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Hoshino A, Picard BH, Polychronopoulou S, Kelaidi C, Azarnoush S, Kracker S, Rieux-Laucat F, Boutboul D, Latour S. Loss-of-phosphorylation of IKZF1 results in gain-of-function associated with immune dysregulation. J Allergy Clin Immunol 2024; 154:229-236.e2. [PMID: 38438084 DOI: 10.1016/j.jaci.2024.01.029] [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: 04/12/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Immune dysregulation often presents as autoimmunity, inflammation, and/or lymphoproliferation. Several germline genetic defects have been associated with immune dysregulation; they include heterozygous gain-of-function (GOF) mutations in IKZF1, an essential transcription factor for hematopoiesis containing zinc finger domains (ZFs). However, in a large percentage of patients, the genetic origin of their immunedysregulation remains undetermined. OBJECTIVE A family with 2 members presenting immune dysregulation signs was studied to identify the genetic cause of their disease. METHODS Whole exome sequencing, analysis of immunologic parameters, and functional assays (including Western blotting, electrophoretic mobility shift assay during the cell cycle, and TH cell differentiation) were performed. RESULTS The 2 patients carried a novel heterozygous mutation in IKZF1 (IKZF1T398M). IKZF1 heterozygous mutations have previously been shown to be responsible for several distinct human immunologic diseases by directly affecting the ability of ZFs to bind to DNA or to dimerize. Herein, we showed that the IKZF1T398M, which is outside the ZFs, caused impaired phosphorylation of IKZF1, resulting in enhanced DNA-binding ability at the S phase of the cell cycle, reduction of the G1-S phase transition, and decreased proliferation. Confirming these data, similar functional alterations were observed with IKZF1T398A, but not with IKZF1T398D, mimicking dephosphorylation and phosphorylation, respectively. In T lymphocytes, expression of IKZF1T398M led to TH cell differentiation skewed toward TH2 cells. Thus, our data indicate that IKZF1T398M behaves as a GOF variant underlying immune dysregulation. CONCLUSION Disturbed IKZF1 phosphorylation represents a novel GOF mechanism (GOF by loss of phosphorylation (termed as GOF-LOP) associated with immune dysregulation, highlighting the regulatory role of IKZF1 during cell cycle progression through phosphorylation.
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Affiliation(s)
- Akihiro Hoshino
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Benoît Heid Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France; Université de Paris-Cité, Paris, France
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Goudi-Athens, Athens, Greece
| | - Charikleia Kelaidi
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Goudi-Athens, Athens, Greece
| | - Saba Azarnoush
- Department of Pediatric Immuno-Hematology, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sven Kracker
- Université de Paris-Cité, Paris, France; Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Frédéric Rieux-Laucat
- Université de Paris-Cité, Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM UMR 1163, Imagine Institute, Paris, France
| | - David Boutboul
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France; Université de Paris-Cité, Paris, France.
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Thomas RM, Pahl MC, Wang L, Grant SFA, Hancock WW, Wells AD. Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function. eLife 2024; 12:RP91392. [PMID: 38655862 PMCID: PMC11042806 DOI: 10.7554/elife.91392] [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] [Indexed: 04/26/2024] Open
Abstract
Ikaros is a transcriptional factor required for conventional T cell development, differentiation, and anergy. While the related factors Helios and Eos have defined roles in regulatory T cells (Treg), a role for Ikaros has not been established. To determine the function of Ikaros in the Treg lineage, we generated mice with Treg-specific deletion of the Ikaros gene (Ikzf1). We find that Ikaros cooperates with Foxp3 to establish a major portion of the Treg epigenome and transcriptome. Ikaros-deficient Treg exhibit Th1-like gene expression with abnormal production of IL-2, IFNg, TNFa, and factors involved in Wnt and Notch signaling. While Ikzf1-Treg-cko mice do not develop spontaneous autoimmunity, Ikaros-deficient Treg are unable to control conventional T cell-mediated immune pathology in response to TCR and inflammatory stimuli in models of IBD and organ transplantation. These studies establish Ikaros as a core factor required in Treg for tolerance and the control of inflammatory immune responses.
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Affiliation(s)
- Rajan M Thomas
- Center for Spatial and Functional Genomics, The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Liqing Wang
- Department of Pathology, Perelman School of Medicine at the University of Pennsylvania and The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Struan FA Grant
- Center for Spatial and Functional Genomics, The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania and The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Wayne W Hancock
- Department of Pathology, Perelman School of Medicine at the University of Pennsylvania and The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
- Department of Pathology, Perelman School of Medicine at the University of Pennsylvania and The Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
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3
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Tiniakou I, Hsu PF, Lopez-Zepeda LS, Garipler G, Esteva E, Adams NM, Jang G, Soni C, Lau CM, Liu F, Khodadadi-Jamayran A, Rodrick TC, Jones D, Tsirigos A, Ohler U, Bedford MT, Nimer SD, Kaartinen V, Mazzoni EO, Reizis B. Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Sci Immunol 2024; 9:eadi1023. [PMID: 38608038 PMCID: PMC11182672 DOI: 10.1126/sciimmunol.adi1023] [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: 04/05/2023] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9-based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, deletion of Trim33 caused rapid loss of DC progenitors, pDCs, and the cross-presenting cDC1 subset. Trim33-deficient Flt3+ progenitors up-regulated pro-inflammatory and macrophage-specific genes but failed to induce the DC differentiation program. Collectively, these data elucidate mechanisms that control Flt3L-driven differentiation of the entire DC lineage and identify Trim33 as its essential regulator.
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Affiliation(s)
- Ioanna Tiniakou
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Pei-Feng Hsu
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Lorena S. Lopez-Zepeda
- Department of Biology, Humboldt Universität zu Berlin; Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine; Berlin, Germany
| | - Görkem Garipler
- Department of Biology, New York University; New York, NY, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Nicholas M. Adams
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Colleen M. Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine; Ithaca, NY, USA
| | - Fan Liu
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine; Miami, FL, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine; New York, NY, USA
| | - Tori C. Rodrick
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine; New York, NY, USA
| | - Drew Jones
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine; New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine; New York, NY, USA
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin; Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine; Berlin, Germany
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center; Houston, TX, USA
| | - Stephen D. Nimer
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine; Miami, FL, USA
| | - Vesa Kaartinen
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry; Ann Arbor, MI, USA
| | | | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
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Zolotarev N, Wang Y, Du M, Bayer M, Grosschedl A, Cisse I, Grosschedl R. Regularly spaced tyrosines in EBF1 mediate BRG1 recruitment and formation of nuclear subdiffractive clusters. Genes Dev 2024; 38:4-10. [PMID: 38233109 PMCID: PMC10903943 DOI: 10.1101/gad.350828.123] [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: 05/26/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
B lineage priming by pioneer transcription factor EBF1 requires the function of an intrinsically disordered region (IDR). Here, we examine the role of regularly spaced tyrosines in the IDR as potential determinants of IDR function and activity of EBF1. We found that four Y > A mutations in EBF1 reduced the formation of condensates in vitro and subdiffractive clusters in vivo. Notably, Y > A mutant EBF1 was inefficient in promoting B cell differentiation and showed impaired chromatin binding, recruitment of BRG1, and activation of specific target genes. Thus, regularly spaced tyrosines in the IDR contribute to the biophysical and functional properties of EBF1.
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Affiliation(s)
- Nikolay Zolotarev
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Yuanting Wang
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Manyu Du
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Marc Bayer
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Anna Grosschedl
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Ibrahim Cisse
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany;
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5
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Kimura H, Onozawa M, Yoshida S, Miyashita N, Yokoyama S, Matsukawa T, Hirabayashi S, Goto H, Endo T, Oguri S, Fujisawa S, Mori A, Kondo T, Hidaka D, Okada K, Ota S, Kakinoki Y, Tsutsumi Y, Yamamoto S, Miyagishima T, Hashiguchi J, Nagashima T, Ibata M, Wakasa K, Haseyama Y, Fujimoto K, Ishihara T, Sakai H, Teshima T. Dominant-negative type of IKZF1 deletion showed a favorable prognosis in adult B-cell acute lymphoblastic leukemia. Ann Hematol 2023; 102:3103-3113. [PMID: 37597110 DOI: 10.1007/s00277-023-05405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/06/2023] [Indexed: 08/21/2023]
Abstract
IKZF1 deletion is a recurrent genomic alteration in B-cell acute lymphoblastic leukemia (B-ALL) and is divided into dominant-negative (DN) and loss of function (LOF) deletions. The prognostic impact of each deletion has not been fully elucidated. We retrospectively analyzed 117 patients with adult B-ALL including 60 patients with BCR::ABL1-positive B-ALL and 57 patients with BCR::ABL1-negative B-ALL by the fluorescence in situ hybridization (FISH) method for IKZF1 deletion and multiplex PCR for the 4 most common IKZF1 deletions (∆4-7, ∆2-7, ∆2-8, and ∆4-8). Samples, in which IKZF1 deletion was detected by FISH but a specific type of deletion was not identified by the PCR, were categorized as "other." Patients were classified into a DN group that had at least 1 allele of ∆4-7 (n = 23), LOF and other group (n = 40), and wildtype group (n = 54). DN type IKZF1 deletions were found in 33.3% of BCR::ABL1-positive cases and 5.2% of BCR::ABL1-negative cases. LOF and other type IKZF1 deletions were found in 43.4% of BCR::ABL1-positive cases and 24.6% of BCR::ABL1-negative cases. Patients with the DN group showed significantly higher overall survival (OS) than that of the LOF and other and WT groups (P = 0.011). Multivariate analysis including age, WBC counts, complex karyotype, and DN type IKZF1 deletion showed that the DN type of IKZF1 deletion (HR = 0.22, P = 0.013) had a positive impact and age ≥ 65 (HR = 1.92, P = 0.029) had a negative impact on OS. The prognostic impact of IKZF1 deletion depends on the type of deletion and DN type of IKZF1 deletion showed better prognosis in adult B-ALL patients.Clinical trial registration This study was part of a prospective observational study (Hokkaido Leukemia Net, UMIN000048611). It was conducted in compliance with ethical principles based on the Helsinki Declaration and was approved by the institutional review board of Hokkaido University Hospital (#015-0344).
