA methyltransferase DNMT3A is highly expressed in GBC tumor tissues compared to matched adjacent normal tissues. Clinicopathological analysis shows that DNMT3A is positively correlated with liver metastasis and poor overall survival outcomes in patients with GBC. Functional analysis confirms that DNMT3A promotes the metastasis of GBC cells in a manner dependent on its DNA methyltransferase activity. Mechanistically, DNMT3A interacts with and is recruited by YAP/TAZ to recognize and access the CpG island within the CDH1 promoter and generates hypermethylation of the CDH1 promoter, which leads to transcriptional silencing of CDH1 and accelerated epithelial-to-mesenchymal transition. Using tissue microarrays, the association between the expression of DNMT3A, YAP/TAZ, and CDH1 is confirmed, which affects the metastatic ability of GBC. These results reveal a novel mechanism through which DNMT3A recruitment by YAP/TAZ guides DNA methylation to drive GBC metastasis and provide insights into the treatment of GBC metastasis by targeting the functional connection between DNMT3A and YAP/TAZ.
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Affiliation(s)
- Sunwang Xu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200125, China
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Zhiqing Yuan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200125, China
| | - Cen Jiang
- Central Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Wei Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200125, China
| | - Qiwei Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200125, China
| | - Tao Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200125, China
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10
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Cox LA, Thompson WJ, Mundt KA. Interventional probability of causation (IPoC) with epidemiological and partial mechanistic evidence: benzene vs. formaldehyde and acute myeloid leukemia (AML). Crit Rev Toxicol 2024; 54:252-289. [PMID: 38753561 DOI: 10.1080/10408444.2024.2337435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/25/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION Causal epidemiology for regulatory risk analysis seeks to evaluate how removing or reducing exposures would change disease occurrence rates. We define interventional probability of causation (IPoC) as the change in probability of a disease (or other harm) occurring over a lifetime or other specified time interval that would be caused by a specified change in exposure, as predicted by a fully specified causal model. We define the closely related concept of causal assigned share (CAS) as the predicted fraction of disease risk that would be removed or prevented by a specified reduction in exposure, holding other variables fixed. Traditional approaches used to evaluate the preventable risk implications of epidemiological associations, including population attributable fraction (PAF) and the Bradford Hill considerations, cannot reveal whether removing a risk factor would reduce disease incidence. We argue that modern formal causal models coupled with causal artificial intelligence (CAI) and realistically partial and imperfect knowledge of underlying disease mechanisms, show great promise for determining and quantifying IPoC and CAS for exposures and diseases of practical interest. METHODS We briefly review key CAI concepts and terms and then apply them to define IPoC and CAS. We present steps to quantify IPoC using a fully specified causal Bayesian network (BN) model. Useful bounds for quantitative IPoC and CAS calculations are derived for a two-stage clonal expansion (TSCE) model for carcinogenesis and illustrated by applying them to benzene and formaldehyde based on available epidemiological and partial mechanistic evidence. RESULTS Causal BN models for benzene and risk of acute myeloid leukemia (AML) incorporating mechanistic, toxicological and epidemiological findings show that prolonged high-intensity exposure to benzene can increase risk of AML (IPoC of up to 7e-5, CAS of up to 54%). By contrast, no causal pathway leading from formaldehyde exposure to increased risk of AML was identified, consistent with much previous mechanistic, toxicological and epidemiological evidence; therefore, the IPoC and CAS for formaldehyde-induced AML are likely to be zero. CONCLUSION We conclude that the IPoC approach can differentiate between likely and unlikely causal factors and can provide useful upper bounds for IPoC and CAS for some exposures and diseases of practical importance. For causal factors, IPoC can help to estimate the quantitative impacts on health risks of reducing exposures, even in situations where mechanistic evidence is realistically incomplete and individual-level exposure-response parameters are uncertain. This illustrates the strength that can be gained for causal inference by using causal models to generate testable hypotheses and then obtaining toxicological data to test the hypotheses implied by the models-and, where necessary, refine the models. This virtuous cycle provides additional insight into causal determinations that may not be available from weight-of-evidence considerations alone.
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Affiliation(s)
- Louis A Cox
- Cox Associates and University of Colorado, Denver, CO, USA
| | | | - Kenneth A Mundt
- Independent Consultants in Epidemiology, Amherst, MA, USA
- Adjunct Professor of Epidemiology, University of Massachusetts, Amherst, MA, USA
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11
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Reyes JM, Tovy A, Zhang L, Bortoletto AS, Rosas C, Chen CW, Waldvogel SM, Guzman AG, Aguilar R, Gupta S, Liu L, Buckley MT, Patel KR, Marcogliese AN, Li Y, Curry CV, Rando T, Brunet A, Parchem RJ, Rau RE, Goodell MA. Hematologic DNMT3A reduction and high-fat diet synergize to promote weight gain and tissue inflammation. iScience 2024; 27:109122. [PMID: 38414863 PMCID: PMC10897855 DOI: 10.1016/j.isci.2024.109122] [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: 07/14/2022] [Revised: 12/11/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
During aging, blood cell production becomes dominated by a limited number of variant hematopoietic stem cell (HSC) clones. Differentiated progeny of variant HSCs are thought to mediate the detrimental effects of such clonal hematopoiesis on organismal health, but the mechanisms are poorly understood. While somatic mutations in DNA methyltransferase 3A (DNMT3A) frequently drive clonal dominance, the aging milieu also likely contributes. Here, we examined in mice the interaction between high-fat diet (HFD) and reduced DNMT3A in hematopoietic cells; strikingly, this combination led to weight gain. HFD amplified pro-inflammatory pathways and upregulated inflammation-associated genes in mutant cells along a pro-myeloid trajectory. Aberrant DNA methylation during myeloid differentiation and in response to HFD led to pro-inflammatory activation and maintenance of stemness genes. These findings suggest that reduced DNMT3A in hematopoietic cells contributes to weight gain, inflammation, and metabolic dysfunction, highlighting a role for DNMT3A loss in the development of metabolic disorders.
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Affiliation(s)
- Jaime M. Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Linda Zhang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Angelina S. Bortoletto
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Chun-Wei Chen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sarah M. Waldvogel
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Anna G. Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Rogelio Aguilar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Sinjini Gupta
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University, Palo Alto, CA, USA
| | | | - Kalyani R. Patel
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | | | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Choladda V. Curry
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Thomas Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University, Palo Alto, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Palo Alto, CA, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University, Palo Alto, CA, USA
| | - Ronald J. Parchem
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Rachel E. Rau
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Margaret A. Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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12
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Kumar V, Stewart JH. Obesity, bone marrow adiposity, and leukemia: Time to act. Obes Rev 2024; 25:e13674. [PMID: 38092420 DOI: 10.1111/obr.13674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 02/28/2024]
Abstract
Obesity has taken the face of a pandemic with less direct concern among the general population and scientific community. However, obesity is considered a low-grade systemic inflammation that impacts multiple organs. Chronic inflammation is also associated with different solid and blood cancers. In addition, emerging evidence demonstrates that individuals with obesity are at higher risk of developing blood cancers and have poorer clinical outcomes than individuals in a normal weight range. The bone marrow is critical for hematopoiesis, lymphopoiesis, and myelopoiesis. Therefore, it is vital to understand the mechanisms by which obesity-associated changes in BM adiposity impact leukemia development. BM adipocytes are critical to maintain homeostasis via different means, including immune regulation. However, obesity increases BM adiposity and creates a pro-inflammatory environment to upregulate clonal hematopoiesis and a leukemia-supportive environment. Obesity further alters lymphopoiesis and myelopoiesis via different mechanisms, which dysregulate myeloid and lymphoid immune cell functions mentioned in the text under different sequentially discussed sections. The altered immune cell function during obesity alters hematological malignancies and leukemia susceptibility. Therefore, obesity-induced altered BM adiposity, immune cell generation, and function impact an individual's predisposition and severity of leukemia, which should be considered a critical factor in leukemia patients.
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Affiliation(s)
- Vijay Kumar
- Department of Surgery, Laboratory of Tumor Immunology and Immunotherapy, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - John H Stewart
- Department of Surgery, Laboratory of Tumor Immunology and Immunotherapy, Morehouse School of Medicine, Atlanta, Georgia, USA
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13
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Jiménez de la Peña M, Rincón-Pérez I, López-Martín S, Albert J, Martín Fernández-Mayoralas D, Fernández-Perrone AL, Jiménez de Domingo A, Tirado P, Calleja-Pérez B, Porta J, Álvarez S, Fernández-Jaén A. Tatton-Brown-Rahman syndrome: Novel pathogenic variants and new neuroimaging findings. Am J Med Genet A 2024; 194:211-217. [PMID: 37795572 DOI: 10.1002/ajmg.a.63434] [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: 05/31/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
Tatton-Brown-Rahman syndrome (TBRS) or DNMT3A-overgrowth syndrome is characterized by overgrowth and intellectual disability associated with minor dysmorphic features, obesity, and behavioral problems. It is caused by variants of the DNMT3A gene. We report four patients with this syndrome due to de novo DNMT3A pathogenic variants, contributing to a deeper understanding of the genetic basis and pathophysiology of this autosomal dominant syndrome. Clinical and magnetic resonance imaging assessments were also performed. All patients showed corpus callosum anomalies, small posterior fossa, and a deep left Sylvian fissure; as well as asymmetry of the uncinate and arcuate fascicles and marked increased cortical thickness. These results suggest that structural neuroimaging anomalies have been previously overlooked, where corpus callosum and brain tract alterations might be unrecognized neuroimaging traits of TBRS syndrome caused by DNMT3A variants.
