1
|
Xu Z, He L, Wu Y, Yang L, Li C, Wu H. PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility. Cell Rep 2023; 42:112967. [PMID: 37561626 DOI: 10.1016/j.celrep.2023.112967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
PTEN loss in fetal liver hematopoietic stem cells (HSCs) leads to alterations in myeloid, T-, and B-lineage potentials and T-lineage acute lymphoblastic leukemia (T-ALL) development. To explore the mechanism underlying PTEN-regulated hematopoietic lineage choices, we carry out integrated assay for transposase-accessible chromatin using sequencing (ATAC-seq), single-cell RNA-seq, and in vitro culture analyses using in vivo-isolated mouse pre-leukemic HSCs and progenitors. We find that PTEN loss alters chromatin accessibility of key lineage transcription factor (TF) binding sites at the prepro-B stage, corresponding to increased myeloid and T-lineage potentials and reduced B-lineage potential. Importantly, we find that PU.1 is an essential TF downstream of PTEN and that altering PU.1 levels can reprogram the chromatin accessibility landscape and myeloid, T-, and B-lineage potentials in Ptennull prepro-B cells. Our study discovers prepro-B as the key developmental stage underlying PTEN-regulated hematopoietic lineage choices and suggests a critical role of PU.1 in modulating the epigenetic state and lineage plasticity of prepro-B progenitors.
Collapse
Affiliation(s)
- Zihan Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Center for Statistical Science, Peking University, Beijing, China
| | - Libing He
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Cheng Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Center for Statistical Science, Peking University, Beijing, China.
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
2
|
Nagel S. The Role of IRX Homeobox Genes in Hematopoietic Progenitors and Leukemia. Genes (Basel) 2023; 14:genes14020297. [PMID: 36833225 PMCID: PMC9957183 DOI: 10.3390/genes14020297] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
IRX genes are members of the TALE homeobox gene class and encode six related transcription factors (IRX1-IRX6) controlling development and cell differentiation of several tissues in humans. Classification of TALE homeobox gene expression patterns for the hematopoietic compartment, termed TALE-code, has revealed exclusive IRX1 activity in pro-B-cells and megakaryocyte erythroid progenitors (MEPs), highlighting its specific contribution to developmental processes at these early stages of hematopoietic lineage differentiation. Moreover, aberrant expression of IRX homeobox genes IRX1, IRX2, IRX3 and IRX5 has been detected in hematopoietic malignancies, including B-cell precursor acute lymphoblastic leukemia (BCP-ALL), T-cell ALL, and some subtypes of acute myeloid leukemia (AML). Expression analyses of patient samples and experimental studies using cell lines and mouse models have revealed oncogenic functions in cell differentiation arrest and upstream and downstream genes, thus, revealing normal and aberrant regulatory networks. These studies have shown how IRX genes play key roles in the development of both normal blood and immune cells, and hematopoietic malignancies. Understanding their biology serves to illuminate developmental gene regulation in the hematopoietic compartment, and may improve diagnostic classification of leukemias in the clinic and reveal new therapeutic targets and strategies.
Collapse
Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Cultures, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| |
Collapse
|
3
|
Abstract
Traditional models of lymphopoiesis present B and T cell development as a linear process that initiates in the fetus and continues after birth in the bone marrow and thymus, respectively. However, this view of lymphocyte development is not in accord with reports, dating back several decades, indicating that the types of lymphocytes generated before and after birth differ. In this regard, selected γδ T cells, and those that utilize the Vγ3 receptor in particular, and innate-like B-1 B cells preferentially arise during fetal blood cell development. This review synthesizes data from multiple laboratories, with an emphasis on our own work using mouse models, demonstrating that innate and conventional B and T cells emerge in hematopoietic stem cell independent and dependent waves of development that are differentially regulated. This layering of lymphocyte development has implications for understanding the composition of the adult immune system and may provide insights into the origin of various lymphocytic leukemias.
Collapse
Affiliation(s)
- Encarnacion Montecino-Rodriguez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kenneth Dorshkind
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| |
Collapse
|
4
|
Flippe L, Gaignerie A, Sérazin C, Baron O, Saulquin X, Anegon I, David L, Guillonneau C. Generation of CD34(+)CD43(+) Hematopoietic Progenitors to Induce Thymocytes from Human Pluripotent Stem Cells. Cells 2022; 11. [PMID: 36552810 DOI: 10.3390/cells11244046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Immunotherapy using primary T cells has revolutionized medical care in some pathologies in recent years, but limitations associated to challenging cell genome edition, insufficient cell number production, the use of only autologous cells, and the lack of product standardization have limited its clinical use. The alternative use of T cells generated in vitro from human pluripotent stem cells (hPSCs) offers great advantages by providing a self-renewing source of T cells that can be readily genetically modified and facilitate the use of standardized universal off-the-shelf allogeneic cell products and rapid clinical access. However, despite their potential, a better understanding of the feasibility and functionality of T cells differentiated from hPSCs is necessary before moving into clinical settings. In this study, we generated human-induced pluripotent stem cells from T cells (T-iPSCs), allowing for the preservation of already recombined TCR, with the same properties as human embryonic stem cells (hESCs). Based on these cells, we differentiated, with high efficiency, hematopoietic progenitor stem cells (HPSCs) capable of self-renewal and differentiation into any cell blood type, in addition to DN3a thymic progenitors from several T-iPSC lines. In order to better comprehend the differentiation, we analyzed the transcriptomic profiles of the different cell types and demonstrated that HPSCs differentiated from hiPSCs had very similar profiles to cord blood hematopoietic stem cells (HSCs). Furthermore, differentiated T-cell progenitors had a similar profile to thymocytes at the DN3a stage of thymic lymphopoiesis. Therefore, utilizing this approach, we were able to regenerate precursors of therapeutic human T cells in order to potentially treat a wide range of diseases.
