1
|
Uehata T, Yamada S, Ori D, Vandenbon A, Giladi A, Jelinski A, Murakawa Y, Watanabe H, Takeuchi K, Toratani K, Mino T, Kiryu H, Standley DM, Tsujimura T, Ikawa T, Kondoh G, Landthaler M, Kawamoto H, Rodewald HR, Amit I, Yamamoto R, Miyazaki M, Takeuchi O. Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz. Blood 2024; 143:243-257. [PMID: 37922454 PMCID: PMC10808253 DOI: 10.1182/blood.2023020903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/05/2023] Open
Abstract
ABSTRACT Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.
Collapse
Affiliation(s)
- Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinnosuke Yamada
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Daisuke Ori
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexis Vandenbon
- Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jelinski
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yasuhiro Murakawa
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Sciences, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuhiro Takeuchi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Kazunori Toratani
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tohru Tsujimura
- Department of Pathology, Hyogo College of Medicine, Hyogo, Japan
| | - Tomokatsu Ikawa
- Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Sciences, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine Berlin, Berlin Institute for Molecular Systems Biology, Berlin, Germany
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hans-Reimer Rodewald
- Division for Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ryo Yamamoto
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
2
|
Takano J, Ito S, Dong Y, Sharif J, Nakajima-Takagi Y, Umeyama T, Han YW, Isono K, Kondo T, Iizuka Y, Miyai T, Koseki Y, Ikegaya M, Sakihara M, Nakayama M, Ohara O, Hasegawa Y, Hashimoto K, Arner E, Klose RJ, Iwama A, Koseki H, Ikawa T. PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment. Nat Commun 2022; 13:7159. [PMID: 36443290 PMCID: PMC9705430 DOI: 10.1038/s41467-022-34856-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Polycomb group proteins (PcG), polycomb repressive complexes 1 and 2 (PRC1 and 2), repress lineage inappropriate genes during development to maintain proper cellular identities. It has been recognized that PRC1 localizes at the replication fork, however, the precise functions of PRC1 during DNA replication are elusive. Here, we reveal that a variant PRC1 containing PCGF1 (PCGF1-PRC1) prevents overloading of activators and chromatin remodeling factors on nascent DNA and thereby mediates proper deposition of nucleosomes and correct downstream chromatin configurations in hematopoietic stem and progenitor cells (HSPCs). This function of PCGF1-PRC1 in turn facilitates PRC2-mediated repression of target genes such as Hmga2 and restricts premature myeloid differentiation. PCGF1-PRC1, therefore, maintains the differentiation potential of HSPCs by linking proper nucleosome configuration at the replication fork with PcG-mediated gene silencing to ensure life-long hematopoiesis.
Collapse
Affiliation(s)
- Junichiro Takano
- grid.509459.40000 0004 0472 0267Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa Japan ,grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan ,grid.136304.30000 0004 0370 1101Department of Cellular and Molecular Medicine, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Shinsuke Ito
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yixing Dong
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Jafar Sharif
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yaeko Nakajima-Takagi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Taichi Umeyama
- grid.7597.c0000000094465255Laboratory for Microbiome Sciences, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Yong-Woon Han
- grid.7597.c0000000094465255Laboratory for Integrative Genomics, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Kyoichi Isono
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan ,grid.412857.d0000 0004 1763 1087Laboratory Animal Center, Wakayama Medical University, Wakayama, Japan
| | - Takashi Kondo
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yusuke Iizuka
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Tomohiro Miyai
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Yoko Koseki
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Mika Ikegaya
- grid.509459.40000 0004 0472 0267Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa Japan ,grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan
| | - Mizuki Sakihara
- grid.143643.70000 0001 0660 6861Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Manabu Nakayama
- grid.410858.00000 0000 9824 2470Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Osamu Ohara