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Affiliation(s)
| | - Irene Rincón-Pérez
- Faculty of Psychology, Universidad Autónoma de Madrid, Madrid, Spain
- Universidad Complutense de Madrid, Madrid, Spain
| | - Sara López-Martín
- Faculty of Psychology, Universidad Autónoma de Madrid, Madrid, Spain
- Neuromottiva, Madrid, Spain
| | - Jacobo Albert
- Faculty of Psychology, Universidad Autónoma de Madrid, Madrid, Spain
| | | | | | | | - Pilar Tirado
- Department of Pediatric Neurology, Hospital Universitario La Paz, Madrid, Spain
| | | | - Javier Porta
- Department of Genomics, Genologica, Málaga, Spain
| | - Sara Álvarez
- Department of Genomics and Medicine, NIMGenetics, Madrid, Spain
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology, Hospital Universitario Quirónsalud, Madrid, Spain
- School of Medicine, Universidad Europea de Madrid, Madrid, Spain
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14
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Yan B, Yuan Q, Guryanova OA. Epigenetic Mechanisms in Hematologic Aging and Premalignant Conditions. EPIGENOMES 2023; 7:32. [PMID: 38131904 PMCID: PMC10743085 DOI: 10.3390/epigenomes7040032] [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: 10/26/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are essential for maintaining overall health by continuously generating blood cells throughout an individual's lifespan. However, as individuals age, the hematopoietic system undergoes significant functional decline, rendering them more susceptible to age-related diseases. Growing research evidence has highlighted the critical role of epigenetic regulation in this age-associated decline. This review aims to provide an overview of the diverse epigenetic mechanisms involved in the regulation of normal HSCs during the aging process and their implications in aging-related diseases. Understanding the intricate interplay of epigenetic mechanisms that contribute to aging-related changes in the hematopoietic system holds great potential for the development of innovative strategies to delay the aging process. In fact, interventions targeting epigenetic modifications have shown promising outcomes in alleviating aging-related phenotypes and extending lifespan in various animal models. Small molecule-based therapies and reprogramming strategies enabling epigenetic rejuvenation have emerged as effective approaches for ameliorating or even reversing aging-related conditions. By acquiring a deeper understanding of these epigenetic mechanisms, it is anticipated that interventions can be devised to prevent or mitigate the rates of hematologic aging and associated diseases later in life. Ultimately, these advancements have the potential to improve overall health and enhance the quality of life in aging individuals.
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Affiliation(s)
- Bowen Yan
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
| | | | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
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15
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Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J. Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res 2023; 51:12476-12491. [PMID: 37941146 PMCID: PMC10711551 DOI: 10.1093/nar/gkad972] [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: 03/29/2023] [Revised: 09/08/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023] Open
Abstract
Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains interplay with the C-terminal methyltransferase (MTase) domain in regulating the dynamic assembly of DNMT3B remains unclear. Here, we report the cryo-EM structure of DNMT3B under various oligomerization states. The ADD domain of DNMT3B interacts with the MTase domain to form an autoinhibitory conformation, resembling the previously observed DNMT3A autoinhibition. Our combined structural and biochemical study further identifies a role for the PWWP domain and its associated ICF mutation in the allosteric regulation of DNMT3B tetramer, and a differential functional impact on DNMT3B by potential ADD-H3K4me0 and PWWP-H3K36me3 bindings. In addition, our comparative structural analysis reveals a coupling between DNMT3B oligomerization and folding of its substrate-binding sites. Together, this study provides mechanistic insights into the allosteric regulation and dynamic assembly of DNMT3B.
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Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA92521, USA
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16
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Jassim A, Rahrmann EP, Simons BD, Gilbertson RJ. Cancers make their own luck: theories of cancer origins. Nat Rev Cancer 2023; 23:710-724. [PMID: 37488363 DOI: 10.1038/s41568-023-00602-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Cancer has been a leading cause of death for decades. This dismal statistic has increased efforts to prevent the disease or to detect it early, when treatment is less invasive, relatively inexpensive and more likely to cure. But precisely how tissues are transformed continues to provoke controversy and debate, hindering cancer prevention and early intervention strategies. Various theories of cancer origins have emerged, including the suggestion that it is 'bad luck': the inevitable consequence of random mutations in proliferating stem cells. In this Review, we discuss the principal theories of cancer origins and the relative importance of the factors that underpin them. The body of available evidence suggests that developing and ageing tissues 'walk a tightrope', retaining adequate levels of cell plasticity to generate and maintain tissues while avoiding overstepping into transformation. Rather than viewing cancer as 'bad luck', understanding the complex choreography of cell intrinsic and extrinsic factors that characterize transformation holds promise to discover effective new ways to prevent, detect and stop cancer before it becomes incurable.
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Affiliation(s)
- Amir Jassim
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Eric P Rahrmann
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ben D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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17
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Sobieralski P, Wasąg B, Leszczyńska A, Żuk M, Bieniaszewska M. The molecular profile in patients with polycythemia vera and essential thrombocythemia is dynamic and correlates with disease's phenotype. Front Oncol 2023; 13:1224590. [PMID: 37671053 PMCID: PMC10475996 DOI: 10.3389/fonc.2023.1224590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction Polycythemia vera (PV) and essential thrombocythemia (ET) are diseases driven by canonical mutations in JAK2, CALR, or MPL gene. Previous studies revealed that in addition to driver mutations, patients with PV and ET can harbor other mutations in various genes, with no established impact on disease phenotype. We hypothesized that the molecular profile of patients with PV and ET is dynamic throughout the disease. Methods In this study, we performed a 37-gene targeted next-generation sequencing panel on the DNA samples collected from 49 study participants in two-time points, separated by 78-141 months. We identified 78 variants across 37 analyzed genes in the study population. Results By analyzing the change in variant allele frequencies and revealing the acquisition of new mutations during the disease, we confirmed the dynamic nature of the molecular profile of patients with PV and ET. We found connections between specific variants with the development of secondary myelofibrosis, thrombotic events, and response to treatment. We confronted our results with existing conventional and mutation-enhanced prognostic systems, showing the limited utility of available prognostic tools. Discussion The results of this study underline the significance of repeated molecular testing in patients with PV and ET and indicate the need for further research within this field to better understand the disease and improve available prognostic tools.
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Affiliation(s)
- Patryk Sobieralski
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasąg
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Aleksandra Leszczyńska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Monika Żuk
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Maria Bieniaszewska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
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18
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Noguera NI, Travaglini S, Scalea S, Catalanotto C, Reale A, Zampieri M, Zaza A, Ricciardi MR, Angelini DF, Tafuri A, Ottone T, Voso MT, Zardo G. YY1 Knockdown Relieves the Differentiation Block and Restores Apoptosis in AML Cells. Cancers (Basel) 2023; 15:4010. [PMID: 37568827 PMCID: PMC10417667 DOI: 10.3390/cancers15154010] [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: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
In this study we analyzed the expression of Yin and Yang 1 protein (YY1), a member of the noncanonical PcG complexes, in AML patient samples and AML cell lines and the effect of YY1 downregulation on the AML differentiation block. Our results show that YY1 is significantly overexpressed in AML patient samples and AML cell lines and that YY1 knockdown relieves the differentiation block. YY1 downregulation in two AML cell lines (HL-60 and OCI-AML3) and one AML patient sample restored the expression of members of the CEBP protein family, increased the expression of extrinsic growth factors/receptors and surface antigenic markers, induced morphological cell characteristics typical of myeloid differentiation, and sensitized cells to retinoic acid treatment and to apoptosis. Overall, our data show that YY1 is not a secondary regulator of myeloid differentiation but that, if overexpressed, it can play a predominant role in myeloid differentiation block.
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Affiliation(s)
- Nelida Ines Noguera
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Serena Travaglini
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Stefania Scalea
- Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
| | - Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Anna Reale
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Michele Zampieri
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Alessandra Zaza
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University, 00185 Rome, Italy
| | - Maria Rosaria Ricciardi
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy; (M.R.R.); (A.T.)
| | | | - Agostino Tafuri
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy; (M.R.R.); (A.T.)
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
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19
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Cui W, Huang Z, Jin SG, Johnson J, Lau KH, Hostetter G, Pfeifer GP. Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation. Cancer Res 2023; 83:2480-2495. [PMID: 37272752 PMCID: PMC10391329 DOI: 10.1158/0008-5472.can-23-0269] [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: 01/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023]
Abstract
Hypermethylation of CpG islands (CGI) is a common feature of cancer cells and predominantly affects Polycomb-associated genomic regions. Elucidating the underlying mechanisms leading to DNA hypermethylation in human cancer could help identify chemoprevention strategies. Here, we evaluated the role of Polycomb complexes and 5-methylcytosine (5mC) oxidases in protecting CGIs from DNA methylation and observed that four genes coding for components of Polycomb repressive complex 1 (PRC1) are downregulated in tumors. Inactivation of RYBP, a key activator of variant PRC1 complexes, in combination with all three 5mC oxidases (TET proteins) in nontumorigenic bronchial epithelial cells led to widespread hypermethylation of Polycomb-marked CGIs affecting almost 4,000 target genes, which closely resembled the DNA hypermethylation landscape observed in human squamous cell lung tumors. The RYBP- and TET-deficient cells showed methylation-associated aberrant regulation of cancer-relevant pathways, including defects in the Hippo tumor suppressor network. Notably, the quadruple knockout cells acquired a transformed phenotype, including anchorage-independent growth and formation of squamous cell carcinomas in mice. This work provides a mechanism promoting hypermethylation of CGIs and shows that such hypermethylation can lead to cell transformation. The breakdown of a two-pronged protection mechanism can be a route towards genome-wide hypermethylation of CGIs in tumors. SIGNIFICANCE Dysfunction of the Polycomb component RYBP in combination with loss of 5-methylcytosine oxidases promotes widespread hypermethylation of CpG islands in bronchial cells and induces tumorigenesis, resembling changes seen in human lung tumors.
