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Østergaard A, Boer JM, van Leeuwen FN, Pieters R, Den Boer ML. IKZF1 in acute lymphoblastic leukemia: the rise before the fall? Leuk Lymphoma 2024; 65:2077-2087. [PMID: 39210599 DOI: 10.1080/10428194.2024.2396046] [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: 04/09/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children and adolescents and in recent decades, the survival rates have risen to >90% in children largely due the introduction of risk adapted therapy. Therefore, knowledge of factors influencing risk of relapse is important. The transcription factor IKAROS is a regulator of lymphocyte development and alterations of its coding gene, IKZF1, are frequent in ALL and are associated with higher relapse risk. This concise review will discuss the normal function of IKAROS together with the effect of gene alterations in ALL such as relieved energy restriction and altered response to anti-leukemic drugs. Besides the biology, the clinical impact of gene alterations in the different subtypes of ALL will be discussed. Finally, possibilities for treating ALL with IKZF1 alterations will be considered including novel therapies like cell signaling inhibitors and immunotherapy.
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Affiliation(s)
- Anna Østergaard
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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2
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Liu M, Li Y, Yuan X, Rong S, Du J. Novel insights into RNA polymerase II transcription regulation: transcription factors, phase separation, and their roles in cardiovascular diseases. Biochem Cell Biol 2024. [PMID: 39540550 DOI: 10.1139/bcb-2024-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024] Open
Abstract
Transcription factors (TFs) are specialized proteins that bind DNA in a sequence-specific manner and modulate RNA polymerase II (Pol II) in multiple steps of the transcription process. Phase separation is a spontaneous or driven process that can form membrane-less organelles called condensates. By creating different liquid phases at active transcription sites, the formation of transcription condensates can reduce the water content of the condensate and lower the dielectric constant in biological systems, which in turn alters the structure and function of proteins and nucleic acids in the condensate. In RNA Pol II transcription, phase separation formation shortens the time at which TFs bind to target DNA sites and promotes transcriptional bursting. RNA Pol II transcription is engaged in developing several diseases, such as cardiovascular disease, by regulating different TFs and mediating the occurrence of phase separation. This review aims to summarize the advances in the molecular mechanisms of RNA Pol II transcriptional regulation, in particular the effect of TFs and phase separation. The role of RNA Pol II transcriptional regulation in cardiovascular disease will be elucidated, providing potential therapeutic targets for the management and treatment of cardiovascular disease.
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Affiliation(s)
- Mengmeng Liu
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Yingrui Li
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 4000l0, China
| | - Shunkang Rong
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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3
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Lenz J, Brehm A. Conserved mechanisms of NuRD function in hematopoetic gene expression. Enzymes 2023; 53:7-32. [PMID: 37748838 DOI: 10.1016/bs.enz.2023.07.006] [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] [Indexed: 09/27/2023]
Abstract
The Nucleosome Remodeling and Deacetylating Complex (NuRD) is ubiquitously expressed in all metazoans. It combines nucleosome remodeling and histone deacetylating activities to generate inaccessible chromatin structures and to repress gene transcription. NuRD is involved in the generation and maintenance of a wide variety of lineage-specific gene expression programs during differentiation and in differentiated cells. A close cooperation with a large number of lineage-specific transcription factors is key to allow NuRD to function in many distinct differentiation contexts. The molecular nature of this interplay between transcription factors and NuRD is complex and not well understood. This review uses hematopoiesis as a paradigm to highlight recent advances in our understanding of how transcription factors and NuRD cooperate at the molecular level during differentiation. A comparison of vertebrate and invertebrate systems serves to identify the conserved and fundamental concepts guiding functional interactions between transcription factors and NuRD. We also discuss how the transcription factor-NuRD axis constitutes a potential therapeutic target for the treatment of hemoglobinopathies.
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Affiliation(s)
- Jonathan Lenz
- Institute for Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University Marburg, Marburg, Germany
| | - Alexander Brehm
- Institute for Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University Marburg, Marburg, Germany.