Collapse
|
5
|
Stamos DB, Clubb LM, Mitra A, Chopp LB, Nie J, Ding Y, Das A, Venkataganesh H, Lee J, El-Khoury D, Li L, Bhandoola A, Bosselut R, Love PE. The histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development. J Exp Med 2021; 218:e20202012. [PMID: 34726730 PMCID: PMC8570297 DOI: 10.1084/jem.20202012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 08/27/2021] [Accepted: 09/30/2021] [Indexed: 11/27/2022] Open
Abstract
Analysis of the transcriptional profiles of developing thymocytes has shown that T lineage commitment is associated with loss of stem cell and early progenitor gene signatures and the acquisition of T cell gene signatures. Less well understood are the epigenetic alterations that accompany or enable these transcriptional changes. Here, we show that the histone demethylase Lsd1 (Kdm1a) performs a key role in extinguishing stem/progenitor transcriptional programs in addition to key repressive gene programs during thymocyte maturation. Deletion of Lsd1 caused a block in late T cell development and resulted in overexpression of interferon response genes as well as genes regulated by the Gfi1, Bcl6, and, most prominently, Bcl11b transcriptional repressors in CD4+CD8+ thymocytes. Transcriptional overexpression in Lsd1-deficient thymocytes was not always associated with increased H3K4 trimethylation at gene promoters, indicating that Lsd1 indirectly affects the expression of many genes. Together, these results identify a critical function for Lsd1 in the epigenetic regulation of multiple repressive gene signatures during T cell development.
Collapse
Affiliation(s)
- Daniel B. Stamos
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Lauren M. Clubb
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Apratim Mitra
- Bioinformatics and Scientific Programing Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Laura B. Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jan Lee
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Dalal El-Khoury
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - LiQi Li
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Paul E. Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| |
Collapse
|
6
|
Bigas A, Rodriguez-Sevilla JJ, Espinosa L, Gallardo F. Recent advances in T-cell lymphoid neoplasms. Exp Hematol 2021; 106:3-18. [PMID: 34879258 DOI: 10.1016/j.exphem.2021.12.191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022]
Abstract
T Cells comprise many subtypes of specified lymphocytes, and their differentiation and function take place in different tissues. This cellular diversity is also observed in the multiple ways T-cell transformation gives rise to a variety of T-cell neoplasms. This review covers the main types of T-cell malignancies and their specific characteristics, emphasizing recent advances at the cellular and molecular levels as well as differences and commonalities among them.
Collapse
Affiliation(s)
- Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain; Institut Josep Carreras contra la Leucemia, Barcelona, Spain.
| | | | - Lluis Espinosa
- Program in Cancer Research, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
| | - Fernando Gallardo
- Dermatology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain.
| |
Collapse
|
7
|
Cheng ZY, He TT, Gao XM, Zhao Y, Wang J. ZBTB Transcription Factors: Key Regulators of the Development, Differentiation and Effector Function of T Cells. Front Immunol 2021; 12:713294. [PMID: 34349770 PMCID: PMC8326903 DOI: 10.3389/fimmu.2021.713294] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
The development and differentiation of T cells represents a long and highly coordinated, yet flexible at some points, pathway, along which the sequential and dynamic expressions of different transcriptional factors play prominent roles at multiple steps. The large ZBTB family comprises a diverse group of transcriptional factors, and many of them have emerged as critical factors that regulate the lineage commitment, differentiation and effector function of hematopoietic-derived cells as well as a variety of other developmental events. Within the T-cell lineage, several ZBTB proteins, including ZBTB1, ZBTB17, ZBTB7B (THPOK) and BCL6 (ZBTB27), mainly regulate the development and/or differentiation of conventional CD4/CD8 αβ+ T cells, whereas ZBTB16 (PLZF) is essential for the development and function of innate-like unconventional γδ+ T & invariant NKT cells. Given the critical role of T cells in host defenses against infections/tumors and in the pathogenesis of many inflammatory disorders, we herein summarize the roles of fourteen ZBTB family members in the development, differentiation and effector function of both conventional and unconventional T cells as well as the underlying molecular mechanisms.
