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Garcia C, Miller-Awe MD, Witkowski MT. Concepts in B cell acute lymphoblastic leukemia pathogenesis. J Leukoc Biol 2024; 116:18-32. [PMID: 38243586 DOI: 10.1093/jleuko/qiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
B cell acute lymphoblastic leukemia (B-ALL) arises from genetic alterations impacting B cell progenitors, ultimately leading to clinically overt disease. Extensive collaborative efforts in basic and clinical research have significantly improved patient prognoses. Nevertheless, a subset of patients demonstrate resistance to conventional chemotherapeutic approaches and emerging immunotherapeutic interventions. This review highlights the mechanistic underpinnings governing B-ALL transformation. Beginning with exploring normative B cell lymphopoiesis, we delineate the influence of recurrent germline and somatic genetic aberrations on the perturbation of B cell progenitor differentiation and protumorigenic signaling, thereby facilitating the neoplastic transformation underlying B-ALL progression. Additionally, we highlight recent advances in the multifaceted landscape of B-ALL, encompassing metabolic reprogramming, microbiome influences, inflammation, and the discernible impact of socioeconomic and racial disparities on B-ALL transformation and patient survival.
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Affiliation(s)
- Clarissa Garcia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Megan D Miller-Awe
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Matthew T Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
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2
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Ma L, Yin C, Zhang Y, Li J, Shi L, Zhou T, Huang X, Liu Y, Cao J, Wu G, Gu H, He L. KCTD5 regulates Ikaros degradation induced by chemotherapeutic drug etoposide in hematological cells. Biol Chem 2024; 405:341-349. [PMID: 38424700 DOI: 10.1515/hsz-2023-0333] [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: 10/24/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
Therapy-related leukemia carries a poor prognosis, and leukemia after chemotherapy is a growing risk in clinic, whose mechanism is still not well understood. Ikaros transcription factor is an important regulator in hematopoietic cells development and differentiation. In the absence of Ikaros, lymphoid cell differentiation is blocked at an extremely early stage, and myeloid cell differentiation is also significantly affected. In this work, we showed that chemotherapeutic drug etoposide reduced the protein levels of several isoforms of Ikaros including IK1, IK2 and IK4, but not IK6 or IK7, by accelerating protein degradation, in leukemic cells. To investigate the molecular mechanism of Ikaros degradation induced by etoposide, immunoprecipitation coupled with LC-MS/MS analysis was conducted to identify changes in protein interaction with Ikaros before and after etoposide treatment, which uncovered KCTD5 protein. Our further study demonstrates that KCTD5 is the key stabilizing factor of Ikaros and chemotherapeutic drug etoposide induces Ikaros protein degradation through decreasing the interaction of Ikaros with KCTD5. These results suggest that etoposide may induce leukemic transformation by downregulating Ikaros via KCTD5, and our work may provide insights to attenuate the negative impact of chemotherapy on hematopoiesis.
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Affiliation(s)
- Lan Ma
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
- Department of Nephropathy, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310007, China
| | - Changqing Yin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Yi Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Jie Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Liuzhi Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Tong Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Xixi Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Yaqi Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Jiawei Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Guang Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Haihua Gu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Licai He
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou 325035, China
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3
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Goh W, Sudholz H, Foroutan M, Scheer S, Pfefferle A, Delconte RB, Meng X, Shen Z, Hennessey R, Kong IY, Schuster IS, Andoniou CE, Davis MJ, Hediyeh-Zadeh S, Souza-Fonseca-Guimaraes F, Parish IA, Beavis P, Thiele D, Chopin M, Degli-Esposti MA, Cursons J, Kallies A, Rautela J, Nutt SL, Huntington ND. IKAROS and AIOLOS directly regulate AP-1 transcriptional complexes and are essential for NK cell development. Nat Immunol 2024; 25:240-255. [PMID: 38182668 DOI: 10.1038/s41590-023-01718-4] [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: 10/23/2022] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
Ikaros transcription factors are essential for adaptive lymphocyte function, yet their role in innate lymphopoiesis is unknown. Using conditional genetic inactivation, we show that Ikzf1/Ikaros is essential for normal natural killer (NK) cell lymphopoiesis and IKZF1 directly represses Cish, a negative regulator of interleukin-15 receptor resulting in impaired interleukin-15 receptor signaling. Both Bcl2l11 and BIM levels, and intrinsic apoptosis were increased in Ikzf1-null NK cells, which in part accounts for NK lymphopenia as both were restored to normal levels when Ikzf1 and Bcl2l11 were co-deleted. Ikzf1-null NK cells presented extensive transcriptional alterations with reduced AP-1 transcriptional complex expression and increased expression of Ikzf2/Helios and Ikzf3/Aiolos. IKZF1 and IKZF3 directly bound AP-1 family members and deletion of both Ikzf1 and Ikzf3 in NK cells resulted in further reductions in Jun/Fos expression and complete loss of peripheral NK cells. Collectively, we show that Ikaros family members are important regulators of apoptosis, cytokine responsiveness and AP-1 transcriptional activity.
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Affiliation(s)
- Wilford Goh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Harrison Sudholz
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Momeneh Foroutan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Sebastian Scheer
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Aline Pfefferle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiangpeng Meng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Zihan Shen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Robert Hennessey
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Iona S Schuster
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Christopher E Andoniou
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
- The South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Thiele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Michael Chopin
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Joe Cursons
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology & Immunology, Faculty of Medicine, Dentistry and Health Sciences & Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jai Rautela
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas D Huntington
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia.
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4
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Yomogida K, Trsan T, Sudan R, Rodrigues PF, Ulezko Antonova A, Ingle H, Luccia BD, Collins PL, Cella M, Gilfillan S, Baldridge MT, Oltz EM, Colonna M. The transcription factor Aiolos restrains the activation of intestinal intraepithelial lymphocytes. Nat Immunol 2024; 25:77-87. [PMID: 38049581 DOI: 10.1038/s41590-023-01693-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 10/27/2023] [Indexed: 12/06/2023]
Abstract
Intestinal intraepithelial lymphocytes (IELs) exhibit prompt innate-like responses to microenvironmental cues and require strict control of effector functions. Here we showed that Aiolos, an Ikaros zinc-finger family member encoded by Ikzf3, acted as a regulator of IEL activation. Ikzf3-/- CD8αα+ IELs had elevated expression of NK receptors, cytotoxic enzymes, cytokines and chemokines. Single-cell RNA sequencing of Ikzf3-/- and Ikzf3+/+ IELs showed an amplified effector machinery in Ikzf3-/- CD8αα+ IELs compared to Ikzf3+/+ counterparts. Ikzf3-/- CD8αα+ IELs had increased responsiveness to interleukin-15, which explained a substantial part, but not all, of the observed phenotypes. Aiolos binding sites were close to those for the transcription factors STAT5 and RUNX, which promote interleukin-15 signaling and cytolytic programs, and Ikzf3 deficiency partially increased chromatin accessibility and histone acetylation in these regions. Ikzf3 deficiency in mice enhanced susceptibility to colitis, underscoring the relevance of Aiolos in regulating the effector function in IELs.
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Affiliation(s)
- Kentaro Yomogida
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Denver, CO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Raki Sudan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick F Rodrigues
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Harshad Ingle
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Blanda Di Luccia
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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5
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Kastner P, Chan S. IKAROS Family Transcription Factors in Lymphocyte Differentiation and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:33-52. [PMID: 39017838 DOI: 10.1007/978-3-031-62731-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The IKAROS family of transcription factors comprises four zinc-finger proteins (IKAROS, HELIOS, AIOLOS, and EOS), which over the last decades have been established to be critical regulators of the development and function of lymphoid cells. These factors act as homo- or heterodimers and are involved both in gene activation and repression. Their function often involves cross-talk with other regulatory circuits, such as the JAK/STAT, NF-κB, and NOTCH pathways. They control lymphocyte differentiation at multiple stages and are notably critical for lymphoid commitment in multipotent hematopoietic progenitors and for T and B cell differentiation downstream of pre-TCR and pre-BCR signaling. They also control many aspects of effector functions in mature B and T cells. They are dysregulated or mutated in multiple pathologies affecting the lymphoid system, which range from leukemia to immunodeficiencies. In this chapter, we review the molecular and physiological function of these factors in lymphocytes and their implications in human pathologies.
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Affiliation(s)
- Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch-Graffenstaden, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch-Graffenstaden, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch-Graffenstaden, France.
- Université de Strasbourg, Illkirch-Graffenstaden, France.
- Faculté de Médecine, Université de Strasbourg, Strasbourg, France.
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch-Graffenstaden, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch-Graffenstaden, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch-Graffenstaden, France.
- Université de Strasbourg, Illkirch-Graffenstaden, France.
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6
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da Silva Lima F, da Silva Gonçalves CE, Fock RA. A review of the role of zinc finger proteins on hematopoiesis. J Trace Elem Med Biol 2023; 80:127290. [PMID: 37659124 DOI: 10.1016/j.jtemb.2023.127290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
The bone marrow is responsible for producing an incredible number of cells daily in order to maintain blood homeostasis through a process called hematopoiesis. Hematopoiesis is a greatly demanding process and one entirely dependent on complex interactions between the hematopoietic stem cell (HSC) and its surrounding microenvironment. Zinc (Zn2+) is considered an important trace element, playing diverse roles in different tissues and cell types, and zinc finger proteins (ZNF) are proteins that use Zn2+ as a structural cofactor. In this way, the ZNF structure is supported by a Zn2+ that coordinates many possible combinations of cysteine and histidine, with the most common ZNF being of the Cys2His2 (C2H2) type, which forms a family of transcriptional activators that play an important role in different cellular processes such as development, differentiation, and suppression, all of these being essential processes for an adequate hematopoiesis. This review aims to shed light on the relationship between ZNF and the regulation of the hematopoietic tissue. We include works with different designs, including both in vitro and in vivo studies, detailing how ZNF might regulate hematopoiesis.