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4
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Affar M, Bottardi S, Quansah N, Lemarié M, Ramón AC, Affar EB, Milot E. IKAROS: from chromatin organization to transcriptional elongation control. Cell Death Differ 2023:10.1038/s41418-023-01212-2. [PMID: 37620540 DOI: 10.1038/s41418-023-01212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
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Affiliation(s)
- Malik Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Norreen Quansah
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Maud Lemarié
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Ailyn C Ramón
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - El Bachir Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
| | - Eric Milot
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
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5
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Tsukumo SI, Subramani PG, Seija N, Tabata M, Maekawa Y, Mori Y, Ishifune C, Itoh Y, Ota M, Fujio K, Di Noia JM, Yasutomo K. AFF3, a susceptibility factor for autoimmune diseases, is a molecular facilitator of immunoglobulin class switch recombination. SCIENCE ADVANCES 2022; 8:eabq0008. [PMID: 36001653 PMCID: PMC9401627 DOI: 10.1126/sciadv.abq0008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Immunoglobulin class switch recombination (CSR) plays critical roles in controlling infections and inflammatory tissue injuries. Here, we show that AFF3, a candidate gene for both rheumatoid arthritis and type 1 diabetes, is a molecular facilitator of CSR with an isotype preference. Aff3-deficient mice exhibit low serum levels of immunoglobulins, predominantly immunoglobulin G2c (IgG2c) followed by IgG1 and IgG3 but not IgM. Furthermore, Aff3-deficient mice show weak resistance to Plasmodium yoelii infection, confirming that Aff3 modulates immunity to this pathogen. Mechanistically, the AFF3 protein binds to the IgM and IgG1 switch regions via a C-terminal domain, and Aff3 deficiency reduces the binding of AID to the switch regions less efficiently. One AFF3 risk allele for rheumatoid arthritis is associated with high mRNA expression of AFF3, IGHG2, and IGHA2 in human B cells. These findings demonstrate that AFF3 directly regulates CSR by facilitating the recruitment of AID to the switch regions.
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Affiliation(s)
- Shin-ichi Tsukumo
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
- Department of Interdisciplinary Research on Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Noé Seija
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Mizuho Tabata
- Department of Parasitology and Infectious Diseases, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoichi Maekawa
- Department of Parasitology and Infectious Diseases, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuya Mori
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Chieko Ishifune
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
| | - Yasushi Itoh
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Division of Experimental Medicine, McGill University, Montréal, QC, Canada
- Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Koji Yasutomo
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
- Department of Interdisciplinary Research on Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan
- The Research Cluster Program on Immunological Diseases, Tokushima University, Tokushima, Japan
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6
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Ne E, Crespo R, Izquierdo-Lara R, Rao S, Koçer S, Górska A, van Staveren T, Kan TW, van de Vijver D, Dekkers D, Rokx C, Moulos P, Hatzis P, Palstra RJ, Demmers J, Mahmoudi T. Catchet-MS identifies IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents. Nucleic Acids Res 2022; 50:5577-5598. [PMID: 35640596 PMCID: PMC9177988 DOI: 10.1093/nar/gkac407] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/11/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has been challenging. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to probe the differential protein composition of the latent and activated HIV-1 5′LTR. Catchet-MS identified known and novel latent 5′LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs. We demonstrate that, by targeting IKZF1 for degradation, these compounds reverse HIV-1 latency in CD4+ T-cells isolated from virally suppressed people living with HIV-1 and that they are able to synergize with other known LRAs.
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Affiliation(s)
- Enrico Ne
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Ray Izquierdo-Lara
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Selin Koçer
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Alicja Górska
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Center, The Netherlands
| | - Dick Dekkers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rg-530, PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Ee679a PO Box 2040, 3000CA Rotterdam, The Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee622 PO Box 2040, 3000CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, The Netherlands.,Department of Urology, Erasmus University Medical Center, The Netherlands
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7
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IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia. NATURE CANCER 2022; 3:595-613. [PMID: 35534777 PMCID: PMC9404532 DOI: 10.1038/s43018-022-00366-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukemia (AML) remains difficult to treat and requires new therapeutic approaches. Potent inhibitors of the chromatin-associated protein MENIN have recently entered human clinical trials, opening new therapeutic opportunities for some genetic subtypes of this disease. Using genome-scale functional genetic screens, we identified IKAROS (encoded by IKZF1) as an essential transcription factor in KMT2A (MLL1)-rearranged (MLL-r) AML that maintains leukemogenic gene expression while also repressing pathways for tumor suppression, immune regulation and cellular differentiation. Furthermore, IKAROS displays an unexpected functional cooperativity and extensive chromatin co-occupancy with mixed lineage leukemia (MLL)1-MENIN and the regulator MEIS1 and an extensive hematopoietic transcriptional complex involving homeobox (HOX)A10, MEIS1 and IKAROS. This dependency could be therapeutically exploited by inducing IKAROS protein degradation with immunomodulatory imide drugs (IMiDs). Finally, we demonstrate that combined IKAROS degradation and MENIN inhibition effectively disrupts leukemogenic transcriptional networks, resulting in synergistic killing of leukemia cells and providing a paradigm for improved drug targeting of transcription and an opportunity for rapid clinical translation.
