1
|
Gao H, Zhao Y, Zhao S, Dai XQ, Qin XY, Zheng WL, He TT, Zhang N, Zhu C, Wang HM, Pan W, Zhu XM, Gao XM, Dai JF, Gong FY, Wang J. The ICF2 gene Zbtb24 specifically regulates the differentiation of B1 cells via promoting heme synthesis. Cell Mol Biol Lett 2024; 29:123. [PMID: 39277732 PMCID: PMC11401330 DOI: 10.1186/s11658-024-00641-2] [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: 03/11/2024] [Accepted: 08/29/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Loss-of-function mutations of ZBTB24 cause immunodeficiency, centromeric instability, and facial anomalies syndrome 2 (ICF2). ICF2 is a rare autosomal recessive disorder with immunological defects in serum antibodies and circulating memory B cells, resulting in recurrent and sometimes fatal respiratory and gastrointestinal infections. The genotype-phenotype correlation in patients with ICF2 indicates an essential role of ZBTB24 in the terminal differentiation of B cells. METHODS We used the clustered regularly interspaced short palindromic repeats (CRISPER)/Cas9 technology to generate B cell specific Zbtb24-deficient mice and verified the deletion specificity and efficiency by quantitative polymerase chain reaction (Q-PCR) and western blotting analyses in fluorescence-activated cell sorting (FACS)-sorted cells. The development, phenotype of B cells and in vivo responses to T cell dependent or independent antigens post immunization were analyzed by flow cytometry and enzyme-linked immunosorbent assay (ELISA). Adoptive transfer experiment in combination with in vitro cultures of FACS-purified B cells and RNA-Seq analysis were utilized to specifically determine the impact of Zbtb24 on B cell biology as well as the underlying mechanisms. RESULTS Zbtb24 is dispensable for B cell development and maintenance in naive mice. Surprisingly, B cell specific deletion of Zbtb24 does not evidently compromise germinal center reactions and the resulting primary and secondary antibody responses induced by T cell dependent antigens (TD-Ags), but significantly inhibits T cell independent antigen-elicited antibody productions in vivo. At the cellular level, Zbtb24-deficiency specifically impedes the plasma cell differentiation of B1 cells without impairing their survival, activation and proliferation in vitro. Mechanistically, Zbtb24-ablation attenuates heme biosynthesis partially through mTORC1 in B1 cells, and addition of exogenous hemin abrogates the differentiation defects of Zbtb24-null B1 cells. CONCLUSIONS Zbtb24 seems to regulate antibody responses against TD-Ags B cell extrinsically, but it specifically promotes the plasma cell differentiation of B1 cells via heme synthesis in mice. Our study also suggests that defected B1 functions contribute to recurrent infections in patients with ICF2.
Collapse
Affiliation(s)
- He Gao
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Ying Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Sai Zhao
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xiao-Qiu Dai
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xiao-Yuan Qin
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Wei-Long Zheng
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Nan Zhang
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Can Zhu
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Hong-Min Wang
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Wen Pan
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xue-Mei Zhu
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Jian-Feng Dai
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China.
| | - Fang-Yuan Gong
- Department of Immunology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China.
| | - Jun Wang
- Institutes of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Suzhou Medical College of Soochow University, Suzhou, 215123, China.
| |
Collapse
|
2
|
Barone S, Cerchia C, Summa V, Brindisi M. Methyl-Transferase-Like Protein 16 (METTL16): The Intriguing Journey of a Key Epitranscriptomic Player Becoming an Emerging Biological Target. J Med Chem 2024; 67:14786-14806. [PMID: 39150226 DOI: 10.1021/acs.jmedchem.4c01247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Key epitranscriptomic players have been increasingly characterized for their structural features and their involvement in several diseases. Accordingly, the design and synthesis of novel epitranscriptomic modulators have started opening a glimmer for drug discovery. m6A is a reversible modification occurring on a specific site and is catalyzed by three sets of proteins responsible for opposite functions. Writers (e.g., methyl-transferase-like protein (METTL) 3/METTL14 complex and METTL16) introduce the methyl group on adenosine N-6, by transferring the methyl group from the methyl donor S-adenosyl-methionine (SAM) to the substrate. Despite the rapidly advancing drug discovery progress on METTL3/METTL14, the METTL16 m6A writer has been marginally explored so far. We herein provide the first comprehensive overview of structural and biological features of METTL16, highlighting the state of the art in the field of its biological and structural characterization. We also showcase initial efforts in the identification of structural templates and preliminary structure-activity relationships for METTL16 modulators.
Collapse
Affiliation(s)
- Simona Barone
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Carmen Cerchia
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Summa
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Margherita Brindisi
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| |
Collapse
|
3
|
Mance L, Bigot N, Zhamungui Sánchez E, Coste F, Martín-González N, Zentout S, Biliškov M, Pukało Z, Mishra A, Chapuis C, Arteni AA, Lateur A, Goffinont S, Gaudon V, Talhaoui I, Casuso I, Beaufour M, Garnier N, Artzner F, Cadene M, Huet S, Castaing B, Suskiewicz MJ. Dynamic BTB-domain filaments promote clustering of ZBTB proteins. Mol Cell 2024; 84:2490-2510.e9. [PMID: 38996459 DOI: 10.1016/j.molcel.2024.05.029] [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: 07/28/2023] [Revised: 04/11/2024] [Accepted: 05/31/2024] [Indexed: 07/14/2024]
Abstract
The formation of dynamic protein filaments contributes to various biological functions by clustering individual molecules together and enhancing their binding to ligands. We report such a propensity for the BTB domains of certain proteins from the ZBTB family, a large eukaryotic transcription factor family implicated in differentiation and cancer. Working with Xenopus laevis and human proteins, we solved the crystal structures of filaments formed by dimers of the BTB domains of ZBTB8A and ZBTB18 and demonstrated concentration-dependent higher-order assemblies of these dimers in solution. In cells, the BTB-domain filamentation supports clustering of full-length human ZBTB8A and ZBTB18 into dynamic nuclear foci and contributes to the ZBTB18-mediated repression of a reporter gene. The BTB domains of up to 21 human ZBTB family members and two related proteins, NACC1 and NACC2, are predicted to behave in a similar manner. Our results suggest that filamentation is a more common feature of transcription factors than is currently appreciated.
Collapse
Affiliation(s)
- Lucija Mance
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Nicolas Bigot
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT - UAR3480, 35000 Rennes, France
| | - Edison Zhamungui Sánchez
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Franck Coste
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France.
| | - Natalia Martín-González
- Aix-Marseille Université, INSERM, DyNaMo, Turing Centre for Living Systems (CENTURI), 13288 Marseille Cedex 09, France; Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288 Marseille Cedex 09, France
| | - Siham Zentout
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT - UAR3480, 35000 Rennes, France
| | - Marin Biliškov
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Zofia Pukało
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Aanchal Mishra
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Catherine Chapuis
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT - UAR3480, 35000 Rennes, France
| | - Ana-Andreea Arteni
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Cryo-Electron Microscopy Facility, CRYOEM-Gif, 91198 Gif-sur-Yvette, France
| | - Axelle Lateur
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Stéphane Goffinont
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Ibtissam Talhaoui
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Ignacio Casuso
- Aix-Marseille Université, INSERM, DyNaMo, Turing Centre for Living Systems (CENTURI), 13288 Marseille Cedex 09, France
| | - Martine Beaufour
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Franck Artzner
- Université Rennes, CNRS, IPR (Institut de Physique de Rennes) - UMR 6251, 35000 Rennes, France
| | - Martine Cadene
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Sébastien Huet
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT - UAR3480, 35000 Rennes, France; Institut Universitaire de France, 75005 Paris, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France
| | - Marcin Józef Suskiewicz
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, affiliated with Université d'Orléans, 45071 Orléans Cedex 2, France.
| |
Collapse
|
4
|
Chatzilygeroudi T, Chondrou V, Boers R, Siamoglou S, Athanasopoulou K, Verigou E, Gribnau J, Alexis S, Labropoulou V, Kourakli A, Patrinos GP, Sgourou A, Symeonidis A. Fetal hemoglobin induction in azacytidine responders enlightens methylation patterns related to blast clearance in higher-risk MDS and CMML. Clin Epigenetics 2024; 16:79. [PMID: 38879530 PMCID: PMC11180405 DOI: 10.1186/s13148-024-01687-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/27/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND As new treatment options for patients with higher-risk myelodysplastic syndromes are emerging, identification of prognostic markers for hypomethylating agent (HMA) treatment and understanding mechanisms of their delayed and short-term responses are essential. Early fetal hemoglobin (HbF) induction has been suggested as a prognostic indicator for decitabine-treated patients. Although epigenetic mechanisms are assumed, responding patients' epigenomes have not been thoroughly examined. We aimed to clarify HbF kinetics and prognostic value for azacytidine treated patients, as well as the epigenetic landscape that might influence HbF re-expression and its clinical relevance. RESULTS Serial HbF measurements by high-performance liquid chromatography (n = 20) showed induction of HbF only among responders (p = 0.030). Moreover, HbF increase immediately after the first azacytidine cycle demonstrated prognostic value for progression-free survival (PFS) (p = 0.032, HR = 0.19, CI 0.24-1.63). Changes in methylation patterns were revealed with methylated DNA genome-wide sequencing analysis (n = 7) for FOG-1, RCOR-1, ZBTB7A and genes of the NuRD-complex components. Targeted pyrosequencing methodology (n = 28) revealed a strong inverse correlation between the degree of γ-globin gene (HBG2) promoter methylation and baseline HbF levels (p = 0.003, rs = - 0.663). A potential epigenetic mechanism of HbF re-expression in azacytidine responders was enlightened by targeted methylation analysis, through hypomethylation of site -53 of HBG2 promoter (p = 0.039, rs = - 0.504), which corresponds to MBD2-NuRD binding site, and to hypermethylation of the CpG326 island of ZBTB7A (p = 0.05, rs = 0.482), a known HbF repressor. These changes were associated to blast cell clearance (pHBG2 = 0.011, rs = 0.480/pZBTB7A = 0.026, rs = 0.427) and showed prognostic value for PFS (pZBTB7A = 0.037, HR = 1.14, CI 0.34-3.8). CONCLUSIONS Early HbF induction is featured as an accessible prognostic indicator for HMA treatment and the proposed potential epigenetic mechanism of HbF re-expression in azacytidine responders includes hypomethylation of the γ-globin gene promoter region and hypermethylation of the CpG326 island of ZBTB7A. The association of these methylation patterns with blast clearance and their prognostic value for PFS paves the way to discuss in-depth azacytidine epigenetic mechanism of action.