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Affiliation(s)
- Hiroyuki Kimura
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Masahiro Onozawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan.
| | - Shota Yoshida
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Naoki Miyashita
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Shota Yokoyama
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Toshihiro Matsukawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | | | - Hideki Goto
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Tomoyuki Endo
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Satoshi Oguri
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Akio Mori
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Takeshi Kondo
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Daisuke Hidaka
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Kohei Okada
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Shuichi Ota
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | | | - Yutaka Tsutsumi
- Department of Hematology, Hakodate Municipal Hospital, Hakodate, Japan
| | - Satoshi Yamamoto
- Department of Hematology, Sapporo City General Hospital, Sapporo, Japan
| | | | - Junichi Hashiguchi
- Department of Internal Medicine, Kitami Red Cross Hospital, Kitami, Japan
| | - Takahiro Nagashima
- Department of Internal Medicine, Kitami Red Cross Hospital, Kitami, Japan
| | - Makoto Ibata
- Department of Hematology, Sapporo Kosei General Hospital, Sapporo, Japan
| | - Kentaro Wakasa
- Department of Hematology, Obihiro Kosei Hospital, Obihiro, Japan
| | | | - Katsuya Fujimoto
- Department of Hematology, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | | | - Hajime Sakai
- Department of Hematology, Teine Keijinkai Hospital, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
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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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7
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Ikzf1 as a novel regulator of microglial homeostasis in inflammation and neurodegeneration. Brain Behav Immun 2023; 109:144-161. [PMID: 36702234 DOI: 10.1016/j.bbi.2023.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/28/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
In the last two decades, microglia have emerged as key contributors to disease progression in many neurological disorders, not only by exerting their classical immunological functions but also as extremely dynamic cells with the ability to modulate synaptic and neural activity. This dynamic behavior, together with their heterogeneous roles and response to diverse perturbations in the brain parenchyma has raised the idea that microglia activation is more diverse than anticipated and that understanding the molecular mechanisms underlying microglial states is essential to unravel their role in health and disease from development to aging. The Ikzf1 (a.k.a. Ikaros) gene plays crucial roles in modulating the function and maturation of circulating monocytes and lymphocytes, but whether it regulates microglial functions and states is unknown. Using genetic tools, here we describe that Ikzf1 is specifically expressed in the adult microglia in brain regions such as cortex and hippocampus. By characterizing the Ikzf1 deficient mice, we observed that these mice displayed spatial learning deficits, impaired hippocampal CA3-CA1 long-term potentiation, and decreased spine density in pyramidal neurons of the CA1, which correlates with an increased expression of synaptic markers within microglia. Additionally, these Ikzf1 deficient microglia exhibited a severe abnormal morphology in the hippocampus, which is accompanied by astrogliosis, an aberrant composition of the inflammasome, and an altered expression of disease-associated microglia molecules. Interestingly, the lack of Ikzf1 induced changes on histone 3 acetylation and methylation levels in the hippocampus. Since the lack of Ikzf1 in mice appears to induce the internalization of synaptic markers within microglia, and severe gliosis we then analyzed hippocampal Ikzf1 levels in several models of neurological disorders. Ikzf1 levels were increased in the hippocampus of these neurological models, as well as in postmortem hippocampal samples from Alzheimer's disease patients. Finally, over-expressing Ikzf1 in cultured microglia made these cells hyporeactive upon treatment with lipopolysaccharide, and less phagocytic compared to control microglia. Altogether, these results suggest that altered Ikzf1 levels in the adult hippocampus are sufficient to induce synaptic plasticity and memory deficits via altering microglial state and function.
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Conserva MR, Redavid I, Anelli L, Zagaria A, Tarantini F, Cumbo C, Tota G, Parciante E, Coccaro N, Minervini CF, Minervini A, Specchia G, Musto P, Albano F. IKAROS in Acute Leukemia: A Positive Influencer or a Mean Hater? Int J Mol Sci 2023; 24:ijms24043282. [PMID: 36834692 PMCID: PMC9961161 DOI: 10.3390/ijms24043282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
One key process that controls leukemogenesis is the regulation of oncogenic gene expression by transcription factors acting as tumor suppressors. Understanding this intricate mechanism is crucial to elucidating leukemia pathophysiology and discovering new targeted treatments. In this review, we make a brief overview of the physiological role of IKAROS and the molecular pathway that contributes to acute leukemia pathogenesis through IKZF1 gene lesions. IKAROS is a zinc finger transcription factor of the Krüppel family that acts as the main character during hematopoiesis and leukemogenesis. It can activate or repress tumor suppressors or oncogenes, regulating the survival and proliferation of leukemic cells. More than 70% of Ph+ and Ph-like cases of acute lymphoblastic leukemia exhibit IKZF1 gene variants, which are linked to worse treatment outcomes in both childhood and adult B-cell precursor acute lymphoblastic leukemia. In the last few years, much evidence supporting IKAROS involvement in myeloid differentiation has been reported, suggesting that loss of IKZF1 might also be a determinant of oncogenesis in acute myeloid leukemia. Considering the complicated "social" network that IKAROS manages in hematopoietic cells, we aim to focus on its involvement and the numerous alterations of molecular pathways it can support in acute leukemias.
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Affiliation(s)
- Maria Rosa Conserva
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Immacolata Redavid
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Luisa Anelli
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Antonella Zagaria
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Francesco Tarantini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Cosimo Cumbo
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Giuseppina Tota
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Elisa Parciante
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Crescenzio Francesco Minervini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Angela Minervini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Giorgina Specchia
- School of Medicine, University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Pellegrino Musto
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Francesco Albano
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
- Correspondence:
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9
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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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10
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Kuijpers TW, Tromp SAM, van Leeuwen EMM, de Bree GJ. Case Report: A Highly Variable Clinical and Immunological Presentation of IKAROS Deficiency in a Single Family. Front Immunol 2022; 13:865838. [PMID: 35479066 PMCID: PMC9036438 DOI: 10.3389/fimmu.2022.865838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022] Open
Abstract
Here we describe a novel mutation in the IKZF gene encoding IKAROS, as the cause of common variable immunodeficiency (CVID). The identification of the same defect in the IKZF gene with manifestations of asymptomatic selective IgA deficiency and chronic ITP in the father and her younger brother, respectively, demonstrates the large variability of this genetic defect in one single family, while living in the same environment with a relatively similar genetic background. As discussed, clinical penetrance of the molecular defects identified by mutations in IKZF and other common gene defects in CVID in familial immune-related abnormalities makes genetic testing a necessary step for diagnosis, management, and counseling, as part of the routine immunological workup.
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Affiliation(s)
- Taco W. Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory of Immunology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Samantha A. M. Tromp
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Samantha A. M. Tromp,
| | - Ester M. M. van Leeuwen
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Godelieve J. de Bree
- Department of Internal Medicine, Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
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11
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Kadono K, Kageyama S, Nakamura K, Hirao H, Ito T, Kojima H, Dery KJ, Li X, Kupiec-Weglinski JW. Myeloid Ikaros-SIRT1 signaling axis regulates hepatic inflammation and pyroptosis in ischemia-stressed mouse and human liver. J Hepatol 2022; 76:896-909. [PMID: 34871625 PMCID: PMC9704689 DOI: 10.1016/j.jhep.2021.11.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Although Ikaros (IKZF1) is a well-established transcriptional regulator in leukocyte lymphopoiesis and differentiation, its role in myeloid innate immune responses remains unclear. Sirtuin 1 (SIRT1) is a histone/protein deacetylase involved in cellular senescence, inflammation, and stress resistance. Whether SIRT1 signaling is essential in myeloid cell activation remains uncertain, while the molecular communication between Ikaros and SIRT1, two major transcriptional regulators, has not been studied. METHODS We undertook molecular and functional studies to interrogate the significance of the myeloid Ikaros-SIRT1 axis in innate immune activation and whether it may serve as a homeostatic sentinel in human liver transplant recipients (hepatic biopsies) and murine models of sterile hepatic inflammation (liver warm ischemia-reperfusion injury in wild-type, myeloid-specific Sirt1-knockout, and CD11b-DTR mice) as well as primary bone marrow-derived macrophage (BMM) cultures (Ikaros silencing vs. overexpression). RESULTS In our clinical study, we identified increased post-reperfusion hepatic Ikaros levels, accompanied by augmented inflammasome signaling yet depressed SIRT1, as a mechanism of hepatocellular damage in liver transplant recipients. In our experimental studies, we identified infiltrating macrophages as the major source of Ikaros in IR-stressed mouse livers. Then, we demonstrated that Ikaros-regulated pyroptosis - induced by canonical inflammasome signaling in BMM cultures - was SIRT1 dependent. Consistent with the latter, myeloid-specific Ikaros signaling augmented hepatic pyroptosis to aggravate pro-inflammatory responses in vivo by negatively regulating SIRT1 in an AMPK-dependent manner. Finally, myeloid-specific SIRT1 was required to suppress pyroptosis, pro-inflammatory phenotype, and ultimately mitigate hepatocellular injury in ischemia-stressed murine livers. CONCLUSION These findings identify the Ikaros-SIRT1 axis as a novel mechanistic biomarker of pyroptosis and a putative checkpoint regulator of homeostasis in response to acute hepatic stress/injury in mouse and human livers. LAY SUMMARY This report describes how crosstalk between Ikaros and SIRT1, two major transcriptional regulators, influence acute hepatic inflammation in murine models of liver ischemia-reperfusion injury and liver transplant recipients. We show that the myeloid Ikaros-SIRT1 axis regulates inflammasome-pyroptotic cell death and hepatocellular damage in stressed livers. Thus, the Ikaros-SIRT1 axis may serve as a novel checkpoint regulator that is required for homeostasis in response to acute liver injury in mice and humans.
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Affiliation(s)
- Kentaro Kadono
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Shoichi Kageyama
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA;,Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kojiro Nakamura
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA;,Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hirofumi Hirao
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Takahiro Ito
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Hidenobu Kojima
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Kenneth J. Dery
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA
| | - Jerzy W. Kupiec-Weglinski
- Dumont-UCLA Transplantation Center, Department of Surgery, Division of Liver and Pancreas Transplantation, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA;,Corresponding author. Address: Dumont-UCLA Transplant Center, 77-120 CHS, 10833 Le Conte Ave, Los Angeles, CA 90095, USA. Tel: (310) 825-4196; Fax: (310) 267-2358. (J.W. Kupiec-Weglinski)
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12
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Flynn ED, Tsu AL, Kasela S, Kim-Hellmuth S, Aguet F, Ardlie KG, Bussemaker HJ, Mohammadi P, Lappalainen T. Transcription factor regulation of eQTL activity across individuals and tissues. PLoS Genet 2022; 18:e1009719. [PMID: 35100260 PMCID: PMC8830792 DOI: 10.1371/journal.pgen.1009719] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/10/2022] [Accepted: 01/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tens of thousands of genetic variants associated with gene expression (cis-eQTLs) have been discovered in the human population. These eQTLs are active in various tissues and contexts, but the molecular mechanisms of eQTL variability are poorly understood, hindering our understanding of genetic regulation across biological contexts. Since many eQTLs are believed to act by altering transcription factor (TF) binding affinity, we hypothesized that analyzing eQTL effect size as a function of TF level may allow discovery of mechanisms of eQTL variability. Using GTEx Consortium eQTL data from 49 tissues, we analyzed the interaction between eQTL effect size and TF level across tissues and across individuals within specific tissues and generated a list of 10,098 TF-eQTL interactions across 2,136 genes that are supported by at least two lines of evidence. These TF-eQTLs were enriched for various TF binding measures, supporting with orthogonal evidence that these eQTLs are regulated by the implicated TFs. We also found that our TF-eQTLs tend to overlap genes with gene-by-environment regulatory effects and to colocalize with GWAS loci, implying that our approach can help to elucidate mechanisms of context-specificity and trait associations. Finally, we highlight an interesting example of IKZF1 TF regulation of an APBB1IP gene eQTL that colocalizes with a GWAS signal for blood cell traits. Together, our findings provide candidate TF mechanisms for a large number of eQTLs and offer a generalizable approach for researchers to discover TF regulators of genetic variant effects in additional QTL datasets.
