1
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Nagel S, Meyer C. Identification of Gene Regulatory Networks in B-Cell Progenitor Differentiation and Leukemia. Genes (Basel) 2024; 15:978. [PMID: 39202339 PMCID: PMC11353346 DOI: 10.3390/genes15080978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/09/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
Pro-B- and pre-B-cells are consecutive entities in early B-cell development, representing cells of origin for B-cell precursor acute lymphoid leukemia (BCP-ALL). Normal B-cell differentiation is critically regulated by specific transcription factors (TFs). Accordingly, TF-encoding genes are frequently deregulated or mutated in BCP-ALL. Recently, we described TF-codes which delineate physiological activities of selected groups of TF-encoding genes in hematopoiesis including B-cell development. Here, we exploited these codes to uncover regulatory connections between particular TFs in pro-B- and pre-B-cells via an analysis of developmental TFs encoded by NKL and TALE homeobox genes and by ETS and T-box genes. Comprehensive expression analyses in BCP-ALL cell lines helped identify validated models to study their mutual regulation in vitro. Knockdown and overexpression experiments and subsequent RNA quantification of TF-encoding genes in selected model cell lines revealed activating, inhibitory or absent connections between nine TFs operating in early B-cell development, including HLX, MSX1, IRX1, MEIS1, ETS2, ERG, SPIB, EOMES, and TBX21. In addition, genomic profiling revealed BCP-ALL subtype-specific copy number alterations of ERG at 21q22, while a deletion of the TGFbeta-receptor gene TGFBR2 at 3p24 resulted in an upregulation of EOMES. Finally, we combined the data to uncover gene regulatory networks which control normal differentiation of early B-cells, collectively endorsing more detailed evaluation of BCP-ALL subtypes.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
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2
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Sams MP, Iansavitchous J, Astridge M, Rysan H, Xu LS, Rodrigues de Oliveira B, DeKoter RP. N-Acetylcysteine Alters Disease Progression and Increases Janus Kinase Mutation Frequency in a Mouse Model of Precursor B-Cell Acute Lymphoblastic Leukemia. J Pharmacol Exp Ther 2024; 389:40-50. [PMID: 38336380 DOI: 10.1124/jpet.123.002000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is the most prevalent type of cancer in young children and is associated with high levels of reactive oxygen species (ROS). The antioxidant N-acetylcysteine (NAC) was tested for its ability to alter disease progression in a mouse model of B-ALL. Mb1-CreΔPB mice have deletions in genes encoding PU.1 and Spi-B in B cells and develop B-ALL at 100% incidence. Treatment of Mb1-CreΔPB mice with NAC in drinking water significantly reduced the frequency of CD19+ pre-B-ALL cells infiltrating the thymus at 11 weeks of age. However, treatment with NAC did not reduce leukemia progression or increase survival by a median 16 weeks of age. NAC significantly altered gene expression in leukemias in treated mice. Mice treated with NAC had increased frequencies of activating mutations in genes encoding Janus kinases 1 and 3. In particular, frequencies of Jak3 R653H mutations were increased in mice treated with NAC compared with control drinking water. NAC opposed oxidization of PTEN protein ROS in cultured leukemia cells. These results show that NAC alters leukemia progression in this mouse model, ultimately selecting for leukemias with high Jak3 R653H mutation frequencies. SIGNIFICANCE STATEMENT: In a mouse model of precursor B-cell acute lymphoblastic leukemia associated with high levels of reactive oxygen species, treatment with N-acetylcysteine did not delay disease progression but instead selected for leukemic clones with activating R653H mutations in Janus kinase 3.
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Affiliation(s)
- Mia P Sams
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - James Iansavitchous
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Madeline Astridge
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Heidi Rysan
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Li S Xu
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Bruno Rodrigues de Oliveira
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
| | - Rodney P DeKoter
- Department of Microbiology and Immunology and the Western Infection, Immunity and Inflammation Centre, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (M.P.S., J.I., M.A., H.R., L.S.X., B.R.dO.) and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada (R.P.D.)