- grid.410858.00000 0000 9824 2470Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yoshinori Hasegawa
- grid.410858.00000 0000 9824 2470Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kosuke Hashimoto
- grid.136593.b0000 0004 0373 3971Laboratory of Computational Biology, Institute for Protein Research, Osaka University Osaka, Japan ,grid.7597.c0000000094465255Laboratory for Transcriptome Technology, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Erik Arner
- grid.7597.c0000000094465255Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN-IMS, Yokohama, Kanagawa Japan
| | - Robert J. Klose
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Atsushi Iwama
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Haruhiko Koseki
- grid.509459.40000 0004 0472 0267Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa Japan ,grid.136304.30000 0004 0370 1101Department of Cellular and Molecular Medicine, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Tomokatsu Ikawa
- grid.509459.40000 0004 0472 0267Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa Japan ,grid.143643.70000 0001 0660 6861Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| |
Collapse
|
3
|
Singh S, Sarkar T, Jakubison B, Gadomski S, Spradlin A, Gudmundsson KO, Keller JR. Inhibitor of DNA binding proteins revealed as orchestrators of steady state, stress and malignant hematopoiesis. Front Immunol 2022; 13:934624. [PMID: 35990659 PMCID: PMC9389078 DOI: 10.3389/fimmu.2022.934624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
Adult mammalian hematopoiesis is a dynamic cellular process that provides a continuous supply of myeloid, lymphoid, erythroid/megakaryocyte cells for host survival. This process is sustained by regulating hematopoietic stem cells (HSCs) quiescence, proliferation and activation under homeostasis and stress, and regulating the proliferation and differentiation of downstream multipotent progenitor (MPP) and more committed progenitor cells. Inhibitor of DNA binding (ID) proteins are small helix-loop-helix (HLH) proteins that lack a basic (b) DNA binding domain present in other family members, and function as dominant-negative regulators of other bHLH proteins (E proteins) by inhibiting their transcriptional activity. ID proteins are required for normal T cell, B cell, NK and innate lymphoid cells, dendritic cell, and myeloid cell differentiation and development. However, recent evidence suggests that ID proteins are important regulators of normal and leukemic hematopoietic stem and progenitor cells (HSPCs). This chapter will review our current understanding of the function of ID proteins in HSPC development and highlight future areas of scientific investigation.
Collapse
Affiliation(s)
- Shweta Singh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Tanmoy Sarkar
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Brad Jakubison
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen Gadomski
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Andrew Spradlin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Kristbjorn O. Gudmundsson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Jonathan R. Keller
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
- *Correspondence: Jonathan R. Keller,
| |
Collapse
|
4
|
van Gils N, Verhagen HJ, Broux M, Martiáñez T, Denkers F, Vermue E, Rutten A, Csikós T, Demeyer S, Çil M, Al M, Cools J, Janssen JJ, Ossenkoppele GJ, Menezes RX, Smit L. Targeting histone methylation to reprogram the transcriptional state that drives survival of drug-tolerant myeloid leukemia persisters. iScience 2022; 25:105013. [PMID: 36097617 PMCID: PMC9463578 DOI: 10.1016/j.isci.2022.105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Although chemotherapy induces complete remission in the majority of acute myeloid leukemia (AML) patients, many face a relapse. This relapse is caused by survival of chemotherapy-resistant leukemia (stem) cells (measurable residual disease; MRD). Here, we demonstrate that the anthracycline doxorubicin epigenetically reprograms leukemia cells by inducing histone 3 lysine 27 (H3K27) and H3K4 tri-methylation. Within a doxorubicin-sensitive leukemia cell population, we identified a subpopulation of reversible anthracycline-tolerant cells (ATCs) with leukemic stem cell (LSC) features lacking doxorubicin-induced H3K27me3 or H3K4me3 upregulation. These ATCs have a distinct transcriptional landscape than the leukemia bulk and could be eradicated by KDM6 inhibition. In primary AML, reprogramming the transcriptional state by targeting KDM6 reduced MRD load and survival of LSCs residing within MRD, and enhanced chemotherapy response in vivo. Our results reveal plasticity of anthracycline resistance in AML cells and highlight the potential of transcriptional reprogramming by epigenetic-based therapeutics to target chemotherapy-resistant AML cells. Reversible anthracycline-tolerant leukemia cells (ATCs) have low H3K27me3 or H3K4me3 ATCs exhibit stem cell features similar to leukemic stem cells Reprogramming the transcriptional state by inhibition of KDM6 depletes ATCs Inhibiting KDM6 adds to doxorubicin treatment and eradicates AML MRD (stem) cells