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Affiliation(s)
- Elise D. Flynn
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
| | - Athena L. Tsu
- New York Genome Center, New York, New York, United States of America
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
| | - Silva Kasela
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
| | - Sarah Kim-Hellmuth
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kristin G. Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Harmen J. Bussemaker
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (PM); (TL)
| | - Tuuli Lappalainen
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
- KTH Royal Institute of Technology, Stockholm, Sweden
- * E-mail: (PM); (TL)
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13
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Xia R, Cheng Y, Han X, Wei Y, Wei X. Ikaros Proteins in Tumor: Current Perspectives and New Developments. Front Mol Biosci 2021; 8:788440. [PMID: 34950704 PMCID: PMC8689071 DOI: 10.3389/fmolb.2021.788440] [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: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023] Open
Abstract
Ikaros is a zinc finger transcription factor (TF) of the Krüppel family member, which significantly regulates normal lymphopoiesis and tumorigenesis. Ikaros can directly initiate or suppress tumor suppressors or oncogenes, consequently regulating the survival and proliferation of cancer cells. Over recent decades, a series of studies have been devoted to exploring and clarifying the relationship between Ikaros and associated tumors. Therapeutic strategies targeting Ikaros have shown promising therapeutic effects in both pre-clinical and clinical trials. Nevertheless, the increasingly prominent problem of drug resistance targeted to Ikaros and its analog is gradually appearing in our field of vision. This article reviews the role of Ikaros in tumorigenesis, the mechanism of drug resistance, the progress of targeting Ikaros in both pre-clinical and clinical trials, and the potential use of associated therapy in cancer therapy.
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Affiliation(s)
- Ruolan Xia
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuejiao Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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14
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Shahin T, Kuehn HS, Shoeb MR, Gawriyski L, Giuliani S, Repiscak P, Hoeger B, Yüce Petronczki Ö, Bal SK, Zoghi S, Dmytrus J, Seruggia D, Castanon I, Rezaei N, Varjosalo M, Halbritter F, Rosenzweig SD, Boztug K. Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. Sci Immunol 2021; 6:eabe3981. [PMID: 34826259 DOI: 10.1126/sciimmunol.abe3981] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tala Shahin
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa Gawriyski
- Institute of Biotechnology, Helsinki Institute of Life Science, Proteomics Unit, University of Helsinki, Helsinki, Finland
| | - Sarah Giuliani
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Peter Repiscak
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Birgit Hoeger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Özlem Yüce Petronczki
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Sevgi Köstel Bal
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Samaneh Zoghi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Jasmin Dmytrus
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Davide Seruggia
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irinka Castanon
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, Proteomics Unit, University of Helsinki, Helsinki, Finland
| | | | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20814, USA
| | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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15
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Shibata S. Chromatin dynamics and epigenetics in skin stress adaptation. J Dermatol Sci 2021; 103:66-72. [PMID: 34238638 DOI: 10.1016/j.jdermsci.2021.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/28/2022]
Abstract
The skin, which is constantly exposed to a wide variety of environmental insults, maintains its integrity by rapidly responding to external signals. In the epidermis, most genes are set in transcriptionally poised conditions to prepare for the prompt induction of stress responding genes. Local chromatin dynamics, supported by an interplay between epigenetic regulators and transcription factors, underlies transcriptional responses upon stress exposure. This review summarizes the epigenetic mechanism regulating gene expression and discusses how stress signaling provokes chromatin reprogramming in the epidermis. Epigenetic regulators play a leading role in chromatin remodeling during stress adaptation, and the timely release and restoration of these factors are indispensable for an appropriate skin repair. Evidence for the epigenetic regulation of physiological responses in the skin is accumulating. The epigenetic environment under continuous stress stimuli may lead to the acquisition of stress tolerance, but at the same time, may also induce pathological hypersensitivity. This review describes the current understanding of epigenetics and provides the potential of epigenetic regulation in skin disease development.
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Affiliation(s)
- Sayaka Shibata
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan.
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16
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Germline IKAROS dimerization haploinsufficiency causes hematologic cytopenias and malignancies. Blood 2021; 137:349-363. [PMID: 32845957 DOI: 10.1182/blood.2020007292] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
IKAROS is a transcription factor forming homo- and heterodimers and regulating lymphocyte development and function. Germline mutations affecting the IKAROS N-terminal DNA binding domain, acting in a haploinsufficient or dominant-negative manner, cause immunodeficiency. Herein, we describe 4 germline heterozygous IKAROS variants affecting its C-terminal dimerization domain, via haploinsufficiency, in 4 unrelated families. Index patients presented with hematologic disease consisting of cytopenias (thrombocytopenia, anemia, neutropenia)/Evans syndrome and malignancies (T-cell acute lymphoblastic leukemia, Burkitt lymphoma). These dimerization defective mutants disrupt homo- and heterodimerization in a complete or partial manner, but they do not affect the wild-type allele function. Moreover, they alter key mechanisms of IKAROS gene regulation, including sumoylation, protein stability, and the recruitment of the nucleosome remodeling and deacetylase complex; none affected in N-terminal DNA binding defects. These C-terminal dimerization mutations are largely associated with hematologic disorders, display dimerization haploinsufficiency and incomplete clinical penetrance, and differ from previously reported allelic variants in their mechanism of action. Dimerization mutants contribute to the growing spectrum of IKAROS-associated diseases displaying a genotype-phenotype correlation.
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17
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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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18
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Xing Y, Wang Q, Zhang J, Li W, Duan A, Yang J, Liu Z. Chromatin accessibility of kidney tubular cells under stress reveals key transcription factor mediating acute and chronic kidney disease. FEBS J 2021; 288:5446-5458. [PMID: 33713542 DOI: 10.1111/febs.15818] [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: 09/17/2020] [Revised: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 11/28/2022]
Abstract
Cellular injury caused by stimuli plays an important role in the progression of various diseases including acute and chronic kidney diseases. The dynamic transcriptional regulation responding to stimuli underlies the important mechanism of injury. In this study, we investigated the regulatory elements and their dynamic activities in kidney tubular epithelial cells. We captured the chromatin accessibility and gene expression with ATAC-seq and RNA sequencing under a variety of extracellular stimuli including H2 O2 , TGF-β1, and FG4592 which is an agonist of hypoxia-inducible factor. Our results revealed both condition-specific and condition-shared transcription regulation. Interestingly, the shared regulation program revealed that the key transcription factor HNF1B-mediated cellular reprogramming leads to a common change among the stimuli. We found the HNF1B regulatory network was significantly disrupted in various kidney diseases.
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Affiliation(s)
- Yuexian Xing
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, School of Medicine, Southeast University, Nanjing, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Qi Wang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Jing Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Wenju Li
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Aiping Duan
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Jingping Yang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, School of Medicine, Southeast University, Nanjing, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
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19
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Wang F, Qi Z, Yao Y, Yu G, Feng T, Zhao T, Xue HH, Zhao Y, Jiang P, Bao L, Yu S. Exploring the stage-specific roles of Tcf-1 in T cell development and malignancy at single-cell resolution. Cell Mol Immunol 2021; 18:644-659. [PMID: 32868912 PMCID: PMC8027857 DOI: 10.1038/s41423-020-00527-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/04/2020] [Indexed: 01/04/2023] Open
Abstract
Tcf-1 (encoded by Tcf7) not only plays critical roles in promoting T cell development and differentiation but also has been identified as a tumor suppressor involved in preventing T cell malignancy. However, the comprehensive mechanisms of Tcf-1 involved in T cell transformation remain poorly understood. In this study, Tcf7fl/fl mice were crossed with Vav-cre, Lck-cre, or Cd4-cre mice to delete Tcf-1 conditionally at the beginning of the HSC, DN2-DN3, or DP stage, respectively. The defective T cell development phenotypes became gradually less severe as the deletion stage became more advanced in distinct mouse models. Interestingly, consistent with Tcf7-/- mice, Tcf7fl/flVav-cre mice developed aggressive T cell lymphoma within 45 weeks, but no tumors were generated in Tcf7fl/flLck-cre or Tcf7fl/flCd4-cre mice. Single-cell RNA-seq (ScRNA-seq) indicated that ablation of Tcf-1 at distinct phases can subdivide DN1 cells into three clusters (C1, C2, and C3) and DN2-DN3 cells into three clusters (C4, C5, and C6). Moreover, Tcf-1 deficiency redirects bifurcation among divergent cell fates, and clusters C1 and C4 exhibit high potential for leukemic transformation. Mechanistically, we found that Tcf-1 directly binds and mediates chromatin accessibility for both typical T cell regulators and proto-oncogenes, including Myb, Mycn, Runx1, and Lyl1 in the DN1 phase and Lef1, Id2, Dtx1, Fyn, Bcl11b, and Zfp36l2 in the DN2-DN3 phase. The aberrant expression of these genes due to Tcf-1 deficiency in very early T cells contributes to subsequent tumorigenesis. Thus, we demonstrated that Tcf-1 plays stage-specific roles in regulating early thymocyte development and transformation, providing new insights and evidence for clinical trials on T-ALL leukemia.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Profiling
- Hepatocyte Nuclear Factor 1-alpha/physiology
- Lymphocyte Activation
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/physiology
- Lymphoma, T-Cell/etiology
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Single-Cell Analysis/methods
- T-Lymphocytes, Regulatory/immunology
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Zhihong Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Yingpeng Yao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Guotao Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Tao Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Tianyan Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Hai-Hui Xue
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Peng Jiang
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI, 53707, USA
| | - Li Bao
- Department Hematology, Beijing Jishuitan Hospital, 100096, Beijing, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China.