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3
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Sigvardsson M. Early B-Cell Factor 1: An Archetype for a Lineage-Restricted Transcription Factor Linking Development to Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:143-156. [PMID: 39017843 DOI: 10.1007/978-3-031-62731-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The development of highly specialized blood cells from hematopoietic stem cells (HSCs) in the bone marrow (BM) is dependent upon a stringently orchestrated network of stage- and lineage-restricted transcription factors (TFs). Thus, the same stem cell can give rise to various types of differentiated blood cells. One of the key regulators of B-lymphocyte development is early B-cell factor 1 (EBF1). This TF belongs to a small, but evolutionary conserved, family of proteins that harbor a Zn-coordinating motif and an IPT/TIG (immunoglobulin-like, plexins, transcription factors/transcription factor immunoglobulin) domain, creating a unique DNA-binding domain (DBD). EBF proteins play critical roles in diverse developmental processes, including body segmentation in the Drosophila melanogaster embryo, and retina formation in mice. While several EBF family members are expressed in neuronal cells, adipocytes, and BM stroma cells, only B-lymphoid cells express EBF1. In the absence of EBF1, hematopoietic progenitor cells (HPCs) fail to activate the B-lineage program. This has been attributed to the ability of EBF1 to act as a pioneering factor with the ability to remodel chromatin, thereby creating a B-lymphoid-specific epigenetic landscape. Conditional inactivation of the Ebf1 gene in B-lineage cells has revealed additional functions of this protein in relation to the control of proliferation and apoptosis. This may explain why EBF1 is frequently targeted by mutations in human leukemia cases. This chapter provides an overview of the biochemical and functional properties of the EBF family proteins, with a focus on the roles of EBF1 in normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
- Division of Molecular Hematology, Lund University, Lund, Sweden.
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4
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Xu H, Tan S, Zhao Y, Zhang L, Cao W, Li X, Tian J, Wang X, Li X, Wang F, Cao J, Zhao T. Lin - PU.1 dim GATA-1 - defines haematopoietic stem cells with long-term multilineage reconstitution activity. Cell Prolif 2023; 56:e13490. [PMID: 37147872 PMCID: PMC10623959 DOI: 10.1111/cpr.13490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
Despite extensive characterization of the state and function of haematopoietic stem cells (HSCs), the use of transcription factors to define the HSC population is still limited. We show here that the HSC population in mouse bone marrow can be defined by the distinct expression levels of Spi1 and Gata1. By using a double fluorescence knock-in mouse model, PGdKI, in which the expression levels of PU.1 and GATA-1 are indicated by the expression of GFP and mCherry, respectively, we uncover that the HSCs with lymphoid and myeloid repopulating activity are specifically enriched in a Lin- PU.1dim GATA-1- (LPG) cell subset. In vivo competitive repopulation assays demonstrate that bone marrow cells gated by LPG exhibit haematopoietic reconstitution activity which is comparable to that of classical Lin- Sca1+ c-kit+ (LSK). The integrated analysis of single-cell RNA sequence data from LPG and LSK-gated cells reveals that a transcriptional network governed by core TFs contributes to regulation of HSC multipotency. These discoveries provide new clues for HSC characterization and functional study.
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Affiliation(s)
- Haoyu Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaojing Tan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weiyun Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xing Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jiayi Tian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaojing Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoyan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fengchao Wang
- National Institute of Biological Sciences (NIBS)BeijingChina
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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5
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Sharma R, Zhang C, Narendran A. The Small-Molecule E26-Transformation-Specific Inhibitor TK216 Attenuates the Oncogenic Properties of Pediatric Leukemia. Genes (Basel) 2023; 14:1916. [PMID: 37895265 PMCID: PMC10606408 DOI: 10.3390/genes14101916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
The E26-transformation-specific (ETS) transcription factors regulate multiple aspects of the normal hematopoietic system. There is an increasing body of evidence suggesting aberrant ETS activity and its contribution to leukemia initiation and progression. In this study, we evaluated the small-molecule ETS inhibitor TK216 and demonstrated its anti-tumor activity in pediatric leukemia. We found TK216 induced growth inhibition, cell cycle arrest and apoptosis and inhibited the migratory capability of leukemic cells, without significantly inhibiting the cell viability of normal blood mononuclear cells. Priming the leukemic cells with 5-Azacitidine enhanced the cytotoxic effects of TK216 on pediatric leukemia cells. Importantly, we found purine-rich box1 (PU.1) to be a potential target of TK216 in myeloid and B-lymphoid leukemic cells. In addition, TK216 sharply decreased Mcl-1 protein levels in a dose-dependent manner. Consistent with this, TK216 also potentiated the cytotoxic effects of Bcl-2 inhibition in venetoclax-resistant cells. The sustained survival benefit provided to leukemic cells in the presence of bone-marrow-derived conditioned media is also found to be modulated by TK216. Taken together, our data indicates that TK216 could be a promising targeted therapeutic agent for the treatment of acute myeloid and B-lymphoid leukemia.