Collapse
|
5
|
Aubrey M, Warburg ZJ, Murre C. Helix-Loop-Helix Proteins in Adaptive Immune Development. Front Immunol 2022; 13:881656. [PMID: 35634342 PMCID: PMC9134016 DOI: 10.3389/fimmu.2022.881656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The E/ID protein axis is instrumental for defining the developmental progression and functions of hematopoietic cells. The E proteins are dimeric transcription factors that activate gene expression programs and coordinate changes in chromatin organization. Id proteins are antagonists of E protein activity. Relative levels of E/Id proteins are modulated throughout hematopoietic development to enable the progression of hematopoietic stem cells into multiple adaptive and innate immune lineages including natural killer cells, B cells and T cells. In early progenitors, the E proteins promote commitment to the T and B cell lineages by orchestrating lineage specific programs of gene expression and regulating VDJ recombination of antigen receptor loci. In mature B cells, the E/Id protein axis functions to promote class switch recombination and somatic hypermutation. E protein activity further regulates differentiation into distinct CD4+ and CD8+ T cells subsets and instructs mature T cell immune responses. In this review, we discuss how the E/Id proteins define the adaptive immune system lineages, focusing on their role in directing developmental gene programs.
Collapse
Affiliation(s)
- Megan Aubrey
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Zachary J Warburg
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Cornelis Murre
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| |
Collapse
|
6
|
Different cell imaging methods did not significantly improve immune cell image classification performance. PLoS One 2022; 17:e0262397. [PMID: 35085287 PMCID: PMC8794178 DOI: 10.1371/journal.pone.0262397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/23/2021] [Indexed: 11/29/2022] Open
Abstract
Developments in high-throughput microscopy have made it possible to collect huge amounts of cell image data that are difficult to analyse manually. Machine learning (e.g., deep learning) is often employed to automate the extraction of information from these data, such as cell counting, cell type classification and image segmentation. However, the effects of different imaging methods on the accuracy of image processing have not been examined systematically. We studied the effects of different imaging methods on the performance of machine learning-based cell type classifiers. We observed lymphoid-primed multipotential progenitor (LMPP) and pro-B cells using three imaging methods: differential interference contrast (DIC), phase contrast (Ph) and bright-field (BF). We examined the classification performance of convolutional neural networks (CNNs) with each of them and their combinations. CNNs achieved an area under the receiver operating characteristic (ROC) curve (AUC) of ~0.9, which was significantly better than when the classifier used only cell size or cell contour shape as input. However, no significant differences were found between imaging methods and focal positions.
Collapse
|
7
|
Torres-Montaner A. The telomere complex and the origin of the cancer stem cell. Biomark Res 2021; 9:81. [PMID: 34736527 PMCID: PMC8567692 DOI: 10.1186/s40364-021-00339-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/21/2021] [Indexed: 11/15/2022] Open
Abstract
Exquisite regulation of telomere length is essential for the preservation of the lifetime function and self-renewal of stem cells. However, multiple oncogenic pathways converge on induction of telomere attrition or telomerase overexpression and these events can by themselves trigger malignant transformation. Activation of NFκB, the outcome of telomere complex damage, is present in leukemia stem cells but absent in normal stem cells and can activate DOT1L which has been linked to MLL-fusion leukemias. Tumors that arise from cells of early and late developmental stages appear to follow two different oncogenic routes in which the role of telomere and telomerase signaling might be differentially involved. In contrast, direct malignant transformation of stem cells appears to be extremely rare. This suggests an inherent resistance of stem cells to cancer transformation which could be linked to a stem cell’specific mechanism of telomere maintenance. However, tumor protection of normal stem cells could also be conferred by cell extrinsic mechanisms.