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Affiliation(s)
- Fabiana da Silva Lima
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Ricardo Ambrósio Fock
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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7
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Mohajeri A, Vaseghi-Shanjani M, Rosenfeld JA, Yang GX, Lu H, Sharma M, Lin S, Salman A, Waqas M, Sababi Azamian M, Worley KC, Del Bel KL, Kozak FK, Rahmanian R, Biggs CM, Hildebrand KJ, Lalani SR, Nicholas SK, Scott DA, Mostafavi S, van Karnebeek C, Henkelman E, Halparin J, Yang CL, Armstrong L, Turvey SE, Lehman A. Dominant negative variants in IKZF2 cause ICHAD syndrome, a new disorder characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay. J Med Genet 2023; 60:1092-1104. [PMID: 37316189 PMCID: PMC11206234 DOI: 10.1136/jmg-2022-109127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/29/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Helios (encoded by IKZF2), a member of the Ikaros family of transcription factors, is a zinc finger protein involved in embryogenesis and immune function. Although predominantly recognised for its role in the development and function of T lymphocytes, particularly the CD4+ regulatory T cells (Tregs), the expression and function of Helios extends beyond the immune system. During embryogenesis, Helios is expressed in a wide range of tissues, making genetic variants that disrupt the function of Helios strong candidates for causing widespread immune-related and developmental abnormalities in humans. METHODS We performed detailed phenotypic, genomic and functional investigations on two unrelated individuals with a phenotype of immune dysregulation combined with syndromic features including craniofacial differences, sensorineural hearing loss and congenital abnormalities. RESULTS Genome sequencing revealed de novo heterozygous variants that alter the critical DNA-binding zinc fingers (ZFs) of Helios. Proband 1 had a tandem duplication of ZFs 2 and 3 in the DNA-binding domain of Helios (p.Gly136_Ser191dup) and Proband 2 had a missense variant impacting one of the key residues for specific base recognition and DNA interaction in ZF2 of Helios (p.Gly153Arg). Functional studies confirmed that both these variant proteins are expressed and that they interfere with the ability of the wild-type Helios protein to perform its canonical function-repressing IL2 transcription activity-in a dominant negative manner. CONCLUSION This study is the first to describe dominant negative IKZF2 variants. These variants cause a novel genetic syndrome characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay.
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Affiliation(s)
- Arezoo Mohajeri
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Maryam Vaseghi-Shanjani
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Gui Xiang Yang
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Henry Lu
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Mehul Sharma
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Susan Lin
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Areesha Salman
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Meriam Waqas
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Mahshid Sababi Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kate L Del Bel
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Frederick K Kozak
- Department of Surgery, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ronak Rahmanian
- Department of Surgery, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Catherine M Biggs
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Kyla J Hildebrand
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Sarah K Nicholas
- Department of Pediatrics, Texas Children's Hospital, Houston, Texas, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Sara Mostafavi
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Erika Henkelman
- Department of Surgery, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica Halparin
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Connie L Yang
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
- Provincial Medical Genetics Program, BC Children's & Women's Hosp, Vancouver, British Columbia, Canada
| | - Stuart E Turvey
- Department of Pediatrics, The University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Anna Lehman
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
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8
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Sin JH, Sucharov J, Kashyap S, Wang Y, Proekt I, Liu X, Parent AV, Gupta A, Kastner P, Chan S, Gardner JM, Ntranos V, Miller CN, Anderson MS, Schjerven H, Waterfield MR. Ikaros is a principal regulator of Aire + mTEC homeostasis, thymic mimetic cell diversity, and central tolerance. Sci Immunol 2023; 8:eabq3109. [PMID: 37889983 DOI: 10.1126/sciimmunol.abq3109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.
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Affiliation(s)
- Jun Hyung Sin
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Juliana Sucharov
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Sujit Kashyap
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Yi Wang
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Irina Proekt
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Xian Liu
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Audrey V Parent
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Gupta
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - James M Gardner
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Vasilis Ntranos
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Corey N Miller
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hilde Schjerven
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Waterfield
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
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9
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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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10
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Sigvardsson M. Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia. Genes Dev 2023; 37:703-723. [PMID: 37673459 PMCID: PMC10546977 DOI: 10.1101/gad.349879.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
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11
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Chalise JP, Ehsani A, Lemecha M, Hung YW, Zhang G, Larson GP, Itakura K. ARID5B regulates fatty acid metabolism and proliferation at the Pre-B cell stage during B cell development. Front Immunol 2023; 14:1170475. [PMID: 37483604 PMCID: PMC10360657 DOI: 10.3389/fimmu.2023.1170475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
During B cell development in bone marrow, large precursor B cells (large Pre-B cells) proliferate rapidly, exit the cell cycle, and differentiate into non-proliferative (quiescent) small Pre-B cells. Dysregulation of this process may result in the failure to produce functional B cells and pose a risk of leukemic transformation. Here, we report that AT rich interacting domain 5B (ARID5B), a B cell acute lymphoblastic leukemia (B-ALL) risk gene, regulates B cell development at the Pre-B stage. In both mice and humans, we observed a significant upregulation of ARID5B expression that initiates at the Pre-B stage and is maintained throughout later stages of B cell development. In mice, deletion of Arid5b in vivo and ex vivo exhibited a significant reduction in the proportion of immature B cells but an increase in large and small Pre-B cells. Arid5b inhibition ex vivo also led to an increase in proliferation of both Pre-B cell populations. Metabolic studies in mouse and human bone marrow revealed that fatty acid uptake peaked in proliferative B cells then decreased during non-proliferative stages. We showed that Arid5b ablation enhanced fatty acid uptake and oxidation in Pre-B cells. Furthermore, decreased ARID5B expression was observed in tumor cells from B-ALL patients when compared to B cells from non-leukemic individuals. In B-ALL patients, ARID5B expression below the median was associated with decreased survival particularly in subtypes originating from Pre-B cells. Collectively, our data indicated that Arid5b regulates fatty acid metabolism and proliferation of Pre-B cells in mice, and reduced expression of ARID5B in humans is a risk factor for B cell leukemia.
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Affiliation(s)
- Jaya Prakash Chalise
- Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Ali Ehsani
- Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Mengistu Lemecha
- Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Yu-Wen Hung
- Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Guoxiang Zhang
- Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Garrett P. Larson
- Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Keiichi Itakura
- Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, Duarte, CA, United States
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12
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Bogush D, Schramm J, Ding Y, He B, Singh C, Sharma A, Tukaramrao DB, Iyer S, Desai D, Nalesnik G, Hengst J, Bhalodia R, Gowda C, Dovat S. Signaling pathways and regulation of gene expression in hematopoietic cells. Adv Biol Regul 2023; 88:100942. [PMID: 36621151 DOI: 10.1016/j.jbior.2022.100942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Cellular functions are regulated by signal transduction pathway networks consisting of protein-modifying enzymes that control the activity of many downstream proteins. Protein kinases and phosphatases regulate gene expression by reversible phosphorylation of transcriptional factors, which are their direct substrates. Casein kinase II (CK2) is a serine/threonine kinase that phosphorylates a large number of proteins that have critical roles in cellular proliferation, metabolism and survival. Altered function of CK2 has been associated with malignant transformation, immunological disorders and other types of diseases. Protein phosphatase 1 (PP1) is a serine/threonine phosphatase, which regulates the phosphorylation status of many proteins that are essential for cellular functions. IKAROS is a DNA-binding protein, which functions as a regulator of gene transcription in hematopoietic cells. CK2 directly phosphorylates IKAROS at multiple phosphosites which determines IKAROS activity as a regulator of gene expression. PP1 binds to IKAROS via the PP1-consensus recognition site and dephosphorylates serine/threonine residues that are phosphorylated by CK2. Thus, the interplay between CK2 and PP1 signaling pathways have opposing effects on the phosphorylation status of their mutual substrate - IKAROS. This review summarizes the effects of CK2 and PP1 on IKAROS role in regulation of gene expression and its function as a tumor suppressor in leukemia.