Collapse
Affiliation(s)
- Zhong-Yan Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| |
Collapse
|
8
|
Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
Collapse
Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
| |
Collapse
|
9
|
Wang F, Qi Z, Yao Y, Yu G, Feng T, Zhao T, Xue HH, Zhao Y, Jiang P, Bao L, Yu S. Exploring the stage-specific roles of Tcf-1 in T cell development and malignancy at single-cell resolution. Cell Mol Immunol 2021; 18:644-659. [PMID: 32868912 PMCID: PMC8027857 DOI: 10.1038/s41423-020-00527-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/04/2020] [Indexed: 01/04/2023] Open
Abstract
Tcf-1 (encoded by Tcf7) not only plays critical roles in promoting T cell development and differentiation but also has been identified as a tumor suppressor involved in preventing T cell malignancy. However, the comprehensive mechanisms of Tcf-1 involved in T cell transformation remain poorly understood. In this study, Tcf7fl/fl mice were crossed with Vav-cre, Lck-cre, or Cd4-cre mice to delete Tcf-1 conditionally at the beginning of the HSC, DN2-DN3, or DP stage, respectively. The defective T cell development phenotypes became gradually less severe as the deletion stage became more advanced in distinct mouse models. Interestingly, consistent with Tcf7-/- mice, Tcf7fl/flVav-cre mice developed aggressive T cell lymphoma within 45 weeks, but no tumors were generated in Tcf7fl/flLck-cre or Tcf7fl/flCd4-cre mice. Single-cell RNA-seq (ScRNA-seq) indicated that ablation of Tcf-1 at distinct phases can subdivide DN1 cells into three clusters (C1, C2, and C3) and DN2-DN3 cells into three clusters (C4, C5, and C6). Moreover, Tcf-1 deficiency redirects bifurcation among divergent cell fates, and clusters C1 and C4 exhibit high potential for leukemic transformation. Mechanistically, we found that Tcf-1 directly binds and mediates chromatin accessibility for both typical T cell regulators and proto-oncogenes, including Myb, Mycn, Runx1, and Lyl1 in the DN1 phase and Lef1, Id2, Dtx1, Fyn, Bcl11b, and Zfp36l2 in the DN2-DN3 phase. The aberrant expression of these genes due to Tcf-1 deficiency in very early T cells contributes to subsequent tumorigenesis. Thus, we demonstrated that Tcf-1 plays stage-specific roles in regulating early thymocyte development and transformation, providing new insights and evidence for clinical trials on T-ALL leukemia.
Collapse
MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Profiling
- Hepatocyte Nuclear Factor 1-alpha/physiology
- Lymphocyte Activation
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/physiology
- Lymphoma, T-Cell/etiology
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Single-Cell Analysis/methods
- T-Lymphocytes, Regulatory/immunology
Collapse
Affiliation(s)
- Fang Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Zhihong Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Yingpeng Yao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Guotao Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Tao Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Tianyan Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Hai-Hui Xue
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Peng Jiang
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI, 53707, USA
| | - Li Bao
- Department Hematology, Beijing Jishuitan Hospital, 100096, Beijing, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China.
| |
Collapse
|
10
|
Loontiens S, Dolens AC, Strubbe S, Van de Walle I, Moore FE, Depestel L, Vanhauwaert S, Matthijssens F, Langenau DM, Speleman F, Van Vlierberghe P, Durinck K, Taghon T. PHF6 Expression Levels Impact Human Hematopoietic Stem Cell Differentiation. Front Cell Dev Biol 2020; 8:599472. [PMID: 33251223 PMCID: PMC7672048 DOI: 10.3389/fcell.2020.599472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 01/10/2023] Open
Abstract
Transcriptional control of hematopoiesis involves complex regulatory networks and functional perturbations in one of these components often results in malignancies. Loss-of-function mutations in PHF6, encoding a presumed epigenetic regulator, have been primarily described in T cell acute lymphoblastic leukemia (T-ALL) and the first insights into its function in normal hematopoiesis only recently emerged from mouse modeling experiments. Here, we investigated the role of PHF6 in human blood cell development by performing knockdown studies in cord blood and thymus-derived hematopoietic precursors to evaluate the impact on lineage differentiation in well-established in vitro models. Our findings reveal that PHF6 levels differentially impact the differentiation of human hematopoietic progenitor cells into various blood cell lineages, with prominent effects on lymphoid and erythroid differentiation. We show that loss of PHF6 results in accelerated human T cell development through reduced expression of NOTCH1 and its downstream target genes. This functional interaction in developing thymocytes was confirmed in vivo using a phf6-deficient zebrafish model that also displayed accelerated developmental kinetics upon reduced phf6 or notch1 activation. In summary, our work reveals that appropriate control of PHF6 expression is important for normal human hematopoiesis and provides clues towards the role of PHF6 in T-ALL development.