Collapse
Affiliation(s)
- A Torres-Montaner
- Department of Pathology, Queen's Hospital, Rom Valley Way, London, Romford, RM7 OAG, UK. .,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
| |
Collapse
|
8
|
Kandarakov OF, Kravatsky YV, Polyakova NS, Bruter AV, Gordeeva EG, Belyavsky AV. Mitomycin C Treatment of Stromal Layers Enhances the Support of In Vitro Hematopoiesis in Co-Culture Systems. Mol Biol 2021. [DOI: 10.1134/s0026893321010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Kimura Y, Iwanaga E, Iwanaga K, Endo S, Inoue Y, Tokunaga K, Nagahata Y, Masuda K, Kawamoto H, Matsuoka M. A regulatory element in the 3'-untranslated region of CEBPA is associated with myeloid/NK/T-cell leukemia. Eur J Haematol 2020; 106:327-339. [PMID: 33197296 DOI: 10.1111/ejh.13551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/01/2022]
Abstract
OBJECTIVES CCAAT/enhancer-binding protein α (CEBPA) is an essential transcription factor for myeloid differentiation. Not only mutation of the CEBPA gene, but also promoter methylation, which results in silencing of CEBPA, contributes to the pathogenesis of acute myeloid leukemia (AML). We sought for another differentially methylated region (DMR) that associates with the CEBPA silencing and disease phenotype. METHODS Using databases, we identified a conserved DMR in the CEBPA 3'-untranslated region (UTR). RESULTS Methylation-specific PCR analysis of 231 AML cases showed that hypermethylation of the 3'-UTR was associated with AML that had a myeloid/NK/T-cell phenotype and downregulated CEBPA. Most of these cases were of an immature phenotype with CD7/CD56 positivity. These cases were significantly associated with lower hemoglobin levels than the others. Furthermore, we discovered that the CEBPA 3'-UTR DMR can enhance transcription from the CEBPA native promoter. In vitro experiments identified IKZF1-binding sites in the 3'-UTR that are responsible for this increased transcription of CEBPA. CONCLUSIONS These results indicate that the CEBPA 3'-UTR DMR is a novel regulatory element of CEBPA related to myeloid/NK/T-cell lineage leukemogenesis. Transcriptional regulation of CEBPA by IKZF1 may provide a clue for understanding the fate determination of myeloid vs. NK/T-lymphoid progenitors.
Collapse
Affiliation(s)
- Yukiko Kimura
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Eisaku Iwanaga
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Kouta Iwanaga
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Shinya Endo
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Yoshitaka Inoue
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Kenji Tokunaga
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Yousuke Nagahata
- Laboratory of Immunology, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto, Japan
| | - Kyoko Masuda
- Laboratory of Immunology, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto, Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan.,Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| |
Collapse
|
10
|
Koniaeva E, Stahlhut M, Lange L, Sauer MG, Kustikova OS, Schambach A. Conditional Immortalization of Lymphoid Progenitors via Tetracycline-Regulated LMO2 Expression. Hum Gene Ther 2019; 31:183-198. [PMID: 31760808 DOI: 10.1089/hum.2019.212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Conditional immortalization of hematopoietic progenitors through lentiviral expression of selected transcription factors in hematopoietic stem and progenitor cells provides a promising tool to study stem cell and leukemia biology. In this study, to generate conditionally immortalized lymphoid progenitor (ciLP) cell lines, murine hematopoietic progenitor cells were transduced with an inducible lentiviral "all-in-one" vector expressing LMO2 under doxycycline (DOX) stimulation and the reverse tetracycline-regulated transactivator (rtTA3). For selection of LMO2-expressing ciLPs (LMO2-ciLPs) and longitudinal manipulation in T cell differentiation lymphoid conditions, we developed a robust approach based on coculture with OP9-DL1 stromal cells and improved cytokine conditions allowing a controlled balance between cell proliferation and differentiation in vitro. LMO2-ciLP cell lines with the highest proliferation, vector copy number, and similar insertion pattern were selected for LMO2 "on/off" in vitro study. LMO2 expression under DOX induction resulted in a double negative (DN) 2 differentiation arrest and a propagation of CD44+CD25- myeloid cell