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20
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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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21
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Astrakhantseva IV, Tomilin AN, Tarabykin VS, Nedospasov SA. Genome-Wide Mutagenesis in Mice: In Search for Genes Regulating Immune Responses and Inflammation. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795420120029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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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: 23] [Impact Index Per Article: 5.8] [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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23
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Wang Y, Zolotarev N, Yang CY, Rambold A, Mittler G, Grosschedl R. A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin. Immunity 2020; 53:1151-1167.e6. [DOI: 10.1016/j.immuni.2020.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023]
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24
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Helios Expression in Tumor-Infiltrating Lymphocytes Correlates with Overall Survival of Advanced Gastric Cancer Patients. Life (Basel) 2020; 10:life10090189. [PMID: 32927747 PMCID: PMC7555661 DOI: 10.3390/life10090189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/06/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022] Open
Abstract
Immunotherapy is a highly promising approach for the treatment of gastric cancer, the third-leading cause of overall cancer death worldwide. In particular, tumor-infiltrating lymphocytes and peripheral blood mononuclear cells are believed to mediate host immune responses, although this activity may vary depending on the activation status and/ or their microenvironments. Here, we examined the expression of a specific zinc finger transcription factor, Helios (IKZF2), in gastric tumor-infiltrating lymphocytes by immunohistochemistry and the correlation with survival. Segregation of gastric cancer patients into high- vs. low-Helios-expressing tumor-infiltrating lymphocytes showed those with high expression to exhibit longer survival in gastric cancer patients, Helicobacter pylori-infected gastric cancer patients and advanced stage (III–IV) gastric cancer patients. In particular, Helios expression was an independent factor for survival in advanced gastric cancer patients. We performed immunofluorescence staining to detect Helios expression in tumor-infiltrating lymphocytes and peripheral blood mononuclear cells. We found that Helios is expressed more in CD4+ T cells and little in CD8+ T cells in infiltrated lymphocytes in gastric cancer. In summary, we believe that the study of specific characteristics of tumor-infiltrating lymphocytes can delineate the interactions of immune and tumor cells to improve upon immunotherapy strategies.
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25
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Chromatin and transcriptome changes in human myoblasts show spatio-temporal correlations and demonstrate DPP4 inhibition in differentiated myotubes. Sci Rep 2020; 10:14336. [PMID: 32868771 PMCID: PMC7459101 DOI: 10.1038/s41598-020-70756-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/03/2020] [Indexed: 12/03/2022] Open
Abstract
Although less attention was paid to understanding physical localization changes in cell nuclei recently, depicting chromatin interaction maps is a topic of high interest. Here, we focused on defining extensive physical changes in chromatin organization in the process of skeletal myoblast differentiation. Based on RNA profiling data and 3D imaging of myogenic (NCAM1, DES, MYOG, ACTN3, MYF5, MYF6, ACTN2, and MYH2) and other selected genes (HPRT1, CDH15, DPP4 and VCAM1), we observed correlations between the following: (1) expression change and localization, (2) a gene and its genomic neighbourhood expression and (3) intra-chromosome and microscopical locus-centromere distances. In particular, we demonstrated the negative regulation of DPP4 mRNA (p < 0.001) and protein (p < 0.05) in differentiated myotubes, which coincided with a localization change of the DPP4 locus towards the nuclear lamina (p < 0.001) and chromosome 2 centromere (p < 0.001). Furthermore, we discuss the possible role of DPP4 in myoblasts (supported by an inhibition assay). We also provide positive regulation examples (VCAM1 and MYH2). Overall, we describe for the first time existing mechanisms of spatial gene expression regulation in myoblasts that might explain the issue of heterogenic responses observed during muscle regenerative therapies.
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26
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Regulation of Small GTPase Rab20 by Ikaros in B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:ijms21051718. [PMID: 32138279 PMCID: PMC7084408 DOI: 10.3390/ijms21051718] [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: 01/25/2020] [Revised: 02/20/2020] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Ikaros is a DNA-binding protein that regulates gene expression and functions as a tumor suppressor in B-cell acute lymphoblastic leukemia (B-ALL). The full cohort of Ikaros target genes have yet to be identified. Here, we demonstrate that Ikaros directly regulates expression of the small GTPase, Rab20. Using ChIP-seq and qChIP we assessed Ikaros binding and the epigenetic signature at the RAB20 promoter. Expression of Ikaros, CK2, and RAB20 was determined by qRT-PCR. Overexpression of Ikaros was achieved by retroviral transduction, whereas shRNA was used to knockdown Ikaros and CK2. Regulation of transcription from the RAB20 promoter was analyzed by luciferase reporter assay. The results showed that Ikaros binds the RAB20 promoter in B-ALL. Gain-of-function and loss-of-function experiments demonstrated that Ikaros represses RAB20 transcription via chromatin remodeling. Phosphorylation by CK2 kinase reduces Ikaros’ affinity toward the RAB20 promoter and abolishes its ability to repress RAB20 transcription. Dephosphorylation by PP1 phosphatase enhances both Ikaros’ DNA-binding affinity toward the RAB20 promoter and RAB20 repression. In conclusion, the results demonstrated opposing effects of CK2 and PP1 on expression of Rab20 via control of Ikaros’ activity as a transcriptional regulator. A novel regulatory signaling network in B-cell leukemia that involves CK2, PP1, Ikaros, and Rab20 is identified.
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27
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Oliveira VCD, Lacerda MPD, Moraes BBM, Gomes CP, Maricato JT, Souza OF, Schenkman S, Pesquero JB, Moretti NS, Rodrigues CA, Popi AF. Deregulation of Ikaros expression in B-1 cells: New insights in the malignant transformation to chronic lymphocytic leukemia. J Leukoc Biol 2019; 106:581-594. [PMID: 31299112 DOI: 10.1002/jlb.ma1118-454r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/16/2019] [Accepted: 06/10/2019] [Indexed: 01/10/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a chronic form of leukemia that originates from an abnormal expansion of CD5+ B-1 cells. Deregulation in the BCR signaling is associated with B-cell transformation. Contrariwise to B-2 cells, BCR engagement in B-1 cells results in low proliferation rate and increased apoptosis population, whereas overactivation may be associated with lymphoproliferative disorders. It has been demonstrated that several transcription factors that are involved in the B cell development play a role in the regulation of BCR function. Among them, Ikaros is considered an essential regulator of lymphoid differentiation and activation. Several reports suggest that Ikaros expression is deregulated in different forms of leukemia. Herein, we demonstrated that CLL cells show decreased Ikaros expression and abnormal cytoplasmic cell localization. These alterations were also observed in radioresistant B-1 cells, which present high proliferative activity, suggesting that abnormal localization of Ikaros could determine its loss of function. Furthermore, Ikaros knockdown increased the expression of BCR pathway components in murine B-1 cells, such as Lyn, Blnk, and CD19. Additionally, in the absence of Ikaros, B-1 cells become responsive to BCR stimulus, increasing cell proliferation even in the absence of antigen stimulation. These results suggested that Ikaros is an important controller of B-1 cell proliferation by interfering with the BCR activity. Therefore, altered Ikaros expression in CLL or radioresistant B-1 cells could determine a responsive status of BCR to self-antigens, which would culminate in the clonal expansion of B-1 cells.
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Affiliation(s)
- Vivian Cristina de Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Marcelo Pitombeira de Lacerda
- Disciplina de Hematologia e Hemoterapia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Bárbara Bomfim Muniz Moraes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Caio Perez Gomes
- Departamento de Biologia Molecular, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Juliana Terzi Maricato
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Olivia Fonseca Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - João Bosco Pesquero
- Departamento de Biologia Molecular, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Celso Arrais Rodrigues
- Disciplina de Hematologia e Hemoterapia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | - Ana Flavia Popi
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
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28
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Latour YL, Gobert AP, Wilson KT. The role of polyamines in the regulation of macrophage polarization and function. Amino Acids 2019; 52:151-160. [PMID: 31016375 DOI: 10.1007/s00726-019-02719-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/04/2019] [Indexed: 01/18/2023]
Abstract
Naturally occurring polyamines are ubiquitously distributed and play important roles in cell development, amino acid and protein synthesis, oxidative DNA damage, proliferation, and cellular differentiation. Macrophages are essential in the innate immune response, and contribute to tissue remodeling. Naïve macrophages have two major potential fates: polarization to (1) the classical pro-inflammatory M1 defense response to bacterial pathogens and tumor cells, and (2) the alternatively activated M2 response, induced in the presence of parasites and wounding, and also implicated in the development of tumor-associated macrophages. ODC, the rate-limiting enzyme in polyamine synthesis, leads to an increase in putrescine levels, which impairs M1 gene transcription. Additionally, spermidine and spermine can regulate translation of pro-inflammatory mediators in activated macrophages. In this review, we focus on polyamines in macrophage activation patterns in the context of gastrointestinal inflammation and carcinogenesis. We seek to clarify mechanisms of innate immune regulation by polyamine metabolism and potential novel therapeutic targets.
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Affiliation(s)
- Yvonne L Latour
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 2215 Garland Avenue, Room 1030C Medical Research Building IV, Nashville, TN, 37232, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain P Gobert
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 2215 Garland Avenue, Room 1030C Medical Research Building IV, Nashville, TN, 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 2215 Garland Avenue, Room 1030C Medical Research Building IV, Nashville, TN, 37232, USA. .,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA. .,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, USA. .,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
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29
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Yi L, Hu Q, Zhou J, Liu Z, Li H. Alternative splicing of Ikaros regulates the FUT4/Le X-α5β1 integrin-FAK axis in acute lymphoblastic leukemia. Biochem Biophys Res Commun 2019; 510:128-134. [PMID: 30683310 DOI: 10.1016/j.bbrc.2019.01.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/12/2019] [Indexed: 12/24/2022]
Abstract
Unveiling the mechanism of the relapse of acute lymphoblastic leukemia (ALL) is the key to improve the prognosis of ALL and remains a huge challenge. Glycan-based interactions play a vital role in immune surveillance, cell-cell adhesion and cell-matrix interaction, contributing to treatment failure in tumor. However, the glycan essential for leukemia development and its upstream regulatory mechanism by oncogenic drivers were rarely reported. Here, we demonstrated that LeX, a well-characterized cancer-related glycan epitope, strengthened the cell-matrix interaction via glycosylating α5β1 integrin under the control of the driver oncogenic Ikaros isoform (IK6) in ALL. By analyzing the expression profile of Ikaros and the level of FUT4/LeX in clinical samples, we found that FUT4/LeX was positively correlated with dysfunctional Ikaros isoforms. IK1 (Full length Ikaros) regulates the level of FUT4 as a transcription repressor, while IK6 abolished the wild-type Ikaros mediated transcriptional repression and resulted in higher level of FUT4 expression. Moreover, we demonstrated that FUT4 could activate α5β1-mediated sequential signal transduction and accelerate adhesion and invasion between integrin α5β1 in leukemia cells and fibronectin in extracellular matrix (ECM) via increasing glycosylation. Together, our study provides a new insight into the mechanisms by which Ikaros mutation induced ALL cells invasion and a potential strategy for drug-resistance ALL by blocking LeX in combination with common chemotherapy.