Collapse
Affiliation(s)
- Theodora Chatzilygeroudi
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Vasiliki Chondrou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Ruben Boers
- Department of Developmental Biology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rio, Patras, Greece
| | - Katerina Athanasopoulou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Evgenia Verigou
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - Joost Gribnau
- Department of Developmental Biology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Spyridon Alexis
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - Vassiliki Labropoulou
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - Alexandra Kourakli
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece
| | - George P Patrinos
- Department of Developmental Biology, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rio, Patras, Greece
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Argyro Sgourou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Argiris Symeonidis
- School of Health Sciences, Faculty of Medicine, Hematology Division, University of Patras, Patras, Greece.
| |
Collapse
|
5
|
Liu G, Kim J, Nguyen N, Zhou L, Dean A. Long noncoding RNA GATA2AS influences human erythropoiesis by transcription factor and chromatin landscape modulation. Blood 2024; 143:2300-2313. [PMID: 38447046 PMCID: PMC11181357 DOI: 10.1182/blood.2023021287] [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: 05/24/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024] Open
Abstract
ABSTRACT Long noncoding RNAs (lncRNAs) are extensively expressed in eukaryotic cells and have been revealed to be important for regulating cell differentiation. Many lncRNAs have been found to regulate erythroid differentiation in the mouse. However, given the low sequence conservation of lncRNAs between mouse and human, our understanding of lncRNAs in human erythroid differentiation remains incomplete. lncRNAs are often transcribed opposite to protein coding genes and regulate their expression. Here, we characterized a human erythrocyte-expressed lncRNA, GATA2AS, which is transcribed opposite to erythroid transcription regulator GATA2. GATA2AS is a 2080-bp long, primarily nucleus-localized noncoding RNA that is expressed in erythroid progenitor cells and decreases during differentiation. Knockout of GATA2AS in human HUDEP2 erythroid progenitor cells using CRISPR-Cas9 genome editing to remove the transcription start site accelerated erythroid differentiation and dysregulated erythroblast gene expression. We identified GATA2AS as a novel GATA2 and HBG activator. Chromatin isolation by RNA purification showed that GATA2AS binds to thousands of genomic sites and colocalizes at a subset of sites with erythroid transcription factors including LRF and KLF1. RNA pulldown and RNA immunoprecipitation confirmed interaction between GATA2AS and LRF and KLF1. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that knockout of GATA2AS reduces binding of these transcription factors genome wide. Assay for transposase-accessible chromatin sequencing (ATAC-seq) and H3K27ac ChIP-seq showed that GATA2AS is essential to maintain the chromatin regulatory landscape during erythroid differentiation. Knockdown of GATA2AS in human primary CD34+ cells mimicked results in HUDEP2 cells. Overall, our results implicate human-specific lncRNA GATA2AS as a regulator of erythroid differentiation by influencing erythroid transcription factor binding and the chromatin regulatory landscape.
Collapse
Affiliation(s)
- Guoyou Liu
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Juhyun Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Nicole Nguyen
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Lecong Zhou
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| |
Collapse
|
6
|
Miyake K, Ito J, Karasuyama H. Novel insights into the ontogeny of basophils. FRONTIERS IN ALLERGY 2024; 5:1402841. [PMID: 38803659 PMCID: PMC11128600 DOI: 10.3389/falgy.2024.1402841] [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: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024] Open
Abstract
Basophils are the least common granulocytes, accounting for <1% of peripheral blood leukocytes. In the last 20 years, analytical tools for mouse basophils have been developed, and we now recognize that basophils play critical roles in various immune reactions, including the development of allergic inflammation and protective immunity against parasites. Moreover, the combined use of flow cytometric analyses and knockout mice has uncovered several progenitor cells committed to basophils in mice. Recently, advancements in single-cell RNA sequencing (scRNA-seq) technologies have challenged the classical view of the differentiation of various hematopoietic cell lineages. This is also true for basophil differentiation, and studies using scRNA-seq analysis have provided novel insights into basophil differentiation, including the association of basophil differentiation with that of erythrocyte/megakaryocyte and the discovery of novel basophil progenitor cells in the mouse bone marrow. In this review, we summarize the recent findings of basophil ontogeny in both mice and humans, mainly focusing on studies using scRNA-seq analyses.
Collapse
Affiliation(s)
- Kensuke Miyake
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | | |
Collapse
|
7
|
Fang Z, Deng Y, Wang H, Zhou J. SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity. PeerJ 2024; 12:e17234. [PMID: 38666079 PMCID: PMC11044885 DOI: 10.7717/peerj.17234] [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: 10/06/2023] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Background Post-translational modification by Small Ubiquitin-like MOdifier (SUMO) is an important mechanism to regulate protein activity, protein stability, and localization of substrates. Zbtb21 is a zinc finger and BTB (Broad-complex, Tram-track and Bric à brac) domain-containing transcription factor. Bioinformatic prediction suggests several putative SUMOylated sites in Zbtb21 protein. Methods Two evolutionarily conserved lysine residues in Zbtb21 protein were mutated alone or in combination to disrupt the binding with SUMO molecules. Western blot and co-immunoprecipitation analyses were performed to detect the SUMOylation state of wild type and mutant Zbtb21 proteins, respectively. Luciferase reporter assays were conducted to evaluate their transcription activities. Meanwhile, immunofluorescence staining was carried out to show their sub-nuclear localizations. Finally, co-immunoprecipitation was performed to detect the interaction between Zbtb21 and its partners. Results Phylogenetically conserved lysines 419 and 845 of zebrafish Zbtb21 protein can be conjugated with SUMO molecules. SUMOylation does not affect the subcellular localization and protein stability of Zbtb21, as well as the interaction with Zbtb14 or Zbtb21. Nevertheless, luciferase reporter assays revealed that Zbtb21 is a dual-function transcription factor which exerts activation or repression effect on different promoters, and SUMOylation can modulate the transcriptional activity of Zbtb21 in regulating downstream target genes. Hence, Zbtb21 is identified as a novel substrate of SUMOylation, which would be important for its function. Conclusions Zebrafish Zbtb21 protein can be SUMOylated on lysines 419 and 845, which is evolutionary conserved. SUMOylation affects the dual role of Zbtb21 on transcription.
Collapse
Affiliation(s)
- Zhou Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Deng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haihong Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
8
|
Xu W, Yao H, Wu Z, Yan X, Jiao Z, Liu Y, Zhang M, Wang D. Oncoprotein SET-associated transcription factor ZBTB11 triggers lung cancer metastasis. Nat Commun 2024; 15:1362. [PMID: 38355937 PMCID: PMC10867109 DOI: 10.1038/s41467-024-45585-5] [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: 07/21/2022] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Metastasis is the major cause of lung cancer-related death, but the mechanisms governing lung tumor metastasis remain incompletely elucidated. SE translocation (SET) is overexpressed in lung tumors and correlates with unfavorable prognosis. Here we uncover SET-associated transcription factor, zinc finger and BTB domain-containing protein 11 (ZBTB11), as a prometastatic regulator in lung tumors. SET interacts and collaborates with ZBTB11 to promote lung cancer cell migration and invasion, primarily through SET-ZBTB11 complex-mediated transcriptional activation of matrix metalloproteinase-9 (MMP9). Additionally, by transcriptional repression of proline-rich Gla protein 2 (PRRG2), ZBTB11 links Yes-associated protein 1 (YAP1) activation to drive lung tumor metastasis independently of SET-ZBTB11 complex. Loss of ZBTB11 suppresses distal metastasis in a lung tumor mouse model. Overexpression of ZBTB11 is recapitulated in human metastatic lung tumors and correlates with diminished survival. Our study demonstrates ZBTB11 as a key metastatic regulator and reveals diverse mechanisms by which ZBTB11 modulates lung tumor metastasis.
Collapse
Affiliation(s)
- Wenbin Xu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Han Yao
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zhen Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zishan Jiao
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yajing Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| |
Collapse
|
9
|
Wei ZX, Cai XX, Fei YD, Wang Q, Hu XL, Li C, Hou JW, Yang YL, Chen TZ, Xu XL, Wang YP, Li YG. Zbtb16 increases susceptibility of atrial fibrillation in type 2 diabetic mice via Txnip-Trx2 signaling. Cell Mol Life Sci 2024; 81:88. [PMID: 38349408 PMCID: PMC10864461 DOI: 10.1007/s00018-024-05125-2] [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: 05/25/2023] [Revised: 12/10/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
Atrial fibrillation (AF) is the most prevalent sustained cardiac arrhythmia, and recent epidemiological studies suggested type 2 diabetes mellitus (T2DM) is an independent risk factor for the development of AF. Zinc finger and BTB (broad-complex, tram-track and bric-a-brac) domain containing 16 (Zbtb16) serve as transcriptional factors to regulate many biological processes. However, the potential effects of Zbtb16 in AF under T2DM condition remain unclear. Here, we reported that db/db mice displayed higher AF vulnerability and Zbtb16 was identified as the most significantly enriched gene by RNA sequencing (RNA-seq) analysis in atrium. In addition, thioredoxin interacting protein (Txnip) was distinguished as the key downstream gene of Zbtb16 by Cleavage Under Targets and Tagmentation (CUT&Tag) assay. Mechanistically, increased Txnip combined with thioredoxin 2 (Trx2) in mitochondrion induced excess reactive oxygen species (ROS) release, calcium/calmodulin-dependent protein kinase II (CaMKII) overactivation, and spontaneous Ca2+ waves (SCWs) occurrence, which could be inhibited through atrial-specific knockdown (KD) of Zbtb16 or Txnip by adeno-associated virus 9 (AAV9) or Mito-TEMPO treatment. High glucose (HG)-treated HL-1 cells were used to mimic the setting of diabetic in vitro. Zbtb16-Txnip-Trx2 signaling-induced excess ROS release and CaMKII activation were also verified in HL-1 cells under HG condition. Furthermore, atrial-specific Zbtb16 or Txnip-KD reduced incidence and duration of AF in db/db mice. Altogether, we demonstrated that interrupting Zbtb16-Txnip-Trx2 signaling in atrium could decrease AF susceptibility via reducing ROS release and CaMKII activation in the setting of T2DM.
Collapse
Affiliation(s)
- Zhi-Xing Wei
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Xing-Xing Cai
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Yu-Dong Fei
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Qian Wang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Xiao-Liang Hu
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Cheng Li
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Jian-Wen Hou
- Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu-Li Yang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Tai-Zhong Chen
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Xiao-Lei Xu
- Department of Biochemistry and Molecular Biology, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yue-Peng Wang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Yi-Gang Li
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China.
| |
Collapse
|
10
|
Liu J, Zhang H. Zinc Finger and BTB Domain-Containing 20: A Newly Emerging Player in Pathogenesis and Development of Human Cancers. Biomolecules 2024; 14:192. [PMID: 38397429 PMCID: PMC10887282 DOI: 10.3390/biom14020192] [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: 01/12/2024] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Zinc finger and BTB domain-containing 20 (ZBTB20), which was initially identified in human dendritic cells, belongs to a family of transcription factors (TFs) with an N-terminal BTB domain and one or more C-terminal DNA-binding zinc finger domains. Under physiological conditions, ZBTB20 acts as a transcriptional repressor in cellular development and differentiation, metabolism, and innate immunity. Interestingly, multiple lines of evidence from mice and human systems have revealed the importance of ZBTB20 in the pathogenesis and development of cancers. ZBTB20 is not only a hotspot of genetic variation or fusion in many types of human cancers, but also a key TF or intermediator involving in the dysregulation of cancer cells. Given the diverse functions of ZBTB20 in both health and disease, we herein summarize the structure and physiological roles of ZBTB20, with an emphasis on the latest findings on tumorigenesis and cancer progression.