Collapse
Affiliation(s)
- Siebe Loontiens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Finola E. Moore
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, United States
| | - Lisa Depestel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Filip Matthijssens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - David M. Langenau
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, United States
- Harvard Stem Cell Institute, Cambridge, MA, United States
| | - Frank Speleman
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kaat Durinck
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
11
|
Abstract
PTEN is one of the most frequently mutated tumor suppressor genes in human cancers. By counteracting the PI3K/AKT/mTOR pathway, PTEN plays an essential role in regulating hematopoietic stem cells (HSCs) self-renewal, migration, lineage commitment, and differentiation. PTEN also plays important roles in suppressing leukemogenesis, especially T-cell acute lymphoblastic leukemia (T-ALL). Herein, we will review the function of PTEN in regulating hematopoiesis and leukemogenesis and discuss potential therapeutic approaches against leukemia with PTEN mutations.
Collapse
Affiliation(s)
- Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| |
Collapse
|
12
|
Sacco KA, Stack M, Notarangelo LD. Targeted pharmacologic immunomodulation for inborn errors of immunity. Br J Clin Pharmacol 2020; 88:2500-2508. [PMID: 32738057 DOI: 10.1111/bcp.14509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022] Open
Abstract
Inborn errors of immunity consist of over 400 known single gene disorders that may manifest with infection susceptibility, autoimmunity, autoinflammation, hypersensitivity and cancer predisposition. Most patients are treated symptomatically with immunoglobulin replacement, prophylactic antimicrobials or broad immunosuppression pertaining to their disease phenotype. Other than haematopoietic stem cell transplantation, the aforementioned treatments do little to alter disease morbidity or mortality. Further, many patients may not be transplant candidates. In this review, we describe monogenic disorders affecting leucocyte migration, disorders of immune synapse formation and dysregulation of immune cell signal transduction. We highlight the use of off-label small molecules and biologics mechanistically targeted to altered disease pathophysiology of such diseases.
Collapse
Affiliation(s)
- Keith A Sacco
- Laboratory of Clinical Immunology and Microbiology, National Institute for Allergy and Infectious Diseases, NIH, Maryland, USA
| | - Michael Stack
- Laboratory of Clinical Immunology and Microbiology, National Institute for Allergy and Infectious Diseases, NIH, Maryland, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute for Allergy and Infectious Diseases, NIH, Maryland, USA
| |
Collapse
|
13
|
Dolens A, Durinck K, Lavaert M, Van der Meulen J, Velghe I, De Medts J, Weening K, Roels J, De Mulder K, Volders P, De Preter K, Kerre T, Vandekerckhove B, Leclercq G, Vandesompele J, Mestdagh P, Van Vlierberghe P, Speleman F, Taghon T. Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development. EMBO Rep 2020; 21:e49006. [PMID: 32255245 PMCID: PMC7202205 DOI: 10.15252/embr.201949006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/03/2020] [Accepted: 03/12/2020] [Indexed: 12/22/2022] Open
Abstract
γδ and αβ T cells have unique roles in immunity and both originate in the thymus from T-lineage committed precursors through distinct but unclear mechanisms. Here, we show that Notch1 activation is more stringently required for human γδ development compared to αβ-lineage differentiation and performed paired mRNA and miRNA profiling across 11 discrete developmental stages of human T cell development in an effort to identify the potential Notch1 downstream mechanism. Our data suggest that the miR-17-92 cluster is a Notch1 target in immature thymocytes and that miR-17 can restrict BCL11B expression in these Notch-dependent T cell precursors. We show that enforced miR-17 expression promotes human γδ T cell development and, consistently, that BCL11B is absolutely required for αβ but less for γδ T cell development. This study suggests that human γδ T cell development is mediated by a stage-specific Notch-driven negative feedback loop through which miR-17 temporally restricts BCL11B expression and provides functional insights into the developmental role of the disease-associated genes BCL11B and the miR-17-92 cluster in a human context.
Collapse
Affiliation(s)
| | - Kaat Durinck
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Marieke Lavaert
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | | | - Imke Velghe
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Jelle De Medts
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Karin Weening
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Juliette Roels
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | | | | | | | - Tessa Kerre
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | | | | | - Jo Vandesompele
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Pieter Mestdagh
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | | | - Frank Speleman
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Tom Taghon
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| |
Collapse
|
14
|
Abstract
In this review, Rothenburg discusses the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors in the primary establishment of T-cell identity. T-cell development in mammals is a model for lineage choice and differentiation from multipotent stem cells. Although T-cell fate choice is promoted by signaling in the thymus through one dominant pathway, the Notch pathway, it entails a complex set of gene regulatory network and chromatin state changes even before the cells begin to express their signature feature, the clonal-specific T-cell receptors (TCRs) for antigen. This review distinguishes three developmental modules for T-cell development, which correspond to cell type specification, TCR expression and selection, and the assignment of cells to different effector types. The first is based on transcriptional regulatory network events, the second is dominated by somatic gene rearrangement and mutation and cell selection, and the third corresponds to establishing a poised state of latent regulator priming through an unknown mechanism. Interestingly, in different lineages, the third module can be deployed at variable times relative to the completion of the first two modules. This review focuses on the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors TCF1, GATA3, PU.1, Bcl11b, Runx1, and E proteins in the primary establishment of T-cell identity.