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Affiliation(s)
- Lijun Yi
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China
| | - Qinghua Hu
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China
| | - Jing Zhou
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China
| | - Zhiqiang Liu
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China
| | - Hong Li
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China.
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30
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Kouprina N, Petrov N, Molina O, Liskovykh M, Pesenti E, Ohzeki JI, Masumoto H, Earnshaw WC, Larionov V. Human Artificial Chromosome with Regulated Centromere: A Tool for Genome and Cancer Studies. ACS Synth Biol 2018; 7:1974-1989. [PMID: 30075081 PMCID: PMC6154217 DOI: 10.1021/acssynbio.8b00230] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since their description in the late 1990s, Human Artificial Chromosomes (HACs) bearing functional kinetochores have been considered as promising systems for gene delivery and expression. More recently a HAC assembled from a synthetic alphoid DNA array has been exploited in studies of centromeric chromatin and in assessing the impact of different epigenetic modifications on kinetochore structure and function in human cells. This HAC was termed the alphoidtetO-HAC, as the synthetic monomers each contained a tetO sequence in place of the CENP-B box that can be targeted specifically with tetR-fusion proteins. Studies in which the kinetochore chromatin of the alphoidtetO-HAC was specifically modified, revealed that heterochromatin is incompatible with centromere function and that centromeric transcription is important for centromere assembly and maintenance. In addition, the alphoidtetO-HAC was modified to carry large gene inserts that are expressed in target cells under conditions that recapitulate the physiological regulation of endogenous loci. Importantly, the phenotypes arising from stable gene expression can be reversed when cells are "cured" of the HAC by inactivating its kinetochore in proliferating cell populations, a feature that provides a control for phenotypic changes attributed to expression of HAC-encoded genes. AlphoidtetO-HAC-based technology has also been used to develop new drug screening and assessment strategies to manipulate the CIN phenotype in cancer cells. In summary, the alphoidtetO-HAC is proving to be a versatile tool for studying human chromosome transactions and structure as well as for genome and cancer studies.
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Affiliation(s)
- Natalay Kouprina
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States,E-mail: . Tel: +1-240-760-7325
| | - Nikolai Petrov
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States
| | - Oscar Molina
- Josep
Carreras Leukaemia Research Institute, School of Medicine, University
of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Mikhail Liskovykh
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States
| | - Elisa Pesenti
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Jun-ichirou Ohzeki
- Laboratory
of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818d Japan
| | - Hiroshi Masumoto
- Laboratory
of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818d Japan,E-mail: . Tel: +81-438-52-395
| | - William C. Earnshaw
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland,E-mail: . Tel: +44-(0)131-650-7101
| | - Vladimir Larionov
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States,E-mail: . Tel: +1-240-760-7325
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31
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Oh KS, Gottschalk RA, Lounsbury NW, Sun J, Dorrington MG, Baek S, Sun G, Wang Z, Krauss KS, Milner JD, Dutta B, Hager GL, Sung MH, Fraser IDC. Dual Roles for Ikaros in Regulation of Macrophage Chromatin State and Inflammatory Gene Expression. THE JOURNAL OF IMMUNOLOGY 2018; 201:757-771. [PMID: 29898962 DOI: 10.4049/jimmunol.1800158] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. The transcription factor Ikaros has been shown to play a critical role in lymphoid cell development and differentiation; however, its function in myeloid cells and innate immune responses is less appreciated. Using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility, we describe unexpected dual repressor and activator functions for Ikaros in the LPS response of murine macrophages. Consistent with the described function of Ikaros as transcriptional repressor, Ikzf1-/- macrophages showed enhanced induction for select responses. In contrast, we observed a dramatic defect in expression of many delayed LPS response genes, and chromatin immunoprecipitation sequencing analyses support a key role for Ikaros in sustained NF-κB chromatin binding. Decreased Ikaros expression in Ikzf1+/- mice and human cells dampens these Ikaros-enhanced inflammatory responses, highlighting the importance of quantitative control of Ikaros protein level for its activator function. In the absence of Ikaros, a constitutively open chromatin state was coincident with dysregulation of LPS-induced chromatin remodeling, gene expression, and cytokine responses. Together, our data suggest a central role for Ikaros in coordinating the complex macrophage transcriptional program in response to pathogen challenge.
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Affiliation(s)
- Kyu-Seon Oh
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Rachel A Gottschalk
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nicolas W Lounsbury
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jing Sun
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Michael G Dorrington
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Guangping Sun
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Ze Wang
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kathleen S Krauss
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Bhaskar Dutta
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Iain D C Fraser
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
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Boutboul D, Kuehn HS, Van de Wyngaert Z, Niemela JE, Callebaut I, Stoddard J, Lenoir C, Barlogis V, Farnarier C, Vely F, Yoshida N, Kojima S, Kanegane H, Hoshino A, Hauck F, Lhermitte L, Asnafi V, Roehrs P, Chen S, Verbsky JW, Calvo KR, Husami A, Zhang K, Roberts J, Amrol D, Sleaseman J, Hsu AP, Holland SM, Marsh R, Fischer A, Fleisher TA, Picard C, Latour S, Rosenzweig SD. Dominant-negative IKZF1 mutations cause a T, B, and myeloid cell combined immunodeficiency. J Clin Invest 2018; 128:3071-3087. [PMID: 29889099 DOI: 10.1172/jci98164] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/17/2018] [Indexed: 01/20/2023] Open
Abstract
Ikaros/IKZF1 is an essential transcription factor expressed throughout hematopoiesis. IKZF1 is implicated in lymphocyte and myeloid differentiation and negative regulation of cell proliferation. In humans, somatic mutations in IKZF1 have been linked to the development of B cell acute lymphoblastic leukemia (ALL) in children and adults. Recently, heterozygous germline IKZF1 mutations have been identified in patients with a B cell immune deficiency mimicking common variable immunodeficiency. These mutations demonstrated incomplete penetrance and led to haploinsufficiency. Herein, we report 7 unrelated patients with a novel early-onset combined immunodeficiency associated with de novo germline IKZF1 heterozygous mutations affecting amino acid N159 located in the DNA-binding domain of IKZF1. Different bacterial and viral infections were diagnosed, but Pneumocystis jirovecii pneumonia was reported in all patients. One patient developed a T cell ALL. This immunodeficiency was characterized by innate and adaptive immune defects, including low numbers of B cells, neutrophils, eosinophils, and myeloid dendritic cells, as well as T cell and monocyte dysfunctions. Notably, most T cells exhibited a naive phenotype and were unable to evolve into effector memory cells. Functional studies indicated these mutations act as dominant negative. This defect expands the clinical spectrum of human IKZF1-associated diseases from somatic to germline, from haploinsufficient to dominant negative.
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Affiliation(s)
- David Boutboul
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Zoé Van de Wyngaert
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France.,University Paris Descartes Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Isabelle Callebaut
- Centre National de la Recherche Scientifique UMR 7590, Sorbonne Universities, University Pierre et Marie Curie-Paris 6-MNHN-IRD-IUC, Paris, France
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Christelle Lenoir
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France
| | - Vincent Barlogis
- Department of Paediatric Haematology-Oncology, La Timone Hospital, Marseille, France
| | - Catherine Farnarier
- Assistance Publique - Hôpitaux de Marseille (APHM) Hôpital Timone Enfants, Service d'Immunologie - Marseille Immunopôle, Marseille, France
| | - Frédéric Vely
- Aix Marseille University, APHM, CNRS, Inserm, Centre d'Immunologie de Marseille-Luminy (CIML), Hôpital Timone Enfants, Service d'Immunologie - Marseille Immunopôle, Marseille, France
| | - Nao Yoshida
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akihiro Hoshino
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fabian Hauck
- Department of Pediatric Immunology and Rheumatology, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Ludovic Lhermitte
- University Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Inserm 1151 and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (APHP), Necker-Enfants Malades Hospital, Paris, France
| | - Vahid Asnafi
- University Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Inserm 1151 and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (APHP), Necker-Enfants Malades Hospital, Paris, France
| | - Philip Roehrs
- Levine Children's Hospital, Carolinas Healthcare System, Charlotte, North Carolina, USA
| | - Shaoying Chen
- Department of Pediatrics, Division of Rheumatology, Medical College of Wisconsin, Madison, Wisconsin, USA
| | - James W Verbsky
- Department of Pediatrics, Division of Rheumatology, Medical College of Wisconsin, Madison, Wisconsin, USA
| | - Katherine R Calvo
- Hematology section, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Ammar Husami
- Division of Human Genetics and Division of Immune Deficiency and Bone Marrow Transplant, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Kejian Zhang
- Division of Human Genetics and Division of Immune Deficiency and Bone Marrow Transplant, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Joseph Roberts
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - David Amrol
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - John Sleaseman
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Amy P Hsu
- Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Rebecca Marsh
- Division of Human Genetics and Division of Immune Deficiency and Bone Marrow Transplant, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Alain Fischer
- University Paris Descartes Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, APHP, Paris, France.,Collège de France, Paris, France
| | - Thomas A Fleisher
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Capucine Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France.,Centre d'Etude des Déficits Immunitaires, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
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Jedi M, Young GP, Pedersen SK, Symonds EL. Methylation and Gene Expression of BCAT1 and IKZF1 in Colorectal Cancer Tissues. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2018; 12:1179554918775064. [PMID: 29780264 PMCID: PMC5952276 DOI: 10.1177/1179554918775064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/12/2018] [Indexed: 12/20/2022]
Abstract
The genes BCAT1 and IKZF1 are hypermethylated in colorectal cancer (CRC), but little is known about how this relates to gene expression. This study assessed the relationship between methylation and gene expression of BCAT1 and IKZF1 in CRC and adjacent non-neoplastic tissues. The tissues were obtained at surgery from 36 patients diagnosed with different stages of CRC (stage I n = 8, stage II n = 13, stage III n = 10, stage IV n = 5). Methylated BCAT1 and IKZF1 were detected in 92% and 72% CRC tissues, respectively, with levels independent of stage (P > .05). In contrast, only 31% and 3% of non-neoplastic tissues were methylated for BCAT1 and IKZF1, respectively (P < .001). The IKZF1 messenger RNA (mRNA) expression was significantly lower in the cancer tissues compared with that of non-neoplastic tissues, whereas the BCAT1 mRNA levels were similar. The latter may be due to the BCAT1 polymerase chain reaction assay detecting more than 1 mRNA transcript. Further studies are warranted to establish the role of the epigenetic silencing of IKZF1 in colorectal oncogenesis.