Collapse
Affiliation(s)
| | - Han Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China;
| |
Collapse
|
11
|
Barakat S, Ezen E, Devecioğlu İ, Gezen M, Piepoli S, Erman B. Dimerization choice and alternative functions of ZBTB transcription factors. FEBS J 2024; 291:237-255. [PMID: 37450366 DOI: 10.1111/febs.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Zinc Finger DNA-binding domain-containing proteins are the most populous family among eukaryotic transcription factors. Among these, members of the BTB domain-containing ZBTB sub-family are mostly known for their transcriptional repressive functions. In this Viewpoint article, we explore molecular mechanisms that potentially diversify the function of ZBTB proteins based on their homo and heterodimerization, alternative splicing and post-translational modifications. We describe how the BTB domain is as much a scaffold for the assembly of co-repressors, as a domain that regulates protein stability. We highlight another mechanism that regulates ZBTB protein stability: phosphorylation in the zinc finger domain. We explore the non-transcriptional, structural roles of ZBTB proteins and highlight novel findings that describe the ability of ZBTB proteins to associate with poly adenosine ribose in the nucleus during the DNA damage response. Herein, we discuss the contribution of BTB domain scaffolds to the formation of transcriptional repressive complexes, to chromosome compartmentalization and their non-transcriptional, purely structural functions in the nucleus.
Collapse
Affiliation(s)
- Sarah Barakat
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - İzem Devecioğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Melike Gezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| |
Collapse
|
12
|
da Silva Lima F, da Silva Gonçalves CE, Fock RA. A review of the role of zinc finger proteins on hematopoiesis. J Trace Elem Med Biol 2023; 80:127290. [PMID: 37659124 DOI: 10.1016/j.jtemb.2023.127290] [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: 04/03/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
The bone marrow is responsible for producing an incredible number of cells daily in order to maintain blood homeostasis through a process called hematopoiesis. Hematopoiesis is a greatly demanding process and one entirely dependent on complex interactions between the hematopoietic stem cell (HSC) and its surrounding microenvironment. Zinc (Zn2+) is considered an important trace element, playing diverse roles in different tissues and cell types, and zinc finger proteins (ZNF) are proteins that use Zn2+ as a structural cofactor. In this way, the ZNF structure is supported by a Zn2+ that coordinates many possible combinations of cysteine and histidine, with the most common ZNF being of the Cys2His2 (C2H2) type, which forms a family of transcriptional activators that play an important role in different cellular processes such as development, differentiation, and suppression, all of these being essential processes for an adequate hematopoiesis. This review aims to shed light on the relationship between ZNF and the regulation of the hematopoietic tissue. We include works with different designs, including both in vitro and in vivo studies, detailing how ZNF might regulate hematopoiesis.
Collapse
Affiliation(s)
- Fabiana da Silva Lima
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Ricardo Ambrósio Fock
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
13
|
Cao H, Naik SH, Amann-Zalcenstein D, Hickey P, Salim A, Cao B, Nilsson SK, Keightley MC, Lieschke GJ. Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification. Blood Adv 2023; 7:6506-6519. [PMID: 37567157 PMCID: PMC10632610 DOI: 10.1182/bloodadvances.2022009580] [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: 12/19/2022] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023] Open
Abstract
Hematopoiesis produces diverse blood cell lineages to meet the basal needs and sudden demands of injury or infection. A rapid response to such challenges requires the expansion of specific lineages and a prompt return to balanced steady-state levels, necessitating tightly coordinated regulation. Previously we identified a requirement for the zinc finger and broad complex, tramtrak, bric-a-brac domain-containing 11 (ZBTB11) transcription factor in definitive hematopoiesis using a forward genetic screen for zebrafish myeloid mutants. To understand its relevance to mammalian systems, we extended these studies to mice. When Zbtb11 was deleted in the hematopoietic compartment, embryos died at embryonic day (E) 18.5 with hematopoietic failure. Zbtb11 hematopoietic knockout (Zbtb11hKO) hematopoietic stem cells (HSCs) were overabundantly specified from E14.5 to E17.5 compared with those in controls. Overspecification was accompanied by loss of stemness, inability to differentiate into committed progenitors and mature lineages in the fetal liver, failure to seed fetal bone marrow, and total hematopoietic failure. The Zbtb11hKO HSCs did not proliferate in vitro and were constrained in cell cycle progression, demonstrating the cell-intrinsic role of Zbtb11 in proliferation and cell cycle regulation in mammalian HSCs. Single-cell RNA sequencing analysis identified that Zbtb11-deficient HSCs were underrepresented in an erythroid-primed subpopulation and showed downregulation of oxidative phosphorylation pathways and dysregulation of genes associated with the hematopoietic niche. We identified a cell-intrinsic requirement for Zbtb11-mediated gene regulatory networks in sustaining a pool of maturation-capable HSCs and progenitor cells.
Collapse
Affiliation(s)
- Huimin Cao
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Shalin H. Naik
- Department of Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Daniela Amann-Zalcenstein
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Advanced Genomics Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Peter Hickey
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Advanced Genomics Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Agus Salim
- Mathematics and Statistics, La Trobe University, Bundoora, VIC, Australia
- Melbourne School of Population and Global Health, School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
| | - Benjamin Cao
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Susan K. Nilsson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - M. Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Rural Clinical Sciences, La Trobe Rural Health School, Bendigo, VIC, Australia
| | - Graham J. Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| |
Collapse
|
14
|
Golovnin A, Melnikova L, Babosha V, Pokholkova GV, Slovohotov I, Umnova A, Maksimenko O, Zhimulev IF, Georgiev P. The N-Terminal Part of Drosophila CP190 Is a Platform for Interaction with Multiple Architectural Proteins. Int J Mol Sci 2023; 24:15917. [PMID: 37958900 PMCID: PMC10648081 DOI: 10.3390/ijms242115917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
CP190 is a co-factor in many Drosophila architectural proteins, being involved in the formation of active promoters and insulators. CP190 contains the N-terminal BTB/POZ (Broad-Complex, Tramtrack and Bric a brac/POxvirus and Zinc finger) domain and adjacent conserved regions involved in protein interactions. Here, we examined the functional roles of these domains of CP190 in vivo. The best-characterized architectural proteins with insulator functions, Pita, Su(Hw), and dCTCF, interacted predominantly with the BTB domain of CP190. Due to the difficulty of mutating the BTB domain, we obtained a transgenic line expressing a chimeric CP190 with the BTB domain of the human protein Kaiso. Another group of architectural proteins, M1BP, Opbp, and ZIPIC, interacted with one or both of the highly conserved regions in the N-terminal part of CP190. Transgenic lines of D. melanogaster expressing CP190 mutants with a deletion of each of these domains were obtained. The results showed that these mutant proteins only partially compensated for the functions of CP190, weakly binding to selective chromatin sites. Further analysis confirmed the essential role of these domains in recruitment to regulatory regions associated with architectural proteins. We also found that the N-terminal of CP190 was sufficient for recruiting Z4 and Chromator proteins and successfully achieving chromatin opening. Taken together, our results and the results of previous studies showed that the N-terminal region of CP190 is a platform for simultaneous interaction with various DNA-binding architectural proteins and transcription complexes.
Collapse
Affiliation(s)
- Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Galina V. Pokholkova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, Novosibirsk 630090, Russia (I.F.Z.)
| | - Ivan Slovohotov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Anastasia Umnova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Igor F. Zhimulev
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, Novosibirsk 630090, Russia (I.F.Z.)
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| |
Collapse
|
15
|
Preiss NK, Kamal Y, Wilkins OM, Li C, Kolling FW, Trask HW, Usherwood YK, Cheng C, Frost HR, Usherwood EJ. Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20. Life Sci Alliance 2023; 6:e202201683. [PMID: 37414528 PMCID: PMC10326419 DOI: 10.26508/lsa.202201683] [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: 08/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
Members of the BTB-ZF transcription factor family regulate the immune system. Our laboratory identified that family member Zbtb20 contributes to the differentiation, recall responses, and metabolism of CD8 T cells. Here, we report a characterization of the transcriptional and epigenetic signatures controlled by Zbtb20 at single-cell resolution during the effector and memory phases of the CD8 T cell response. Without Zbtb20, transcriptional programs associated with memory CD8 T cell formation were up-regulated throughout the CD8 T response. A signature of open chromatin was associated with genes controlling T cell activation, consistent with the known impact on differentiation. In addition, memory CD8 T cells lacking Zbtb20 were characterized by open chromatin regions with overrepresentation of AP-1 transcription factor motifs and elevated RNA- and protein-level expressions of the corresponding AP-1 components. Finally, we describe motifs and genomic annotations from the DNA targets of Zbtb20 in CD8 T cells identified by cleavage under targets and release under nuclease (CUT&RUN). Together, these data establish the transcriptional and epigenetic networks contributing to the control of CD8 T cell responses by Zbtb20.
Collapse
Affiliation(s)
- Nicholas K Preiss
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Yasmin Kamal
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Owen M Wilkins
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Chenyang Li
- Genomic Medicine Department, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX, USA
| | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Heidi W Trask
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Young-Kwang Usherwood
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Hildreth R Frost
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Edward J Usherwood
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| |
Collapse
|
16
|
Phoenix JT, Budreika A, Kostlan RJ, Hwang JH, Fanning SW, Kregel S. Editorial: Hormone resistance in cancer. Front Endocrinol (Lausanne) 2023; 14:1272932. [PMID: 37693345 PMCID: PMC10484586 DOI: 10.3389/fendo.2023.1272932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/17/2023] [Indexed: 09/12/2023] Open
Affiliation(s)
- John T. Phoenix
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Integrated Program in Biomedical Science, Biochemistry, Molecular and Cancer Biology, Loyola University Chicago, Maywood, IL, United States
| | - Audris Budreika
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Raymond J. Kostlan
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Integrated Program in Biomedical Science, Biochemistry, Molecular and Cancer Biology, Loyola University Chicago, Maywood, IL, United States
| | - Justin H. Hwang
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Sean W. Fanning
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Steven Kregel
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| |
Collapse
|
17
|
Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [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: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
Collapse
Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
18
|
Paschoudi K, Yannaki E, Psatha N. Precision Editing as a Therapeutic Approach for β-Hemoglobinopathies. Int J Mol Sci 2023; 24:9527. [PMID: 37298481 PMCID: PMC10253463 DOI: 10.3390/ijms24119527] [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: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Beta-hemoglobinopathies are the most common genetic disorders worldwide, caused by a wide spectrum of mutations in the β-globin locus, and associated with morbidity and early mortality in case of patient non-adherence to supportive treatment. Allogeneic transplantation of hematopoietic stem cells (allo-HSCT) used to be the only curative option, although the indispensable need for an HLA-matched donor markedly restricted its universal application. The evolution of gene therapy approaches made possible the ex vivo delivery of a therapeutic β- or γ- globin gene into patient-derived hematopoietic stem cells followed by the transplantation of corrected cells into myeloablated patients, having led to high rates of transfusion independence (thalassemia) or complete resolution of painful crises (sickle cell disease-SCD). Hereditary persistence of fetal hemoglobin (HPFH), a syndrome characterized by increased γ-globin levels, when co-inherited with β-thalassemia or SCD, converts hemoglobinopathies to a benign condition with mild clinical phenotype. The rapid development of precise genome editing tools (ZFN, TALENs, CRISPR/Cas9) over the last decade has allowed the targeted introduction of mutations, resulting in disease-modifying outcomes. In this context, genome editing tools have successfully been used for the introduction of HPFH-like mutations both in HBG1/HBG2 promoters or/and in the erythroid enhancer of BCL11A to increase HbF expression as an alternative curative approach for β-hemoglobinopathies. The current investigation of new HbF modulators, such as ZBTB7A, KLF-1, SOX6, and ZNF410, further expands the range of possible genome editing targets. Importantly, genome editing approaches have recently reached clinical translation in trials investigating HbF reactivation in both SCD and thalassemic patients. Showing promising outcomes, these approaches are yet to be confirmed in long-term follow-up studies.