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Younis H, Anwar MW, Khan MUG, Sikandar A, Bajwa UI. A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs). Interdiscip Sci 2021; 13:371-388. [PMID: 33959851 DOI: 10.1007/s12539-021-00433-8] [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: 06/20/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Protein-protein interaction plays an important role in the understanding of biological processes in the body. A network of dynamic protein complexes within a cell that regulates most biological processes is known as a protein-protein interaction network (PPIN). Complex prediction from PPINs is a challenging task. Most of the previous computation approaches mine cliques, stars, linear and hybrid structures as complexes from PPINs by considering topological features and fewer of them focus on important biological information contained within protein amino acid sequence. In this study, we have computed a wide variety of topological features and integrate them with biological features computed from protein amino acid sequence such as bag of words, physicochemical and spectral domain features. We propose a new Sequential Forward Feature Selection (SFFS) algorithm, i.e., random forest-based Boruta feature selection for selecting the best features from computed large feature set. Decision tree, linear discriminant analysis and gradient boosting classifiers are used as learners. We have conducted experiments by considering two reference protein complex datasets of yeast, i.e., CYC2008 and MIPS. Human and mouse complex information is taken from CORUM 3.0 dataset. Protein interaction information is extracted from the database of interacting proteins (DIP). Our proposed SFFS, i.e., random forest-based Brouta feature selection in combination with decision trees, linear discriminant analysis and Gradient Boosting Classifiers outperforms other state of art algorithms by achieving precision, recall and F-measure rates, i.e. 94.58%, 94.92% and 94.45% for MIPS, 96.31%, 93.55% and 96.02% for CYC2008, 98.84%, 98.00%, 98.87 % for CORUM humans and 96.60%, 96.70%, 96.32% for CORUM mouse dataset complexes, respectively.
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Affiliation(s)
- Haseeb Younis
- School of Professional Advancement, University of Management and Technology, Lahore, Pakistan.,Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan
| | | | - Muhammad Usman Ghani Khan
- Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Aisha Sikandar
- Govt. Girls Post Graduate College No.1 Abbottabad, Abbottabad, Pakistan
| | - Usama Ijaz Bajwa
- Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan
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9
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Lemarié M, Bottardi S, Mavoungou L, Pak H, Milot E. IKAROS is required for the measured response of NOTCH target genes upon external NOTCH signaling. PLoS Genet 2021; 17:e1009478. [PMID: 33770102 PMCID: PMC8026084 DOI: 10.1371/journal.pgen.1009478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/07/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
The tumor suppressor IKAROS binds and represses multiple NOTCH target genes. For their induction upon NOTCH signaling, IKAROS is removed and replaced by NOTCH Intracellular Domain (NICD)-associated proteins. However, IKAROS remains associated to other NOTCH activated genes upon signaling and induction. Whether IKAROS could participate to the induction of this second group of NOTCH activated genes is unknown. We analyzed the combined effect of IKAROS abrogation and NOTCH signaling on the expression of NOTCH activated genes in erythroid cells. In IKAROS-deleted cells, we observed that many of these genes were either overexpressed or no longer responsive to NOTCH signaling. IKAROS is then required for the organization of bivalent chromatin and poised transcription of NOTCH activated genes belonging to either of the aforementioned groups. Furthermore, we show that IKAROS-dependent poised organization of the NOTCH target Cdkn1a is also required for its adequate induction upon genotoxic insults. These results highlight the critical role played by IKAROS in establishing bivalent chromatin and transcriptional poised state at target genes for their activation by NOTCH or other stress signals. NOTCH1 deregulation can favor hematological malignancies. In addition to RBP-Jκ/NICD/MAML1, other regulators are required for the measured activation of NOTCH target genes. IKAROS is a known repressor of many NOTCH targets. Since it can also favor transcriptional activation and control gene expression levels, we questioned whether IKAROS could participate to the activation of specific NOTCH target genes. We are reporting that upon NOTCH induction, the absence of IKAROS impairs the measured activation of two groups of NOTCH target genes: (i) those overexpressed and characterized by an additive effect imposed by the absence of IKAROS and NOTCH induction; and (ii) those ‘desensitized’ and no more activated by NOTCH. At genes of both groups, IKAROS controls the timely recruitment of the chromatin remodelers CHD4 and BRG1. IKAROS then influences the activation of these genes through the organization of chromatin and poised transcription or through transcriptional elongation control. The importance of the IKAROS controlled and measured activation of genes is not limited to NOTCH signaling as it also characterizes Cdkn1a expression upon genotoxic stress. Thus, these results provide a new perspective on the importance of IKAROS for the adequate cellular response to stress, whether imposed by NOTCH or genotoxic insults.