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Affiliation(s)
- Maher Jedi
- Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia
| | | | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia
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Ueta M, Hamuro J, Nishigaki H, Nakamura N, Shinomiya K, Mizushima K, Hitomi Y, Tamagawa-Mineoka R, Yokoi N, Naito Y, Tokunaga K, Katoh N, Sotozono C, Kinoshita S. Mucocutaneous inflammation in the Ikaros Family Zinc Finger 1-keratin 5-specific transgenic mice. Allergy 2018; 73:395-404. [PMID: 28914974 DOI: 10.1111/all.13308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Our genomewide association study documented an association between cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis (CM-SJS/TEN) and Ikaros Family Zinc Finger 1 (IKZF1). Few studies examined biological and pathological functions of IKZF1 in mucosal immunity. We hypothesized that IKZF1 contributes to the mucocutaneous inflammation. METHODS Human skin and conjunctival tissues were obtained for immunohistological studies. Primary human conjunctival epithelial cells (PHCjECs) and adult human epidermal keratinocytes (HEKa) also used for gene expression analysis. We also generated K5-Ikzf1-EGFP transgenic mice (Ikzf1 Tg) by introducing the Ik1 isoform into cells expressing keratin 5, which is expressed in epithelial tissues such as the epidermis and conjunctiva, and then examined them histologically and investigated gene expression of the epidermis. Moreover, Ikzf1 Tg were induced allergic contact dermatitis. RESULTS We found that human epidermis and conjunctival epithelium expressed IKZF1, and in PHCjECs and HEKa, the expression of IKZF1 mRNA was upregulated by stimulation with polyI:C, a TLR3 ligand. In Ikzf1 Tg, we observed dermatitis and mucosal inflammation including the ocular surface. In contact dermatitis model, inflammatory infiltrates in the skin of Ikzf1 Tg were significantly increased compared with wild type. Microarray analysis showed that Lcn2, Adh7, Epgn, Ifi202b, Cdo1, Gpr37, Duoxa1, Tnfrsf4, and Enpp5 genes were significantly upregulated in the epidermis of Ikzf1 Tg compared with wild type. CONCLUSION Our findings support the hypothesis that Ikaros might participate in mucocutaneous inflammation.
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Affiliation(s)
- M. Ueta
- Department of Frontier Medical Science and Technology for Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - J. Hamuro
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - H. Nishigaki
- Department of Frontier Medical Science and Technology for Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - N. Nakamura
- Department of Dermatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - K. Shinomiya
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - K. Mizushima
- Department of Molecular Gastroenterology and Hepatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - Y. Hitomi
- Department of Human Genetics; Graduate School of Medicine; University of Tokyo; Tokyo Japan
| | - R. Tamagawa-Mineoka
- Department of Dermatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - N. Yokoi
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - Y. Naito
- Department of Molecular Gastroenterology and Hepatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - K. Tokunaga
- Department of Human Genetics; Graduate School of Medicine; University of Tokyo; Tokyo Japan
| | - N. Katoh
- Department of Dermatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - C. Sotozono
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - S. Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
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35
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Oliveira VCD, Sodré ACP, Gomes CP, Moretti NS, Pesquero JB, Popi AF. Alteration in Ikaros expression promotes B-1 cell differentiation into phagocytes. Immunobiology 2017; 223:252-257. [PMID: 29107383 DOI: 10.1016/j.imbio.2017.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/29/2017] [Accepted: 10/03/2017] [Indexed: 12/11/2022]
Abstract
Ikaros is a broad transcription factor pointed as a critical regulator of lymphocyte development. Recent reports have emphasized that distinct isoforms of Ikaros control the dichotomy of the hematopoietic system into lymphoid and myeloid lineages. In addition, expression of dominant-negative isoforms of Ikaros is linked to abnormal hematopoiesis, which could culminate in hematological disorders due to loss of function of the protein. B-1 cells are an intriguing subtype of B-lymphocytes that preserves some myeloid characteristics. These cells are able to differentiate into phagocytes (B-1CDP - B-1 cell derived phagocytes) in vitro and in vivo. During such process, reprogramming of gene expression occurs: lymphoid genes are turned off, while expression of myeloid genes is increased. This study aims to investigate whether Ikaros could be related to the control of B-1 cell plasticity. Interestingly, Ikaros expression by B-1CDP cells was found to be relatively low, and the protein is abnormally localized in the cytoplasm. Moreover, the isoforms expressed by B-1 cells are different from those expressed by other lymphocytes, with expression of active isoforms being almost absent in B-1CDP. Based on these findings, Ikaros could be an important factor driving the differentiation and proliferation of B-1 cells.
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Affiliation(s)
- Vivian Cristina de Oliveira
- Disciplina de Imunologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Brazil
| | - Ana Clara Pires Sodré
- Disciplina de Imunologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Brazil
| | - Caio Perez Gomes
- Departamento de Biologia Molecular, Universidade Federal de São Paulo, Brazil
| | - Nilmar Silvio Moretti
- Disciplina de Parasitologia Departamento de Microbiologia, Imunologia e Parasitologia Universidade Federal de São Paulo, Brazil
| | - João Bosco Pesquero
- Departamento de Biologia Molecular, Universidade Federal de São Paulo, Brazil
| | - Ana Flavia Popi
- Disciplina de Imunologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Brazil.
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Bose P, Verstovsek S. Prognosis of Primary Myelofibrosis in the Genomic Era. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2017; 16 Suppl:S105-13. [PMID: 27521306 DOI: 10.1016/j.clml.2016.02.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 02/07/2023]
Abstract
Currently, prognostication in primary myelofibrosis (PMF) relies on the International Prognostic Scoring System (IPSS), dynamic IPSS (DIPSS), and DIPSS-plus, which incorporate age, blood counts, constitutional symptoms, circulating blasts, red cell transfusion need, and karyotype. Although the JAK2 V617F mutation was discovered a decade ago and MPL mutations shortly thereafter, it was the recent discovery of CALR mutations in the vast majority of JAK2/MPL-unmutated patients and recognition of the powerful impact of CALR mutations and triple-negative (JAK2/MPL/CALR-negative) status on outcome that set the stage for revision of traditional prognostic models to include molecular information. Additionally, the advent of next-generation sequencing has identified a host of previously unrecognized somatic mutations across hematologic malignancies. As in the myelodysplastic syndromes, the majority of common and prognostically informative mutations in PMF affect epigenetic regulation and mRNA splicing. Thus, a need has arisen to incorporate mutational information on genes such as ASXL1 and SRSF2 into risk stratification systems. Mutations in yet other genes appear to be important players in leukemic transformation, and new insights into disease pathogenesis are emerging. Finally, the number of prognostically detrimental mutations may affect both survival and response to ruxolitinib, which has significant implications for clinical decision making. In this review, we briefly summarize the prognostic models in use today and discuss in detail the somatic mutations commonly encountered in patients with PMF, along with their prognostic implications and role in leukemic transformation. Emerging prognostic models that incorporate new molecular information into existing systems or exclude clinical variables are also presented.
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Affiliation(s)
- Prithviraj Bose
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX.
| | - Srdan Verstovsek
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
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Schischlik F, Kralovics R. Mutations in myeloproliferative neoplasms - their significance and clinical use. Expert Rev Hematol 2017; 10:961-973. [PMID: 28914569 DOI: 10.1080/17474086.2017.1380515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Clonal hematologic diseases of the blood such as polycythemia vera, essential thrombocythemia and primary myelofibrosis belong to the BCR-ABL negative Myeloproliferative Neoplasms (MPN). These diseases are characterized by clonal expansion of hematopoietic precursor cells followed by increased production of differentiated cells of the myeloid lineage. Initiation of clonal hematopoiesis, formation of a clinical phenotype as well as disease progression form part of MPN disease evolution. The disease is driven by acquired somatic mutations in critical pathways such as cytokine signaling, epigenetic regulation, RNA splicing, and transcription factor signaling. Areas covered: The following review aims to provide an overview of the mutational landscape of MPN, the impact of these mutations in MPN pathogenesis as well as their prognostic value. Finally, a summary of how these mutations are being used or could potentially be used for the treatment of MPN patients is presented. Expert commentary: The genetic landscape of MPN patients has been successfully dissected within the past years with the advent of new sequencing technologies. Integrating the genetic information within a clinical setting is already benefitting patients in terms of disease monitoring and prognostic information of disease progression but will be further intensified within the next years.
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Affiliation(s)
- Fiorella Schischlik
- a CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna , Austria
| | - Robert Kralovics
- a CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna , Austria
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Kobitzsch B, Gökbuget N, Schwartz S, Reinhardt R, Brüggemann M, Viardot A, Wäsch R, Starck M, Thiel E, Hoelzer D, Burmeister T. Loss-of-function but not dominant-negative intragenic IKZF1 deletions are associated with an adverse prognosis in adult BCR-ABL-negative acute lymphoblastic leukemia. Haematologica 2017; 102:1739-1747. [PMID: 28751559 PMCID: PMC5622858 DOI: 10.3324/haematol.2016.161273] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/18/2017] [Indexed: 12/17/2022] Open
Abstract
Genetic alterations of the transcription factor IKZF1 ("IKAROS") are detected in around 15-30% of cases of BCR-ABL-negative B-cell precursor acute lymphoblastic leukemia. Different types of intragenic deletions have been observed, resulting in a functionally inactivated allele ("loss-of-function") or in "dominant-negative" isoforms. The prognostic impact of these alterations especially in adult acute lymphoblastic leukemia is not well defined. We analyzed 482 well-characterized cases of adult BCR-ABL-negative B-precursor acute lymphoblastic leukemia uniformly treated in the framework of the GMALL studies and detected IKZF1 alterations in 128 cases (27%). In 20%, the IKZF1 alteration was present in a large fraction of leukemic cells ("high deletion load") while in 7% it was detected only in small subclones ("low deletion load"). Some patients showed more than one IKZF1 alteration (8%). Patients exhibiting a loss-of-function isoform with high deletion load had a shorter overall survival (OS at 5 years 28% vs. 59%; P<0.0001), also significant in a subgroup analysis of standard risk patients according to GMALL classification (OS at 5 years 37% vs. 68%; P=0.0002). Low deletion load or dominant-negative IKZF1 alterations had no prognostic impact. The results thus suggest that there is a clear distinction between loss-of-function and dominant-negative IKZF1 deletions. Affected patients should thus be monitored for minimal residual disease carefully to detect incipient relapses at an early stage and they are potential candidates for alternative or intensified treatment regimes. (clinicaltrials.gov identifiers: 00199056 and 00198991).