Collapse
Affiliation(s)
- Kiriaki Paschoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece;
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece;
- Department of Hematology, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nikoletta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| |
Collapse
|
19
|
Ct Chow C, Kobayashi M, Kambe G, Harada H. ZBTB2 is recruited to a specific subset of HIF-1 target loci to facilitate full gene expression under hypoxia. J Mol Biol 2023:168162. [PMID: 37257772 DOI: 10.1016/j.jmb.2023.168162] [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: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
The cellular response to hypoxia is mainly governed by a transcription factor, hypoxia-inducible factor 1 (HIF-1). Although upregulation of HIF-1 target genes has been hypothesized to require interaction of HIF-1 with other coactivators, much remains to be elucidated regarding the underlying mechanisms. Here, we demonstrate that zinc finger and BTB domain-containing protein 2 (ZBTB2) enhances the expression of certain HIF-1 target genes under hypoxia. ChIP-Seq analysis showed that there is a subset of HIF-1 target genes with overlapping HIF-1 and ZBTB2 peaks. Examination of a representative gene, EGFR antisense RNA 1 (EGFR-AS1), showed that HIF-1 binding to the consensus hypoxia-responsive element (HRE) sequence resulted in the recruitment of ZBTB2 to the gene locus and increased p300-mediated histone acetylation, leading to enhanced gene expression under hypoxia. In contrast, expression of HIF-1 target genes lacking ZBTB2 peaks, such as carbonic anhydrase 9 (CA9), was not upregulated by ZBTB2. These findings demonstrate that ZBTB2 is a novel factor that can be recruited to the vicinity of HREs on a subset of HIF-1 target gene loci, and is required for their full expression under hypoxia.
Collapse
Affiliation(s)
- Christalle Ct Chow
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Gouki Kambe
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
| |
Collapse
|
20
|
Cui Y, Zhou M, He Q, He Z. Zbtb40 Deficiency Leads to Morphological and Phenotypic Abnormalities of Spermatocytes and Spermatozoa and Causes Male Infertility. Cells 2023; 12:cells12091264. [PMID: 37174664 PMCID: PMC10177581 DOI: 10.3390/cells12091264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Studies on the gene regulation of spermatogenesis are of unusual significance for maintaining male reproduction and treating male infertility. Here, we have demonstrated, for the first time, that a loss of ZBTB40 function leads to abnormalities in the morphological and phenotypic characteristics of mouse spermatocytes and spermatids as well as male infertility. We revealed that Zbtb40 was expressed in spermatocytes of mouse testes, and it was co-localized with γH2AX in mouse secondary spermatocytes. Interestingly, spermatocytes of Zbtb40 knockout mice had longer telomeres, compromised double-strand break (DSB) repair in the sex chromosome, and a higher apoptosis ratio compared to wild-type (WT) mice. The testis weight, testicular volume, and cauda epididymis body weight of the Zbtb40+/- male mice were significantly lower than in WT mice. Mating tests indicated that Zbtb40+/- male mice were able to mate normally, but they failed to produce any pups. Notably, sperm of Zbtb40+/- mice showed flagellum deformities and abnormal acrosome biogenesis. Furthermore, a ZBTB40 mutation was associated with non-obstructive azoospermia. Our results implicate that ZBTB40 deficiency leads to morphological and phenotypic abnormalities of spermatocytes and spermatids and causes male infertility. This study thus offers a new genetic mechanism regulating mammalian spermatogenesis and provides a novel target for gene therapy in male infertility.
Collapse
Affiliation(s)
- Yinghong Cui
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha 410013, China
- The Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha 410013, China
- The Manufacture-Based Learning & Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| | - Mingqing Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha 410013, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha 410013, China
| | - Zuping He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha 410013, China
- The Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha 410013, China
- The Manufacture-Based Learning & Research Demonstration Center for Human Reproductive Health New Technology of Hunan Normal University, Changsha 410013, China
| |
Collapse
|
21
|
Jeong JH, Park SH, Kim H, Nam HY, Kim SH, Jeong M, Kong MJ, Son J, Jeong JE, Song JH, Kim SW, Choi KC. ZBTB7A suppresses glioblastoma tumorigenesis through the transcriptional repression of EPB41L5. Exp Mol Med 2023; 55:43-54. [PMID: 36596853 PMCID: PMC9898510 DOI: 10.1038/s12276-022-00908-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 01/05/2023] Open
Abstract
Glioblastoma multiforme (GBM), the most aggressive and malignant glioma, has a poor prognosis. Although patients with GBM are treated with surgery, chemotherapy, and radiation therapy, GBM is highly resistant to treatment, making it difficult and expensive to treat. In this study, we analyzed the Gene Expression Profiling Interactive Analysis dataset, the Cancer Genome Atlas dataset, and Gene Expression Omnibus array data. ZBTB7A (also called FBI1/POKEMON/LRF) was found to be highly expressed in low-grade glioma but significantly downregulated in patients with GBM. ZBTB7A is a transcription factor that plays an important role in many developmental stages, including cell proliferation. The activation of epithelial-mesenchymal transition (EMT) is a key process in cancer progression and metastasis. Erythrocyte membrane protein band 4.1 like 5 (EPB41L5) is an essential protein for EMT progression and metastasis in various types of cancer. We found that ZBTB7A depletion in U87 cells induced GBM progression and metastasis. Based on RNA sequencing data, ZBTB7A directly binds to the promoter of the EPB41L5 gene, reducing its expression and inhibiting GBM progression. We demonstrated that ZBTB7A dramatically inhibits GBM tumor growth through transcriptional repression of EPB41L5. Thus, both ZBTB7A and EPB41L5 may be potential biomarkers and novel therapeutic targets for GBM treatment. Overall, we discovered the role of a novel tumor suppressor that directly inhibits GBM progression (ZBTB7A) and identified EPB41L5 as a therapeutic target protein for patients with GBM.
Collapse
Affiliation(s)
- Ji-Hoon Jeong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seung-Ho Park
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunhee Kim
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hae Yun Nam
- grid.413967.e0000 0001 0842 2126Department of Biochemistry and Molecular Biology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung-Hak Kim
- grid.14005.300000 0001 0356 9399Department of Animal Science, Chonnam National University, Gwangju, Korea
| | - Minseok Jeong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min-Jeong Kong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jihyun Son
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji-Eun Jeong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji-Hye Song
- grid.418974.70000 0001 0573 0246Korea Food Research Institute, Wanju-gun, 55365 Korea
| | - Seong Who Kim
- Department of Biochemistry and Molecular Biology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Kyung-Chul Choi
- Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| |
Collapse
|
22
|
The remodeling of Z-DNA in the mammalian germ line. Biochem Soc Trans 2022; 50:1875-1884. [PMID: 36454621 PMCID: PMC9788570 DOI: 10.1042/bst20221015] [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: 10/17/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
We recently discovered a novel biological process, the scheduled remodeling of Z-DNA structures in the developing fetal mouse male germ cells [Nat. Cell Biol. 24, 1141-1153]. This process affects purine/pyrimidine dinucleotide repeat (PPR) rich sequences, which can form stable left-handed Z-DNA structures. The protein that carries out this function is identified as ZBTB43, member of a large family of ZBTB proteins. Z-DNA remodeling by ZBTB43 not only coincides with global remodeling of DNA methylation and chromatin events in the male germ line, but it also is a prerequisite for de novo DNA methylation. When ZBTB43 changes DNA structure from the left-handed zigzag shaped Z-DNA to the regular smooth right-handed B-DNA, it also generates a suitable substrate for the de novo DNA methyltransferase, DNMT3A. By instructing de novo DNA methylation at PPRs in prospermatogonia, ZBTB43 safeguards epigenomic integrity of the male gamete. PPRs are fragile sequences, sites of large deletions and rearrangements in mammalian cells, and this fragility is thought to be due to Z-DNA structure formation rather than the sequence itself. This idea is now supported by the in vivo finding that DNA double strand breaks accumulate in mutant prospermatogonia which lack ZBTB43-dependent Z-DNA remodeling. If unrepaired, double stranded DNA breaks can lead to germ line mutations. Therefore, by preventing such breaks ZBTB43 is critical for guarding genome stability between generations. Here, we discuss the significance and implications of these findings in more detail.
Collapse
|
23
|
Yoshinaga M, Han K, Morgens DW, Horii T, Kobayashi R, Tsuruyama T, Hia F, Yasukura S, Kajiya A, Cai T, Cruz PHC, Vandenbon A, Suzuki Y, Kawahara Y, Hatada I, Bassik MC, Takeuchi O. The N 6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity. Nat Commun 2022; 13:6435. [PMID: 36307435 PMCID: PMC9616860 DOI: 10.1038/s41467-022-34078-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/12/2022] [Indexed: 02/07/2023] Open
Abstract
During erythroid differentiation, the maintenance of genome integrity is key for the success of multiple rounds of cell division. However, molecular mechanisms coordinating the expression of DNA repair machinery in erythroid progenitors are poorly understood. Here, we discover that an RNA N6-methyladenosine (m6A) methyltransferase, METTL16, plays an essential role in proper erythropoiesis by safeguarding genome integrity via the control of DNA-repair-related genes. METTL16-deficient erythroblasts exhibit defective differentiation capacity, DNA damage and activation of the apoptotic program. Mechanistically, METTL16 controls m6A deposition at the structured motifs in DNA-repair-related transcripts including Brca2 and Fancm mRNAs, thereby upregulating their expression. Furthermore, a pairwise CRISPRi screen revealed that the MTR4-nuclear RNA exosome complex is involved in the regulation of METTL16 substrate mRNAs in erythroblasts. Collectively, our study uncovers that METTL16 and the MTR4-nuclear RNA exosome act as essential regulatory machinery to maintain genome integrity and erythropoiesis.