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Affiliation(s)
- Maud Lemarié
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
| | - Lionel Mavoungou
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
| | - Helen Pak
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
| | - Eric Milot
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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10
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Role of Aiolos and Ikaros in the Antitumor and Immunomodulatory Activity of IMiDs in Multiple Myeloma: Better to Lose Than to Find Them. Int J Mol Sci 2021; 22:ijms22031103. [PMID: 33499314 PMCID: PMC7865245 DOI: 10.3390/ijms22031103] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022] Open
Abstract
The Ikaros zing-finger family transcription factors (IKZF TFs) are important regulators of lymphocyte development and differentiation and are also highly expressed in B cell malignancies, including Multiple Myeloma (MM), where they are required for cancer cell growth and survival. Moreover, IKZF TFs negatively control the functional properties of many immune cells. Thus, the targeting of these proteins has relevant therapeutic implications in cancer. Indeed, accumulating evidence demonstrated that downregulation of Ikaros and Aiolos, two members of the IKZF family, in malignant plasma cells as well as in adaptative and innate lymphocytes, is key for the anti-myeloma activity of Immunomodulatory drugs (IMiDs). This review is focused on IKZF TF-related pathways in MM. In particular, we will address how the depletion of IKZF TFs exerts cytotoxic effects on MM cells, by reducing their survival and proliferation, and concomitantly potentiates the antitumor immune response, thus contributing to therapeutic efficacy of IMiDs, a cornerstone in the treatment of this neoplasia.
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11
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Liu M, Jin J, Ji Y, Shan H, Zou Z, Cao Y, Yang L, Liu L, Zhou L, Lei H, Wu Y, Xu H, Wu Y. Hsp90/C terminal Hsc70-interacting protein regulates the stability of Ikaros in acute myeloid leukemia cells. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1481-1490. [PMID: 33439458 DOI: 10.1007/s11427-020-1860-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022]
Abstract
The stability of Ikaros family zinc finger protein 1 (Ikaros), a critical hematopoietic transcription factor, can be regulated by cereblon (CRBN) ubiquitin ligase stimulated by immunomodulatory drugs in multiple myeloma. However, other stabilization mechanisms of Ikaros have yet to be elucidated. In this study, we show that the pharmacologic inhibition or knockdown of Hsp90 downregulates Ikaros in acute myeloid leukemia (AML) cells. Proteasome inhibitor MG132 but not autophagy inhibitor chloroquine could suppress the Hsp90 inhibitor STA-9090-induced reduction of Ikaros, which is accompanied with the increased ubiquitination of Ikaros. Moreover, Ikaros interacts with E3 ubiquitin-ligase C terminal Hsc70 binding protein (CHIP), which mediates the STA-9090-induced ubiquitination of Ikaros. In addition, the knockdown of Ikaros effectively inhibits the proliferation of leukemia cells, but this phenomenon could be rescued by Ikaros overexpression. Collectively, our findings indicate that the interplay between HSP90 and CHIP regulates the stability of Ikaros in AML cells, which provides a novel strategy for AML treatment through targeting the HSP90/Ikaros/CHIP axis.