population characterized by lymphoid and myeloid phenotypes, respectively. Both DN2 and CD44+CD25- myeloid cell subpopulations expressed c-KIT, suggesting that LMO2-ciLPs were similar to uncommitted progenitors under DOX supplementation. DOX removal resulted in cessation of ectopic LMO2 expression and LMO2-ciLPs continued T cell lymphoid differentiation accompanied by c-KIT downregulation and interleukin 7 receptor expression. Switching off LMO2 expression was accompanied by increased Notch signaling and significant reduction of the CD44+CD25- myeloid cell population under T cell differentiation lymphoid conditions. Although vector insertions in cooperation with LMO2 expression could influence the fate of LMO2-ciLPs and additional experiments are required to evaluate it, our approach provides a promising tool to investigate mechanisms underlying stem cell, leukemia, and lymphocyte biology, leading to novel approaches for disease modeling and therapy evaluation.
Collapse
Affiliation(s)
- Ekaterina Koniaeva
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Maike Stahlhut
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Lucas Lange
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Martin G Sauer
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Olga S Kustikova
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
11
|
Johari B, Asadi Z, Rismani E, Maghsood F, Sheikh Rezaei Z, Farahani S, Madanchi H, Kadivar M. Inhibition of transcription factor T-cell factor 3 (TCF3) using the oligodeoxynucleotide strategy increases embryonic stem cell stemness: possible application in regenerative medicine. Cell Biol Int 2019; 43:852-862. [PMID: 31033094 DOI: 10.1002/cbin.11153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 03/10/2019] [Accepted: 04/24/2019] [Indexed: 12/22/2022]
Abstract
The transcription factor T-cell factor 3 (TCF3), one component of the Wnt pathway, is known as a cell-intrinsic inhibitor of many pluripotency genes in embryonic stem cells (ESCs) that influences the balance between pluripotency and differentiation. In this study, the effects of inhibition of TCF3 transcription factor on the stemness of mouse ESCs (mESCs) were investigated using the decoy oligodeoxynucleotides (ODNs) strategy. The TCF3 decoy and its scramble ODNs were designed and synthesized. The interaction specificity of the TCF3 decoy with the TCF3 transcription factor was evaluated by the electrophoretic mobility shift assay. Subcellular localization was carried out using fluorescence and confocal microscopy. Self-renewal and pluripotency of mESCs were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), cell cycle and apoptosis, alkaline phosphatase (ALP), embryoid body (EB) formation, and real-time assays. All experiments were performed in triplicate. The results showed that knockdown of TCF3 by decoy ODNs transfection in mESCs led to an increase in the cell proliferation, ALP enzyme activity, and master regulatory stemness genes and a decrease in the number and diameter of EBs. These results supported TCF3 as a potential target to maintain the pluripotency and self-renewal capacity of mESCs. Knockdown of the TCF3 transcription factor using decoy ODNs can be a promising method to maintain the stemness of stem cells in regenerative medicine and cell therapy researches.
Collapse
Affiliation(s)
- Behrooz Johari
- Student Research Committee, Zanjan University of Medical Sciences, Zanjan, Iran.,Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Zoleykha Asadi
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Elham Rismani
- Deartment of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Faezeh Maghsood
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | | | - Sima Farahani
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Madanchi
- Department and Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran
| | - Mehdi Kadivar
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
12
|
Stable lines and clones of long-term proliferating normal, genetically unmodified murine common lymphoid progenitors. Blood 2018; 131:2026-2035. [DOI: 10.1182/blood-2017-09-805259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/11/2018] [Indexed: 01/15/2023] Open
Abstract
Key Points
We have established a novel culture system for long-term proliferating murine lymphoid progenitors without any genetic manipulation. The cultured lymphoid progenitors can differentiate to lymphoid and myeloid lineages in vitro and in vivo.