Collapse
Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
15
|
Harly C, Kenney D, Ren G, Lai B, Raabe T, Yang Q, Cam MC, Xue HH, Zhao K, Bhandoola A. The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage. Nat Immunol 2019; 20:1150-60. [PMID: 31358996 DOI: 10.1038/s41590-019-0445-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 06/12/2019] [Indexed: 01/25/2023]
Abstract
Innate lymphoid cells (ILCs) play important functions in immunity and tissue homeostasis, but their development is poorly understood. Through the use of single-cell approaches, we examined the transcriptional and functional heterogeneity of ILC progenitors, and studied the precursor-product relationships that link the subsets identified. This analysis identified two successive stages of ILC development within T cell factor 1-positive (TCF-1+) early innate lymphoid progenitors (EILPs), which we named 'specified EILPs' and 'committed EILPs'. Specified EILPs generated dendritic cells, whereas this potential was greatly decreased in committed EILPs. TCF-1 was dispensable for the generation of specified EILPs, but required for the generation of committed EILPs. TCF-1 used a pre-existing regulatory landscape established in upstream lymphoid precursors to bind chromatin in EILPs. Our results provide insight into the mechanisms by which TCF-1 promotes developmental progression of ILC precursors, while constraining their dendritic cell lineage potential and enforcing commitment to ILC fate.
Collapse
|
16
|
Khalsa JK, Chawla AS, Prabhu SB, Vats M, Dhar A, Dev G, Das N, Mukherjee S, Tanwar S, Banerjee H, Durdik JM, Bal V, George A, Rath S, Arimbasseri GA. Functionally significant metabolic differences between B and T lymphocyte lineages. Immunology 2019; 158:104-120. [PMID: 31318442 DOI: 10.1111/imm.13098] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/13/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022] Open
Abstract
Activation of B and T lymphocytes leads to major remodelling of the metabolic landscape of the cells enabling their post-activation functions. However, naive B and T lymphocytes also show metabolic differences, and the genesis, nature and functional significance of these differences are not yet well understood. Here we show that resting B-cells appeared to have lower energy demands than resting T-cells as they consumed lower levels of glucose and fatty acids and produced less ATP. Resting B-cells are more dependent on OXPHOS, while T-cells show more dependence on aerobic glycolysis. However, despite an apparently higher energy demand, T lineage cells showed lower rates of protein synthesis than equivalent B lineage stages. These metabolic differences between the two lineages were established early during lineage differentiation, and were functionally significant. Higher levels of protein synthesis in B-cells were associated with increased synthesis of MHC class II molecules and other proteins associated with antigen internalization, transport and presentation. The combination of higher energy demand and lower protein synthesis in T-cells was consistent with their higher ATP-dependent motility. Our data provide an integrated perspective of the metabolic differences and their functional implications between the B and T lymphocyte lineages.
Collapse
Affiliation(s)
| | | | - Savit B Prabhu
- Wellcome Laboratory, Christian Medical College, Vellore, India
| | - Mukti Vats
- National Institute of Immunology, New Delhi, India
| | - Atika Dhar
- National Institute of Immunology, New Delhi, India
| | - Gagan Dev
- National Institute of Immunology, New Delhi, India
| | - Nabanita Das
- Indian Institute of Chemical Biology, Kolkata, India
| | | | | | | | | | - Vineeta Bal
- National Institute of Immunology, New Delhi, India
| | - Anna George
- National Institute of Immunology, New Delhi, India
| | | | | |
Collapse
|
17
|
Patrick MS, Cheng NL, Kim J, An J, Dong F, Yang Q, Zou I, Weng NP. Human T Cell Differentiation Negatively Regulates Telomerase Expression Resulting in Reduced Activation-Induced Proliferation and Survival. Front Immunol 2019; 10:1993. [PMID: 31497023 PMCID: PMC6712505 DOI: 10.3389/fimmu.2019.01993] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/07/2019] [Indexed: 01/10/2023] Open
Abstract
Maintenance of telomeres is essential for preserving T cell proliferative responses yet the precise role of telomerase in human T cell differentiation, function, and aging is not fully understood. Here we analyzed human telomerase reverse transcriptase (hTERT) expression and telomerase activity in six T cell subsets from 111 human adults and found that levels of hTERT mRNA and telomerase activity had an ordered decrease from naïve (TN) to central memory (TCM) to effector memory (TEM) cells and were higher in CD4+ than their corresponding CD8+ subsets. This differentiation-related reduction of hTERT mRNA and telomerase activity was preserved after activation. Furthermore, the levels of hTERT mRNA and telomerase activity were positively correlated with the degree of activation-induced proliferation and survival of T cells in vitro. Partial knockdown of hTERT by an anti-sense oligo in naïve CD4+ cells led to a modest but significant reduction of cell proliferation. Finally, we found that activation-induced levels of telomerase activity in CD4+ TN and TCM cells were significantly lower in old than in young subjects. These findings reveal that hTERT/telomerase expression progressively declines during T cell differentiation and age-associated reduction of activation-induced expression of hTERT/telomerase mainly affects naïve CD4+ T cells and suggest that enhancing telomerase activity could be a strategy to improve T cell function in the elderly.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| |
Collapse
|
18
|
Abstract