Collapse
Affiliation(s)
- Masanori Yoshinaga
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Kyuho Han
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - David W. Morgens
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Takuro Horii
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Ryosuke Kobayashi
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Tatsuaki Tsuruyama
- grid.258799.80000 0004 0372 2033Department of Drug and Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Fabian Hia
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Shota Yasukura
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Asako Kajiya
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Ting Cai
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Pedro H. C. Cruz
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Alexis Vandenbon
- grid.258799.80000 0004 0372 2033Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507 Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XLaboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Yukio Kawahara
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Izuho Hatada
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan ,grid.256642.10000 0000 9269 4097Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), Gunma, 371-8512 Japan
| | - Michael C. Bassik
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Osamu Takeuchi
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| |
Collapse
|
24
|
Xu X, Shobuike T, Shiraki M, Kamohara A, Hirata H, Murayama M, Mawatari D, Ueno M, Morimoto T, Kukita T, Mawatari M, Kukita A. Leukemia/lymphoma-related factor (LRF) or osteoclast zinc finger protein (OCZF) overexpression promotes osteoclast survival by increasing Bcl-xl mRNA: A novel regulatory mechanism mediated by the RNA binding protein SAM68. J Transl Med 2022; 102:1000-1010. [PMID: 36775415 DOI: 10.1038/s41374-022-00792-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022] Open
Abstract
RANKL induces NFATc1, a key transcriptional factor to induce osteoclast-specific genes such as cathepsin K, whereas transcriptional control of osteoclast survival is not fully understood. Leukemia/lymphoma-related factor (LRF) in mouse and osteoclast zinc finger protein (OCZF) in rat are zinc finger and BTB domain-containing protein (zBTB) family of transcriptional regulators, and are critical regulators of hematopoiesis. We have previously shown that differentiation and survival were enhanced in osteoclasts from OCZF-Transgenic (Tg) mice. In the present study, we show a possible mechanism of osteoclast survival regulated by LRF/OCZF and the role of OCZF overexpression in pathological bone loss. In the in vitro cultures, LRF was highly colocalized with NFATc1 in cells of early stage in osteoclastogenesis, but only LRF expression persisted after differentiation into mature osteoclasts. LRF expression was further enhanced in resorbing osteoclasts formed on dentin slices. Osteoclast survival inhibitor such as alendronate, a bisphosphonate reduced LRF expression. Micro CT evaluation revealed that femurs of OCZF-Tg mice showed significantly lower bone volume compared to that of WT mice. Furthermore, OCZF overexpression markedly promoted bone loss in ovariectomy-induced osteolytic mouse model. The expression of anti-apoptotic Bcl-xl mRNA, which is formed by alternative splicing, was enhanced in the cultures in which osteoclasts are formed from OCZF-Tg mice. In contrast, the expression of pro-apoptotic Bcl-xs mRNA was lost in the culture derived from OCZF-Tg mice. We found that the expression levels of RNA binding splicing regulator, Src substrate associated in mitosis of 68 kDa (Sam68) protein were markedly decreased in OCZF-Tg mice-derived osteoclasts. In addition, shRNA-mediated knockdown of Sam68 expression increased the expression of Bcl-xl mRNA, suggesting that SAM68 regulates the expression of Bcl-xl. These results indicate that OCZF overexpression reduces protein levels of Sam68, thereby promotes osteoclast survival, and suggest that LRF/OCZF is a promising target for regulating pathological bone loss.
Collapse
Affiliation(s)
- Xianghe Xu
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
- Department of Molecular Cell Biology & Oral Anatomy, Faculty of Dentistry, Kyushu University, Fukuoka, Japan
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Takeo Shobuike
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - Makoto Shiraki
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Asana Kamohara
- Department of Oral & Maxillofacial Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Hirohito Hirata
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Masatoshi Murayama
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Daisuke Mawatari
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Masaya Ueno
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Tadatsugu Morimoto
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Toshio Kukita
- Department of Molecular Cell Biology & Oral Anatomy, Faculty of Dentistry, Kyushu University, Fukuoka, Japan
| | - Masaaki Mawatari
- Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Akiko Kukita
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan.
- Research Center of Arthroplasty, Faculty of Medicine, Saga University, Saga, Japan.
| |
Collapse
|
25
|
Bachu VS, Kandoi S, Park KU, Kaufman ML, Schwanke M, Lamba DA, Brzezinski JA. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas. Dev Biol 2022; 488:131-150. [PMID: 35644251 PMCID: PMC10676565 DOI: 10.1016/j.ydbio.2022.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
How cone photoreceptors are formed during retinal development is only partially known. This is in part because we do not fully understand the gene regulatory network responsible for cone genesis. We reasoned that cis-regulatory elements (enhancers) active in nascent cones would be regulated by the same upstream network that controls cone formation. To dissect this network, we searched for enhancers active in developing cones. By electroporating enhancer-driven fluorescent reporter plasmids, we observed that a sequence within an intron of the cone-specific Pde6c gene acted as an enhancer in developing mouse cones. Similar fluorescent reporter plasmids were used to generate stable transgenic human induced pluripotent stem cells that were then grown into three-dimensional human retinal organoids. These organoids contained fluorescently labeled cones, demonstrating that the Pde6c enhancer was also active in human cones. We observed that enhancer activity was transient and labeled a minor population of developing rod photoreceptors in both mouse and human systems. This cone-enriched pattern argues that the Pde6c enhancer is activated in cells poised between rod and cone fates. Additionally, it suggests that the Pde6c enhancer is activated by the same regulatory network that selects or stabilizes cone fate choice. To further understand this regulatory network, we identified essential enhancer sequence regions through a series of mutagenesis experiments. This suggested that the Pde6c enhancer was regulated by transcription factor binding at five or more locations. Binding site predictions implicated transcription factor families known to control photoreceptor formation and families not previously associated with cone development. These results provide a framework for deciphering the gene regulatory network that controls cone genesis in both human and mouse systems. Our new transgenic human stem cell lines provide a tool for determining which cone developmental mechanisms are shared and distinct between mice and humans.
Collapse
Affiliation(s)
- Vismaya S Bachu
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
26
|
Nie J, Carpenter AC, Chopp LB, Chen T, Balmaceno-Criss M, Ciucci T, Xiao Q, Kelly MC, McGavern DB, Belkaid Y, Bosselut R. The transcription factor LRF promotes integrin β7 expression by and gut homing of CD8αα + intraepithelial lymphocyte precursors. Nat Immunol 2022; 23:594-604. [PMID: 35354951 PMCID: PMC9290758 DOI: 10.1038/s41590-022-01161-x] [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: 01/20/2021] [Accepted: 02/10/2022] [Indexed: 11/08/2022]
Abstract
While T cell receptor (TCR) αβ+CD8α+CD8β- intraepithelial lymphocytes (CD8αα+ IELs) differentiate from thymic IEL precursors (IELps) and contribute to gut homeostasis, the transcriptional control of their development remains poorly understood. In the present study we showed that mouse thymocytes deficient for the transcription factor leukemia/lymphoma-related factor (LRF) failed to generate TCRαβ+CD8αα+ IELs and their CD8β-expressing counterparts, despite giving rise to thymus and spleen CD8αβ+ T cells. LRF-deficient IELps failed to migrate to the intestine and to protect against T cell-induced colitis, and had impaired expression of the gut-homing integrin α4β7. Single-cell RNA-sequencing found that LRF was necessary for the expression of genes characteristic of the most mature IELps, including Itgb7, encoding the β7 subunit of α4β7. Chromatin immunoprecipitation and gene-regulatory network analyses both defined Itgb7 as an LRF target. Our study identifies LRF as an essential transcriptional regulator of IELp maturation in the thymus and subsequent migration to the intestinal epithelium.
Collapse
Affiliation(s)
- Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Andrea C Carpenter
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Laura B Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
- Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Ting Chen
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Mariah Balmaceno-Criss
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Qi Xiao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michael C Kelly
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yasmine Belkaid
- Metaorganism Immunology Section, Laboratory of Immune System Biology, Bethesda, MD, USA
- Microbiome core, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA.
| |
Collapse
|
27
|
Down-regulation of the transcriptional repressor ZNF802 (JAZF1) reactivates fetal hemoglobin in β 0-thalassemia/HbE. Sci Rep 2022; 12:4952. [PMID: 35322124 PMCID: PMC8943019 DOI: 10.1038/s41598-022-08920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Reactivating of fetal hemoglobin (HbF; α2γ2) can ameliorate the severity of β-thalassemia disease by compensating for adult hemoglobin deficiency in patients. Previously, microarray analysis revealed that zinc finger protein (ZNF)802 (also known as Juxta-posed with another zinc finger gene-1 (JAZF1)) was upregulated in human erythroblasts derived from adult peripheral blood compared with fetal liver-derived cells, implying a potential role as a HbF repressor. However, deficiency in ZNF802 induced by lentiviral shRNA in β0-thalassemia/hemoglobinE erythroblasts had no effect on erythroblast proliferation and differentiation. Remarkably, the induction of HBG expression was observed at the transcriptional and translational levels resulting in an increase of HbF to 35.0 ± 3.5%. Interestingly, the embryonic globin transcripts were also upregulated but the translation of embryonic globin was not detected. These results suggest ZNF802 might be a transcriptional repressor of the γ-globin gene in adult erythroid cells.
Collapse
|
28
|
Garipler G, Lu C, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Zen Petisco Fiore AP, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO. The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes. Cell Rep 2022; 38:110524. [PMID: 35294876 PMCID: PMC8972945 DOI: 10.1016/j.celrep.2022.110524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/21/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid activation. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ∼1,700 TFs with CRISPR loss-of-function screen, we found that ZBTB11 and ZFP131 are required for embryonic stem cell (ESC) pluripotency. ESCs without ZBTB11 or ZFP131 lose colony morphology, reduce proliferation rate, and upregulate transcription of genes associated with three germ layers. ZBTB11 and ZFP131 bind proximally to pro-differentiation genes. ZBTB11 or ZFP131 loss leads to an increase in H3K4me3, negative elongation factor (NELF) complex release, and concomitant transcription at associated genes. Together, our results suggest that ZBTB11 and ZFP131 maintain pluripotency by preventing premature expression of pro-differentiation genes and present a generalizable framework to maintain cellular potency.
Collapse
Affiliation(s)
- Görkem Garipler
- Department of Biology, New York University, New York, NY 10003, USA
| | - Congyi Lu
- Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Alexis Morrissey
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lorena S Lopez-Zepeda
- Department of Biology, Humboldt Universität zu Berlin, Berlin 10117, Germany; Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Yingzhen Pei
- Department of Biology, New York University, New York, NY 10003, USA
| | - Simon E Vidal
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Begüm Aydin
- Department of Biology, New York University, New York, NY 10003, USA
| | - Matthias Stadtfeld
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, Berlin 10117, Germany; Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA.
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY 10003, USA.
| |
Collapse
|
29
|
Discovery of a novel megakaryopoiesis enhancer, ingenol, promoting thrombopoiesis through PI3K-Akt signaling independent of thrombopoietin. Pharmacol Res 2022; 177:106096. [PMID: 35077844 DOI: 10.1016/j.phrs.2022.106096] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 01/09/2023]
Abstract
Thrombocytopenia, a most common complication of radiotherapy and chemotherapy, is an important cause of morbidity and mortality in cancer patients. However, there are still no approved agents for the treatment of radiation- and chemotherapy-induced thrombocytopenia (RIT and CIT, respectively). In this study, a drug screening model for predicting compounds with activity in promoting megakaryocyte (MK) differentiation and platelet production was established based on machine learning (ML), and a natural product ingenol was predicted as a potential active compound. Then, in vitro experiments showed that ingenol significantly promoted MK differentiation in K562 and HEL cells. Furthermore, a RIT mice model and c-MPL knock-out (c-MPL-/-) mice constructed by CRISPR/Cas9 technology were used to assess the therapeutic action of ingenol on thrombocytopenia. The results showed that ingenol accelerated megakaryopoiesis and thrombopoiesis both in RIT mice and c-MPL-/- mice. Next, RNA-sequencing (RNA-seq) was carried out to analyze the gene expression profile induced by ingenol during MK differentiation. Finally, through experimental verifications, we demonstrated that the activation of PI3K/Akt signaling pathway was involved in ingenol-induced MK differentiation. Blocking PI3K/Akt signaling pathway abolished the promotion of ingenol on MK differentiation. Nevertheless, inhibition of TPO/c-MPL signaling pathway could not suppress ingenol-induced MK differentiation. In conclusion, our study builds a drug screening model to discover active compounds against thrombocytopenia, reveals the critical roles of ingenol in promoting MK differentiation and platelet production, and provides a promising avenue for the treatment of RIT.