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Affiliation(s)
- Daniel Bogush
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Joseph Schramm
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Yali Ding
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Bing He
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chingakham Singh
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Arati Sharma
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | | | - Soumya Iyer
- University of Chicago, Chicago, IL, 60637, USA
| | - Dhimant Desai
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Gregory Nalesnik
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Jeremy Hengst
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Riya Bhalodia
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chandrika Gowda
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
| | - Sinisa Dovat
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
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13
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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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14
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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15
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Yamashita M, Morio T. AIOLOS Variants Causing Immunodeficiency in Human and Mice. Front Immunol 2022; 13:866582. [PMID: 35444653 PMCID: PMC9014263 DOI: 10.3389/fimmu.2022.866582] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
AIOLOS is encoded by IKZF3 and is a member of the IKAROS zinc finger transcription factor family. Heterozygous missense variants in the second zinc finger of AIOLOS have recently been reported to be found in the families of patients with inborn errors of immunity. The AIOLOSG159R variant was identified in patients with B-lymphopenia and familial Epstein–Barr virus-associated lymphoma. Early B-cell progenitors were significantly reduced in the bone marrow of patients with AIOLOSG159R. Another variant, AIOLOSN160S was identified in the patients presented with hypogammaglobulinemia, susceptibility to Pneumocystis jirovecii pneumonia, and chronic lymphocytic leukemia. Patients with AIOLOSN160S had mostly normal B cell counts but showed increased levels of CD21lo B cells, decreased CD23 expression, and abrogated CD40 response. Both variants were determined to be loss-of-function. Mouse models harboring the corresponding patient’s variants recapitulated the phenotypes of the patients. AIOLOS is therefore a novel disease-causing gene in human adaptive immune deficiency.
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Affiliation(s)
- Motoi Yamashita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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16
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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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17
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T-ALL can evolve to oncogene independence. Leukemia 2021; 35:2205-2219. [PMID: 33483615 DOI: 10.1038/s41375-021-01120-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/09/2020] [Accepted: 01/07/2021] [Indexed: 01/29/2023]
Abstract
The majority of cases of T-cell acute lymphoblastic leukemia (T-ALL) contain chromosomal abnormalities that drive overexpression of oncogenic transcription factors. However, whether these initiating oncogenes are required for leukemia maintenance is poorly understood. To address this, we developed a tetracycline-regulated mouse model of T-ALL driven by the oncogenic transcription factor Lmo2. This revealed that whilst thymus-resident pre-Leukemic Stem Cells (pre-LSCs) required continuous Lmo2 expression, the majority of leukemias relapsed despite Lmo2 withdrawal. Relapse was associated with a mature phenotype and frequent mutation or loss of tumor suppressor genes including Ikzf1 (Ikaros), with targeted deletion Ikzf1 being sufficient to transform Lmo2-dependent leukemias to Lmo2-independence. Moreover, we found that the related transcription factor TAL1 was dispensable in several human T-ALL cell lines that contain SIL-TAL1 chromosomal deletions driving its overexpression, indicating that evolution to oncogene independence can also occur in human T-ALL. Together these results indicate an evolution of oncogene addiction in murine and human T-ALL and show that loss of Ikaros is a mechanism that can promote self-renewal of T-ALL lymphoblasts in the absence of an initiating oncogenic transcription factor.
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18
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Boast B, Nunes-Santos CDJ, Kuehn HS, Rosenzweig SD. Ikaros-Associated Diseases: From Mice to Humans and Back Again. Front Pediatr 2021; 9:705497. [PMID: 34354970 PMCID: PMC8330404 DOI: 10.3389/fped.2021.705497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
The normal expression of Ikaros (IKZF1) is important for the proper functioning of both the human and murine immune systems. Whilst our understanding of IKZF1 in the immune system has been greatly enhanced by the study of mice carrying mutations in Ikzf1, analyses of human patients carrying germline IKZF1 mutations have been instrumental in understanding its biological role within the human immune system and its effect on human disease. A myriad of different mutations in IKZF1 have been identified, spanning across the entire gene causing differential clinical outcomes in patients including immunodeficiency, immune dysregulation, and cancer. The majority of mutations in humans leading to IKAROS-associated diseases are single amino acid heterozygous substitutions that affect the overall function of the protein. The majority of mutations studied in mice however, affect the expression of the protein rather than its function. Murine studies would suggest that the complete absence of IKZF1 expression leads to severe and sometimes catastrophic outcomes, yet these extreme phenotypes are not commonly observed in patients carrying IKZF1 heterozygous mutations. It is unknown whether this discrepancy is simply due to differences in zygosity, the role and regulation of IKZF1 in the murine and human immune systems, or simply due to a lack of similar controls across both groups. This review will focus its analysis on the current literature surrounding what is known about germline IKZF1 defects in both the human and the murine immune systems, and whether existing mice models are indeed accurate tools to study the effects of IKZF1-associated diseases.
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Affiliation(s)
- Brigette Boast
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
| | - Cristiane de Jesus Nunes-Santos
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
| | - Sergio D. Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
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19
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Yamashita M, Morio T. Inborn errors of IKAROS and AIOLOS. Curr Opin Immunol 2021; 72:239-248. [PMID: 34265590 DOI: 10.1016/j.coi.2021.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/06/2021] [Accepted: 06/15/2021] [Indexed: 11/27/2022]
Abstract
IKAROS is a pioneer protein of the IKZF family of transcription factors that plays an essential role in lymphocyte development. Recently, inborn errors of IKAROS have been identified in patients with B cell deficiency and hypogammaglobulinemia, and these patients often present with recurrent sinopulmonary infection. Autoimmunity and hematologic malignancies are other characteristic complications seen in the patients with IKAROS deficiency. Missense mutation involving asparagine at the 159th position results in combined immunodeficiency, often presenting with Pneumocystis jirovecii pneumonia. Inborn errors of AIOLOS, HELIOS, and PEGASUS have also been reported in patients with B cell deficiency, Evans syndrome, and hereditary thrombocytopenia, respectively. Here, we briefly review the phenotype and genotype of IKZF mutations, especially IKAROS.
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Affiliation(s)
- Motoi Yamashita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan.
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20
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YILMAZ E, KUEHN HS, ODAKIR E, NIEMELA JE, OZCAN A, EKEN A, ROHLFS M, CANSEVER M, GOK V, AYDIN F, KARAKUKCU M, HAUCK F, KLEIN C, UNAL E, ROSENZWEIG SD, PATIROGLU T. Common Variable Immunodeficiency, Autoimmune Hemolytic Anemia, and Pancytopenia Associated With a Defect in IKAROS. J Pediatr Hematol Oncol 2021; 43:e351-e357. [PMID: 33122583 PMCID: PMC7987842 DOI: 10.1097/mph.0000000000001976] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Mutations in IKZF1, which encodes Ikaros family zinc finger 1 (IKAROS) transcription factor, are associated with recurrent infections, cytopenia, autoimmune diseases, and hematologic malignancies. Diverse clinical phenotypes resulting from IKZF1 mutations include pulmonary fungal infections, cytopenia, autoimmune hemolytic anemia (AIHA), and malignancies. In this study, we aimed to assess the DNA-binding ability and pericentromeric (PC) localization of a variant of IKZF discovered in a patient. MATERIALS AND METHODS DNA-binding ability of a pathogenic IKZF variant was tested using electrophoretic mobility shift assay and PC localization of the variant was assessed by immunofluorescent microscopy in NIH3T3 cells. RESULTS Clinical features of a 3-month-old male infant who underwent hematopoietic stem cell transplantation because of an IKZF1 mutation-associated common variable immunodeficiency, AIHA, and pancytopenia are described. DNA studies revealed a heterozygous missense variant (IKZF1 NM_006060 c.427C>T; p.R143W). Cotransfection studies revealed that mutant R143W has a partial dominant-negative effect over PC targeting and DNA binding. CONCLUSIONS IKZF1 mutation must be kept in mind if neonatal AIHA, common variable immunodeficiency, and pancytopenia are observed.
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Affiliation(s)
- Ebru YILMAZ
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Hye Sun KUEHN
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National, Institutes of Health, Bethesda, Md, USA
| | - Eda ODAKIR
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Julie E. NIEMELA
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National, Institutes of Health, Bethesda, Md, USA
| | - Alper OZCAN
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Ahmet EKEN
- Department of Medical Biology, Erciyes University, Faculty of Medicine, Kayseri, Turkey
- Molecular Biology and Genetics Department, Gevher Nesibe Genom and Stem Cell Institution, Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Meino ROHLFS
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Murat CANSEVER
- Department of Pediatrics, Division of Pediatric Immunology, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Veysel GOK
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Firdevs AYDIN
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Musa KARAKUKCU
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Fabian HAUCK
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
| | - Christoph KLEIN
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
| | - Ekrem UNAL
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
- Molecular Biology and Genetics Department, Gevher Nesibe Genom and Stem Cell Institution, Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Sergio D. ROSENZWEIG
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National, Institutes of Health, Bethesda, Md, USA
| | - Turkan PATIROGLU
- Department of Pediatrics, Division of Pediatric Hematology and Oncology & Pediatric HSCT Unit, Erciyes University, Faculty of Medicine, Kayseri, Turkey
- Department of Pediatrics, Division of Pediatric Immunology, Erciyes University, Faculty of Medicine, Kayseri, Turkey
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21
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Boast B, Miosge LA, Kuehn HS, Cho V, Athanasopoulos V, McNamara HA, Sontani Y, Mei Y, Howard D, Sutton HJ, Omari SA, Yu Z, Nasreen M, Andrews TD, Cockburn IA, Goodnow CC, Rosenzweig SD, Enders A. A Point Mutation in IKAROS ZF1 Causes a B Cell Deficiency in Mice. THE JOURNAL OF IMMUNOLOGY 2021; 206:1505-1514. [PMID: 33658297 DOI: 10.4049/jimmunol.1901464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/27/2021] [Indexed: 12/26/2022]
Abstract
IKZF1 (IKAROS) is essential for normal lymphopoiesis in both humans and mice. Previous Ikzf1 mouse models have demonstrated the dual role for IKZF1 in both B and T cell development and have indicated differential requirements of each zinc finger. Furthermore, mutations in IKZF1 are known to cause common variable immunodeficiency in patients characterized by a loss of B cells and reduced Ab production. Through N-ethyl-N-nitrosourea mutagenesis, we have discovered a novel Ikzf1 mutant mouse with a missense mutation (L132P) in zinc finger 1 (ZF1) located in the DNA binding domain. Unlike other previously reported murine Ikzf1 mutations, this L132P point mutation (Ikzf1L132P ) conserves overall protein expression and has a B cell-specific phenotype with no effect on T cell development, indicating that ZF1 is not required for T cells. Mice have reduced Ab responses to immunization and show a progressive loss of serum Igs compared with wild-type littermates. IKZF1L132P overexpressed in NIH3T3 or HEK293T cells failed to localize to pericentromeric heterochromatin and bind target DNA sequences. Coexpression of wild-type and mutant IKZF1, however, allows for localization to pericentromeric heterochromatin and binding to DNA indicating a haploinsufficient mechanism of action for IKZF1L132P Furthermore, Ikzf1+/L132P mice have late onset defective Ig production, similar to what is observed in common variable immunodeficiency patients. RNA sequencing revealed a total loss of Hsf1 expression in follicular B cells, suggesting a possible functional link for the humoral immune response defects observed in Ikzf1L132P/L132P mice.