Gene regulatory network modeling has played a major role in advancing the understanding of developmental systems, by crystallizing structures of relevant extant information, by formally posing hypothetical functional relationships between network elements, and by offering clear predictive tests to improve understanding of the mechanisms driving developmental progression. Both ordinary differential equation (ODE)-based and Boolean models have also been highly successful in explaining dynamics within subcircuits of more complex processes. In a very small number of cases, gene regulatory network models of much more global scope have been proposed that successfully predict the dynamics of the processes establishing most of an embryonic body plan. Can such successes be expanded to very different developmental systems, including post-embryonic mammalian systems? This perspective discusses several problems that must be solved in more quantitative and predictive theoretical terms, to make this possible. These problems include: the effects of cellular history on chromatin state and how these affect gene accessibility; the dose dependence of activities of many transcription factors (a problem for Boolean models); stochasticity of some transcriptional outputs (a problem for simple ODE models); response timing delays due to epigenetic remodeling requirements; functionally different kinds of repression; and the regulatory syntax that governs responses of genes with multiple enhancers.
Collapse
Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| |
Collapse
|
19
|
Simons L, Cavazzana M, André I. Concise Review: Boosting T-Cell Reconstitution Following Allogeneic Transplantation-Current Concepts and Future Perspectives. Stem Cells Transl Med 2019; 8:650-657. [PMID: 30887712 PMCID: PMC6591542 DOI: 10.1002/sctm.18-0248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/06/2019] [Indexed: 12/14/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is the treatment of choice for a large number of malignant and nonmalignant (inherited) diseases of the hematopoietic system. Nevertheless, non‐HLA identical transplantations are complicated by a severe T‐cell immunodeficiency associated with a high rate of infection, relapse and graft‐versus‐host disease. Initial recovery of T‐cell immunity following HSCT relies on peripheral expansion of memory T cells mostly driven by cytokines. The reconstitution of a diverse, self‐tolerant, and naive T‐cell repertoire, however, may take up to 2 years and crucially relies on the interaction of T‐cell progenitors with the host thymic epithelium, which may be altered by GvHD, age or transplant‐related toxicities. In this review, we summarize current concepts to stimulate reconstitution of a peripheral and polyclonal T‐cell compartment following allogeneic transplantation such as graft manipulation (i.e., T‐cell depletion), transfusion of ex vivo manipulated donor T cells or the exogenous administration of cytokines and growth factors to stimulate host‐thymopoiesis with emphasis on approaches which have led to clinical trials. Particular attention will be given to the development of cellular therapies such as the ex vivo generation of T‐cell precursors to fasten generation of a polyclonal and functional host‐derived T‐cell repertoire. Having been tested so far only in preclinical mouse models, clinical studies are now on the way to validate the efficacy of such T‐cell progenitors in enhancing immune reconstitution following HSCT in various clinical settings. stem cells translational medicine2019;00:1–8
Collapse
Affiliation(s)
- Laura Simons
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes University-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Biotherapy, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Marina Cavazzana
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM CIC, Paris, France.,Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes University-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Biotherapy, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Isabelle André
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes University-Sorbonne Paris Cité, Imagine Institute, Paris, France
| |
Collapse
|
20
|
Rothenberg EV, Hosokawa H, Ungerbäck J. Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development. Front Immunol 2019; 10:228. [PMID: 30842770 PMCID: PMC6391351 DOI: 10.3389/fimmu.2019.00228] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
PU.1 is an ETS-family transcription factor that plays a broad range of roles in hematopoiesis. A direct regulator of myeloid, dendritic-cell, and B cell functional programs, and a well-known antagonist of terminal erythroid cell differentiation, it is also expressed in the earliest stages of T-cell development of each cohort of intrathymic pro-T cells. Its expression in this context appears to give T-cell precursors initial, transient access to myeloid and dendritic cell developmental competence and therefore to represent a source of antagonism or delay of T-cell lineage commitment. However, it has remained uncertain until recently why T-cell development is also intensely dependent upon PU.1. Here, we review recent work that sheds light on the molecular biology of PU.1 action across the genome in pro-T cells and identifies the genes that depend on PU.1 for their correct regulation. This work indicates modes of chromatin engagement, pioneering, and cofactor recruitment (“coregulator theft”) by PU.1 as well as gene network interactions that not only affect specific target genes but also have system-wide regulatory consequences, amplifying the impact of PU.1 beyond its own direct binding targets. The genes directly regulated by PU.1 also suggest a far-reaching transformation of cell biology and signaling potential between the early stages of T-cell development when PU.1 is expressed and when it is silenced. These cell-biological functions can be important to distinguish fetal from adult T-cell development and have the potential to illuminate aspects of thymic function that have so far remained the most mysterious.