Collapse
|
13
|
Miyai T, Takano J, Endo TA, Kawakami E, Agata Y, Motomura Y, Kubo M, Kashima Y, Suzuki Y, Kawamoto H, Ikawa T. Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells. Genes Dev 2018; 32:112-126. [PMID: 29440259 PMCID: PMC5830925 DOI: 10.1101/gad.309575.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/29/2017] [Indexed: 02/04/2023]
Abstract
Miyai et al. used multipotent progenitors harboring a tamoxifen-inducible form of Id3—where virtually all cells became B cells within 6 d by withdrawing 4-OHT—to identify a three-step transcription factor network model during specification of multipotent progenitors toward the B-cell lineage. Stem cell fate is orchestrated by core transcription factors (TFs) and epigenetic modifications. Although regulatory genes that control cell type specification are identified, the transcriptional circuit and the cross-talk among regulatory factors during cell fate decisions remain poorly understood. To identify the “time-lapse” TF networks during B-lineage commitment, we used multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system in which virtually all cells became B cells within 6 d by simply withdrawing 4-hydroxytamoxifen (4-OHT). Transcriptome and epigenome analysis at multiple time points revealed that ∼10%–30% of differentially expressed genes were virtually controlled by the core TFs, including E2A, EBF1, and PAX5. Strikingly, we found unexpected transcriptional priming before the onset of the key TF program. Inhibition of the immediate early genes such as Nr4a2, Klf4, and Egr1 severely impaired the generation of B cells. Integration of multiple data sets, including transcriptome, protein interactome, and epigenome profiles, identified three representative transcriptional circuits. Single-cell RNA sequencing (RNA-seq) analysis of lymphoid progenitors in bone marrow strongly supported the three-step TF network model during specification of multipotent progenitors toward B-cell lineage in vivo. Thus, our findings will provide a blueprint for studying the normal and neoplastic development of B lymphocytes.
Collapse
Affiliation(s)
- Tomohiro Miyai
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Disease Biology Group, Medical Science Innovation Hub Program, RIKEN Cluster for Science and Technology Hub, Yokohama 230-0045, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Junichiro Takano
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Immune Regulation Research, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba 260-8670, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Eiryo Kawakami
- Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Healthcare and Medical Data-Driven AI-based Predictive Reasoning Development Unit, Medical Science Innovation Hub Program, RIKEN Cluster for Science and Technology Hub, Yokohama 230-0045, Japan
| | - Yasutoshi Agata
- Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan
| | - Yasutaka Motomura
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda 278-0022, Japan.,Laboratory for Cytokine Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda 278-0022, Japan.,Laboratory for Cytokine Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yukie Kashima
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 272-8562, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 272-8562, Japan
| | - Hiroshi Kawamoto
- Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Tomokatsu Ikawa
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| |
Collapse
|
14
|
Li Y, Xiao Y, Liu C. The Horizon of Materiobiology: A Perspective on Material-Guided Cell Behaviors and Tissue Engineering. Chem Rev 2017; 117:4376-4421. [PMID: 28221776 DOI: 10.1021/acs.chemrev.6b00654] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the biological functions of cell and tissue can be regulated by biochemical factors (e.g., growth factors, hormones), the biophysical effects of materials on the regulation of biological activity are receiving more attention. In this Review, we systematically summarize the recent progress on how biomaterials with controllable properties (e.g., compositional/degradable dynamics, mechanical properties, 2D topography, and 3D geometry) can regulate cell behaviors (e.g., cell adhesion, spreading, proliferation, cell alignment, and the differentiation or self-maintenance of stem cells) and tissue/organ functions. How the biophysical features of materials influence tissue/organ regeneration have been elucidated. Current challenges and a perspective on the development of novel materials that can modulate specific biological functions are discussed. The interdependent relationship between biomaterials and biology leads us to propose the concept of "materiobiology", which is a scientific discipline that studies the biological effects of the properties of biomaterials on biological functions at cell, tissue, organ, and the whole organism levels. This Review highlights that it is more important to develop ECM-mimicking biomaterials having a self-regenerative capacity to stimulate tissue regeneration, instead of attempting to recreate the complexity of living tissues or tissue constructs ex vivo. The principles of materiobiology may benefit the development of novel biomaterials providing combinative bioactive cues to activate the migration of stem cells from endogenous reservoirs (i.e., cell niches), stimulate robust and scalable self-healing mechanisms, and unlock the body's innate powers of regeneration.