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Affiliation(s)
- Meng Liu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jin Jin
- Department of Ultrasound, Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009, China
| | - Yanjie Ji
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Huizhuang Shan
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhihui Zou
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yang Cao
- Department of Hematology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Li Yang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ligen Liu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hu Lei
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yunzhao Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hanzhang Xu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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12
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Read KA, Jones DM, Freud AG, Oestreich KJ. Established and emergent roles for Ikaros transcription factors in lymphoid cell development and function. Immunol Rev 2020; 300:82-99. [PMID: 33331000 DOI: 10.1111/imr.12936] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Ikaros zinc finger transcription factors are important regulators of the gene programs underlying the development of hematopoietic cell lineages. The family consists of five members: Ikaros, Helios, Aiolos, Eos, and Pegasus, which engage in both homo- and heterotypic intrafamilial interactions to exert diverse functional effects. Pioneering studies focused on the role of these factors in early lymphoid development, as their absence resulted in severe defects in lymphocyte populations. More recent work has now begun to define nuanced, stage-specific roles for Ikaros family members in the differentiation and function of mature T, B, and innate lymphoid cell populations including natural killer (NK) cells. The precise transcriptional mechanisms by which these factors function, both independently and collaboratively, is an area of active investigation. However, several key themes appear to be emerging regarding the pathways influenced by Ikaros family members, including the end-to-end regulation of cytokine signaling. Here, we review roles for Ikaros factors in lymphoid cell development, differentiation, and function, including a discussion of the current understanding of the transcriptional mechanisms they employ and considerations for the future study of this important transcription factor family.
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Affiliation(s)
- Kaitlin A Read
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA.,Biomedical Sciences Graduate Program, Columbus, OH, USA
| | - Devin M Jones
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA.,Biomedical Sciences Graduate Program, Columbus, OH, USA
| | - Aharon G Freud
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA.,Department of Pathology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA
| | - Kenneth J Oestreich
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA
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13
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Darracq A, Pak H, Bourgoin V, Zmiri F, Dellaire G, Affar EB, Milot E. NPM and NPM-MLF1 interact with chromatin remodeling complexes and influence their recruitment to specific genes. PLoS Genet 2019; 15:e1008463. [PMID: 31675375 PMCID: PMC6853375 DOI: 10.1371/journal.pgen.1008463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 11/13/2019] [Accepted: 10/04/2019] [Indexed: 11/18/2022] Open
Abstract
Nucleophosmin (NPM1) is frequently mutated or subjected to chromosomal translocation in acute myeloid leukemia (AML). NPM protein is primarily located in the nucleus, but the recurrent NPMc+ mutation, which creates a nuclear export signal, is characterized by cytoplasmic localization and leukemogenic properties. Similarly, the NPM-MLF1 translocation product favors the partial cytoplasmic retention of NPM. Regardless of their common cellular distribution, NPM-MLF1 malignancies engender different effects on hematopoiesis compared to NPMc+ counterparts, highlighting possible aberrant nuclear function(s) of NPM in NPMc+ and NPM-MLF1 AML. We performed a proteomic analysis and found that NPM and NPM-MLF1 interact with various nuclear proteins including subunits of the chromatin remodeling complexes ISWI, NuRD and P/BAF. Accordingly, NPM and NPM-MLF1 are recruited to transcriptionally active or repressed genes along with NuRD subunits. Although the overall gene expression program in NPM knockdown cells is similar to that resulting from NPMc+, NPM-MLF1 expression differentially altered gene transcription regulated by NPM. The abnormal gene regulation imposed by NPM-MLF1 can be characterized by the enhanced recruitment of NuRD to gene regulatory regions. Thus, different mechanisms would orchestrate the dysregulation of NPM function in NPMc+- versus NPM1-MLF1-associated leukemia. NPMc+ mutation is the most common mutation in acute myeloid leukemia (AML) with prevalence in one third of all AML cases. NPM can also be involved in leukemogenic translocation including the t(3;5)(q25;q34) NPM-MLF1 translocation, which is associated to bad clinical course but remains poorly defined. We are reporting that NPM and the leukemogenic NPM-MLF1 play central role in chromatin organization and gene regulation in hematopoietic cells. A proteomic analysis provided the evidence that NPM and NPM-MLF1 are interacting with the chromatin remodeling complexes NuRD, P/BAF and ISWI in hematopoietic cells. The NPM nuclear depletion, such as imposed by the leukemogenic NPMc+ mutation, or the expression of NPM-MLF1 favors the uncontrolled recruitment of the CHD4/NuRD to chromatin and the abnormal regulation of NPM-target genes. Our results suggest that the abnormal gene regulation forced by NPM-MLF1 is different than the loss of nuclear function imposed by NPMc+, and it can be characterized by the enhanced recruitment of CHD4/NuRD to genes. Thus, NPM-MLF1 is likely to promote hematopoietic malignancies by disruption of gene regulation imposed by the NuRD activity.