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Affiliation(s)
- Wei Cui
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Zhijun Huang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Gerd P. Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
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20
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Balandrán JC, Lasry A, Aifantis I. The Role of Inflammation in the Initiation and Progression of Myeloid Neoplasms. Blood Cancer Discov 2023; 4:254-266. [PMID: 37052531 PMCID: PMC10320626 DOI: 10.1158/2643-3230.bcd-22-0176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 04/14/2023] Open
Abstract
Myeloid malignancies are devastating hematologic cancers with limited therapeutic options. Inflammation is emerging as a novel driver of myeloid malignancy, with important implications for tumor composition, immune response, therapeutic options, and patient survival. Here, we discuss the role of inflammation in normal and malignant hematopoiesis, from clonal hematopoiesis to full-blown myeloid leukemia. We discuss how inflammation shapes clonal output from hematopoietic stem cells, how inflammation alters the immune microenvironment in the bone marrow, and novel therapies aimed at targeting inflammation in myeloid disease. SIGNIFICANCE Inflammation is emerging as an important factor in myeloid malignancies. Understanding the role of inflammation in myeloid transformation, and the interplay between inflammation and other drivers of leukemogenesis, may yield novel avenues for therapy.
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Affiliation(s)
- Juan Carlos Balandrán
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Audrey Lasry
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
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21
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Cumbo C, Orsini P, Anelli L, Zagaria A, Iannò MF, De Cecco L, Minervini CF, Coccaro N, Tota G, Parciante E, Conserva MR, Redavid I, Tarantini F, Minervini A, Carluccio P, De Grassi A, Pierri CL, Specchia G, Musto P, Albano F. Case report: biallelic DNMT3A mutations in acute myeloid leukemia. Front Oncol 2023; 13:1205220. [PMID: 37448520 PMCID: PMC10336536 DOI: 10.3389/fonc.2023.1205220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
DNMT3A gene mutations, detected in 20-25% of de novo acute myeloid leukemia (AML) patients, are typically heterozygous. Biallelic variants are uncommon, affecting ~3% of cases and identifying a worse prognosis. Indeed, two concomitant DNMT3A mutations were recently associated with shorter event-free survival and overall survival in AML. We present an AML case bearing an unusual DNMT3A molecular status, strongly affecting its function and strangely impacting the global genomic methylation profile. A 56-year-old Caucasian male with a diagnosis of AML not otherwise specified (NOS) presented a complex DNMT3A molecular profile consisting of four different somatic variants mapping on different alleles (in trans). 3D modelling analysis predicted the effect of the DNMT3A mutational status, showing that all the investigated mutations decreased or abolished DNMT3A activity. Although unexpected, DNMT3A's severe loss of function resulted in a global genomic hypermethylation in genes generally involved in cell differentiation. The mechanisms through which DNMT3A contributes to AML remain elusive. We present a unique AML case bearing multiple biallelic DNMT3A variants abolishing its activity and resulting in an unexpected global hypermethylation. The unusual DNMT3A behavior described requires a reflection on its role in AML development and persistence, highlighting the heterogeneity of its deregulation.
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Affiliation(s)
- Cosimo Cumbo
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Orsini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Luisa Anelli
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Antonella Zagaria
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | | | - Loris De Cecco
- Molecular Mechanisms Unit, Department of Research Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Crescenzio Francesco Minervini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Nicoletta Coccaro
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Giuseppina Tota
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Elisa Parciante
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Maria Rosa Conserva
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Immacolata Redavid
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Tarantini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Angela Minervini
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Carluccio
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Computational Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Computational Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | | | - Pellegrino Musto
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Albano
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), Hematology and Stem Cell Transplantation Unit, University of Bari "Aldo Moro", Bari, Italy
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22
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Drieux F, Lemonnier F, Gaulard P. How molecular advances may improve the diagnosis and management of PTCL patients. Front Oncol 2023; 13:1202964. [PMID: 37427095 PMCID: PMC10328093 DOI: 10.3389/fonc.2023.1202964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Peripheral T-cell lymphomas (PTCL) comprised more than 30 rare heterogeneous entities, representing 10 to 15% of adult non-Hodgkin lymphomas. Although their diagnosis is still mainly based on clinical, pathological, and phenotypic features, molecular studies have allowed for a better understanding of the oncogenic mechanisms involved and the refinement of many PTCL entities in the recently updated classifications. The prognosis remains poor for most entities (5-year overall survival < 30%), with current conventional therapies based on anthracyclin-based polychemotherapy regimen, despite many years of clinical trials. The recent use of new targeted therapies appears to be promising for relapsed/refractory patients, such as demethylating agents in T-follicular helper (TFH) PTCL. However further studies are needed to evaluate the proper combination of these drugs in the setting of front-line therapy. In this review, we will summarize the oncogenic events for the main PTCL entities and report the molecular targets that have led to the development of new therapies. We will also discuss the development of innovative high throughput technologies that aid the routine workflow for the histopathological diagnosis and management of PTCL patients.
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Affiliation(s)
- Fanny Drieux
- Service d’Anatomie et de Cytologie Pathologiques, INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - François Lemonnier
- Unité hémopathies Lymphoïdes, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris Est Créteil, Créteil, France
| | - Philippe Gaulard
- Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris Est Créteil, Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris, Créteil, France
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23
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Liu S, Su J, Xie X, Huang R, Li H, Luo R, Li J, Liu X, He J, Huang Y, Wu P. Detection of methyltransferase activity and inhibitor screening based on rGO-mediated silver enhancement signal amplification strategy. Anal Biochem 2023:115207. [PMID: 37290576 DOI: 10.1016/j.ab.2023.115207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/20/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
DNA methylation refers to the chemical modification process of obtaining a methyl group by the covalent bonding of a specific base in DNA sequence with S-adenosyl methionine (SAM) as a methyl donor under the catalysis of methyltransferase (MTase), which is related to the occurrence of multiple diseases. Therefore, the detection of MTase activity is of great significance for disease diagnosis and drug screening. Because reduced graphene oxide (rGO) has a unique planar structure and remarkable catalytic performance, it is not clear whether rGO can rapidly catalyze silver deposition as an effective way of signal amplification. However, in this study, we were pleasantly surprised to find that using H2O2 as a reducing agent, rGO can rapidly catalyze silver deposition, and its catalytic efficiency of silver deposition is significantly better than that of GO. Therefore, based on further verifying the mechanism of catalytic properties of rGO, we constructed a novel electrochemical biosensor (rGO/silver biosensor) for the detection of dam MTase activity, which has high selectivity and sensitivity to MTase in the range of 0.1 U/mL to 10.0 U/mL, and the detection limit is as low as 0.07 U/mL. Besides, this study also used Gentamicin and 5-Fluorouracil as inhibitor models, confirming that the biosensor has a good application prospect in the high-throughput screening of dam MTase inhibitors.
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Affiliation(s)
- Shuyan Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China; State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jing Su
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China; College of Chemistry & Chemical Engineering, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Xixiang Xie
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Rongping Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Haiping Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Ruiyu Luo
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jinghua Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jian He
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Yong Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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24
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Estes J, Malus M, Wilson L, Grayson PC, Maz M. A Case of VEXAS: Vacuoles, E1 Enzyme, X-linked, Autoinflammatory, Somatic Syndrome With Co-existing DNA (Cytosine-5)-Methyltransferase 3A Mutation Complicated by Localized Skin Reaction to Tocilizumab and Azacitidine. Cureus 2023; 15:e39906. [PMID: 37404435 PMCID: PMC10317045 DOI: 10.7759/cureus.39906] [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] [Accepted: 06/03/2023] [Indexed: 07/06/2023] Open
Abstract
Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome is a recently identified autoinflammatory condition with a correlating missense somatic mutation of the X chromosome. Here we present a unique case of a patient with VEXAS syndrome with coinciding ubiquitin-like modifier activating enzyme 1 (UBA1) and DNA (cytosine-5)-methyltransferase 3A (DNMT3A) mutations who developed cutaneous and systemic reactions to tocilizumab and azacitidine therapy, respectively.
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Affiliation(s)
- Jordan Estes
- Department of Medicine, University of Kansas Medical Center, Kansas City, USA
| | - Matthew Malus
- Department of Medicine, Division of Allergy, Clinical Immunology, and Rheumatology, University of Kansas Medical Center, Kansas City, USA
| | - Lorena Wilson
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Peter C Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, USA
| | - Mehrdad Maz
- Department of Medicine, Division of Allergy, Clinical Immunology, and Rheumatology, University of Kansas Medical Center, Kansas City, USA
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25
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Eckardt JN, Röllig C, Metzeler K, Heisig P, Stasik S, Georgi JA, Kroschinsky F, Stölzel F, Platzbecker U, Spiekermann K, Krug U, Braess J, Görlich D, Sauerland C, Woermann B, Herold T, Hiddemann W, Müller-Tidow C, Serve H, Baldus CD, Schäfer-Eckart K, Kaufmann M, Krause SW, Hänel M, Berdel WE, Schliemann C, Mayer J, Hanoun M, Schetelig J, Wendt K, Bornhäuser M, Thiede C, Middeke JM. Unsupervised meta-clustering identifies risk clusters in acute myeloid leukemia based on clinical and genetic profiles. COMMUNICATIONS MEDICINE 2023; 3:68. [PMID: 37198246 DOI: 10.1038/s43856-023-00298-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Increasingly large and complex biomedical data sets challenge conventional hypothesis-driven analytical approaches, however, data-driven unsupervised learning can detect inherent patterns in such data sets. METHODS While unsupervised analysis in the medical literature commonly only utilizes a single clustering algorithm for a given data set, we developed a large-scale model with 605 different combinations of target dimensionalities as well as transformation and clustering algorithms and subsequent meta-clustering of individual results. With this model, we investigated a large cohort of 1383 patients from 59 centers in Germany with newly diagnosed acute myeloid leukemia for whom 212 clinical, laboratory, cytogenetic and molecular genetic parameters were available. RESULTS Unsupervised learning identifies four distinct patient clusters, and statistical analysis shows significant differences in rate of complete remissions, event-free, relapse-free and overall survival between the four clusters. In comparison to the standard-of-care hypothesis-driven European Leukemia Net (ELN2017) risk stratification model, we find all three ELN2017 risk categories being represented in all four clusters in varying proportions indicating unappreciated complexity of AML biology in current established risk stratification models. Further, by using assigned clusters as labels we subsequently train a supervised model to validate cluster assignments on a large external multicenter cohort of 664 intensively treated AML patients. CONCLUSIONS Dynamic data-driven models are likely more suitable for risk stratification in the context of increasingly complex medical data than rigid hypothesis-driven models to allow for a more personalized treatment allocation and gain novel insights into disease biology.