Collapse
Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Jonas Ungerbäck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
21
|
Zhu H, Zhang L, Wu Y, Dong B, Guo W, Wang M, Yang L, Fan X, Tang Y, Liu N, Lei X, Wu H. T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1. eLife 2018; 7:38314. [PMID: 30412053 PMCID: PMC6251627 DOI: 10.7554/elife.38314] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022] Open
Abstract
Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC 'stemness'. Using single-cell RNA-seq analysis, we identify a master regulator, SPI1, the LSC-specific expression of which determines the molecular signature and activity of LSCs in the murine Pten-null T-ALL model. Although initiated by PTEN-controlled β-catenin activation, Spi1 expression and LSC 'stemness' are maintained by a β-catenin-SPI1-HAVCR2 regulatory circuit independent of the leukemogenic driver mutation. Perturbing any component of this circuit either genetically or pharmacologically can prevent LSC formation or eliminate existing LSCs. LSCs lose their 'stemness' when Spi1 expression is silenced by DNA methylation, but Spi1 expression can be reactivated by 5-AZ treatment. Importantly, similar regulatory mechanisms may be also present in human T-ALL.
Collapse
Affiliation(s)
- Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Liuzhen Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Bingjie Dong
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Weilong Guo
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Mei Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Xiaoying Fan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yuliang Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ningshu Liu
- Drug Discovery Oncology, Bayer Pharmaceuticals, Berlin, Germany
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| |
Collapse
|
22
|
Abstract
As our catalog of cell states expands, appropriate characterization of these states and the transitions between them is crucial. Here we discuss the roles of intermediate cell states (ICSs) in this growing collection. We begin with definitions and discuss evidence for the existence of ICSs and their relevance in various tissues. We then provide a list of possible functions for ICSs with examples. Finally, we describe means by which ICSs and their functional roles can be identified from single-cell data or predicted from models.
Collapse
Affiliation(s)
- Adam L. MacLean
- Department of Mathematics and Center for Complex Biological Systems, University of California, Irvine, CA 92697, United States
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37966, United States
| | - Qing Nie
- Department of Mathematics and Center for Complex Biological Systems, University of California, Irvine, CA 92697, United States,Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| |
Collapse
|
23
|
Longabaugh WJR, Zeng W, Zhang JA, Hosokawa H, Jansen CS, Li L, Romero-Wolf M, Liu P, Kueh HY, Mortazavi A, Rothenberg EV. Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proc Natl Acad Sci U S A 2017; 114:5800-7. [PMID: 28584128 DOI: 10.1073/pnas.1610617114] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing bases for a comprehensively updated model of the T-cell specification gene regulatory network presented herein. However, the role of lineage commitment factor Bcl11b has been unclear. We use self-organizing maps on 63 RNA-seq datasets from normal and perturbed T-cell development to identify functional targets of Bcl11b during commitment and relate them to other regulomes. We show that both activation and repression target genes can be bound by Bcl11b in vivo, and that Bcl11b effects overlap with E2A-dependent effects. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid, myeloid, and dendritic, and B-cell fate alternatives are excluded by different mechanisms.
Collapse
|
24
|
Wallaert A, Durinck K, Taghon T, Van Vlierberghe P, Speleman F. T-ALL and thymocytes: a message of noncoding RNAs. J Hematol Oncol 2017; 10:66. [PMID: 28270163 PMCID: PMC5341419 DOI: 10.1186/s13045-017-0432-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/24/2017] [Indexed: 02/06/2023] Open
Abstract
In the last decade, the role for noncoding RNAs in disease was clearly established, starting with microRNAs and later expanded towards long noncoding RNAs. This was also the case for T cell acute lymphoblastic leukemia, which is a malignant blood disorder arising from oncogenic events during normal T cell development in the thymus. By studying the transcriptomic profile of protein-coding genes, several oncogenic events leading to T cell acute lymphoblastic leukemia (T-ALL) could be identified. In recent years, it became apparent that several of these oncogenes function via microRNAs and long noncoding RNAs. In this review, we give a detailed overview of the studies that describe the noncoding RNAome in T-ALL oncogenesis and normal T cell development.