Collapse
Affiliation(s)
- Yulin Li
- Key Laboratory for Ultrafine Materials of Ministry of Education, East China University of Science and Technology , Meilong Road 130, Shanghai 200237, People's Republic of China
| | - Yin Xiao
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove, Brisbane, Queensland 4059, Australia
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, East China University of Science and Technology , Meilong Road 130, Shanghai 200237, People's Republic of China
| |
Collapse
|
15
|
Masuda J, Kawamoto H, Strober W, Takayama E, Mizutani A, Murakami H, Ikawa T, Kitani A, Maeno N, Shigehiro T, Satoh A, Seno A, Arun V, Kasai T, Fuss IJ, Katsura Y, Seno M. Transient Tcf3 Gene Repression by TALE-Transcription Factor Targeting. Appl Biochem Biotechnol 2016; 180:1559-1573. [PMID: 27406037 DOI: 10.1007/s12010-016-2187-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/04/2016] [Indexed: 12/14/2022]
Abstract
Transplantation of hematopoietic stem and progenitor cells (HSCs) i.e., self-renewing cells that retain multipotentiality, is now a widely performed therapy for many hematopoietic diseases. However, these cells are present in low number and are subject to replicative senescence after extraction; thus, the acquisition of sufficient numbers of cells for transplantation requires donors able to provide repetitive blood samples and/or methods of expanding cell numbers without disturbing cell multipotentiality. Previous studies have shown that HSCs maintain their multipotentiality and self-renewal activity if TCF3 transcription function is blocked under B cell differentiating conditions. Taking advantage of this finding to devise a new approach to HSC expansion in vitro, we constructed an episomal expression vector that specifically targets and transiently represses the TCF3 gene. This consisted of a vector encoding a transcription activator-like effector (TALE) fused to a Krüppel-associated box (KRAB) repressor. We showed that this TALE-KRAB vector repressed expression of an exogenous reporter gene in HEK293 and COS-7 cell lines and, more importantly, efficiently repressed endogenous TCF3 in a human B lymphoma cell line. These findings suggest that this vector can be used to maintain multipotentiality in HSC being subjected to a long-term expansion regimen prior to transplantation.
Collapse
Affiliation(s)
- Junko Masuda
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Hiroshi Kawamoto
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama, 230-0045, Japan
- Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eiji Takayama
- Department of Oral Biochemistry, Asahi University School of Dentistry, Hozumi 1851, Gifu, 501-0296, Japan
| | - Akifumi Mizutani
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Hiroshi Murakami
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Tomokatsu Ikawa
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama, 230-0045, Japan
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Atsushi Kitani
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Narumi Maeno
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Tsukasa Shigehiro
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Ayano Satoh
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Akimasa Seno
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Vaidyanath Arun
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Tomonari Kasai
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Ivan J Fuss
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yoshimoto Katsura
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama, 230-0045, Japan
- Division of Cell Regeneration and Transplantation, Advanced Medical Research Center, School of Medicine, Nihon University, Tokyo, 173-8610, Japan
| | - Masaharu Seno
- Division of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| |
Collapse
|