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Affiliation(s)
- Benjamin Kobitzsch
- Department of Hematology, Oncology and Tumor Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt/Main, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology, Charité Universitätsmedizin Berlin, Germany
| | | | - Monika Brüggemann
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andreas Viardot
- Department of Medicine III (Hematology, Oncology), Ulm University, Munich, Germany
| | - Ralph Wäsch
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Munich, Germany
| | - Michael Starck
- Department of Hematology, Klinikum München-Schwabing, Munich, Germany
| | - Eckhard Thiel
- Department of Hematology, Oncology and Tumor Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Dieter Hoelzer
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt/Main, Germany
| | - Thomas Burmeister
- Department of Hematology, Oncology and Tumor Immunology, Charité Universitätsmedizin Berlin, Germany
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Kim J, Lu C, Srinivasan S, Awe S, Brehm A, Fuller MT. Blocking promiscuous activation at cryptic promoters directs cell type-specific gene expression. Science 2017; 356:717-721. [PMID: 28522526 PMCID: PMC5572561 DOI: 10.1126/science.aal3096] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/13/2017] [Indexed: 12/18/2022]
Abstract
To selectively express cell type-specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. By blocking transcription from normally cryptic promoters, Kmg restricts activation by Aly, a component of the testis-meiotic arrest complex, to transcripts for male germ cell differentiation. Our results suggest that as new regions of the genome become open for transcription during terminal differentiation, blocking the action of a promiscuous activator on cryptic promoters is a critical mechanism for specifying precise gene activation.
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Affiliation(s)
- Jongmin Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Chenggang Lu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Shrividhya Srinivasan
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Stephan Awe
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
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Martín-Ibáñez R, Pardo M, Giralt A, Miguez A, Guardia I, Marion-Poll L, Herranz C, Esgleas M, Garcia-Díaz Barriga G, Edel MJ, Vicario-Abejón C, Alberch J, Girault JA, Chan S, Kastner P, Canals JM. Helios expression coordinates the development of a subset of striatopallidal medium spiny neurons. Development 2017; 144:1566-1577. [PMID: 28289129 PMCID: PMC5399659 DOI: 10.1242/dev.138248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 03/03/2017] [Indexed: 12/25/2022]
Abstract
Here, we unravel the mechanism of action of the Ikaros family zinc finger protein Helios (He) during the development of striatal medium spiny neurons (MSNs). He regulates the second wave of striatal neurogenesis involved in the generation of striatopallidal neurons, which express dopamine 2 receptor and enkephalin. To exert this effect, He is expressed in neural progenitor cells (NPCs) keeping them in the G1/G0 phase of the cell cycle. Thus, a lack of He results in an increase of S-phase entry and S-phase length of NPCs, which in turn impairs striatal neurogenesis and produces an accumulation of the number of cycling NPCs in the germinal zone (GZ), which end up dying at postnatal stages. Therefore, He−/− mice show a reduction in the number of dorso-medial striatal MSNs in the adult that produces deficits in motor skills acquisition. In addition, overexpression of He in NPCs induces misexpression of DARPP-32 when transplanted in mouse striatum. These findings demonstrate that He is involved in the correct development of a subset of striatopallidal MSNs and reveal new cellular mechanisms for neuronal development. Summary: The transcription factor Helios regulates G1-S transition to promote neuronal differentiation of a striatopallidal neuronal subpopulation involved in motor skill acquisition.
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Affiliation(s)
- Raquel Martín-Ibáñez
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Research and Development Unit, Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Mónica Pardo
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Albert Giralt
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Pathophysiology of Neurodegenerative Diseases Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Andrés Miguez
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Inés Guardia
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Lucile Marion-Poll
- Inserm UMR-S839; Université Pierre et Marie Curie (UPMC, Paris 6), Sorbonne Universités; Institut du Fer à Moulin, 75005 Paris, France
| | - Cristina Herranz
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Research and Development Unit, Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Miriam Esgleas
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Gerardo Garcia-Díaz Barriga
- Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Pathophysiology of Neurodegenerative Diseases Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Michael J Edel
- Control of Pluripotency Laboratory, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain.,Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010 Australia.,School of Medicine and Pharmacology, Anatomy, Physiology and Human Biology, CCTRM, University of Western Australia, Western Australia, 6009 Australia
| | - Carlos Vicario-Abejón
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Departamento de Neurobiología Molecular, Celular y del Desarrollo, Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), 28002 Madrid, Spain
| | - Jordi Alberch
- Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Jean-Antoine Girault
- Inserm UMR-S839; Université Pierre et Marie Curie (UPMC, Paris 6), Sorbonne Universités; Institut du Fer à Moulin, 75005 Paris, France
| | - Susan Chan
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain
| | - Philippe Kastner
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch-Graffenstaden, France.,Faculté de Médecine, Université de Strasbourg, 67081 Strasbourg, France
| | - Josep M Canals
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain .,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Research and Development Unit, Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
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Ornithine decarboxylase regulates M1 macrophage activation and mucosal inflammation via histone modifications. Proc Natl Acad Sci U S A 2017; 114:E751-E760. [PMID: 28096401 DOI: 10.1073/pnas.1614958114] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macrophage activation is a critical step in host responses during bacterial infections. Ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine metabolism, has been well studied in epithelial cells and is known to have essential roles in many different cellular functions. However, its role in regulating macrophage function during bacterial infections is not well characterized. We demonstrate that macrophage-derived ODC is a critical regulator of M1 macrophage activation during both Helicobacter pylori and Citrobacter rodentium infection. Myeloid-specific Odc deletion significantly increased gastric and colonic inflammation, respectively, and enhanced M1 activation. Add-back of putrescine, the product of ODC, reversed the increased macrophage activation, indicating that ODC and putrescine are regulators of macrophage function. Odc-deficient macrophages had increased histone 3, lysine 4 (H3K4) monomethylation, and H3K9 acetylation, accompanied by decreased H3K9 di/trimethylation both in vivo and ex vivo in primary macrophages. These alterations in chromatin structure directly resulted in up-regulated gene transcription, especially M1 gene expression. Thus, ODC in macrophages tempers antimicrobial, M1 macrophage responses during bacterial infections through histone modifications and altered euchromatin formation, leading to the persistence and pathogenesis of these organisms.
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Lomonte P. Herpesvirus Latency: On the Importance of Positioning Oneself. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 223:95-117. [PMID: 28528441 DOI: 10.1007/978-3-319-53168-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nucleus is composed of multiple compartments and domains, which directly or indirectly influence many cellular processes including gene expression, RNA splicing and maturation, protein post-translational modifications, and chromosome segregation. Nuclear-replicating viruses, especially herpesviruses, have co-evolved with the cell, adopting strategies to counteract and eventually hijack this hostile environment for their own benefit. This allows them to persist in the host for the entire life of an individual and to ensure their maintenance in the target species. Herpesviruses establish latency in dividing or postmitotic cells from which they can efficiently reactivate after sometimes years of a seemingly dormant state. Therefore, herpesviruses circumvent the threat of permanent silencing by reactivating their dormant genomes just enough to escape extinction, but not too much to avoid life-threatening damage to the host. In addition, herpesviruses that establish latency in dividing cells must adopt strategies to maintain their genomes in the daughter cells to avoid extinction by dilution of their genomes following multiple cell divisions. From a biochemical point of view, reactivation and maintenance of viral genomes in dividing cells occur successfully because the viral genomes interact with the nuclear architecture in a way that allows the genomes to be transmitted faithfully and to benefit from the nuclear micro-environments that allow reactivation following specific stimuli. Therefore, spatial positioning of the viral genomes within the nucleus is likely to be essential for the success of the latent infection and, beyond that, for the maintenance of herpesviruses in their respective hosts.
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Affiliation(s)
- Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Assembly, Nuclear Domains, Virus, 69008, Lyon, France.
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43
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Genomic and transcriptional landscape of P2RY8-CRLF2-positive childhood acute lymphoblastic leukemia. Leukemia 2016; 31:1491-1501. [PMID: 27899802 PMCID: PMC5508072 DOI: 10.1038/leu.2016.365] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/07/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
Children with P2RY8-CRLF2-positive acute lymphoblastic leukemia have an increased relapse risk. Their mutational and transcriptional landscape, as well as the respective patterns at relapse remain largely elusive. We, therefore, performed an integrated analysis of whole-exome and RNA sequencing in 41 major clone fusion-positive cases including 19 matched diagnosis/relapse pairs. We detected a variety of frequently subclonal and highly instable JAK/STAT but also RTK/Ras pathway-activating mutations in 76% of cases at diagnosis and virtually all relapses. Unlike P2RY8-CRLF2 that was lost in 32% of relapses, all other genomic alterations affecting lymphoid development (58%) and cell cycle (39%) remained stable. Only IKZF1 alterations predominated in relapsing cases (P=0.001) and increased from initially 36 to 58% in matched cases. IKZF1's critical role is further corroborated by its specific transcriptional signature comprising stem cell features with signs of impaired lymphoid differentiation, enhanced focal adhesion, activated hypoxia pathway, deregulated cell cycle and increased drug resistance. Our findings support the notion that P2RY8-CRLF2 is dispensable for relapse development and instead highlight the prominent rank of IKZF1 for relapse development by mediating self-renewal and homing to the bone marrow niche. Consequently, reverting aberrant IKAROS signaling or its disparate programs emerges as an attractive potential treatment option in these leukemias.
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Chen WM, Wu CS, Liu JL, Yeh CM, Tseng L, Huang HC, Chang PJ, Wu SF. Expression of Helios in gastric tumor cells predicts better survival in gastric cancer patients. J Cancer Res Clin Oncol 2016; 142:2375-82. [PMID: 27576507 DOI: 10.1007/s00432-016-2223-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/20/2016] [Indexed: 12/25/2022]
Abstract
PURPOSE Helios belongs to Ikaros family, which plays an important role in the cell-fate decision and control cell proliferation; abnormal expressions in leukemia are associated with poor prognosis. In this study, we investigated the Helios expression between Helicobacter pylori infection and prognosis in gastric cancer patients. METHODS A total of 67 gastric cancer patients who received partial or full gastrectomies were enrolled. Helios expression by immunohistochemistry and mRNA was investigated with the clinical stage, Helicobacter pylori infection, CD4 expression, FoxP3 expression and prognosis. RESULTS From the immunohistochemistry stain, we found that the Helios was expressed in both cancer cell and tumor-infiltrated lymphocytes. The high expression of Helios in gastric tumor cells had a better median overall survival rate in gastric cancer patients (50.7 ± 3.2 vs. 34.1 ± 4.9 months; P = 0.015), Helicobacter pylori-infected patients (51.1 ± 3.5 vs. 30.4 ± 5.1 months; P = 0.007) and advanced gastric cancer patients (42.1 ± 5.5 vs. 23.2 ± 4.8 months; P = 0.043). From multivariate analysis, the Helios expression in gastric tumor cells was an independent factor to predict better survival in all gastric cancers (HR = 2.78; 95 % confidence interval [CI], 1.09-7.09; P = 0.032) and advanced gastric cancer patients (HR = 2.85; 95 % confidence interval [CI], 1.00-8.13; P = 0.03). CONCLUSIONS Higher expression of Helios in gastric tumor cells predicts better survival in gastric cancer patients, especially for Helicobacter pylori-infected and advanced-stage gastric cancer patients.