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Affiliation(s)
- Anaïs Darracq
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l’Île de Montréal, boulevard l’Assomption, Montreal, Quebec, Canada
- Molecular Biology Program, University of Montreal, Montreal, Quebec, Canada
| | - Helen Pak
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l’Île de Montréal, boulevard l’Assomption, Montreal, Quebec, Canada
| | - Vincent Bourgoin
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l’Île de Montréal, boulevard l’Assomption, Montreal, Quebec, Canada
| | - Farah Zmiri
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l’Île de Montréal, boulevard l’Assomption, Montreal, Quebec, Canada
| | - Graham Dellaire
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - El Bachir Affar
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l’Île de Montréal, boulevard l’Assomption, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Boulevard Edouard-Montpetit, Montreal, Quebec, Canada
| | - Eric Milot
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l’Île de Montréal, boulevard l’Assomption, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Boulevard Edouard-Montpetit, Montreal, Quebec, Canada
- * E-mail:
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14
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Powell MD, Read KA, Sreekumar BK, Oestreich KJ. Ikaros Zinc Finger Transcription Factors: Regulators of Cytokine Signaling Pathways and CD4 + T Helper Cell Differentiation. Front Immunol 2019; 10:1299. [PMID: 31244845 PMCID: PMC6563078 DOI: 10.3389/fimmu.2019.01299] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022] Open
Abstract
CD4+ T helper cells are capable of differentiating into a number of effector subsets that perform diverse functions during adaptive immune responses. The differentiation of each of these subsets is governed, in large part, by environmental cytokine signals and the subsequent activation of downstream, cell-intrinsic transcription factor networks. Ikaros zinc finger (IkZF) transcription factors are known regulators of immune cell development, including that of CD4+ T cell subsets. Over the past decade, members of the IkZF family have also been implicated in the differentiation and function of individual T helper cell subsets, including T helper 1 (TH1), TH2, TH17, T follicular (TFH), and T regulatory (TREG) cells. Now, an increasing body of literature suggests that the distinct cell-specific cytokine environments responsible for the development of each subset result in differential expression of IkZF factors across T helper populations. Intriguingly, recent studies suggest that IkZF members influence T helper subset differentiation in a feed-forward fashion through the regulation of these same cytokine-signaling pathways. Here, we review the increasingly prominent role for IkZF transcription factors in the differentiation of effector CD4+ T helper cell subsets.
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Affiliation(s)
- Michael D Powell
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, United States
| | - Kaitlin A Read
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Biomedical and Veterinary Sciences Graduate Program, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Bharath K Sreekumar
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, United States
| | - Kenneth J Oestreich
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
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15
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Iarovaia OV, Kovina AP, Petrova NV, Razin SV, Ioudinkova ES, Vassetzky YS, Ulianov SV. Genetic and Epigenetic Mechanisms of β-Globin Gene Switching. BIOCHEMISTRY (MOSCOW) 2018; 83:381-392. [PMID: 29626925 DOI: 10.1134/s0006297918040090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and β-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and β-globin genes are of interest from both theoretical and practical points of view. Alteration of balanced expression of globin genes, which usually occurs due to damage to adult β-globin genes, leads to development of severe diseases - hemoglobinopathies. In most cases, reactivation of the fetal hemoglobin gene in patients with β-thalassemia and sickle cell disease can reduce negative consequences of irreversible alterations of expression of the β-globin genes. This review focuses on the current state of research on genetic and epigenetic mechanisms underlying stage-specific switching of β-globin genes.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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16
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Read KA, Powell MD, Baker CE, Sreekumar BK, Ringel-Scaia VM, Bachus H, Martin RE, Cooley ID, Allen IC, Ballesteros-Tato A, Oestreich KJ. Integrated STAT3 and Ikaros Zinc Finger Transcription Factor Activities Regulate Bcl-6 Expression in CD4 + Th Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:2377-2387. [PMID: 28848064 DOI: 10.4049/jimmunol.1700106] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/03/2017] [Indexed: 12/24/2022]
Abstract
B cell lymphoma-6 (Bcl-6) is a transcriptional repressor that is required for the differentiation of T follicular helper (TFH) cell populations. Currently, the molecular mechanisms underlying the transcriptional regulation of Bcl-6 expression are unclear. In this study, we have identified the Ikaros zinc finger transcription factors Aiolos and Ikaros as novel regulators of Bcl-6. We found that increased expression of Bcl-6 in CD4+ Th cell populations correlated with enhanced enrichment of Aiolos and Ikaros at the Bcl6 promoter. Furthermore, overexpression of Aiolos or Ikaros, but not the related family member Eos, was sufficient to induce Bcl6 promoter activity. Intriguingly, STAT3, a known Bcl-6 transcriptional regulator, physically interacted with Aiolos to form a transcription factor complex capable of inducing the expression of Bcl6 and the TFH-associated cytokine receptor Il6ra Importantly, in vivo studies revealed that the expression of Aiolos was elevated in Ag-specific TFH cells compared with that observed in non-TFH effector Th cells generated in response to influenza infection. Collectively, these data describe a novel regulatory mechanism through which STAT3 and the Ikaros zinc finger transcription factors Aiolos and Ikaros cooperate to regulate Bcl-6 expression.