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Affiliation(s)
- Brigette Boast
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Lisa A Miosge
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892
| | - Vicky Cho
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Vicki Athanasopoulos
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia.,Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Hayley A McNamara
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Yovina Sontani
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Yan Mei
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Debbie Howard
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Henry J Sutton
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Sofia A Omari
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia.,Children's Cancer Institute, School of Women's and Children's Health, Lowy Cancer Centre, University of New South Wales, Sydney, New South Wales 2031, Australia
| | - Zhijia Yu
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Mariam Nasreen
- Australian Phenomics Facility, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia; and
| | - T Daniel Andrews
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ian A Cockburn
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Christopher C Goodnow
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892
| | - Anselm Enders
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia;
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22
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Harman CCD, Bailis W, Zhao J, Hill L, Qu R, Jackson RP, Shyer JA, Steach HR, Kluger Y, Goff LA, Rinn JL, Williams A, Henao-Mejia J, Flavell RA. An in vivo screen of noncoding loci reveals that Daedalus is a gatekeeper of an Ikaros-dependent checkpoint during haematopoiesis. Proc Natl Acad Sci U S A 2021; 118:e1918062118. [PMID: 33446502 PMCID: PMC7826330 DOI: 10.1073/pnas.1918062118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Haematopoiesis relies on tightly controlled gene expression patterns as development proceeds through a series of progenitors. While the regulation of hematopoietic development has been well studied, the role of noncoding elements in this critical process is a developing field. In particular, the discovery of new regulators of lymphopoiesis could have important implications for our understanding of the adaptive immune system and disease. Here we elucidate how a noncoding element is capable of regulating a broadly expressed transcription factor, Ikaros, in a lymphoid lineage-specific manner, such that it imbues Ikaros with the ability to specify the lymphoid lineage over alternate fates. Deletion of the Daedalus locus, which is proximal to Ikaros, led to a severe reduction in early lymphoid progenitors, exerting control over the earliest fate decisions during lymphoid lineage commitment. Daedalus locus deletion led to alterations in Ikaros isoform expression and a significant reduction in Ikaros protein. The Daedalus locus may function through direct DNA interaction as Hi-C analysis demonstrated an interaction between the two loci. Finally, we identify an Ikaros-regulated erythroid-lymphoid checkpoint that is governed by Daedalus in a lymphoid-lineage-specific manner. Daedalus appears to act as a gatekeeper of Ikaros's broad lineage-specifying functions, selectively stabilizing Ikaros activity in the lymphoid lineage and permitting diversion to the erythroid fate in its absence. These findings represent a key illustration of how a transcription factor with broad lineage expression must work in concert with noncoding elements to orchestrate hematopoietic lineage commitment.
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Affiliation(s)
- Christian C D Harman
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520
- Howard Hughes Medical Institute, New Haven, CT 06520
| | - Will Bailis
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jun Zhao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
| | - Louisa Hill
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Rihao Qu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
| | - Ruaidhrí P Jackson
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
| | - Justin A Shyer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
| | - Holly R Steach
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
- Applied Mathematics Program, Yale University, New Haven, CT 06511
| | - Loyal A Goff
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - John L Rinn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, CO 80301
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
- Department of Genetics and Genomic Sciences, University of Connecticut Health Center, Farmington, CT 06030
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Richard A Flavell
- Howard Hughes Medical Institute, New Haven, CT 06520;
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
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23
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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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24
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IKZF1 Deletions as a Prognostic Factor in Costa Rican Patients With Pediatric B-Cell Acute Lymphoblastic Leukemia. J Pediatr Hematol Oncol 2020; 42:e401-e406. [PMID: 32324698 DOI: 10.1097/mph.0000000000001807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The IKZF1 gene encodes for Ikaros, a transcriptional factor in B-cell development. Deletions in this gene have been associated with a worse prognosis in B-cell acute lymphoblastic leukemia (B-ALL). We evaluated the presence of these alterations in all Costa Rican pediatric patients diagnosed with B-ALL between 2011 and 2014, treated with a modified Berlin-Frankfurt-Münster therapeutic protocol. Multiplex polymerase chain reaction with 2 detection methods (agarose gel and gene scanning) was used to detect intragenic deletions and multiplex ligation-dependent probe amplification for whole-gene deletions. Differences between groups (normal vs. deleted IKZF1) were analyzed by the χ test, the Kaplan-Meier test was used to calculate relapse-free survival and overall survival, and Cox regression was performed for multivariant analysis. Minimum follow-up was 4.5 years. Incidence of IKZF1 deletions was 12.9% (n=20), with an equal amount of intragenic and complete gene deletions. Adverse karyotype (P=0.048), high-risk category (P=0.030), occurrence of relapse (P=0.021), and medullar relapse (P=0.011) were statistically associated with the presence of deletions in IKZF1. Relapse-free survival at 54 months was lower in patients harboring an IKZF1 deletion than that in patients with IKZF1-wt (40.0% vs. 66.7%; P=0.014). Patients with B-ALL and IKZF1 deletions, showed a poorer relapse-free survival, in comparison with patients with IKZF1-wt, suggesting that IKZF1 status is an independent prognostic factor for pediatric patients with B-ALL.
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25
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Alomairi J, Molitor AM, Sadouni N, Hussain S, Torres M, Saadi W, Dao LTM, Charbonnier G, Santiago-Algarra D, Andrau JC, Puthier D, Sexton T, Spicuglia S. Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene. PLoS One 2020; 15:e0233191. [PMID: 32453736 PMCID: PMC7250416 DOI: 10.1371/journal.pone.0233191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023] Open
Abstract
The Ikzf1 locus encodes the lymphoid specific transcription factor Ikaros, which plays an essential role in both T and B cell differentiation, while deregulation or mutation of IKZF1/Ikzf1 is involved in leukemia. Tissue-specific and cell identity genes are usually associated with clusters of enhancers, also called super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. Several potential regulatory regions have been identified in close proximity of Ikzf1, however, the full extent of the regulatory landscape of the Ikzf1 locus is not yet established. In this study, we combined epigenomics and transcription factor binding along with high-throughput enhancer assay and 4C-seq to prioritize an enhancer element located 120 kb upstream of the Ikzf1 gene. We found that deletion of the E120 enhancer resulted in a significant reduction of Ikzf1 mRNA. However, the epigenetic landscape and 3D topology of the locus were only slightly affected, highlighting the complexity of the regulatory landscape regulating the Ikzf1 locus.