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Affiliation(s)
- Jan-Niklas Eckardt
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany.
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany.
| | - Christoph Röllig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Klaus Metzeler
- Medical Clinic and Policlinic I Hematology and Cell Therapy, University Hospital, Leipzig, Germany
| | - Peter Heisig
- Department of Software and Multimedia Technology, Technical University Dresden, Dresden, Germany
| | - Sebastian Stasik
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Julia-Annabell Georgi
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Frank Kroschinsky
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic I Hematology and Cell Therapy, University Hospital, Leipzig, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Utz Krug
- Department of Medicine III, Hospital Leverkusen, Leverkusen, Germany
| | - Jan Braess
- Hospital Barmherzige Brueder Regensburg, Regensburg, Germany
| | - Dennis Görlich
- Institute for Biostatistics and Clinical Research, University Muenster, Muenster, Germany
| | - Cristina Sauerland
- Institute for Biostatistics and Clinical Research, University Muenster, Muenster, Germany
| | - Bernhard Woermann
- Department of Hematology, Oncology and Tumor Immunology, Charité, Berlin, Germany
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Wolfgang Hiddemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- German Consortium for Translational Cancer Research DKFZ, Heidelberg, Germany
| | - Hubert Serve
- Department of Medicine 2, Hematology and Oncology, Goethe University Frankfurt, Frankfurt, Germany
| | - Claudia D Baldus
- Department of Hematology and Oncology, University Hospital Schleswig Holstein, Kiel, Germany
| | | | - Martin Kaufmann
- Department of Hematology, Oncology and Palliative Care, Robert-Bosch Hospital, Stuttgart, Germany
| | - Stefan W Krause
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Mathias Hänel
- Department of Internal Medicine 3, Klinikum Chemnitz GmbH, Chemnitz, Germany
| | - Wolfgang E Berdel
- Department of Internal Medicine A, University Hospital Muenster, Muenster, Germany
| | - Christoph Schliemann
- Department of Internal Medicine A, University Hospital Muenster, Muenster, Germany
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology, Masaryk University Hospital, Brno, Czech Republic
| | - Maher Hanoun
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Karsten Wendt
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
- Department of Software and Multimedia Technology, Technical University Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- German Consortium for Translational Cancer Research DKFZ, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Christian Thiede
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Jan Moritz Middeke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
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26
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Tong X, Li M, Jin J, Li Y, Li L, Peng Y, Huang L, Xu B, Meng F, Mao X, Huang L, Huang W, Zhang D. Cladribine- and decitabine-containing conditioning regimen has a low post-transplant relapse rate in patients with relapsed or refractory acute myeloid leukemia and high-risk myelodysplastic syndrome. Int J Cancer 2023; 152:2123-2133. [PMID: 36594582 DOI: 10.1002/ijc.34419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/24/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023]
Abstract
To reduce the risk of relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT), there have been continuing efforts to optimize the conditioning regimens. Our study aimed to analyze the risk factors associated with the relapse of relapsed/refractory (R/R), high-risk acute myeloid leukemia (AML) and high-risk myelodysplastic syndrome (MDS) post-transplant and the efficacy of a new conditioning regimen involving decitabine and cladribine. Clinical data of 125 patients with R/R AML, high-risk AML and high-risk MDS who underwent allo-HSCT were collected. In addition, 35 patients with R/R AML, high-risk AML and high-risk MDS received treatment with a new conditioning regimen including decitabine and cladribine. Cox regression analysis was used to identify risk factors associated with OS, RFS and relapse. Among 125 patients who underwent allo-HSCT, CR before allo-HSCT and matched sibling donors were independent protective factors for OS. DNMT3A abnormality was an independent risk factor for both relapse and RFS. Among 35 patients who received a new conditioning regimen containing decitabine and cladribine, only six patients relapsed and 1-year cumulative incidence of relapse was 11.7%. Moreover, this new regimen showed efficient MRD clearance early after allo-HSCT. The combined decitabine- and cladribine-based conditioning regimen showed a low relapse rate and a high survival without an increased incidence of GVHD or adverse effects and thus has potential for use in allo-HSCT for R/R AML, high-risk AML and high-risk MDS.
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Affiliation(s)
- Xiwen Tong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengyuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jie Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yizhou Peng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lifang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bin Xu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fankai Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xia Mao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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27
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Xie X, Su M, Ren K, Ma X, Lv Z, Li Z, Mei Y, Ji P. Clonal hematopoiesis and bone marrow inflammation. Transl Res 2023; 255:159-170. [PMID: 36347490 DOI: 10.1016/j.trsl.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
Abstract
Clonal hematopoiesis (CH) occurs in hematopoietic stem cells with increased risks of progressing to hematologic malignancies. CH mutations are predominantly found in aged populations and correlate with an increased incidence of cardiovascular and other diseases. Increased lines of evidence demonstrate that CH mutations are closely related to the inflammatory bone marrow microenvironment. In this review, we summarize the recent advances in this topic starting from the discovery of CH and its mutations. We focus on the most commonly mutated and well-studied genes in CH and their contributions to the innate immune responses and inflammatory signaling, especially in the hematopoietic cells of bone marrow. We also aimed to discuss the interrelationship between inflammatory bone marrow microenvironment and CH mutations. Finally, we provide our perspectives on the challenges in the field and possible future directions to help understand the pathophysiology of CH.
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Affiliation(s)
- Xinshu Xie
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Meng Su
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Kehan Ren
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Xuezhen Ma
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhiyi Lv
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhaofeng Li
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Yang Mei
- School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China.
| | - Peng Ji
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.
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28
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Kodada D, Hyblova M, Krumpolec P, Janostiakova N, Barath P, Grendar M, Blandova G, Petrovic O, Janega P, Repiska V, Minarik G. The Potential of Liquid Biopsy in Detection of Endometrial Cancer Biomarkers: A Pilot Study. Int J Mol Sci 2023; 24:ijms24097811. [PMID: 37175518 PMCID: PMC10178554 DOI: 10.3390/ijms24097811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Endometrial cancer belongs to the most common gynecologic cancer types globally, with increasing incidence. There are numerous ways of classifying different cases. The most recent decade has brought advances in molecular classification, which show more accurate prognostic factors and the possibility of personalised adjuvant treatment. In addition, diagnostic approaches lag behind these advances, with methods causing patients discomfort while lacking the reproducibility of tissue sampling for biopsy. Minimally invasive liquid biopsies could therefore represent an alternative screening and diagnostic approach in patients with endometrial cancer. The method could potentially detect molecular changes in this cancer type and identify patients at early stages. In this pilot study, we tested such a detection method based on circulating tumour DNA isolated from the peripheral blood plasma of 21 Slovak endometrial cancer patients. We successfully detected oncomutations in the circulating DNA of every single patient, although the prognostic value of the detected mutations failed to offer certainty. Furthermore, we detected changes associated with clonal hematopoiesis, including DNMT3A mutations, which were present in the majority of circulating tumour DNA samples.
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Affiliation(s)
- Dominik Kodada
- Medirex Group Academy, 94905 Nitra, Slovakia
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | | | | | - Nikola Janostiakova
- Medirex Group Academy, 94905 Nitra, Slovakia
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | | | - Marian Grendar
- Medirex Group Academy, 94905 Nitra, Slovakia
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Gabriela Blandova
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | | | - Pavol Janega
- Medirex Group Academy, 94905 Nitra, Slovakia
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Vanda Repiska
- Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia
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29
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Tian H, Liu C, Yu J, Han J, Du J, Liang S, Wang W, Liu Q, Lian R, Zhu T, Wu S, Tao T, Ye Y, Zhao J, Yang Y, Zhu X, Cai J, Wu J, Li M. PHF14 enhances DNA methylation of SMAD7 gene to promote TGF-β-driven lung adenocarcinoma metastasis. Cell Discov 2023; 9:41. [PMID: 37072414 PMCID: PMC10113255 DOI: 10.1038/s41421-023-00528-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/07/2023] [Indexed: 04/20/2023] Open
Abstract
Aberrant activation of TGF-β signaling plays a pivotal role in cancer metastasis and progression. However, molecular mechanisms underlying the dysregulation of TGF-β pathway remain to be understood. Here, we found that SMAD7, a direct downstream transcriptional target and also a key antagonist of TGF-β signaling, is transcriptionally suppressed in lung adenocarcinoma (LAD) due to DNA hypermethylation. We further identified that PHF14 binds DNMT3B and serves as a DNA CpG motif reader, recruiting DNMT3B to the SMAD7 gene locus, resulting in DNA methylation and transcriptional suppression of SMAD7. Our in vitro and in vivo experiments showed that PHF14 promotes metastasis through binding DNMT3B to suppress SMAD7 expression. Moreover, our data revealed that PHF14 expression correlates with lowered SMAD7 level and shorter survival of LAD patients, and importantly that SMAD7 methylation level of circulating tumor DNA (ctDNA) can potentially be used for prognosis prediction. Together, our present study illustrates a new epigenetic mechanism, mediated by PHF14 and DNMT3B, in the regulation of SMAD7 transcription and TGF-β-driven LAD metastasis, and suggests potential opportunities for LAD prognosis.
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Affiliation(s)
- Han Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Cancer Institute, Southern Medical University, Guangzhou, Guangdong, China
| | - Chenying Liu
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jianchen Yu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- School of Chemistry, South China Normal University, Guangzhou, Guangdong, China
| | - Jian Han
- Cancer Institute, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianan Du
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shujun Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenting Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qin Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Rong Lian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Zhu
- Department of Laboratory Medicine, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shanshan Wu
- Department of Biology, School of Basic Medical Science, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Tianyu Tao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yaokai Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingjing Zhao
- Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xun Zhu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junchao Cai
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jueheng Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mengfeng Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Cancer Institute, Southern Medical University, Guangzhou, Guangdong, China.