Collapse
|
30
|
Boogerd CJ, Lacraz GPA, Vértesy Á, van Kampen SJ, Perini I, de Ruiter H, Versteeg D, Brodehl A, van der Kraak P, Giacca M, de Jonge N, Junker JP, van Oudenaarden A, Vink A, van Rooij E. OUP accepted manuscript. Cardiovasc Res 2022; 119:477-491. [PMID: 35576477 PMCID: PMC10064846 DOI: 10.1093/cvr/cvac072] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
AIMS Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that is characterized by progressive loss of myocardium that is replaced by fibro-fatty cells, arrhythmias, and sudden cardiac death. While myocardial degeneration and fibro-fatty replacement occur in specific locations, the underlying molecular changes remain poorly characterized. Here, we aim to delineate local changes in gene expression to identify new genes and pathways that are relevant for specific remodelling processes occurring during ACM. METHODS AND RESULTS Using Tomo-Seq, genome-wide transcriptional profiling with high spatial resolution, we created transmural epicardial-to-endocardial gene expression atlases of explanted ACM hearts to gain molecular insights into disease-driving processes. This enabled us to link gene expression profiles to the different regional remodelling responses and allowed us to identify genes that are potentially relevant for disease progression. In doing so, we identified distinct gene expression profiles marking regions of cardiomyocyte degeneration and fibro-fatty remodelling and revealed Zinc finger and BTB domain-containing protein 11 (ZBTB11) to be specifically enriched at sites of active fibro-fatty replacement of myocardium. Immunohistochemistry indicated ZBTB11 to be induced in cardiomyocytes flanking fibro-fatty areas, which could be confirmed in multiple cardiomyopathy patients. Forced overexpression of ZBTB11 induced autophagy and cell death-related gene programmes in human cardiomyocytes, leading to increased apoptosis. CONCLUSION Our study shows the power of Tomo-Seq to unveil new molecular mechanisms in human cardiomyopathy and uncovers ZBTB11 as a novel driver of cardiomyocyte loss.
Collapse
Affiliation(s)
| | | | | | - Sebastiaan J van Kampen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ilaria Perini
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hesther de Ruiter
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Danielle Versteeg
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andreas Brodehl
- Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Petra van der Kraak
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mauro Giacca
- School of Cardiovascular Medicine and Sciences, King’s College London British Heart Foundation Centre, London, UK
| | - Nicolaas de Jonge
- Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | |
Collapse
|
31
|
Whole-transcriptome analysis in acute lymphoblastic leukemia: a report from the DFCI ALL Consortium Protocol 16-001. Blood Adv 2021; 6:1329-1341. [PMID: 34933343 PMCID: PMC8864659 DOI: 10.1182/bloodadvances.2021005634] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/27/2021] [Indexed: 11/25/2022] Open
Abstract
RNA-seq is feasible in the context of a prospective clinical trial for de novo ALL within a clinically sensitive turnaround time. RNA-seq identified several genetic alterations not detected by conventional methods that confer potential prognostic and therapeutic impact.
The molecular hallmark of childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent, prognostic genetic alterations, many of which are cryptic by conventional cytogenetics. RNA sequencing (RNA-seq) is a powerful next-generation sequencing technology that can simultaneously identify cryptic gene rearrangements, sequence mutations and gene expression profiles in a single assay. We examined the feasibility and utility of incorporating RNA-seq into a prospective multicenter phase 3 clinical trial for children with newly diagnosed ALL. The Dana-Farber Cancer Institute ALL Consortium Protocol 16-001 enrolled 173 patients with ALL who consented to optional studies and had samples available for RNA-seq. RNA-seq identified at least 1 alteration in 157 patients (91%). Fusion detection was 100% concordant with results obtained from conventional cytogenetic analyses. An additional 56 gene fusions were identified by RNA-seq, many of which confer prognostic or therapeutic significance. Gene expression profiling enabled further molecular classification into the following B-cell ALL (B-ALL) subgroups: high hyperdiploid (n = 36), ETV6-RUNX1/-like (n = 31), TCF3-PBX1 (n = 7), KMT2A-rearranged (KMT2A-R; n = 5), intrachromosomal amplification of chromosome 21 (iAMP21) (n = 1), hypodiploid (n = 1), Philadelphia chromosome (Ph)-positive/Ph-like (n = 16), DUX4-R (n = 11), PAX5 alterations (PAX5 alt; n = 11), PAX5 P80R (n = 1), ZNF384-R (n = 4), NUTM1-R (n = 1), MEF2D-R (n = 1), and others (n = 10). RNA-seq identified 141 nonsynonymous mutations in 93 patients (54%); the most frequent were RAS-MAPK pathway mutations. Among 79 patients with both low-density array and RNA-seq data for the Philadelphia chromosome-like gene signature prediction, results were concordant in 74 patients (94%). In conclusion, RNA-seq identified several clinically relevant genetic alterations not detected by conventional methods, which supports the integration of this technology into front-line pediatric ALL trials. This trial was registered at www.clinicaltrials.gov as #NCT03020030.
Collapse
|
32
|
Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing. Sci Rep 2021; 11:23927. [PMID: 34907275 PMCID: PMC8671462 DOI: 10.1038/s41598-021-03474-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
The red-crowned crane (Grus japonensis) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan. Here, we sequenced for the first time the full-length unreferenced transcriptome of red-crowned crane mixed samples using a PacBio Sequel platform. A total of 359,136 circular consensus sequences (CCS) were obtained via clustering to remove redundancy. A total of 303,544 full-length non-chimeric sequences were identified by judging whether CCS contained 5' and 3' adapters, and the poly(A) tail. Eight samples were sequenced using Illumina, and PacBio sequencing data were corrected according to the collected Illumina data to obtain more accurate full-length transcripts. A total of 4,100 long non-coding RNAs, 13,115 simple sequences repeat loci and 29 transcription factor families were identified. The expression of lncRNAs and TFs in pancreas was lowest comparing with other tissues. Many enriched immune-related transmission pathways (MHC and IL receptors) were identified in the spleen. This study will contribute to a better understanding of the gene structure and post-transcriptional regulatory network, and provide references for future studies on red-crowned cranes.
Collapse
|
33
|
Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J. The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. J Biol Chem 2021; 297:100947. [PMID: 34270961 PMCID: PMC8350017 DOI: 10.1016/j.jbc.2021.100947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/21/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) harboring broad-complex, tramtrack, and bric-a-brac (BTB) domains play important roles in development and disease. These BTB domains are thought to recruit transcriptional modulators to target DNA regions. However, a systematic molecular understanding of the mechanism of action of this TF family is lacking. Here, we identify the zinc finger BTB-TF Zbtb2 from a genetic screen for regulators of exit from pluripotency and demonstrate that its absence perturbs embryonic stem cell differentiation and the gene expression dynamics underlying peri-implantation development. We show that ZBTB2 binds the chromatin remodeler Ep400 to mediate downstream transcription. Independently, the BTB domain directly interacts with nucleosome remodeling and deacetylase and histone chaperone histone regulator A. Nucleosome remodeling and deacetylase recruitment is a common feature of BTB TFs, and based on phylogenetic analysis, we propose that this is a conserved evolutionary property. Binding to UBN2, in contrast, is specific to ZBTB2 and requires a C-terminal extension of the BTB domain. Taken together, this study identifies a BTB-domain TF that recruits chromatin modifiers and a histone chaperone during a developmental cell state transition and defines unique and shared molecular functions of the BTB-domain TF family.
Collapse
Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | | | - Anaïs F Bardet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; CNRS, University of Strasbourg, UMR7242 Biotechnology and Cell Signaling, Illkirch, France
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
34
|
Cheng ZY, He TT, Gao XM, Zhao Y, Wang J. ZBTB Transcription Factors: Key Regulators of the Development, Differentiation and Effector Function of T Cells. Front Immunol 2021; 12:713294. [PMID: 34349770 PMCID: PMC8326903 DOI: 10.3389/fimmu.2021.713294] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
The development and differentiation of T cells represents a long and highly coordinated, yet flexible at some points, pathway, along which the sequential and dynamic expressions of different transcriptional factors play prominent roles at multiple steps. The large ZBTB family comprises a diverse group of transcriptional factors, and many of them have emerged as critical factors that regulate the lineage commitment, differentiation and effector function of hematopoietic-derived cells as well as a variety of other developmental events. Within the T-cell lineage, several ZBTB proteins, including ZBTB1, ZBTB17, ZBTB7B (THPOK) and BCL6 (ZBTB27), mainly regulate the development and/or differentiation of conventional CD4/CD8 αβ+ T cells, whereas ZBTB16 (PLZF) is essential for the development and function of innate-like unconventional γδ+ T & invariant NKT cells. Given the critical role of T cells in host defenses against infections/tumors and in the pathogenesis of many inflammatory disorders, we herein summarize the roles of fourteen ZBTB family members in the development, differentiation and effector function of both conventional and unconventional T cells as well as the underlying molecular mechanisms.
Collapse
Affiliation(s)
- Zhong-Yan Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| |
Collapse
|
35
|
Boto P, Gerzsenyi TB, Lengyel A, Szunyog B, Szatmari I. Zbtb46-dependent altered developmental program in embryonic stem cell-derived blood cell progenitors. STEM CELLS (DAYTON, OHIO) 2021; 39:1322-1334. [PMID: 34058047 DOI: 10.1002/stem.3424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 04/13/2021] [Accepted: 05/19/2021] [Indexed: 11/05/2022]
Abstract
Zbtb46 is a recently identified dendritic cell (DC)-specific transcription factor with poorly defined biology. Although Zbtb46 is highly expressed in conventional DCs, evidence also points to its presence in erythroid progenitors and endothelial cells suggesting that this factor might influence the early hematopoietic development. Here, we probe the effect of this transcription factor in embryonic stem cell (ESC)-derived blood cell progenitors using chemically inducible mouse cell lines. Unexpectedly, forced expression of this protein elicited a broad repressive effect at the early stage of ESC differentiation. Ectopic expression of Zbtb46 interfered with the mesoderm formation and cell proliferation was also negatively impacted. More importantly, reduced number of CD11b+ myeloid blood cells were generated from ESC-derived Flk1+ mesoderm cells in the presence of Zbtb46. Consistent with this finding, our gene expression profiling revealed that numerous myeloid and immune response related genes, including Irf8, exhibited lower expression in the Zbtb46-primed cells. Despite these repressive effects, however, Zbtb46 overexpression was associated with enhanced formation of erythroid blood cell colonies and increased adult hemoglobin (Hbb-b1) expression at the early phase of ESC differentiation. Moreover, elevated percent of CD105 (Endoglin) positive cells were detected in the Zbtb46-primed samples. In summary, our results support that Zbtb46 suppresses the ESC-derived myeloid development and diverts mesoderm cells toward erythroid developmental pathway. Moreover, our transcriptomic data provide a resource for exploration of the Zbtb46 regulatory network in ESC-derived progenitors.