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Affiliation(s)
- Kaitlin A Read
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016
| | - Michael D Powell
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061
| | - Chandra E Baker
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016
| | - Bharath K Sreekumar
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061
| | - Veronica M Ringel-Scaia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061
| | - Holly Bachus
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - R Emily Martin
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016
| | - Ian D Cooley
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016.,Virginia Tech Carilion School of Medicine, Roanoke, VA 24016
| | - Irving C Allen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061
| | - Andre Ballesteros-Tato
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Kenneth J Oestreich
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016; .,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061.,Virginia Tech Carilion School of Medicine, Roanoke, VA 24016
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17
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Yang R, Zheng Z, Chen Q, Yang L, Huang H, Miki D, Wu W, Zeng L, Liu J, Zhou JX, Ogas J, Zhu JK, He XJ, Zhang H. The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci. Genome Biol 2017; 18:103. [PMID: 28569170 PMCID: PMC5452414 DOI: 10.1186/s13059-017-1226-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/03/2017] [Indexed: 11/27/2022] Open
Abstract
Background The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana. Results Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant. Conclusions PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences non-coding RNA production, DNA methylation, and transcriptional silencing. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1226-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Zhimin Zheng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Qing Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Wenwu Wu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Liang Zeng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Jun Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.
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18
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Lee WS, McColl B, Maksimovic J, Vadolas J. Epigenetic interplay at the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:393-404. [DOI: 10.1016/j.bbagrm.2017.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 02/02/2023]
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19
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Logie C, Stunnenberg HG. Epigenetic memory: A macrophage perspective. Semin Immunol 2016; 28:359-67. [DOI: 10.1016/j.smim.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/16/2016] [Accepted: 06/23/2016] [Indexed: 01/02/2023]
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20
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DeVilbiss AW, Tanimura N, McIver SC, Katsumura KR, Johnson KD, Bresnick EH. Navigating Transcriptional Coregulator Ensembles to Establish Genetic Networks: A GATA Factor Perspective. Curr Top Dev Biol 2016; 118:205-44. [PMID: 27137658 DOI: 10.1016/bs.ctdb.2016.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Complex developmental programs require orchestration of intrinsic and extrinsic signals to control cell proliferation, differentiation, and survival. Master regulatory transcription factors are vital components of the machinery that transduce these stimuli into cellular responses. This is exemplified by the GATA family of transcription factors that establish cell type-specific genetic networks and control the development and homeostasis of systems including blood, vascular, adipose, and cardiac. Dysregulated GATA factor activity/expression underlies anemia, immunodeficiency, myelodysplastic syndrome, and leukemia. Parameters governing the capacity of a GATA factor expressed in multiple cell types to generate cell type-specific transcriptomes include selective coregulator usage and target gene-specific chromatin states. As knowledge of GATA-1 mechanisms in erythroid cells constitutes a solid foundation, we will focus predominantly on GATA-1, while highlighting principles that can be extrapolated to other master regulators. GATA-1 interacts with ubiquitous and lineage-restricted transcription factors, chromatin modifying/remodeling enzymes, and other coregulators to activate or repress transcription and to maintain preexisting transcriptional states. Major unresolved issues include: how does a GATA factor selectively utilize diverse coregulators; do distinct epigenetic landscapes and nuclear microenvironments of target genes dictate coregulator requirements; and do gene cohorts controlled by a common coregulator ensemble function in common pathways. This review will consider these issues in the context of GATA factor-regulated hematopoiesis and from a broader perspective.
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Affiliation(s)
- A W DeVilbiss
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - N Tanimura
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - S C McIver
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - K R Katsumura
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - K D Johnson
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - E H Bresnick
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States.
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