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Affiliation(s)
- Wei-Ming Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chiayi, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Shyong Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chiayi, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jing-Lan Liu
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Pathology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Chia-Ming Yeh
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, No.168, University Rd., Min-Hsiung, Chia-Yi, 62247, Taiwan, Republic of China
| | - Libby Tseng
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, No.168, University Rd., Min-Hsiung, Chia-Yi, 62247, Taiwan, Republic of China
| | - Hao-Chun Huang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Pey-Jium Chang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shu-Fen Wu
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, No.168, University Rd., Min-Hsiung, Chia-Yi, 62247, Taiwan, Republic of China.
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45
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Yokota T, Kanakura Y. Genetic abnormalities associated with acute lymphoblastic leukemia. Cancer Sci 2016; 107:721-5. [PMID: 26991355 PMCID: PMC4968601 DOI: 10.1111/cas.12927] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 12/27/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) occurs with high frequency in childhood and is associated with high mortality in adults. Recent technical advances in next‐generation sequencing have shed light on genetic abnormalities in hematopoietic stem/progenitor cells as the precursor to ALL pathogenesis. Based on these genetic abnormalities, ALL is now being reclassified into newly identified subtypes. Philadelphia chromosome‐like B‐lineage ALL is one of the new high‐risk subtypes characterized by genetic alterations that activate various signaling pathways, including those involving cytokine receptors, tyrosine kinases, and epigenetic modifiers. Philadelphia chromosome‐like ALL is essentially heterogeneous; however, deletion mutations in the IKZF1 gene encoding the transcription factor IKAROS underlie many cases as a key factor inducing aggressive phenotypes and poor treatment responses. Whole‐genome sequencing studies of ALL patients and ethnically matched controls also identified inherited genetic variations in lymphoid neoplasm‐related genes, which are likely to increase ALL susceptibility. These findings are directly relevant to clinical hematology, and further studies on this aspect could contribute to accurate diagnosis, effective monitoring of residual disease, and patient‐oriented therapies.
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Affiliation(s)
- Takafumi Yokota
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuzuru Kanakura
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Suita, Japan
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46
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Cho SJ, Kang H, Kim MY, Lee JE, Kim SJ, Nam SY, Kim JY, Kim HS, Pyo S, Yang KH. Site-Specific Phosphorylation of Ikaros Induced by Low-Dose Ionizing Radiation Regulates Cell Cycle Progression of B Lymphoblast Through CK2 and AKT Activation. Int J Radiat Oncol Biol Phys 2016; 94:1207-18. [DOI: 10.1016/j.ijrobp.2016.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 11/17/2022]
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47
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Maeng YS, Kwon JY, Kim EK, Kwon YG. Heterochromatin Protein 1 Alpha (HP1α: CBX5) is a Key Regulator in Differentiation of Endothelial Progenitor Cells to Endothelial Cells. Stem Cells 2016; 33:1512-22. [PMID: 25588582 DOI: 10.1002/stem.1954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/23/2014] [Indexed: 11/10/2022]
Abstract
As the ability to control the differentiation of endothelial stem/progenitor cells (EPCs) into vascular endothelial cell lineages could be useful for promoting neovascularization, it is important to obtain a deeper understanding of the epigenetic mechanisms that regulate EPC differentiation and neovascularization. Heterochromatin protein 1α (HP1α) is known to be involved in the epigenetic regulation of gene silencing. However, recent reports demonstrate that HP1α can also activate gene expression during cell differentiation. In this study, microarray analysis revealed that HP1α expression was induced during EPC differentiation and is associated with the expression of outgrowing endothelial cell (OEC)-specific protein markers. To explore the role of HP1α in the differentiation of EPCs to OECs, its expression was knocked-down or over-expressed in differentiating EPCs. Overexpression of HP1α promoted the differentiation and angiogenic activity of EPCs in vitro and in vivo, whereas knockdown of HP1α led to a defect in OEC migration, tube formation, and angiogenic sprouting activity. Gene expression profiling showed increased expression of angiogenic genes, including NOTCH1, cadherin-5, and angiopoietin-like-2, and decreased expression of progenitor cell marker genes, including CD133, CXCR4, and C-KIT, in HP1α-overexpressing EPCs. Also, increased HP1α at an early stage of EPC differentiation may regulate angiogenic gene transcription by interacting with chromatin that modifies epigenetic factors such as the methyl-CpG binding domain, Polycomb group ring finger 2, and DNA methyltransferases. Our findings demonstrate, for the first time, that HP1α plays an important role in the differentiation and angiogenic function of EPCs by regulating endothelial gene expression. Stem Cells 2015;33:1512-1522.
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Affiliation(s)
- Yong-Sun Maeng
- Corneal Dystrophy Research Institute; Department of Ophthalmology, Yonsei University College of Medicine, Seoul, 120-752, Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
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48
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Bertolino E, Reinitz J, Manu. The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Dev Biol 2016; 413:128-44. [PMID: 26945717 DOI: 10.1016/j.ydbio.2016.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/13/2016] [Accepted: 02/15/2016] [Indexed: 11/25/2022]
Abstract
C/EBPα plays an instructive role in the macrophage-neutrophil cell-fate decision and its expression is necessary for neutrophil development. How Cebpa itself is regulated in the myeloid lineage is not known. We decoded the cis-regulatory logic of Cebpa, and two other myeloid transcription factors, Egr1 and Egr2, using a combined experimental-computational approach. With a reporter design capable of detecting both distal enhancers and silencers, we analyzed 46 putative cis-regulatory modules (CRMs) in cells representing myeloid progenitors, and derived early macrophages or neutrophils. In addition to novel enhancers, this analysis revealed a surprisingly large number of silencers. We determined the regulatory roles of 15 potential transcriptional regulators by testing 32,768 alternative sequence-based transcriptional models against CRM activity data. This comprehensive analysis allowed us to infer the cis-regulatory logic for most of the CRMs. Silencer-mediated repression of Cebpa was found to be effected mainly by TFs expressed in non-myeloid lineages, highlighting a previously unappreciated contribution of long-distance silencing to hematopoietic lineage resolution. The repression of Cebpa by multiple factors expressed in alternative lineages suggests that hematopoietic genes are organized into densely interconnected repressive networks instead of hierarchies of mutually repressive pairs of pivotal TFs. More generally, our results demonstrate that de novo cis-regulatory dissection is feasible on a large scale with the aid of transcriptional modeling. Current address: Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
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Affiliation(s)
- Eric Bertolino
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - John Reinitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Statistics, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Manu
- Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
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Saeidi K. Myeloproliferative neoplasms: Current molecular biology and genetics. Crit Rev Oncol Hematol 2015; 98:375-89. [PMID: 26697989 DOI: 10.1016/j.critrevonc.2015.11.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 09/10/2015] [Accepted: 11/09/2015] [Indexed: 12/16/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) are clonal disorders characterized by increased production of mature blood cells. Philadelphia chromosome-negative MPNs (Ph-MPNs) consist of polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). A number of stem cell derived mutations have been identified in the past 10 years. These findings showed that JAK2V617F, as a diagnostic marker involving JAK2 exon 14 with a high frequency, is the best molecular characterization of Ph-MPNs. Somatic mutations in an endoplasmic reticulum chaperone, named calreticulin (CALR), is the second most common mutation in patients with ET and PMF after JAK2 V617F mutation. Discovery of CALR mutations led to the increased molecular diagnostic of ET and PMF up to 90%. It has been shown that JAK2V617F is not the unique event in disease pathogenesis. Some other genes' location such as TET oncogene family member 2 (TET2), additional sex combs-like 1 (ASXL1), casitas B-lineage lymphoma proto-oncogene (CBL), isocitrate dehydrogenase 1/2 (IDH1/IDH2), IKAROS family zinc finger 1 (IKZF1), DNA methyltransferase 3A (DNMT3A), suppressor of cytokine signaling (SOCS), enhancer of zeste homolog 2 (EZH2), tumor protein p53 (TP53), runt-related transcription factor 1 (RUNX1) and high mobility group AT-hook 2 (HMGA2) have also identified to be involved in MPNs phenotypes. Here, current molecular biology and genetic mechanisms involved in MNPs with a focus on the aforementioned factors is presented.
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Affiliation(s)
- Kolsoum Saeidi
- Department of Medical Genetics, Kerman University of Medical Sciences, Kerman, Iran.
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50
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Xia P, Wang S, Du Y, Huang G, Satoh T, Akira S, Fan Z. Insulin-InsR signaling drives multipotent progenitor differentiation toward lymphoid lineages. J Exp Med 2015; 212:2305-21. [PMID: 26573296 PMCID: PMC4683997 DOI: 10.1084/jem.20150618] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 10/09/2015] [Indexed: 12/01/2022] Open
Abstract
Xia et al. report that insulin receptor signaling is required for lymphoid lineage specification in early lymphopoiesis via modulation of Ikaros expression. Disrupted insulin signaling generates more myeloid cells and fewer lymphoid cells, resulting in a skewed myeloid/lymphoid ratio in diabetic mice. The lineage commitment of HSCs generates balanced myeloid and lymphoid populations in hematopoiesis. However, the underlying mechanisms that control this process remain largely unknown. Here, we show that insulin–insulin receptor (InsR) signaling is required for lineage commitment of multipotent progenitors (MPPs). Deletion of Insr in murine bone marrow causes skewed differentiation of MPPs to myeloid cells. mTOR acts as a downstream effector that modulates MPP differentiation. mTOR activates Stat3 by phosphorylation at serine 727 under insulin stimulation, which binds to the promoter of Ikaros, leading to its transcription priming. Our findings reveal that the insulin–InsR signaling drives MPP differentiation into lymphoid lineages in early lymphopoiesis, which is essential for maintaining a balanced immune system for an individual organism.
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Affiliation(s)
- Pengyan Xia
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanling Huang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Takashi Satoh
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka 565-0871, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka 565-0871, Japan
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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