Collapse
Affiliation(s)
- Pal Boto
- Stem Cell Differentiation Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,University of Debrecen, Doctoral School of Molecular Cell and Immune Biology, Debrecen, Hungary
| | - Timea Beatrix Gerzsenyi
- Stem Cell Differentiation Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Adel Lengyel
- Stem Cell Differentiation Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Balint Szunyog
- Stem Cell Differentiation Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Istvan Szatmari
- Stem Cell Differentiation Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
36
|
Singh AK, Verma S, Kushwaha PP, Prajapati KS, Shuaib M, Kumar S, Gupta S. Role of ZBTB7A zinc finger in tumorigenesis and metastasis. Mol Biol Rep 2021; 48:4703-4719. [PMID: 34014468 DOI: 10.1007/s11033-021-06405-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/08/2021] [Indexed: 02/08/2023]
Abstract
The zinc finger and BTB (broad-complex, tramtrack and bric a brac) domain containing protein 7A (ZBTB7A) is a pleiotropic transcription factor that plays an important role in various stages of cell proliferation, differentiation, and other developmental processes. ZBTB7A is a member of the POK family that directly and specifically binds to short DNA recognition sites located near their target genes thereby acting as transcriptional activator or repressor. ZBTB7A overexpression has been associated with tumorigenesis and metastasis in various human cancer types, including breast, prostate, lung, ovarian, and colon cancer. However in some instances downregulation of ZBTB7A results in tumor progression, suggesting its role as a tumor suppressor. ZBTB7A is involved with complicated regulatory networks which include protein-protein and protein-nucleic acid interactions. ZBTB7A involvement in cancer progression and metastasis is perhaps enabled through the regulation of various signaling pathways depending on the type and genetic context of cancer. The association of ZBTB7A with other proteins affects cancer aggressiveness, therapeutic resistance and clinical outcome. This review focuses on the involvement of ZBTB7A in various signaling pathways and its role in cancer progression. We will also review the literature on ZBTB7A and cancer which could be potentially explored for its therapeutic implications.
Collapse
Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Shiv Verma
- Department of Urology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.,Department of Urology, The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Prem Prakash Kushwaha
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Kumari Sunita Prajapati
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Mohd Shuaib
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Shashank Kumar
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India.
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA. .,Department of Urology, The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA. .,Department of Nutrition, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Divison of General Medical Sciences, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA. .,Department of Urology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, 44106, USA.
| |
Collapse
|
37
|
ZNF410 represses fetal globin by singular control of CHD4. Nat Genet 2021; 53:719-728. [PMID: 33859416 PMCID: PMC8180380 DOI: 10.1038/s41588-021-00843-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/10/2021] [Indexed: 02/02/2023]
Abstract
Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes encoding γ-globins, but rather its chromatin occupancy is concentrated solely at CHD4, encoding the NuRD nucleosome remodeler, which is itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for the effects of ZNF410 on fetal globin repression. Knockout of ZNF410 or its mouse homolog Zfp410 reduces CHD4 levels by 60%, enough to substantially de-repress HbF while eluding cellular or organismal toxicity. These studies suggest a potential target for HbF induction for β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved TF with singular devotion to regulation of a chromatin subcomplex.
Collapse
|
38
|
Xie B, Khoyratty TE, Abu-Shah E, F Cespedes P, MacLean AJ, Pirgova G, Hu Z, Ahmed AA, Dustin ML, Udalova IA, Arnon TI. The Zinc Finger Protein Zbtb18 Represses Expression of Class I Phosphatidylinositol 3-Kinase Subunits and Inhibits Plasma Cell Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:1515-1527. [PMID: 33608456 PMCID: PMC7980533 DOI: 10.4049/jimmunol.2000367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/31/2021] [Indexed: 11/24/2022]
Abstract
The PI3K pathway plays a key role in B cell activation and is important for the differentiation of Ab producing plasma cells (PCs). Although much is known about the molecular mechanisms that modulate PI3K signaling in B cells, the transcriptional regulation of PI3K expression is poorly understood. In this study, we identify the zinc finger protein Zbtb18 as a transcriptional repressor that directly binds enhancer/promoter regions of genes encoding class I PI3K regulatory subunits, subsequently limiting their expression, dampening PI3K signaling and suppressing PC responses. Following activation, dividing B cells progressively downregulated Zbtb18, allowing gradual amplification of PI3K signals and enhanced development of PCs. Human Zbtb18 displayed similar expression patterns and function in human B cells, acting to inhibit development of PCs. Furthermore, a number of Zbtb18 mutants identified in cancer patients showed loss of suppressor activity, which was also accompanied by impaired regulation of PI3K genes. Taken together, our study identifies Zbtb18 as a repressor of PC differentiation and reveals its previously unappreciated function as a transcription modulator of the PI3K signaling pathway.
Collapse
Affiliation(s)
- Bin Xie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Tariq E Khoyratty
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Enas Abu-Shah
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Pablo F Cespedes
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Andrew J MacLean
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Gabriela Pirgova
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| | - Tal I Arnon
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; and
| |
Collapse
|
39
|
Barbarani G, Labedz A, Stucchi S, Abbiati A, Ronchi AE. Physiological and Aberrant γ-Globin Transcription During Development. Front Cell Dev Biol 2021; 9:640060. [PMID: 33869190 PMCID: PMC8047207 DOI: 10.3389/fcell.2021.640060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
The expression of the fetal Gγ- and Aγ-globin genes in normal development is confined to the fetal period, where two γ-globin chains assemble with two α-globin chains to form α2γ2 tetramers (HbF). HbF sustains oxygen delivery to tissues until birth, when β-globin replaces γ-globin, leading to the formation of α2β2 tetramers (HbA). However, in different benign and pathological conditions, HbF is expressed in adult cells, as it happens in the hereditary persistence of fetal hemoglobin, in anemias and in some leukemias. The molecular basis of γ-globin differential expression in the fetus and of its inappropriate activation in adult cells is largely unknown, although in recent years, a few transcription factors involved in this process have been identified. The recent discovery that fetal cells can persist to adulthood and contribute to disease raises the possibility that postnatal γ-globin expression could, in some cases, represent the signature of the fetal cellular origin.
Collapse
Affiliation(s)
- Gloria Barbarani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Agata Labedz
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Sarah Stucchi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Alessia Abbiati
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Antonella E Ronchi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| |
Collapse
|
40
|
Maksimenko OG, Fursenko DV, Belova EV, Georgiev PG. CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers. Acta Naturae 2021; 13:31-46. [PMID: 33959385 PMCID: PMC8084297 DOI: 10.32607/actanaturae.11206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.
Collapse
Affiliation(s)
- O. G. Maksimenko
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
| | | | - E. V. Belova
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
| | | |
Collapse
|
41
|
Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner. Biomedicines 2020; 8:biomedicines8120608. [PMID: 33327466 PMCID: PMC7764960 DOI: 10.3390/biomedicines8120608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.
Collapse
|
42
|
ZBTB gene expression in HIV patients: a possible new molecular mechanism of viral control. Arch Virol 2020; 166:167-178. [PMID: 33130911 DOI: 10.1007/s00705-020-04854-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
HIV infects its target cell and integrates into its genome as an essential step in its replication cycle. Proviral DNA is also subjected to the same transcriptional regulation as the host cell genome by its own transcriptional factors, with activating or repressive activity. There is a clear interaction between the presence of transcriptional repressors and a decrease in the rate of HIV replication, promoting gene silencing in infected cells, which serve as viral reservoirs. This represents a major obstacle for HIV eradication. The ZBTB gene family comprises 49 genes that encode transcription factors that have a repressor function in differentiation and development of cells of the lymphopoietic lineage, including the main target cells of HIV, CD4+ T cells. In this cross-sectional study, we evaluated the expression profile of ZBTB genes in CD4+ T cells of HIV-positive individuals with different levels of infection control. We found upregulation of gene expression of ZBTB4 (p < 0.01), ZBTB7B (p < 0.001), and ZBTB38 (p < 0.05) and downregulation of ZBTB16 (p < 0.01) in HIV-positive patients compared to HIV-negative individuals. Interestingly, in a deeper analysis, we observed that elite controllers had the highest levels of expression of the ZBTB38, ZBTB2, HIC1, ZBTB7A, ZBTB7B (ThPOK) and ZBTB4 genes, showing 2.56- to 7.60-fold upregulation compare to the ART-naïve group. These results suggest a possible contribution of these ZBTB transcriptional repressors in HIV-positive patients and a possible new molecular mechanism of viral control.
Collapse
|
43
|
LRF/ZBTB7A conservation accentuates its potential as a therapeutic target for the hematopoietic disorders. Gene 2020; 760:145020. [PMID: 32755656 DOI: 10.1016/j.gene.2020.145020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 11/22/2022]
Abstract
Conserved sequences across species have always provided valuable insights to improve our understanding on the human genome's entity and the interplay among different loci. Lymphoma/leukemia related factor (LRF) is encoded by ZBTB7A gene and belongs to an evolutionarily conserved family of transcription factors, implicated in vital cellular functions. The present data, demonstrating the wide-spread and the high overlap of the LRF/ZBTB7A recognition sites with genomic segments identified as CpG islands in the human genome, suggest that its binding capacity strongly depends on a specific sequence-encoded feature within CpGs. We have previously shown that de-methylation of the CpG island 326 lying in the ZBTB7A gene promoter is associated with impaired pharmacological induction of fetal hemoglobin in β-type hemoglobinopathies patients. Within this context we aimed to investigate the extent of the LRF/ZBTB7A conservation among primates and mouse genome, focusing our interest also on the CpG island flanking the gene's promoter region, in an effort to further establish its epigenetic regulatory role in human hematopoiesis and pharmacological involvement in hematopoietic disorders. Comparative analysis of the human ZBTB7A nucleotide and amino acid sequences and orthologous sequences among non-human primates and mouse, exhibited high conservation scores. Pathway analysis, clearly indicated that LRF/ZBTB7A influences conserved cellular processes. These data in conjunction with the high levels of expression foremost in hematopoietic tissues, highlighted LRF/ZBTB7A as an essential factor operating indisputably during hematopoiesis.
Collapse
|
44
|
He Z, Zhu J, Mo J, Zhao H, Chen Q. HBV DNA integrates into upregulated ZBTB20 in patients with hepatocellular carcinoma. Mol Med Rep 2020; 22:380-386. [PMID: 32319639 PMCID: PMC7248478 DOI: 10.3892/mmr.2020.11074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/18/2020] [Indexed: 12/27/2022] Open
Abstract
Hepatitis B virus (HBV) affects the malignant phenotype of hepatocellular carcinoma (HCC). The aim of the present study was to investigate the integration sites of HBV DNA and the expression of the zinc finger protein, zinc finger and BTB domain containing 20 (ZBTB20) in patients with hepatocellular carcinoma. Integration of the HBV gene was detected using a high-throughput sequencing technique based on the HBV-Alu-PCR method. The expression of ZBTB20 was detected by western blotting. HBVX integration sites were detected in ~70% of the HCC tissue samples. HBV-integrated subgene X detection suggested that 67% of the integrated specimens were inserted into the host X gene in a forward direction, 57% in a reverse direction, 24% in both forward and reverse directions, and 38% had two HBV integration sites. A total of 3,320 HBV integration sites were identified, including 1,397 in HCC tissues, 1,205 in paracancerous tissues and 718 in normal liver tissues. HBV integration fragments displayed enrichment in the 200–800 bp region. Additionally, the results suggested that HBV was highly integrated into transmembrane phosphatase with tensin homology, long intergenic non-protein coding RNA (LINC)00618, LOC101929241, ACTR3 pseudogene 5, LINC00999, LOC101928775, deleted in oesophageal cancer 1, LINC00824, EBF transcription factor 2 and ZBTB20 in tumour tissues. Furthermore, the expression of ZBTB20 was upregulated in HCC tissues compared with normal control liver tissues, and was associated with HBV integration frequency. The present study suggested that HBV DNA integrated into upregulated ZBTB20 in patients with hepatocellular carcinoma, which might promote the occurrence and development of HCC. Furthermore, the results of the present study may provide a theoretical basis for the diagnosis and treatment of HCC.