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Affiliation(s)
- Jaafar Alomairi
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Anne M. Molitor
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Wiam Saadi
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Lan T. M. Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - David Santiago-Algarra
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Jean Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Denis Puthier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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26
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Monzón-Casanova E, Matheson LS, Tabbada K, Zarnack K, Smith CWJ, Turner M. Polypyrimidine tract-binding proteins are essential for B cell development. eLife 2020; 9:e53557. [PMID: 32081131 PMCID: PMC7058386 DOI: 10.7554/elife.53557] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a RNA-binding protein (RBP) expressed throughout B cell development. Deletion of Ptbp1 in mouse pro-B cells results in upregulation of PTBP2 and normal B cell development. We show that PTBP2 compensates for PTBP1 in B cell ontogeny as deletion of both Ptbp1 and Ptbp2 results in a complete block at the pro-B cell stage and a lack of mature B cells. In pro-B cells PTBP1 ensures precise synchronisation of the activity of cyclin dependent kinases at distinct stages of the cell cycle, suppresses S-phase entry and promotes progression into mitosis. PTBP1 controls mRNA abundance and alternative splicing of important cell cycle regulators including CYCLIN-D2, c-MYC, p107 and CDC25B. Our results reveal a previously unrecognised mechanism mediated by a RBP that is essential for B cell ontogeny and integrates transcriptional and post-translational determinants of progression through the cell cycle.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Louise S Matheson
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
| | - Kristina Tabbada
- Next Generation Sequencing Facility, The Babraham InstituteCambridgeUnited Kingdom
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | | | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
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27
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Bastidas Torres AN, Cats D, Mei H, Fanoni D, Gliozzo J, Corti L, Paulli M, Vermeer MH, Willemze R, Berti E, Tensen CP. Whole-genome analysis uncovers recurrent IKZF1 inactivation and aberrant cell adhesion in blastic plasmacytoid dendritic cell neoplasm. Genes Chromosomes Cancer 2019; 59:295-308. [PMID: 31846142 PMCID: PMC7079160 DOI: 10.1002/gcc.22831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/04/2019] [Accepted: 12/12/2019] [Indexed: 01/29/2023] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and highly aggressive hematological malignancy with a poorly understood pathobiology and no effective therapeutic options. Despite a few recurrent genetic defects (eg, single nucleotide changes, indels, large chromosomal aberrations) have been identified in BPDCN, none are disease‐specific, and more importantly, none explain its genesis or clinical behavior. In this study, we performed the first high resolution whole‐genome analysis of BPDCN with a special focus on structural genomic alterations by using whole‐genome sequencing and RNA sequencing. Our study, the first to characterize the landscape of genomic rearrangements and copy number alterations of BPDCN at nucleotide‐level resolution, revealed that IKZF1, a gene encoding a transcription factor required for the differentiation of plasmacytoid dendritic cell precursors, is focally inactivated through recurrent structural alterations in this neoplasm. In concordance with the genomic data, transcriptome analysis revealed that conserved IKZF1 target genes display a loss‐of‐IKZF1 expression pattern. Furthermore, up‐regulation of cellular processes responsible for cell‐cell and cell‐ECM interactions, which is a hallmark of IKZF1 deficiency, was prominent in BPDCN. Our findings suggest that IKZF1 inactivation plays a central role in the pathobiology of the disease, and consequently, therapeutic approaches directed at reestablishing the function of this gene might be beneficial for patients.
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Affiliation(s)
| | - Davy Cats
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniele Fanoni
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Jessica Gliozzo
- Department of Dermatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Corti
- Department of Dermatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marco Paulli
- Unit of Anatomic Pathology, Department of Molecular Medicine, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rein Willemze
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Emilio Berti
- Department of Dermatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cornelis P Tensen
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
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28
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Mazzurana L, Forkel M, Rao A, Van Acker A, Kokkinou E, Ichiya T, Almer S, Höög C, Friberg D, Mjösberg J. Suppression of Aiolos and Ikaros expression by lenalidomide reduces human ILC3-ILC1/NK cell transdifferentiation. Eur J Immunol 2019; 49:1344-1355. [PMID: 31151137 DOI: 10.1002/eji.201848075] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/18/2019] [Accepted: 05/29/2019] [Indexed: 12/17/2022]
Abstract
The Ikaros family of transcription factors (TFs) are important regulators of lymphocyte function. However, their roles in human innate lymphoid cell (ILC) function remain unclear. Here, we found that Ikaros (IKZF1) is expressed by all ILC subsets, including NK cells, in blood, tonsil, and gut, while Helios (IKZF2) is preferentially expressed by ILC3 in tonsil and gut. Aiolos (IKZF3) followed the expression pattern of T-bet and Eomes, being predominantly expressed by ILC1 and NK cells. Differentiation of IFN-γ-producing ILC1 and NK cells from ILC3 by IL-1β plus IL-12-stimulation was associated with upregulation of T-bet and Aiolos. Selective degradation of Aiolos and Ikaros by lenalidomide suppressed ILC1 and NK cell differentiation and expression of ILC1 and NK cell-related transcripts (LEF1, PRF1, GRZB, CD244, NCR3, and IRF8). In line with reduced ILC1/NK cell differentiation, we observed an increase in the expression of the ILC3-related TF Helios, as well as ILC3 transcripts (TNFSF13B, IL22, NRP1, and RORC) and in the frequency of IL-22 producing ILC3 in cultures with IL-1β and IL-23. These data suggest that suppression of Aiolos and Ikaros expression inhibits ILC1 and NK cell differentiation while ILC3 function is maintained. Hence, our results open up for new possibilities in targeting Ikaros family TFs for modulation of type 1/3 immunity in inflammation and cancer.
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Affiliation(s)
- Luca Mazzurana
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Forkel
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Rao
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aline Van Acker
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Efthymia Kokkinou
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tamaki Ichiya
- Department of Medicine Solna, Karolinska Institutet, Center for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Sven Almer
- Department of Medicine, Solna, Karolinska Institutet, and IBD-Center, Division of Gastroenterology, Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Charlotte Höög
- Department of Medicine Solna, Karolinska Institutet and GHP Stockholm Gastro Center, Stockholm, Sweden
| | - Danielle Friberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical and Experimental Medicine, Linköping University, Sweden
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29
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Powell MD, Read KA, Sreekumar BK, Oestreich KJ. Ikaros Zinc Finger Transcription Factors: Regulators of Cytokine Signaling Pathways and CD4 + T Helper Cell Differentiation. Front Immunol 2019; 10:1299. [PMID: 31244845 PMCID: PMC6563078 DOI: 10.3389/fimmu.2019.01299] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022] Open
Abstract
CD4+ T helper cells are capable of differentiating into a number of effector subsets that perform diverse functions during adaptive immune responses. The differentiation of each of these subsets is governed, in large part, by environmental cytokine signals and the subsequent activation of downstream, cell-intrinsic transcription factor networks. Ikaros zinc finger (IkZF) transcription factors are known regulators of immune cell development, including that of CD4+ T cell subsets. Over the past decade, members of the IkZF family have also been implicated in the differentiation and function of individual T helper cell subsets, including T helper 1 (TH1), TH2, TH17, T follicular (TFH), and T regulatory (TREG) cells. Now, an increasing body of literature suggests that the distinct cell-specific cytokine environments responsible for the development of each subset result in differential expression of IkZF factors across T helper populations. Intriguingly, recent studies suggest that IkZF members influence T helper subset differentiation in a feed-forward fashion through the regulation of these same cytokine-signaling pathways. Here, we review the increasingly prominent role for IkZF transcription factors in the differentiation of effector CD4+ T helper cell subsets.
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Affiliation(s)
- Michael D Powell
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, United States
| | - Kaitlin A Read
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Biomedical and Veterinary Sciences Graduate Program, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Bharath K Sreekumar
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, United States
| | - Kenneth J Oestreich
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
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30
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Eskandarian Z, Fliegauf M, Bulashevska A, Proietti M, Hague R, Smulski CR, Schubert D, Warnatz K, Grimbacher B. Assessing the Functional Relevance of Variants in the IKAROS Family Zinc Finger Protein 1 ( IKZF1) in a Cohort of Patients With Primary Immunodeficiency. Front Immunol 2019; 10:568. [PMID: 31057532 PMCID: PMC6477086 DOI: 10.3389/fimmu.2019.00568] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 12/13/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency. Patients with CVID are prone to recurrent bacterial infection due to the failure of adequate immunoglobulin production. Monogenetic defects have been identified in ~25% of CVID patients. Recently, mutations in IKZF1, encoding the zinc-finger transcription factor IKAROS which is broadly expressed in hematopoietic cells, have been associated with a CVID-like phenotype. Herein we describe 11 patients with heterozygous IKZF1 variants from eight different families with autosomal dominant CVID and two siblings with an IKZF1 variant presenting with inflammatory bowel disease (IBD). This study shows that mutations affecting the DNA binding domain of IKAROS can impair the interaction with the target DNA sequence thereby preventing heterochromatin and pericentromeric localization (HC-PC) of the protein. Our results also indicate an impairment of pericentromeric localization of IKAROS by overexpression of a truncated variant, caused by an immature stop codon in IKZF1. We also describe an additional variant in TNFSF10, encoding Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL), additionally presented in individuals of Family A. Our results indicate that this variant may impair the TRAIL-induced apoptosis in target cell lines and prohibit the NFκB activation by TRAIL and may act as a modifier in Family A.
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Affiliation(s)
- Zoya Eskandarian
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Manfred Fliegauf
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany
| | - Alla Bulashevska
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Michele Proietti
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Rosie Hague
- Royal Hospital for Children, Glasgow, United Kingdom
| | - Cristian Roberto Smulski
- Department of Medical Physics, Centro Atómico Bariloche, CONICET, San Carlos de Bariloche, Argentina
| | - Desirée Schubert
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Clinic for Rheumatology and Clinical Immunology, Faculty of Medicine, CCI, Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,Satellite Center Freiburg, RESIST-Cluster of Excellence 2155, Hanover Medical School, Freiburg, Germany.,Satellite Center Freiburg, German Center for Infection Research, Freiburg, Germany.,Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, United Kingdom
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31
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Chen Q, Shi Y, Chen Y, Ji T, Li Y, Yu L. Multiple functions of Ikaros in hematological malignancies, solid tumor and autoimmune diseases. Gene 2019; 684:47-52. [DOI: 10.1016/j.gene.2018.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
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32
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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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33
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Lyon de Ana C, Arakcheeva K, Agnihotri P, Derosia N, Winandy S. Lack of Ikaros Deregulates Inflammatory Gene Programs in T Cells. THE JOURNAL OF IMMUNOLOGY 2019; 202:1112-1123. [PMID: 30635395 DOI: 10.4049/jimmunol.1801270] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/10/2018] [Indexed: 12/15/2022]
Abstract
CD4 Th cells are organizers of the immune response, directing other immune cells to initiate and maintain effective humoral and cellular immunity. CD4 T cells differentiate into distinct Th effector or regulatory subsets in response to signals delivered to them during the course of infection. Ikaros is a transcription factor that is expressed in blood cells from the level of the hematopoietic stem cell. It is required for normal thymic T cell development and serves as a tumor suppressor, as lack of Ikaros in developing lymphoid cells results in leukemia. To study the role of Ikaros in CD4 T cell differentiation and function, an Ikaros conditional knockout mouse was developed such that Ikaros expression was deleted specifically in mature T cells, thus avoiding defects observed in germline Ikaros mutant mice. Using this model system, we have shown that in the absence of Ikaros, CD4 T cells are able to attain Th1, Th2, and Th17, but not inducible regulatory T, cell fates. However, they show enhanced expression of a cohort of proinflammatory cytokines, resulting in differentiation of Th17 cells with a phenotype that has been associated with autoimmunity and pathological inflammation. In addition, we define Ikaros as a repressor of the gene program associated with the response to type I IFNs, another key pathway whose deregulation is linked to autoimmunity. Taken together, these data definitively define Ikaros as a critical regulator at the center of the inflammatory response in T cells and highlight a potential role in suppressing autoimmunity.