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30
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Ramabadran R, Wang JH, Reyes JM, Guzman AG, Gupta S, Rosas C, Brunetti L, Gundry MC, Tovy A, Long H, Gu T, Cullen SM, Tyagi S, Rux D, Kim JJ, Kornblau SM, Kyba M, Stossi F, Rau RE, Takahashi K, Westbrook TF, Goodell MA. DNMT3A-coordinated splicing governs the stem state switch towards differentiation in embryonic and haematopoietic stem cells. Nat Cell Biol 2023; 25:528-539. [PMID: 37024683 PMCID: PMC10337578 DOI: 10.1038/s41556-023-01109-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/17/2023] [Indexed: 04/08/2023]
Abstract
Upon stimulation by extrinsic stimuli, stem cells initiate a programme that enables differentiation or self-renewal. Disruption of the stem state exit has catastrophic consequences for embryogenesis and can lead to cancer. While some elements of this stem state switch are known, major regulatory mechanisms remain unclear. Here we show that this switch involves a global increase in splicing efficiency coordinated by DNA methyltransferase 3α (DNMT3A), an enzyme typically involved in DNA methylation. Proper activation of murine and human embryonic and haematopoietic stem cells depends on messenger RNA processing, influenced by DNMT3A in response to stimuli. DNMT3A coordinates splicing through recruitment of the core spliceosome protein SF3B1 to RNA polymerase and mRNA. Importantly, the DNA methylation function of DNMT3A is not required and loss of DNMT3A leads to impaired splicing during stem cell turnover. Finally, we identify the spliceosome as a potential therapeutic target in DNMT3A-mutated leukaemias. Together, our results reveal a modality through which DNMT3A and the spliceosome govern exit from the stem state towards differentiation.
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Affiliation(s)
- Raghav Ramabadran
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Jarey H Wang
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Anna G Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sinjini Gupta
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael C Gundry
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hali Long
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Tianpeng Gu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sean M Cullen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Siddhartha Tyagi
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Danielle Rux
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Jean J Kim
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kyba
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Rachel E Rau
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas F Westbrook
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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31
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Ghaoui R, Ha TT, Kerkhof J, McConkey H, Gao S, Babic M, King R, Ravenscroft G, Kocyzek B, Otto S, Laing NG, Scott H, Sadikovic B, Kassahn KS. Expanding the phenotype of DNMT3A as a cause a congenital myopathy with rhabdomyolysis. Neuromuscul Disord 2023; 33:484-489. [PMID: 37209493 DOI: 10.1016/j.nmd.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/17/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023]
Abstract
Pathogenic variants in DNMT3A are most commonly associated with Tatton-Brown-Rahman Syndrome (TBRS), but includes other phenotypes such as Heyn-Sproul-Jackson syndrome and acute myeloid leukemia (AML). We describe a patient presenting to the neuromuscular clinic with a de novo missense variant in DNMT3A where the striking clinical feature is that of a congenital myopathy with associated episodes of rhabdomyolysis, severe myalgias and chest pain along with phenotypic features associated with TBRS. Muscle biopsy showed minor myopathic features and cardiac investigations revealed mildly impaired bi-ventricular systolic function. We confirmed the DNA methylation profile matched haplo-insufficient TBRS cases, consistent with a loss of methyltransferase activity. Our report emphasizes the phenotypic overlap of patients with syndromic disorders presenting to neuromuscular clinics and limitations of gene panels in establishing a molecular diagnosis.
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32
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Chianese U, Papulino C, Megchelenbrink W, Tambaro FP, Ciardiello F, Benedetti R, Altucci L. Epigenomic machinery regulating pediatric AML: clonal expansion mechanisms, therapies, and future perspectives. Semin Cancer Biol 2023; 92:84-101. [PMID: 37003397 DOI: 10.1016/j.semcancer.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with a genetic, epigenetic, and transcriptional etiology mainly presenting somatic and germline abnormalities. AML incidence rises with age but can also occur during childhood. Pediatric AML (pAML) accounts for 15-20% of all pediatric leukemias and differs considerably from adult AML. Next-generation sequencing technologies have enabled the research community to "paint" the genomic and epigenomic landscape in order to identify pathology-associated mutations and other prognostic biomarkers in pAML. Although current treatments have improved the prognosis for pAML, chemoresistance, recurrence, and refractory disease remain major challenges. In particular, pAML relapse is commonly caused by leukemia stem cells that resist therapy. Marked patient-to-patient heterogeneity is likely the primary reason why the same treatment is successful for some patients but, at best, only partially effective for others. Accumulating evidence indicates that patient-specific clonal composition impinges significantly on cellular processes, such as gene regulation and metabolism. Although our understanding of metabolism in pAML is still in its infancy, greater insights into these processes and their (epigenetic) modulation may pave the way toward novel treatment options. In this review, we summarize current knowledge on the function of genetic and epigenetic (mis)regulation in pAML, including metabolic features observed in the disease. Specifically, we describe how (epi)genetic machinery can affect chromatin status during hematopoiesis, leading to an altered metabolic profile, and focus on the potential value of targeting epigenetic abnormalities in precision and combination therapy for pAML. We also discuss the possibility of using alternative epidrug-based therapeutic approaches that are already in clinical practice, either alone as adjuvant treatments and/or in combination with other drugs.
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Affiliation(s)
- Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Chiara Papulino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Wout Megchelenbrink
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Princess Máxima Center, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands.
| | - Francesco Paolo Tambaro
- Bone Marrow Transplant Unit, Pediatric Oncology Department AORN Santobono Pausilipon, 80129, Naples Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy; IEOS, Institute for Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131 Naples, Italy.
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33
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Chen Y, Zhu Y, Kramer A, Fang Y, Wilson M, Li YR, Yang L. Genetic engineering strategies to enhance antitumor reactivity and reduce alloreactivity for allogeneic cell-based cancer therapy. Front Med (Lausanne) 2023; 10:1135468. [PMID: 37064017 PMCID: PMC10090359 DOI: 10.3389/fmed.2023.1135468] [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: 12/31/2022] [Accepted: 03/09/2023] [Indexed: 03/31/2023] Open
Abstract
The realm of cell-based immunotherapy holds untapped potential for the development of next-generation cancer treatment through genetic engineering of chimeric antigen receptor (CAR)-engineered T (CAR-T) cell therapies for targeted eradication of cancerous malignancies. Such allogeneic "off-the-shelf" cell products can be advantageously manufactured in large quantities, stored for extended periods, and easily distributed to treat an exponential number of cancer patients. At current, patient risk of graft-versus-host disease (GvHD) and host-versus-graft (HvG) allorejection severely restrict the development of allogeneic CAR-T cell products. To address these limitations, a variety of genetic engineering strategies have been implemented to enhance antitumor efficacy, reduce GvHD and HvG onset, and improve the overall safety profile of T-cell based immunotherapies. In this review, we summarize these genetic engineering strategies and discuss the challenges and prospects these approaches provide to expedite progression of translational and clinical studies for adoption of a universal cell-based cancer immunotherapy.
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Affiliation(s)
- Yuning Chen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yichen Zhu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Adam Kramer
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ying Fang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matthew Wilson
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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34
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Li W, Liu S, Wang C, Cui L, Zhao X, Liu W, Zhang R, Li Z. DNMT3A low-expression is correlated to poor prognosis in childhood B-ALL and confers resistance to daunorubicin on leukemic cells. BMC Cancer 2023; 23:255. [PMID: 36934225 PMCID: PMC10024838 DOI: 10.1186/s12885-023-10724-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Little is known about DNMT3A expression and its prognostic significance in childhood B cell acute lymphoblastic leukemia (B-ALL). METHODS We determined DNMT3A mRNA expression in 102 children with B-ALL. Correlations with relapse-free survival (RFS) and common clinical characteristics were analyzed. DNMT3A was stably knocked out by CRISPR/Cas9 gene editing technology in Reh and 697 B-ALL cell lines. Cell proliferation activity after treated with daunorubicin (DNR) was determined by CCK8 assay in DNMT3A KO Reh and 697 cell lines. RESULTS DNMT3A expression in B-ALL patients who were in continuous complete remission (CCR) was higher than in those who got relapse (P = 0.0111). Receiver operating characteristic curve showed prognostic significance of DNMT3A expression (P = 0.003). Low expression of DNMT3A (≤ 0.197) was significantly correlated with poor RFS (P < 0.001) in children with B-ALL. Knock-out of DNMT3A in Reh and 697 cell lines significantly increased IC50 of DNR (P = 0.0201 and 0.0022 respectively), indicating elevated resistance to DNR. CONCLUSION Low expression of DNMT3A associates with poor prognosis in children with B-ALL. Knock-out of DNMT3A confers resistance to DNR on leukemic cells.
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Affiliation(s)
- Weijing Li
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Shugang Liu
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Chanjuan Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lei Cui
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Xiaoxi Zhao
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Wei Liu
- Department of Hematology Oncology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China.
| | - Ruidong Zhang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China.
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China.
- Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
| | - Zhigang Li
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China.
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China.
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35
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McCallion O, Bilici M, Hester J, Issa F. Regulatory T-cell therapy approaches. Clin Exp Immunol 2023; 211:96-107. [PMID: 35960852 PMCID: PMC10019137 DOI: 10.1093/cei/uxac078] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Regulatory T cells (Tregs) have enormous therapeutic potential to treat a variety of immunopathologies characterized by aberrant immune activation. Adoptive transfer of ex vivo expanded autologous Tregs continues to progress through mid- to late-phase clinical trials in several disease spaces and has generated promising preliminary safety and efficacy signals to date. However, the practicalities of this strategy outside of the clinical trial setting remain challenging. Here, we review the current landscape of regulatory T-cell therapy, considering emergent approaches and technologies presenting novel ways to engage Tregs, and reflect on the progress necessary to deliver their therapeutic potential to patients.
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Affiliation(s)
- Oliver McCallion
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Merve Bilici
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Joanna Hester
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- Correspondence. Fadi Issa, Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK.