Collapse
Affiliation(s)
- Zebao He
- Department of Neurology, Taizhou Enze Medical Center Enze Hospital, Taizhou, Zhejiang 318000, P.R. China
| | - Jiansheng Zhu
- Department of Neurology, Taizhou Enze Medical Center Enze Hospital, Taizhou, Zhejiang 318000, P.R. China
| | - Jinggang Mo
- Department of Neurology, Taizhou Central Hospital, Taizhou University Hospital, Taizhou, Zhejiang 318000, P.R. China
| | - Haihong Zhao
- Department of Neurology, Taizhou Enze Medical Center Enze Hospital, Taizhou, Zhejiang 318000, P.R. China
| | - Qiuyue Chen
- Department of Neurology, Taizhou Central Hospital, Taizhou University Hospital, Taizhou, Zhejiang 318000, P.R. China
| |
Collapse
|
45
|
Lee WY, Pfau RB, Choi SM, Yang J, Xiao H, Putnam EM, Ryan RJ, Bixby DL, Shao L. The diagnostic challenges and clinical course of a myeloid/lymphoid neoplasm with eosinophilia and ZBTB20-JAK2 gene fusion presenting as B-lymphoblastic leukemia. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004937. [PMID: 32238402 PMCID: PMC7133749 DOI: 10.1101/mcs.a004937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/03/2020] [Indexed: 12/03/2022] Open
Abstract
We report the diagnostic challenges and the clinical course of a patient with an extraordinary presentation of B-lymphoblastic leukemia (B-ALL) with eosinophilia. We identified a novel ZBTB20-JAK2 gene fusion as a chimeric RNA transcript using the Archer platform. This gene fusion from the same patient was recently identified by Peterson et al. (2019) at the genomic level using a different sequencing technology platform. The configuration of this gene fusion predicts the production of a kinase-activating JAK2 fusion protein, which would normally lead to a diagnosis of Philadelphia chromosome–like B-ALL (Ph-like B-ALL). However, the unusual presentation of eosinophilia led us to demonstrate the presence of this gene fusion in nonlymphoid hematopoietic cells by fluorescence in situ hybridization (FISH) studies with morphologic correlation. Therefore, we believe this disease, in fact, represents blast crisis arising from an underlying myeloid neoplasm with JAK2 rearrangements. This case illustrates the difficulty in differentiating Ph-like B-ALL and myeloid/lymphoid neoplasm with eosinophilia and gene rearrangements (MLN-EGR) in blast crisis. As currently defined, the diagnosis of MLN-EGR relies on the hematologic presentations and the identification of marker gene fusions (including PCM1-JAK2, ETV6-JAK2, and BCR-JAK2). However, these same gene fusions, when limited to B-lymphoblasts, also define Ph-like B-ALL. Yet, our case does not conform to either condition. Therefore, the assessment for lineage restriction of gene rearrangements to reflect the pathophysiologic difference between B-ALL and MLN-EGR in blast crisis is likely a more robust diagnostic approach and allows the inclusion of MLN-EGR with novel gene fusions.
Collapse
Affiliation(s)
- Winston Y Lee
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Ruthann B Pfau
- Institute of Genomic Medicine, Nationwide Children's Hospital and Department of Pathology, the Ohio State University, Columbus, Ohio 43205-2664, USA
| | - Sarah M Choi
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Jiong Yang
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Hong Xiao
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Eileen M Putnam
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Russell Jh Ryan
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Dale L Bixby
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| | - Lina Shao
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109-2800, USA
| |
Collapse
|
46
|
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X. Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res 2019; 47:8388-8398. [PMID: 31226215 PMCID: PMC6895263 DOI: 10.1093/nar/gkz557] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 01/07/2023] Open
Abstract
ZBTB24, encoding a protein of the ZBTB family of transcriptional regulators, is one of four known genes—the other three being DNMT3B, CDCA7 and HELLS—that are mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a genetic disorder characterized by DNA hypomethylation and antibody deficiency. The molecular mechanisms by which ZBTB24 regulates gene expression and the biological functions of ZBTB24 are poorly understood. Here, we identified a 12-bp consensus sequence [CT(G/T)CCAGGACCT] occupied by ZBTB24 in the mouse genome. The sequence is present at multiple loci, including the Cdca7 promoter region, and ZBTB24 binding is mostly associated with gene activation. Crystallography and DNA-binding data revealed that the last four of the eight zinc fingers (ZFs) (i.e. ZF5-8) in ZBTB24 confer specificity of DNA binding. Two ICF missense mutations have been identified in the ZBTB24 ZF domain, which alter zinc-binding cysteine residues. We demonstrated that the corresponding C382Y and C407G mutations in mouse ZBTB24 abolish specific DNA binding and fail to induce Cdca7 expression. Our analyses indicate and suggest a structural basis for the sequence specific recognition by a transcription factor centrally important for the pathogenesis of ICF syndrome.
Collapse
Affiliation(s)
- Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Anup K Singh
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luis Della Coletta
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Celine Shuet Lin Kong
- Program in Cancer Biology, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| |
Collapse
|
47
|
Constantinou C, Spella M, Chondrou V, Patrinos GP, Papachatzopoulou A, Sgourou A. The multi-faceted functioning portrait of LRF/ZBTB7A. Hum Genomics 2019; 13:66. [PMID: 31823818 PMCID: PMC6905007 DOI: 10.1186/s40246-019-0252-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
Transcription factors (TFs) consisting of zinc fingers combined with BTB (for broad-complex, tram-track, and bric-a-brac) domain (ZBTB) are a highly conserved protein family that comprises a multifunctional and heterogeneous group of TFs, mainly modulating cell developmental events and cell fate. LRF/ZBTB7A, in particular, is reported to be implicated in a wide variety of physiological and cancer-related cell events. These physiological processes include regulation of erythrocyte maturation, B/T cell differentiation, adipogenesis, and thymic insulin expression affecting consequently insulin self-tolerance. In cancer, LRF/ZBTB7A has been reported to act either as oncogenic or as oncosuppressive factor by affecting specific cell processes (proliferation, apoptosis, invasion, migration, metastasis, etc) in opposed ways, depending on cancer type and molecular interactions. The molecular mechanisms via which LRF/ZBTB7A is known to exert either physiological or cancer-related cellular effects include chromatin organization and remodeling, regulation of the Notch signaling axis, cellular response to DNA damage stimulus, epigenetic-dependent regulation of transcription, regulation of the expression and activity of NF-κB and p53, and regulation of aerobic glycolysis and oxidative phosphorylation (Warburg effect). It is a pleiotropic TF, and thus, alterations to its expression status become detrimental for cell survival. This review summarizes its implication in different cellular activities and the commonly invoked molecular mechanisms triggered by LRF/ZBTB7A’s orchestrated action.
Collapse
Affiliation(s)
- Caterina Constantinou
- Biology laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece.,Laboratory of Pharmacology, Department of Medicine, University of Patras, Patras, Greece
| | - Magda Spella
- Biology laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece.,Laboratory for Molecular Respiratory Carcinogenesis, Department of Physiology, Medical Faculty, University of Patras, Patras, Greece
| | - Vasiliki Chondrou
- Biology laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, UAE
| | | | - Argyro Sgourou
- Biology laboratory, School of Science and Technology, Hellenic Open University, Patras, Greece.
| |
Collapse
|
48
|
Ohishi A, Masunaga Y, Iijima S, Yamoto K, Kato F, Fukami M, Saitsu H, Ogata T. De novo ZBTB7A variant in a patient with macrocephaly, intellectual disability, and sleep apnea: implications for the phenotypic development in 19p13.3 microdeletions. J Hum Genet 2019; 65:181-186. [PMID: 31645653 DOI: 10.1038/s10038-019-0690-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022]
Abstract
Interstitial microdeletions at chromosome 19p13.3 are frequently associated with a constellation of clinical features including macrocephaly, characteristic face, intellectual disability, and sleep apnea. Previous studies in 25 patients with 19p13.3 microdeletions have revealed loss of MAP2K2 in 24 patients and that of PIAS4 and ZBTB7A in 23 patients, suggesting that these three adjacent genes are candidate genes for the phenotypic development in 19p13.3 microdeletions. We identified a de novo likely pathogenic heterozygous missense variant of ZBTB7A (NM_015898.3:c.1152C>G, p.(Cys384Trp)) in a Japanese boy with macrocephaly, intellectual disability, and sleep apnea. This variant affects the conserved cysteine residue forming the coordinate bond with Zn2+ ion at the first zinc finger domain, and is predicted to exert a dominant-negative effect because of the generation of homo- and hetero-dimers with the wild-type and variant ZBTB7A proteins. The results argue for a critical relevance of ZBTB7A to the development of most, but probably not all, of the 19p13.3 microdeletion phenotype.
Collapse
Affiliation(s)
- Akira Ohishi
- Maternal-Fetal and Neonatal Care Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shigeo Iijima
- Maternal-Fetal and Neonatal Care Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Fumiko Kato
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University school of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan. .,Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
| |
Collapse
|
49
|
Koubi M, Poplineau M, Vernerey J, N'Guyen L, Tiberi G, Garciaz S, El-Kaoutari A, Maqbool MA, Andrau JC, Guillouf C, Saurin AJ, Duprez E. Regulation of the positive transcriptional effect of PLZF through a non-canonical EZH2 activity. Nucleic Acids Res 2019; 46:3339-3350. [PMID: 29425303 PMCID: PMC5909434 DOI: 10.1093/nar/gky080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
The transcription factor PLZF (promyelocytic leukemia zinc finger protein) acts as an epigenetic regulator balancing self-renewal and differentiation of hematopoietic cells through binding to various chromatin-modifying factors. First described as a transcriptional repressor, PLZF is also associated with active transcription, although the molecular bases underlying the differences are unknown. Here, we reveal that in a hematopoietic cell line, PLZF is predominantly associated with transcribed genes. Additionally, we identify a new association between PLZF and the histone methyltransferase, EZH2 at the genomic level. We find that co-occupancy of PLZF and EZH2 on chromatin at PLZF target genes is not associated with SUZ12 or trimethylated lysine 27 of histone H3 (H3K27me3) but with the active histone mark H3K4me3 and active transcription. Removal of EZH2 leads to an increase of PLZF binding and increased gene expression. Our results suggest a new role of EZH2 in restricting PLZF positive transcriptional activity independently of its canonical PRC2 activity.
Collapse
Affiliation(s)
- Myriam Koubi
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Julien Vernerey
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Lia N'Guyen
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Guillaume Tiberi
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Sylvain Garciaz
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Abdessamad El-Kaoutari
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| | - Muhammad A Maqbool
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, Cedex 5, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, Cedex 5, France
| | - Christel Guillouf
- Gustave Roussy, Université Paris-Saclay, Inserm U1170, CNRS Villejuif, France
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, 13288 Marseille, Cedex 9, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille Cedex 9, France
| |
Collapse
|
50
|
Qin XY, Feng J, Chen G, Dou XW, Dai XQ, Dong HL, Gong FY, Xiao F, Zhao Y, Gao XM, Wang J. ZBTB24 regulates the apoptosis of human T cells via CDCA7/TRAIL-receptor axis. Biochem Biophys Res Commun 2019; 514:259-265. [DOI: 10.1016/j.bbrc.2019.04.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/20/2019] [Indexed: 10/26/2022]
|