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Affiliation(s)
- Carolina Lyon de Ana
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Ksenia Arakcheeva
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Parul Agnihotri
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Nicole Derosia
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Susan Winandy
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
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34
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Fistonich C, Zehentmeier S, Bednarski JJ, Miao R, Schjerven H, Sleckman BP, Pereira JP. Cell circuits between B cell progenitors and IL-7 + mesenchymal progenitor cells control B cell development. J Exp Med 2018; 215:2586-2599. [PMID: 30158115 PMCID: PMC6170173 DOI: 10.1084/jem.20180778] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/05/2018] [Accepted: 08/06/2018] [Indexed: 01/30/2023] Open
Abstract
B cell development is characterized by well-defined transitions. Fistonich et al. demonstrate that two distinct cell circuits formed between proB, preB, and IL-7+ cells regulate the size and quality of B cell progenitors and control B cell development. B cell progenitors require paracrine signals such as interleukin-7 (IL-7) provided by bone marrow stromal cells for proliferation and survival. Yet, how B cells regulate access to these signals in vivo remains unclear. Here we show that proB and IL-7+ cells form a cell circuit wired by IL-7R signaling, which controls CXCR4 and focal adhesion kinase (FAK) expression and restricts proB cell movement due to increased adhesion to IL-7+CXCL12Hi cells. PreBCR signaling breaks this circuit by switching the preB cell behavior into a fast-moving and lower-adhesion state via increased CXCR4 and reduced FAK/α4β1 expression. This behavioral change reduces preB cell exposure to IL-7, thereby attenuating IL-7R signaling in vivo. Remarkably, IL-7 production is downregulated by signals provided by preB cells with unrepaired double-stranded DNA breaks and by preB acute lymphoblastic leukemic cells. Combined, these studies revealed that distinct cell circuits control the quality and homeostasis of B cell progenitors.
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Affiliation(s)
- Chris Fistonich
- Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT
| | - Sandra Zehentmeier
- Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT
| | - Jeffrey J Bednarski
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Runfeng Miao
- Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - João P Pereira
- Department of Immunobiology, Yale University School of Medicine, Yale University, New Haven, CT
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35
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Tang S, Shen H, Qu C, Dai H, Zhu X, Xue S, Ding Z, Lu J, Wu D, Tang X. Ikaros family zinc-finger 1 mutation is an independent factor for the poor prognosis of adult B-cell acute lymphoblastic leukemia, and allogeneic hematopoietic stem cell transplantation can improve clinical outcomes. Bone Marrow Transplant 2018; 54:236-243. [PMID: 29942002 DOI: 10.1038/s41409-018-0249-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 04/11/2018] [Accepted: 04/30/2018] [Indexed: 01/11/2023]
Abstract
To investigate the prognosis of patients with adult B-cell acute lymphoblastic leukemia (B-ALL) with Ikaros family zinc-finger 1 (IKZF1) mutation and determine the role of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in improving the clinical outcome, we detected the IKZF1 mutation and BCR-ABL fusion gene at diagnosis in the bone marrow of 164 adult patients with B-ALL, and analyzed the clinical data of these patients retrospectively. Our analysis showed that grade III-IV acute graft-versus-host disease and IKZF1 mutation in the transplantation group and age and IKZF1 mutation in the non-transplantation group were independent factors for poor prognosis by univariate and multivariate analyses.The 3-year overall survival (OS) and leukemia-free survival (LFS) rates were much lower in the IKZF1+/BCR-ABL+ subgroup than in the IKZF1+/BCR-ABL- and IKZF1-/BCR-ABL- subgroups in both the transplantation and non-transplantation groups. The 3-year OS and LFS rates were significantly higher in the transplantation group than in the non-transplantation group with IKZF1 mutation.The study demonstrated that IKZF1 mutation was an independent factor indicating the poor prognosis of adult B-ALL and much worse prognosis in the BCR-ABL+ subgroup in both non-transplantation and transplantation groups. However, allo-HSCT significantly improved the OS and LFS of patients and also their clinical outcomes.
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Affiliation(s)
- Shanhao Tang
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Department of Hematology, Yinzhou People Hospital, Ningbo, China
| | - Hongjie Shen
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Changju Qu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Haiping Dai
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Xiaming Zhu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Shengli Xue
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Zixuan Ding
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jing Lu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China.,Institute of Blood and Marrow Transplantation, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Depei Wu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China. .,Institute of Blood and Marrow Transplantation, Suzhou, China. .,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
| | - Xiaowen Tang
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Suzhou, China. .,Institute of Blood and Marrow Transplantation, Suzhou, China. .,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
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36
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Symonds EL, Pedersen SK, Murray DH, Jedi M, Byrne SE, Rabbitt P, Baker RT, Bastin D, Young GP. Circulating tumour DNA for monitoring colorectal cancer-a prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection. Clin Epigenetics 2018; 10:63. [PMID: 29796114 PMCID: PMC5956533 DOI: 10.1186/s13148-018-0500-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background Cell-free circulating tumour-derived DNA (ctDNA) can be detected by testing for methylated BCAT1 and IKZF1 DNA, which has proven sensitivity for colorectal cancer (CRC). A prospective correlative biomarker study between presence of methylated BCAT1 and IKZF1 in tissue and blood was conducted in cases with CRC to explore how detection of such ctDNA biomarkers relates to cancer characteristics, methylation in tissue and surgical resection of the primary cancer. Methods Enrolled patients with invasive CRC had blood collected at diagnosis, prior to any treatment or surgery (peri-diagnostic sample). A subgroup of patients also had cancer and adjacent non-neoplastic tissue collected at surgical resection, as well as a second blood sample collected within 12 months of surgery (post-surgery sample). DNA was extracted from all samples and assayed for methylated BCAT1 and IKZF1 to determine the degree of methylation in tissue and the presence of ctDNA in blood. Results Of 187 cases providing peri-diagnostic blood samples, tissue was available in 91, and 93 provided at least one post-surgery blood sample for marker analysis. Significant methylation of either BCAT1 or IKZF1 was seen in 86/91 (94.5%) cancer tissues, with levels independent of stage and higher than that observed in adjacent non-neoplastic specimens (P < 0.001). ctDNA methylated in BCAT1 or IKZF1 was detected in 116 (62.0%) cases at diagnosis and was significantly more likely to be detected with later stage (P < 0.001) and distal tumour location (P = 0.004). Of the 91 patients who provided pre-and post-surgery blood samples, 47 patients were ctDNA-positive at diagnosis and 35 (74.5%) became negative after tumour resection. Conclusion This study has shown that BCAT1 and IKZF1 methylation are common events in CRC with almost all cancer tissues showing significant levels of methylation in the two genes. The presence of ctDNA in blood is stage-related and show rapid reversion to negative following surgical resection. Monitoring methylated BCAT1 and IKZF1 levels could therefore inform adequacy of surgical resection. Trial registration Australian New Zealand Clinical Trial Registry number 12611000318987. Registered 25 March 2011. Electronic supplementary material The online version of this article (10.1186/s13148-018-0500-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erin L Symonds
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia.,2Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia Australia
| | | | - David H Murray
- Clinical Genomics Pty Ltd, North Ryde, New South Wales Australia
| | - Maher Jedi
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Susan E Byrne
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Philippa Rabbitt
- 4Colorectal Surgery, Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Bedford Park, South Australia Australia
| | - Rohan T Baker
- Clinical Genomics Pty Ltd, North Ryde, New South Wales Australia
| | - Dawn Bastin
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Graeme P Young
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
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37
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Heizmann B, Kastner P, Chan S. The Ikaros family in lymphocyte development. Curr Opin Immunol 2018; 51:14-23. [DOI: 10.1016/j.coi.2017.11.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/21/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
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38
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Abstract
Transcription factor IKZF1 (IKAROS) acts as a critical regulator of lymphoid differentiation and is frequently deleted or mutated in B-cell precursor acute lymphoblastic leukemia. IKZF1 gene defects are associated with inferior treatment outcome in both childhood and adult B-cell precursor acute lymphoblastic leukemia and occur in more than 70% of BCR-ABL1-positive and BCR-ABL1-like cases of acute lymphoblastic leukemia. Over the past few years, much has been learned about the tumor suppressive function of IKZF1 during leukemia development and the molecular pathways that relate to its impact on treatment outcome. In this review, we provide a concise overview on the role of IKZF1 during normal lymphopoiesis and the pathways that contribute to leukemia pathogenesis as a consequence of altered IKZF1 function. Furthermore, we discuss different mechanisms by which IKZF1 alterations impose therapy resistance on leukemic cells, including enhanced cell adhesion and modulation of glucocorticoid response.