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36
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Jain S, Goswami A, Lone MR, Ramteke P, Gogia A, Aggarwal M, Viswanathan GK, Kakkar D, Mandal T, Sharma A, Sahoo R, Baldia A, Sharma MC, Bakhshi S, Pramanik R, Dhawan R, Kumar L, Mallick S. Follicular Helper T-Cell-derived Nodal Lymphomas: Study of Histomorphologic, Immunophenotypic, Clinical, and RHOA G17V Mutational Profile. Appl Immunohistochem Mol Morphol 2023; 31:172-180. [PMID: 36806188 DOI: 10.1097/pai.0000000000001105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/03/2023] [Indexed: 02/22/2023]
Abstract
The study was designed to review the demographic, clinical, and pathologic characteristics of follicular helper T cells (TFH)-derived nodal PTCL in India including angioimmunoblastic T-cell lymphoma (AITL), peripheral T-cell lymphoma (PTCL) with follicular helper T cell phenotype (P-TFH), and follicular T-cell lymphoma with additional immunohistochemistry (IHC) and RHOAG17V mutational analysis, as well as their impact on survival. This retrospective study included 88 cases of PTCL that were reclassified using IHC for TFH markers (PD1, ICOS, BCL6, and CD10) and dendritic-meshwork markers (CD21, CD23). Cases of TFH cell origin were evaluated for RHOAG17V mutation using Sanger sequencing and amplification-refractory mutation system-polymerase chain reaction (PCR) (validated using cloning and quantitative PCR) with detailed clinicopathologic correlation. Extensive re-evaluation with added IHC panel resulted in a total of 19 cases being reclassified, and the final subtypes were AITL (37 cases, 42%), PTCL-not otherwise specified (44, 50%), P-TFH (6, 7%), and follicular T-cell lymphoma (1, 1%). The presence of at least 2 TFH markers (>20% immunopositivity) determined the TFH origin. AITL patients tended to be male and showed increased presence of B-symptoms and hepatosplenomegaly. Histomorphology revealed that 92% of AITL cases had pattern 3 involvement. Sanger sequencing with conventional PCR did not yield any mutation, while RHOAG17V was detected by amplification-refractory mutation system-PCR in AITL (51%, P =0.027) and P-TFH (17%), which was validated with cloning followed by sequencing. Cases of RHOAG17V-mutant AITL had a worse Eastern Cooperative Oncology Group performance status initially but fared better in terms of overall outcome ( P =0.029). Although not specific for AITL, RHOAG17V mutation shows an association with diagnosis and requires sensitive methods for detection due to low-tumor burden. The mutant status of AITL could have prognostic implications and translational relevance.
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Affiliation(s)
| | | | | | | | | | - Mukul Aggarwal
- Haematology, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | | | | | | | | | | | | | | | | | | | - Rishi Dhawan
- Haematology, All India Institute of Medical Sciences, New Delhi, Delhi, India
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Eckardt JN, Röllig C, Metzeler K, Kramer M, Stasik S, Georgi JA, Heisig P, Spiekermann K, Krug U, Braess J, Görlich D, Sauerland CM, Woermann B, Herold T, Berdel WE, Hiddemann W, Kroschinsky F, Schetelig J, Platzbecker U, Müller-Tidow C, Sauer T, Serve H, Baldus C, Schäfer-Eckart K, Kaufmann M, Krause S, Hänel M, Schliemann C, Hanoun M, Thiede C, Bornhäuser M, Wendt K, Middeke JM. Prediction of complete remission and survival in acute myeloid leukemia using supervised machine learning. Haematologica 2023; 108:690-704. [PMID: 35708137 PMCID: PMC9973482 DOI: 10.3324/haematol.2021.280027] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 11/09/2022] Open
Abstract
Achievement of complete remission signifies a crucial milestone in the therapy of acute myeloid leukemia (AML) while refractory disease is associated with dismal outcomes. Hence, accurately identifying patients at risk is essential to tailor treatment concepts individually to disease biology. We used nine machine learning (ML) models to predict complete remission and 2-year overall survival in a large multicenter cohort of 1,383 AML patients who received intensive induction therapy. Clinical, laboratory, cytogenetic and molecular genetic data were incorporated and our results were validated on an external multicenter cohort. Our ML models autonomously selected predictive features including established markers of favorable or adverse risk as well as identifying markers of so-far controversial relevance. De novo AML, extramedullary AML, double-mutated CEBPA, mutations of CEBPA-bZIP, NPM1, FLT3-ITD, ASXL1, RUNX1, SF3B1, IKZF1, TP53, and U2AF1, t(8;21), inv(16)/t(16;16), del(5)/del(5q), del(17)/del(17p), normal or complex karyotypes, age and hemoglobin concentration at initial diagnosis were statistically significant markers predictive of complete remission, while t(8;21), del(5)/del(5q), inv(16)/t(16;16), del(17)/del(17p), double-mutated CEBPA, CEBPA-bZIP, NPM1, FLT3-ITD, DNMT3A, SF3B1, U2AF1, and TP53 mutations, age, white blood cell count, peripheral blast count, serum lactate dehydrogenase level and hemoglobin concentration at initial diagnosis as well as extramedullary manifestations were predictive for 2-year overall survival. For prediction of complete remission and 2-year overall survival areas under the receiver operating characteristic curves ranged between 0.77-0.86 and between 0.63-0.74, respectively in our test set, and between 0.71-0.80 and 0.65-0.75 in the external validation cohort. We demonstrated the feasibility of ML for risk stratification in AML as a model disease for hematologic neoplasms, using a scalable and reusable ML framework. Our study illustrates the clinical applicability of ML as a decision support system in hematology.
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Affiliation(s)
- Jan-Niklas Eckardt
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden.
| | - Christoph Röllig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden
| | - Klaus Metzeler
- Medical Clinic and Policlinic I Hematology and Cell Therapy. University Hospital, Leipzig
| | - Michael Kramer
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden
| | - Sebastian Stasik
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden
| | | | - Peter Heisig
- Institute of Software and Multimedia Technology, Technical University Dresden, Dresden
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich
| | - Utz Krug
- Medical Clinic III, Hospital Leverkusen, Leverkusen
| | - Jan Braess
- Hospital Barmherzige Brueder Regensburg, Regensburg
| | - Dennis Görlich
- Institute for Biometrics and Clinical Research, University Muenster, Muenster
| | | | - Bernhard Woermann
- Department of Hematology, Oncology and Tumor Immunology, Charité, Berlin
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich
| | - Wolfgang E Berdel
- Department of Internal Medicine A, University Hospital Muenster, Muenster
| | - Wolfgang Hiddemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich
| | - Frank Kroschinsky
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden
| | - Uwe Platzbecker
- Medical Clinic and Policlinic I Hematology and Cell Therapy. University Hospital, Leipzig
| | - Carsten Müller-Tidow
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany; German Consortium for Translational Cancer Research DKFZ, Heidelberg
| | - Tim Sauer
- Department of Medicine V, University Hospital Heidelberg, Heidelberg
| | - Hubert Serve
- Department of Medicine 2, Hematology and Oncology, Goethe University Frankfurt, Frankfurt
| | - Claudia Baldus
- Department of Hematology and Oncology, University Hospital Schleswig Holstein, Kiel
| | - Kerstin Schäfer-Eckart
- Department of Internal Medicine 5, Paracelsus Medical Private University Nuremberg, Nuremberg
| | - Martin Kaufmann
- Department of Hematology, Oncology and Palliative Care, Robert-Bosch Hospital, Stuttgart
| | - Stefan Krause
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen
| | - Mathias Hänel
- Department of Internal Medicine 3, Klinikum Chemnitz GmbH, Chemnitz, Germany; Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen
| | | | - Maher Hanoun
- Department of Internal Medicine 3, Klinikum Chemnitz GmbH, Chemnitz, Germany; Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen
| | - Christian Thiede
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany; German Consortium for Translational Cancer Research DKFZ, Heidelberg
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany; German Consortium for Translational Cancer Research DKFZ, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Dresden
| | - Karsten Wendt
- Medical Clinic and Policlinic I Hematology and Cell Therapy. University Hospital, Leipzig
| | - Jan Moritz Middeke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden
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NPM 1 Mutations in AML-The Landscape in 2023. Cancers (Basel) 2023; 15:cancers15041177. [PMID: 36831522 PMCID: PMC9954410 DOI: 10.3390/cancers15041177] [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: 01/16/2023] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Acute myeloid leukemia (AML) represents 80% of acute leukemia in adults and is characterized by clonal expansion of hematopoietic stem cells secondary to genomic mutations, rendering a selective growth advantage to the mutant clones. NPM1mut is found in around 30% of AML and clinically presents with leukocytosis, high blast percentage and extramedullary involvement. Considered as a "gate-keeper" mutation, NPM1mut appears to be a "first hit" in the process of leukemogenesis and development of overt leukemia. Commonly associated with other mutations (e.g., FLT 3, DNMT3A, TET2, SF3B1), NPM1 mutation in AML has an important role in diagnosis, prognosis, treatment and post-treatment monitoring. Several novel therapies targeting NPM1 are being developed in various clinical phases with demonstration of efficacy. In this review, we summarize the pathophysiology of the NPM1 gene mutation in AML, clinical implications and the novel targeted therapies to date.
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Oura K, Morishita A, Hamaya S, Fujita K, Masaki T. The Roles of Epigenetic Regulation and the Tumor Microenvironment in the Mechanism of Resistance to Systemic Therapy in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24032805. [PMID: 36769116 PMCID: PMC9917861 DOI: 10.3390/ijms24032805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Primary liver cancer is the sixth most common cancer and the third most common cause of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) is a major histologic type with a poor prognosis owing to the difficulty in early detection, the chemotherapy resistance, and the high recurrence rate of the disease. Despite recent advancements in HCC prevention and diagnosis, over 50% of patients are diagnosed at Barcelona Clinic Liver Cancer Stage B or C. Systemic therapies are recommended for unresectable HCC (uHCC) with major vascular invasion, extrahepatic metastases, or intrahepatic lesions that have a limited response to transcatheter arterial chemoembolization, but the treatment outcome tends to be unsatisfactory due to acquired drug resistance. Elucidation of the mechanisms underlying the resistance to systemic therapies and the appropriate response strategies to solve this issue will contribute to improved outcomes in the multidisciplinary treatment of uHCC. In this review, we summarize recent findings on the mechanisms of resistance to drugs such as sorafenib, regorafenib, and lenvatinib in molecularly targeted therapy, with a focus on epigenetic regulation and the tumor microenvironment and outline the approaches to improve the therapeutic outcome for patients with advanced HCC.