Collapse
Affiliation(s)
- Annelynn Wallaert
- Center for Medical Genetics, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent, Ghent, Belgium.
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Tom Taghon
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| |
Collapse
|
25
|
Nagel S, Pommerenke C, Scherr M, Meyer C, Kaufmann M, Battmer K, MacLeod RA, Drexler HG. NKL homeobox gene activities in hematopoietic stem cells, T-cell development and T-cell leukemia. PLoS One 2017; 12:e0171164. [PMID: 28151996 DOI: 10.1371/journal.pone.0171164] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) cells represent developmentally arrested T-cell progenitors, subsets of which aberrantly express homeobox genes of the NKL subclass, including TLX1, TLX3, NKX2-1, NKX2-5, NKX3-1 and MSX1. Here, we analyzed the transcriptional landscape of all 48 members of the NKL homeobox gene subclass in CD34+ hematopoietic stem and progenitor cells (HSPCs) and during lymphopoiesis, identifying activities of nine particular genes. Four of these were expressed in HSPCs (HHEX, HLX1, NKX2-3 and NKX3-1) and three in common lymphoid progenitors (HHEX, HLX1 and MSX1). Interestingly, our data indicated downregulation of NKL homeobox gene transcripts in late progenitors and mature T-cells, a phenomenon which might explain the oncogenic impact of this group of genes in T-ALL. Using MSX1-expressing T-ALL cell lines as models, we showed that HHEX activates while HLX1, NKX2-3 and NKX3-1 repress MSX1 transcription, demonstrating the mutual regulation and differential activities of these homeobox genes. Analysis of a public T-ALL expression profiling data set comprising 117 patient samples identified 20 aberrantly activated members of the NKL subclass, extending the number of known NKL homeobox oncogene candidates. While 7/20 genes were also active during hematopoiesis, the remaining 13 showed ectopic expression. Finally, comparative analyses of T-ALL patient and cell line profiling data of NKL-positive and NKL-negative samples indicated absence of shared target genes but instead highlighted deregulation of apoptosis as common oncogenic effect. Taken together, we present a comprehensive survey of NKL homeobox genes in early hematopoiesis, T-cell development and T-ALL, showing that these genes generate an NKL-code for the diverse stages of lymphoid development which might be fundamental for regular differentiation.
Collapse
|
26
|
Affiliation(s)
- Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| |
Collapse
|
27
|
Abstract
T cells are continually generated in the thymus in a highly dynamic process comprising discrete steps of lineage commitment, T cell receptor (TCR) gene rearrangement, and selection. These steps are linked to distinct rates of proliferation, survival, and cell death, but a quantitative picture of T cell development is only beginning to emerge. Here we summarize recent technical advances, including genetic fate mapping, barcoding, and molecular timers, that have allowed the implementation of computational models to quantify developmental dynamics in the thymus. Coupling new techniques with mathematical models has recently resulted in the emergence of new paradigms in early hematopoiesis and might similarly open new perspectives on T cell development.
Collapse
Affiliation(s)
- Andreas Krueger
- Institute of Molecular Medicine, Goethe University Frankfurt am Main, 60590 Frankfurt am Main, Germany.
| | - Natalia Ziętara
- Dr von Hauner Children's Hospital, Ludwig Maximilian University, 80337 Munich, Germany
| | - Marcin Łyszkiewicz
- Dr von Hauner Children's Hospital, Ludwig Maximilian University, 80337 Munich, Germany
| |
Collapse
|
28
|
Abstract
Science Immunology will provide a broad platform for the most exciting findings in this growing field.
Collapse
Affiliation(s)
- Angela C Colmone
- Angela C. Colmone is the Editor of Science Immunology, American Association for the Advancement of Science, Washington, DC 20005, USA. .,Federica Sallusto is the Head of the Cellular Immunology Laboratory and Director of the Center of Medical Immunology, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Abul K. Abbas is the Distinguished Professor in Pathology and Chair of Pathology, University of California, San Francisco, San Francisco, CA 94143-0511, USA.
| | - Federica Sallusto
- Angela C. Colmone is the Editor of Science Immunology, American Association for the Advancement of Science, Washington, DC 20005, USA. .,Federica Sallusto is the Head of the Cellular Immunology Laboratory and Director of the Center of Medical Immunology, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Abul K. Abbas is the Distinguished Professor in Pathology and Chair of Pathology, University of California, San Francisco, San Francisco, CA 94143-0511, USA.
| | - Abul K Abbas
- Angela C. Colmone is the Editor of Science Immunology, American Association for the Advancement of Science, Washington, DC 20005, USA. .,Federica Sallusto is the Head of the Cellular Immunology Laboratory and Director of the Center of Medical Immunology, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Abul K. Abbas is the Distinguished Professor in Pathology and Chair of Pathology, University of California, San Francisco, San Francisco, CA 94143-0511, USA.
| |
Collapse
|