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Affiliation(s)
- René Marke
- Laboratory of Pediatric Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frank N van Leeuwen
- Laboratory of Pediatric Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Blanca Scheijen
- Laboratory of Pediatric Oncology, Radboud University Medical Center, Nijmegen, the Netherlands .,Department of Pathology, Radboud University Medical Center; Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
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39
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A novel IKAROS haploinsufficiency kindred with unexpectedly late and variable B-cell maturation defects. J Allergy Clin Immunol 2017; 141:432-435.e7. [PMID: 28927821 PMCID: PMC6588539 DOI: 10.1016/j.jaci.2017.08.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/01/2017] [Accepted: 08/17/2017] [Indexed: 11/20/2022]
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40
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Li S, Heller JJ, Bostick JW, Lee A, Schjerven H, Kastner P, Chan S, Chen ZE, Zhou L. Ikaros Inhibits Group 3 Innate Lymphoid Cell Development and Function by Suppressing the Aryl Hydrocarbon Receptor Pathway. Immunity 2017; 45:185-97. [PMID: 27438771 DOI: 10.1016/j.immuni.2016.06.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/27/2016] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
Group 3 innate lymphoid cells (ILC3s) expressing the transcription factor (TF) RORγt are important for the defense and homeostasis of host intestinal tissues. The zinc finger TF Ikaros, encoded by Ikzf1, is essential for the development of RORγt(+) fetal lymphoid tissue inducer (LTi) cells and lymphoid organogenesis, but its role in postnatal ILC3s is unknown. Here, we show that small-intestinal ILC3s had lower Ikaros expression than ILC precursors and other ILC subsets. Ikaros inhibited ILC3s in a cell-intrinsic manner through zinc-finger-dependent inhibition of transcriptional activity of the aryl hydrocarbon receptor, a key regulator of ILC3 maintenance and function. Ablation of Ikzf1 in RORγt(+) ILC3s resulted in increased expansion and cytokine production of intestinal ILC3s and protection against infection and colitis. Therefore, in contrast to being required for LTi development, Ikaros inhibits postnatal ILC3 development and function to regulate gut immune responses at steady state and in disease.
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Affiliation(s)
- Shiyang Li
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Jennifer J Heller
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John W Bostick
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Chemical and Biological Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Aileen Lee
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Zongming E Chen
- Department of Laboratory Medicine in Geisinger Health System, 100 N. Academy Avenue, MC 19-20, Danville, PA 17822, USA
| | - Liang Zhou
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA.
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41
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Abstract
In this review from Georgopoulos, the role of the IKAROS gene family in lymphocyte differentiation is discussed in light of recent studies on the lineage-specific transcriptional and epigenetic networks through which IKAROS proteins operate. Lymphocyte differentiation is set to produce myriad immune effector cells with the ability to respond to multitudinous foreign substances. The uniqueness of this developmental system lies in not only the great diversity of cellular functions that it can generate but also the ability of its differentiation intermediates and mature effector cells to expand upon demand, thereby providing lifelong immunity. Surprisingly, the goals of this developmental system are met by a relatively small group of DNA-binding transcription factors that work in concert to control the timing and magnitude of gene expression and fulfill the demands for cellular specialization, expansion, and maintenance. The cellular and molecular mechanisms through which these lineage-promoting transcription factors operate have been a focus of basic research in immunology. The mechanisms of development discerned in this effort are guiding clinical research on disorders with an immune cell base. Here, I focus on IKAROS, one of the earliest regulators of lymphoid lineage identity and a guardian of lymphocyte homeostasis.
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Affiliation(s)
- Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
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42
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Read KA, Powell MD, Baker CE, Sreekumar BK, Ringel-Scaia VM, Bachus H, Martin RE, Cooley ID, Allen IC, Ballesteros-Tato A, Oestreich KJ. Integrated STAT3 and Ikaros Zinc Finger Transcription Factor Activities Regulate Bcl-6 Expression in CD4 + Th Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:2377-2387. [PMID: 28848064 DOI: 10.4049/jimmunol.1700106] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/03/2017] [Indexed: 12/24/2022]
Abstract
B cell lymphoma-6 (Bcl-6) is a transcriptional repressor that is required for the differentiation of T follicular helper (TFH) cell populations. Currently, the molecular mechanisms underlying the transcriptional regulation of Bcl-6 expression are unclear. In this study, we have identified the Ikaros zinc finger transcription factors Aiolos and Ikaros as novel regulators of Bcl-6. We found that increased expression of Bcl-6 in CD4+ Th cell populations correlated with enhanced enrichment of Aiolos and Ikaros at the Bcl6 promoter. Furthermore, overexpression of Aiolos or Ikaros, but not the related family member Eos, was sufficient to induce Bcl6 promoter activity. Intriguingly, STAT3, a known Bcl-6 transcriptional regulator, physically interacted with Aiolos to form a transcription factor complex capable of inducing the expression of Bcl6 and the TFH-associated cytokine receptor Il6ra Importantly, in vivo studies revealed that the expression of Aiolos was elevated in Ag-specific TFH cells compared with that observed in non-TFH effector Th cells generated in response to influenza infection. Collectively, these data describe a novel regulatory mechanism through which STAT3 and the Ikaros zinc finger transcription factors Aiolos and Ikaros cooperate to regulate Bcl-6 expression.
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Affiliation(s)
- Kaitlin A Read
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016
| | - Michael D Powell
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061
| | - Chandra E Baker
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016
| | - Bharath K Sreekumar
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061
| | - Veronica M Ringel-Scaia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061
| | - Holly Bachus
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - R Emily Martin
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016
| | - Ian D Cooley
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016.,Virginia Tech Carilion School of Medicine, Roanoke, VA 24016
| | - Irving C Allen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061
| | - Andre Ballesteros-Tato
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Kenneth J Oestreich
- Virginia Tech Carilion Research Institute, Roanoke, VA 24016; .,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061.,Virginia Tech Carilion School of Medicine, Roanoke, VA 24016
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43
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Abnormal hematopoiesis and autoimmunity in human subjects with germline IKZF1 mutations. J Allergy Clin Immunol 2017; 140:223-231. [DOI: 10.1016/j.jaci.2016.09.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/08/2016] [Accepted: 09/23/2016] [Indexed: 01/28/2023]
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44
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Katerndahl CDS, Heltemes-Harris LM, Willette MJL, Henzler CM, Frietze S, Yang R, Schjerven H, Silverstein KAT, Ramsey LB, Hubbard G, Wells AD, Kuiper RP, Scheijen B, van Leeuwen FN, Müschen M, Kornblau SM, Farrar MA. Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival. Nat Immunol 2017; 18:694-704. [PMID: 28369050 PMCID: PMC5540372 DOI: 10.1038/ni.3716] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/28/2017] [Indexed: 12/14/2022]
Abstract
The transcription factor STAT5 has a critical role in B cell acute lymphoblastic leukemia (B-ALL). How STAT5 mediates this effect is unclear. Here we found that activation of STAT5 worked together with defects in signaling components of the precursor to the B cell antigen receptor (pre-BCR), including defects in BLNK, BTK, PKCβ, NF-κB1 and IKAROS, to initiate B-ALL. STAT5 antagonized the transcription factors NF-κB and IKAROS by opposing regulation of shared target genes. Super-enhancers showed enrichment for STAT5 binding and were associated with an opposing network of transcription factors, including PAX5, EBF1, PU.1, IRF4 and IKAROS. Patients with a high ratio of active STAT5 to NF-κB or IKAROS had more-aggressive disease. Our studies indicate that an imbalance of two opposing transcriptional programs drives B-ALL and suggest that restoring the balance of these pathways might inhibit B-ALL.
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Affiliation(s)
- Casey D S Katerndahl
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lynn M Heltemes-Harris
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mark J L Willette
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christine M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Seth Frietze
- MLRS Department, University of Vermont, Burlington, Vermont, USA
| | - Rendong Yang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Kevin A T Silverstein
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura B Ramsey
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Gregory Hubbard
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Blanca Scheijen
- Laboratory of Pediatric Oncology Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Department of Pathology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Frank N van Leeuwen
- Laboratory of Pediatric Oncology Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Markus Müschen
- Department of Systems Biology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Pasadena, California, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Farrar
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
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45
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Mitchell JL, Seng A, Yankee TM. Expression and splicing of Ikaros family members in murine and human thymocytes. Mol Immunol 2017; 87:1-11. [PMID: 28376432 DOI: 10.1016/j.molimm.2017.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 03/08/2017] [Accepted: 03/17/2017] [Indexed: 11/18/2022]
Abstract
The Ikaros family of transcription factors includes five highly homologous members that can homodimerize or heterodimerize in any combination. Dimerization is essential for their ability to bind DNA and function as transcription factors. Previous studies showed that eliminating the function of the entire family blocks lymphocyte development while deletion of individual family members has relatively minor defects. These data indicate that multiple family members function during T cell development, so we examined the changes in expression of each family member as thymocytes progressed from the CD4-CD8- double negative (DN) to the CD4+CD8+ double positive (DP) developmental stage. Further, we compared the expression of each family member in murine and human thymocytes. In both species, Ikaros and Aiolos mRNA levels increased as thymocytes progressed through the DN to DP transition, but the corresponding increases in protein levels were only observed in mice. Further, Ikaros and Aiolos underwent extensive alternative splicing in mice, whereas only Ikaros was extensively spliced in humans. Helios mRNA and protein levels decreased during murine T cell development, but increased during human T cell development. These differences in the expression and splicing of Ikaros family members between human and murine thymocytes strongly suggest that the Ikaros family of transcription factors regulates murine and human T cell development differently, although the similarities across Ikaros family members may allow different proteins to fulfill similar functions.