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Stelmach P, Trumpp A. Leukemic stem cells and therapy resistance in acute myeloid leukemia. Haematologica 2023; 108:353-366. [PMID: 36722405 PMCID: PMC9890038 DOI: 10.3324/haematol.2022.280800] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Indexed: 02/02/2023] Open
Abstract
A major obstacle in the treatment of acute myeloid leukemia (AML) is refractory disease or relapse after achieving remission. The latter arises from a few therapy-resistant cells within minimal residual disease (MRD). Resistant cells with long-term self-renewal capacity that drive clonal outgrowth are referred to as leukemic stem cells (LSC). The cancer stem cell concept considers LSC as relapse-initiating cells residing at the top of each genetically defined AML subclone forming epigenetically controlled downstream hierarchies. LSC display significant phenotypic and epigenetic plasticity, particularly in response to therapy stress, which results in various mechanisms mediating treatment resistance. Given the inherent chemotherapy resistance of LSC, targeted strategies must be incorporated into first-line regimens to prevent LSC-mediated AML relapse. The combination of venetoclax and azacitidine is a promising current strategy for the treatment of AML LSC. Nevertheless, the selection of patients who would benefit either from standard chemotherapy or venetoclax + azacitidine treatment in first-line therapy has yet to be established and the mechanisms of resistance still need to be discovered and overcome. Clinical trials are currently underway that investigate LSC susceptibility to first-line therapies. The era of single-cell multi-omics has begun to uncover the complex clonal and cellular architectures and associated biological networks. This should lead to a better understanding of the highly heterogeneous AML at the inter- and intra-patient level and identify resistance mechanisms by longitudinal analysis of patients' samples. This review discusses LSC biology and associated resistance mechanisms, potential therapeutic LSC vulnerabilities and current clinical trial activities.
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Affiliation(s)
- Patrick Stelmach
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH),Department of Medicine V, Heidelberg University Hospital
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH); Faculty of Biosciences, Heidelberg University; German Cancer Consortium (DKTK), Heidelberg.
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Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation. Int J Mol Sci 2023; 24:ijms24021727. [PMID: 36675240 PMCID: PMC9863985 DOI: 10.3390/ijms24021727] [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: 12/24/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The mammalian DNA methylation landscape is established and maintained by the combined activities of the two key epigenetic modifiers, DNA methyltransferases (DNMT) and Ten-eleven-translocation (TET) enzymes. Once DNMTs produce 5-methylcytosine (5mC), TET proteins fine-tune the DNA methylation status by consecutively oxidizing 5mC to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives. The 5mC and oxidized methylcytosines are essential for the maintenance of cellular identity and function during differentiation. Cytosine modifications with DNMT and TET enzymes exert pleiotropic effects on various aspects of hematopoiesis, including self-renewal of hematopoietic stem/progenitor cells (HSPCs), lineage determination, differentiation, and function. Under pathological conditions, these enzymes are frequently dysregulated, leading to loss of function. In particular, the loss of DNMT3A and TET2 function is conspicuous in diverse hematological disorders, including myeloid and lymphoid malignancies, and causally related to clonal hematopoiesis and malignant transformation. Here, we update recent advances in understanding how the maintenance of DNA methylation homeostasis by DNMT and TET proteins influences normal hematopoiesis and malignant transformation, highlighting the potential impact of DNMT3A and TET2 dysregulation on clonal dominance and evolution of pre-leukemic stem cells to full-blown malignancies. Clarification of the normal and pathological functions of DNA-modifying epigenetic regulators will be crucial to future innovations in epigenetic therapies for treating hematological disorders.
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Makkar H, Majhi RK, Goel H, Gupta AK, Chopra A, Tanwar P, Seth R. Acute myeloid leukemia: novel mutations and their clinical implications. AMERICAN JOURNAL OF BLOOD RESEARCH 2023; 13:12-27. [PMID: 36937458 PMCID: PMC10017594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/09/2023] [Indexed: 03/21/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogenous and challenging hematological malignancy with suboptimal outcomes. The implications of advanced technologies in the genetic characterization of AML have enhanced the understanding of individualized patient risk, which has also led to the development of new therapeutic strategies. A comprehensive study of novel mutations is essential to moderate the complicacies in patient management and achieve optimal outcomes in AML. In this review, we summarized the clinical relevance of important novel mutations, including TET2, ETV6, SATB1, EZH2, PTPN11, and U2AF1, which impact the prognosis of AML. TET2 mutation can lead to DNA hypermethylation, and gene fusion, and mutation in ETV6 disrupts hematopoietic transcription machinery, SATB1 downregulation aggravates the disease, and EZH2 mutation confers resistance to chemotherapy. PTPN11 mutation influences the RAS-MAPK signaling pathway, and U2AF1 alters the splicing of downstream mRNA. The systemic influence of these mutations has adverse consequences. Therefore, extensive research on novel mutations and their mechanism of action in the pathogenesis of AML is vital. This study lays out the perspective of expanding the apprehension about AML and novel drug targets. The combination of advanced genetic techniques, risk stratification, ongoing improvements, and innovations in treatment strategy will undoubtedly lead to improved survival outcomes in AML.
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Affiliation(s)
- Harshita Makkar
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical SciencesNew Delhi 110029, India
| | - Ravi Kumar Majhi
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical SciencesNew Delhi 110029, India
| | - Harsh Goel
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical SciencesNew Delhi 110029, India
| | - Aditya Kumar Gupta
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical SciencesNew Delhi 110029, India
| | - Anita Chopra
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical SciencesNew Delhi 110029, India
| | - Pranay Tanwar
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical SciencesNew Delhi 110029, India
| | - Rachna Seth
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical SciencesNew Delhi 110029, India
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Natarajan P. Genomic Aging, Clonal Hematopoiesis, and Cardiovascular Disease. Arterioscler Thromb Vasc Biol 2023; 43:3-14. [PMID: 36353993 PMCID: PMC9780188 DOI: 10.1161/atvbaha.122.318181] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Chronologic age is the dominant risk factor for coronary artery disease but the features of aging promoting coronary artery disease are poorly understood. Advances in human genetics and population-based genetic profiling of blood cells have uncovered the surprising role of age-related subclinical leukemogenic mutations in blood cells, termed "clonal hematopoiesis of indeterminate potential," in coronary artery disease. Such mutations typically occur in DNMT3A, TET2, ASXL1, and JAK2. Murine and human studies prioritize the role of key inflammatory pathways linking clonal hematopoiesis with coronary artery disease. Increasingly larger, longitudinal, multiomics analyses are enabling further dissection into mechanistic insights. These observations expand the genetic architecture of coronary artery disease, now linking hallmark features of hematologic neoplasia with a much more common cardiovascular condition. Implications of these studies include the prospect of novel precision medicine paradigms for coronary artery disease.
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Affiliation(s)
- Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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44
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Aryal S, Zhang Y, Wren S, Li C, Lu R. Molecular regulators of HOXA9 in acute myeloid leukemia. FEBS J 2023; 290:321-339. [PMID: 34743404 DOI: 10.1111/febs.16268] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/30/2021] [Accepted: 11/05/2021] [Indexed: 02/05/2023]
Abstract
Dysregulation of the oncogenic transcription factor HOXA9 is a prominent feature for most aggressive acute myeloid leukemia cases and a strong indicator of poor prognosis in patients. Leukemia subtypes with hallmark overexpression of HOXA9 include those carrying MLL gene rearrangements, NPM1c mutations, and other genetic alternations. A growing body of evidence indicates that HOXA9 dysregulation is both sufficient and necessary for leukemic transformation. The HOXA9 mRNA and protein regulation includes multilayered controls by transcription factors (such as CDX2/4 and USF2/1), epigenetic factors (such as MLL-menin-LEDGF, DOT1L, ENL, HBO1, NPM1c-XPO1, and polycomb proteins), microRNAs (such as miR-126 and miR-196b), long noncoding RNAs (such as HOTTIP), three-dimensional chromatin interactions, and post-translational protein modifications. Recently, insights into the dynamic regulation of HOXA9 have led to an advanced understanding of the HOXA9 regulome and provided new cancer therapeutic opportunities, including developing inhibitors targeting DOT1L, menin, and ENL proteins. This review summarizes recent advances in understanding the molecular mechanisms controlling HOXA9 regulation and the pharmacological approaches that target HOXA9 regulators to treat HOXA9-driven acute myeloid leukemia.
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Affiliation(s)
- Sajesan Aryal
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
| | - Yang Zhang
- Department of Tumor Cell Biology & Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Wren
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
| | - Chunliang Li
- Department of Tumor Cell Biology & Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rui Lu
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
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Wang Y, Quesada AE, Zuo Z, Medeiros LJ, Yin CC, Li S, Xu J, Borthakur G, Li Y, Yang C, Abaza Y, Gao J, Lu X, You MJ, Zhang Y, Lin P. The Impact of Mutation of Myelodysplasia-Related Genes in De Novo Acute Myeloid Leukemia Carrying NPM1 Mutation. Cancers (Basel) 2022; 15:cancers15010198. [PMID: 36612194 PMCID: PMC9818485 DOI: 10.3390/cancers15010198] [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: 10/04/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Background: The impact of gene mutations typically associated with myelodysplastic syndrome (MDS) in acute myeloid leukemia (AML) with NPM1 mutation is unclear. Methods: Using a cohort of 107 patients with NPM1-mutated AML treated with risk-adapted therapy, we compared survival outcomes of patients without MDS-related gene mutations (group A) with those carrying concurrent FLT3-ITD (group B) or with MDS-related gene mutations (group C). Minimal measurable disease (MMD) status assessed by multiparameter flow cytometry (MFC), polymerase chain reaction (PCR), and/or next-generation sequencing (NGS) were reviewed. Results: Among the 69 patients treated intensively, group C showed significantly inferior progression-free survival (PFS, p < 0.0001) but not overall survival (OS, p = 0.055) compared to group A. Though groups A and C had a similar MMD rate, group C patients had a higher relapse rate (p = 0.016). Relapse correlated with MMD status at the end of cycle 2 induction (p = 0.023). Survival of group C patients was similar to that of group B. Conclusion: MDS-related gene mutations are associated with an inferior survival in NPM1-mutated AML.
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Affiliation(s)
- Yi Wang
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andres E. Quesada
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhuang Zuo
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shaoying Li
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Xu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yisheng Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Yang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yasmin Abaza
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Juehua Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - M. James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yizhuo Zhang
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Correspondence: (Y.Z.); (P.L.); Tel.: +86-18622221239 (Y.Z.); +1-(713)-794-1746 (P.L.); Fax: +86-022-23340123 (Y.Z.); +1-(713)-563-2977 (P.L.)
| | - Pei Lin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (Y.Z.); (P.L.); Tel.: +86-18622221239 (Y.Z.); +1-(713)-794-1746 (P.L.); Fax: +86-022-23340123 (Y.Z.); +1-(713)-563-2977 (P.L.)
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The R736H cancer mutation in DNMT3A modulates the properties of the FF-subunit interface. Biochimie 2022; 208:66-74. [PMID: 36528185 DOI: 10.1016/j.biochi.2022.12.005] [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: 09/18/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The DNMT3A DNA methyltransferase is an important epigenetic enzyme that is frequently mutated in cancers, particularly in AML. The heterozygous R736H mutation in the FF-interface of the tetrameric enzyme is the second most frequently observed DNMT3A cancer mutation, but its pathogenic mechanism is unclear. We show here that R736H leads to a moderate reduction in catalytic activity of 20-40% depending on the substrate, but no changes in CpG specificity, flanking sequence preferences and subnuclear localization. Strikingly, R736H showed a very strong stimulation by DNMT3L and the R736H/DNMT3L complex was 3-fold more active than WT/DNMT3L. Similarly, formation of mixed R736H/DNMT3A WT FF-interfaces led to an increased activity. R736H/DNMT3L and mixed R736H/DNMT3A WT FF-interfaces were less stable than interfaces not involving R736H, suggesting that an increased flexibility of the mixed interfaces stimulates catalytic activity. Our data suggest that aberrant activity of DNMT3A R736H may lead to DNA hypermethylation in cancer cells which could cause changes in gene expression.
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DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation. Nat Struct Mol Biol 2022; 29:1252-1265. [PMID: 36510023 DOI: 10.1038/s41594-022-00885-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/02/2022] [Indexed: 12/14/2022]
Abstract
In mammalian embryos, DNA methylation is initialized to maximum levels in the epiblast by the de novo DNA methyltransferases DNMT3A and DNMT3B before gastrulation diversifies it across regulatory regions. Here we show that DNMT3A and DNMT3B are differentially regulated during endoderm and mesoderm bifurcation and study the implications in vivo and in meso-endoderm embryoid bodies. Loss of both Dnmt3a and Dnmt3b impairs exit from the epiblast state. More subtly, independent loss of Dnmt3a or Dnmt3b leads to small biases in mesoderm-endoderm bifurcation and transcriptional deregulation. Epigenetically, DNMT3A and DNMT3B drive distinct methylation kinetics in the epiblast, as can be predicted from their strand-specific sequence preferences. The enzymes compensate for each other in the epiblast, but can later facilitate lineage-specific methylation kinetics as their expression diverges. Single-cell analysis shows that differential activity of DNMT3A and DNMT3B combines with replication-linked methylation turnover to increase epigenetic plasticity in gastrulation. Together, these findings outline a dynamic model for the use of DNMT3A and DNMT3B sequence specificity during gastrulation.
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Li X, Feng C, Peng S. Epigenetics alternation in lung fibrosis and lung cancer. Front Cell Dev Biol 2022; 10:1060201. [PMID: 36420141 PMCID: PMC9676258 DOI: 10.3389/fcell.2022.1060201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/20/2022] [Indexed: 09/10/2023] Open
Abstract
Respiratory disease including interstitial lung diseases (ILDs) and lung cancer is a group of devastating diseases that linked with increased morbidity and healthcare burden. However, respiratory diseases cannot be fully explained by the alternation of genetic information. Genetic studies described that epigenetic mechanisms also participate to transmit genetic information. Recently, many studies demonstrated the role of altered epigenetic modification in the pathogenesis of lung cancer and pulmonary fibrosis. Due to lacking effective medication, the underlying pathophysiological processes and causal relationships of lung diseases with epigenetic mechanisms still need to be better understood. Our present review provided a systematic revision of current knowledge concerning diverse epigenetic aberrations in major lung diseases, with special emphasis on DNA methylation, histone modifications, lncRNAs profiles, telomere patterns, as well as chromatin-remodelling complexes. We believed that a new target therapy for lung disease based on findings of the involved epigenetic pathway is a promising future direction.
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Affiliation(s)
- Xueren Li
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin, China
- Tianjin Institute of Respiratory Diseases, Tianjin, China
| | - Chunjing Feng
- The Institute Includes H&B(Tianjin) Stem Cell Research Institute, Tianjin, China
| | - Shouchun Peng
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin, China
- Tianjin Institute of Respiratory Diseases, Tianjin, China
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Chu X, Zhong L, Dan W, Wang X, Zhang Z, Liu Z, Lu Y, Shao X, Zhou Z, Chen S, Liu B. DNMT3A R882H mutation drives daunorubicin resistance in acute myeloid leukemia via regulating NRF2/NQO1 pathway. Cell Commun Signal 2022; 20:168. [PMID: 36303144 PMCID: PMC9615155 DOI: 10.1186/s12964-022-00978-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methyltransferase 3A (DNMT3A) often mutate on arginine 882 (DNMT3AR882) in acute myeloid leukemia (AML). AML patients with DNMT3A R882 mutation are usually resistant to daunorubicin treatment; however, the associated mechanism is still unclear. Therefore, it is urgent to investigate daunorubicin resistance in AML patients with DNMT3A R882 mutant. METHOD AML cell lines with DNMT3A-wild type (DNMT3A-WT), and DNMT3A-Arg882His (DNMT3A-R882H) mutation were constructed to investigate the role of DNMT3A R882H mutation on cell proliferation, apoptosis and cells' sensitivity to Danunorubin. Bioinformatics was used to analyze the role of nuclear factor-E2-related factor (NRF2) in AML patients with DNMT3A R882 mutation. The regulatory mechanism of DNMT3A R882H mutation on NRF2 was studied by Bisulfite Sequencing and CO-IP. NRF2 inhibitor Brusatol (Bru) was used to explore the role of NRF2 in AML cells carried DNMT3A R882H mutation. RESULTS AML cells with a DNMT3A R882H mutation showed high proliferative and anti-apoptotic activities. In addition, mutant cells were less sensitive to daunorubicin and had a higher NRF2 expression compared with those in WT cells. Furthermore, the NRF2/NQO1 pathway was activated in mutant cells in response to daunorubicin treatment. DNMT3A R882H mutation regulated the expression of NRF2 via influencing protein stability rather than decreasing methylation of NRF2 promoter. Also, NRF2/NQO1 pathway inhibition improved mutant cells' sensitivity to daunorubicin significantly. CONCLUSION Our findings identified NRF2 as an important player in the regulation of cell apoptosis through which helps mediate chemoresistance to daunorubicin in AML cells with DNMT3A R882H mutation. Targeting NRF2 might be a novel therapeutic approach to treat AML patients with a DNMT3A R882H mutation. Video abstract.
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Affiliation(s)
- Xuan Chu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Liang Zhong
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wenran Dan
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Xiao Wang
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Zhonghui Zhang
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Zhenyan Liu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Yang Lu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Xin Shao
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Ziwei Zhou
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Shuyu Chen
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Beizhong Liu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing, 402160, China. .,Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Association of H-Type Hypertension with miR-21, miR-29, and miR-199 in Kazahks of Xinjiang, China. Int J Hypertens 2022; 2022:4632087. [PMID: 36200021 PMCID: PMC9529513 DOI: 10.1155/2022/4632087] [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: 05/26/2022] [Revised: 07/30/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Objective This study aims to analyze the expressions of miR-21, miR-29, and miR-199 in the serum of the patients with H-type hypertension among Kazakhs. Then, we analyzed the effect of MTHFR 677C > T polymorphism on the association between the above miRNA and H-type hypertension. Method In this study, the expression of miR-21, miR-29, and miR-199 was quantitatively measured in 120 serum samples and then stratified according to the C677T polymorphism to analyze the relationship between target miRNAs and HHcy. Results The expression of miR-21/-29 in the hypertension group was higher than the normal group (P < 0.001). And the expression of miR-199 was higher in the hcy group than in the normal group (P < 0.001). In the CC and CT genotypes of MTHFR 677C > T, the expression of miR-21 was lower in the HHcy patients than in the normal individuals (P = 0.005 and P = 0.001) and miR-199 was significantly higher in the HHcy patients than in the normal ones (P = 0.002 and P = 0.048). No such difference was found in the TT genotype. Logistic regression analysis showed that after adjusting for sex, age, BMI, systolic blood pressure, diastolic blood pressure, and MTHFRC677 T gene polymorphism, miR-21 was negatively correlated with hcy (OR = 0.222, 95% CI (0.101–0.485), P < 0.001) and miR-199 was positively correlated with hcy (OR = 1.823,95%CI (1.272∼2.614), P = 0.001). Conclusion miR-21, miR-29, and miR-199 are associated with H-type hypertension in the Kazakhs, especially hyperhomocysteinemia. And these three miRNAs may serve as biomarkers to provide clues to the potential pathogenesis of H-type hypertension.
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