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Affiliation(s)
- Julie L Mitchell
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Amara Seng
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Thomas M Yankee
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, United States.
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46
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Zhong C, Zhu J. Transcriptional regulators dictate innate lymphoid cell fates. Protein Cell 2017; 8:242-254. [PMID: 28108952 PMCID: PMC5359184 DOI: 10.1007/s13238-017-0369-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 12/15/2022] Open
Abstract
Research on innate lymphoid cells (ILC) has recently been a fast paced topic of immunological research. As ILCs are able to produce signature Th cytokine, ILCs have garnered considerable attention and have been described to represent the innate counterpart of the CD4+ T helper (Th) cells. The development and function of ILCs are precisely regulated by a network of crucial transcription factors, which are also involved in the development or differentiation of conventional natural killer (cNK) cells and T cells. In this review, we will summarize the key transcriptional regulators and their functions through each phases of ILC development. With the phase of ILC lineage commitment, we will focus in particular on the roles of the transcription regulators Id2 and GATA-3, which in collaboration with other transcriptional factors, are critically involved in the generation of ILC fate determined progenitors. Once an ILC lineage has been established, several other transcription factors are required for the specification and functional regulation of distinct mature ILC subsets. Thus, a comprehensive understanding of the interactions and regulatory mechanisms mediated by these transcription factors will help us to further understand how ILCs exert their helper-like functions and bridge the innate and adaptive immunity.
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Affiliation(s)
- Chao Zhong
- Molecular and Cellular Immunoregulation Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
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47
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Seng A, Yankee TM. The Role of the Ikaros Family of Transcription Factors in Regulatory T cell Development and Function. ACTA ACUST UNITED AC 2017; 8. [PMID: 28758047 PMCID: PMC5531196 DOI: 10.4172/2155-9899.1000495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regulatory T (Treg) cells are a subset of immune cells that maintain homeostasis by promoting immune tolerance and suppressing the immune response via a variety of mechanisms such as secreting cytokines, killing reactive immune cells, and inducing anergy. Dysfunction of Treg cells has been implicated in inflammatory diseases such as autoimmunity and transplant rejection. Conversely, too many or hyperresponsive Treg cells has been observed in cancer and chronic infections. Treg cells have proven to be difficult to study as there are no definitive Treg surface markers. Additionally, Tregs can gain pro-inflammatory phenotype depending on stimuli. In this commentary, we discuss the expression and function of members of the Ikaros family of transcription factors during Treg cell development and activation.
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Affiliation(s)
- Amara Seng
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Thomas M Yankee
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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48
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Regulation of PI3K signaling in T-cell acute lymphoblastic leukemia: a novel PTEN/Ikaros/miR-26b mechanism reveals a critical targetable role for PIK3CD. Leukemia 2017; 31:2355-2364. [PMID: 28280276 PMCID: PMC5986278 DOI: 10.1038/leu.2017.80] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 01/07/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic
malignancy, and T-ALL patients are prone to early disease relapse and suffer
from poor outcomes. The PTEN, PI3K/AKT, and Notch pathways are frequently
altered in T-ALL. PTEN is a tumor suppressor that inactivates the PI3K pathway.
We profiled miRNAs in Pten-deficient mouse T-ALL and identified
miR-26b as a potentially dysregulated gene. We validated decreased expression
levels of miR-26b in mouse and human T-ALL cells. In addition, expression of
exogenous miR-26b reduced proliferation and promoted apoptosis of T-ALL cells
in vitro, and hindered progression of T-ALL in
vivo. Furthermore, miR-26b inhibited the PI3K/AKT pathway by
directly targeting PIK3CD, the gene encoding PI3Kδ, in
human T-ALL cell lines. ShRNA for PIK3CD and CAL-101, a PIK3CD
inhibitor, reduced the growth and increased apoptosis of T-ALL cells. Finally,
we showed that PTEN induced miR-26b expression by regulating the differential
expression of Ikaros isoforms that are transcriptional regulators of miR-26b.
These results suggest that miR-26b functions as a tumor suppressor in the
development of T-ALL. Further characterization of targets and regulators of
miR-26b may be promising for the development of novel therapies.
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49
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Comeaux EQ, Mullighan CG. TP53 Mutations in Hypodiploid Acute Lymphoblastic Leukemia. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026286. [PMID: 28003275 DOI: 10.1101/cshperspect.a026286] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is an aggressive neoplasm of B- or T-lymphoid progenitors and is the commonest childhood tumor. ALL comprises multiple subtypes characterized by distinct genetic alterations, with stereotyped patterns of aneuploidy present in many cases. Although alterations of TP53 are common in many tumors, they are infrequent in ALL, with the exception of two ALL subtypes associated with poor outcome: relapsed disease and ALL with hypodiploidy. TP53 alterations are present in almost all cases of ALL with low hypodiploidy and are associated with alterations of the lymphoid transcription factor IKZF2 and the tumor-suppressor gene loci CDKN2A and CDKN2B. Remarkably, more than half of TP53 mutations in low-hypodiploid ALL in children are present in nontumor cells, indicating that low-hypodiploid ALL is a manifestation of Li-Fraumeni syndrome. These findings have profound implications for our understanding of the genetic pathogenesis of hypodiploid ALL, suggesting that alteration of TP53 function may promote the distinctive aneuploidy characteristic of hypodiploid ALL. Moreover, the identification of hypodiploidy mandates offering testing for TP53 mutational status to patients and their relatives, with appropriate counseling and disease surveillance.
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Affiliation(s)
- Evan Q Comeaux
- Departments of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles G Mullighan
- Departments of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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50
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Witkowski MT, Hu Y, Roberts KG, Boer JM, McKenzie MD, Liu GJ, Le Grice OD, Tremblay CS, Ghisi M, Willson TA, Horstmann MA, Aifantis I, Cimmino L, Frietze S, den Boer ML, Mullighan CG, Smyth GK, Dickins RA. Conserved IKAROS-regulated genes associated with B-progenitor acute lymphoblastic leukemia outcome. J Exp Med 2017; 214:773-791. [PMID: 28190000 PMCID: PMC5339666 DOI: 10.1084/jem.20160048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 10/05/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022] Open
Abstract
Genetic alterations disrupting the transcription factor IKZF1 (encoding IKAROS) are associated with poor outcome in B lineage acute lymphoblastic leukemia (B-ALL) and occur in >70% of the high-risk BCR-ABL1+ (Ph+) and Ph-like disease subtypes. To examine IKAROS function in this context, we have developed novel mouse models allowing reversible RNAi-based control of Ikaros expression in established B-ALL in vivo. Notably, leukemias driven by combined BCR-ABL1 expression and Ikaros suppression rapidly regress when endogenous Ikaros is restored, causing sustained disease remission or ablation. Comparison of transcriptional profiles accompanying dynamic Ikaros perturbation in murine B-ALL in vivo with two independent human B-ALL cohorts identified nine evolutionarily conserved IKAROS-repressed genes. Notably, high expression of six of these genes is associated with inferior event-free survival in both patient cohorts. Among them are EMP1, which was recently implicated in B-ALL proliferation and prednisolone resistance, and the novel target CTNND1, encoding P120-catenin. We demonstrate that elevated Ctnnd1 expression contributes to maintenance of murine B-ALL cells with compromised Ikaros function. These results suggest that IKZF1 alterations in B-ALL leads to induction of multiple genes associated with proliferation and treatment resistance, identifying potential new therapeutic targets for high-risk disease.
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Affiliation(s)
- Matthew T Witkowski
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Yifang Hu
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Judith M Boer
- Department of Pediatric Oncology, Erasmus MC - Sophia Children's Hospital, 3015 CN Rotterdam, Netherlands
| | - Mark D McKenzie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Grace J Liu
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Oliver D Le Grice
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
| | - Cedric S Tremblay
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Margherita Ghisi
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Tracy A Willson
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
| | - Martin A Horstmann
- Research Institute Children's Cancer Center, Department of Pediatric Hematology and Oncology, University Medical Center Hamburg, 20246 Hamburg, Germany
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY 10016
| | - Luisa Cimmino
- Department of Pathology, NYU School of Medicine, New York, NY 10016
| | - Seth Frietze
- Department of Medical Laboratory and Radiation Science, University of Vermont, Burlington, VT 05405
| | - Monique L den Boer
- Department of Pediatric Oncology, Erasmus MC - Sophia Children's Hospital, 3015 CN Rotterdam, Netherlands.,Dutch Childhood Oncology Group, 2545 The Hague, Netherlands
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Gordon K Smyth
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Mathematics and Statistics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia .,Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville 3010, Victoria, Australia
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