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Affiliation(s)
| | | | - Aru Narendran
- Department of Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, Canada
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6
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Sigvardsson M. Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia. Genes Dev 2023; 37:703-723. [PMID: 37673459 PMCID: PMC10546977 DOI: 10.1101/gad.349879.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
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7
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Potts MA, Mizutani S, Garnham AL, Li Wai Suen CSN, Kueh AJ, Tai L, Pal M, Strasser A, Herold MJ. Deletion of the transcriptional regulator TFAP4 accelerates c-MYC-driven lymphomagenesis. Cell Death Differ 2023:10.1038/s41418-023-01145-w. [PMID: 36894688 DOI: 10.1038/s41418-023-01145-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
Many lymphoid malignancies arise from deregulated c-MYC expression in cooperation with additional genetic lesions. While many of these cooperative genetic lesions have been discovered and their functions characterised, DNA sequence data of primary patient samples suggest that many more do exist. However, the nature of their contributions to c-MYC driven lymphomagenesis have not yet been investigated. We identified TFAP4 as a potent suppressor of c-MYC driven lymphoma development in a previous genome-wide CRISPR knockout screen in primary cells in vivo [1]. CRISPR deletion of TFAP4 in Eµ-MYC transgenic haematopoietic stem and progenitor cells (HSPCs) and transplantation of these manipulated HSPCs into lethally irradiated animals significantly accelerated c-MYC-driven lymphoma development. Interestingly, TFAP4 deficient Eµ-MYC lymphomas all arose at the pre-B cell stage of B cell development. This observation prompted us to characterise the transcriptional profile of pre-B cells from pre-leukaemic mice transplanted with Eµ-MYC/Cas9 HSPCs that had been transduced with sgRNAs targeting TFAP4. This analysis revealed that TFAP4 deletion reduced expression of several master regulators of B cell differentiation, such as Spi1, SpiB and Pax5, which are direct target genes of both TFAP4 and MYC. We therefore conclude that loss of TFAP4 leads to a block in differentiation during early B cell development, thereby accelerating c-MYC-driven lymphoma development.
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Affiliation(s)
- Margaret A Potts
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Shinsuke Mizutani
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Connie S N Li Wai Suen
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia
| | - Martin Pal
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Blood Cells and Blood Cancer Division, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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8
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Das Gupta D, Lohoff M. Puppet masters of B-cell progenitor acute lymphoblastic leukemia: The preB cell receptor and the interleukin 7 receptor α. Eur J Immunol 2023; 53:e2250093. [PMID: 36805963 DOI: 10.1002/eji.202250093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/02/2022] [Accepted: 01/13/2023] [Indexed: 02/23/2023]
Abstract
B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) is enriched for a preB cell phenotype, hinting at a specific vulnerability of this cell stage. Two signaling pathways via the preB cell receptor (preBCR) and the interleukin 7 receptor α (IL-7Rα) chain govern the balance between differentiation and proliferation at this stage and both receptor pathways are routinely altered in human BCP-ALL. Here, we review the immunobiology of both the preBCR as well as the IL-7Rα and analyze the human BCP-ALL spectrum in the light of these signaling complexes. Finally, we present a terminology for preBCR signaling modules that distinguishes a pro-proliferative "phase-I" module from a pro-differentiative "phase-II" module. This terminology might serve as a framework to better address shared oncogenic mechanics of preB cell stage BCP-ALL.
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Affiliation(s)
- Dennis Das Gupta
- Institute for Medical Microbiology & Hospital Hygiene, Philipps University Marburg, Marburg, Germany.,Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Michael Lohoff
- Institute for Medical Microbiology & Hospital Hygiene, Philipps University Marburg, Marburg, Germany
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9
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Ariga Y, Low S, Hoshino H, Nakada T, Akama TO, Muramoto A, Fukushima M, Yamauchi T, Ohshima Y, Kobayashi M. Expression and Clinical Significance of Spi-B in B-cell Acute Lymphoblastic Leukemia. J Histochem Cytochem 2022; 70:683-694. [PMID: 36169277 PMCID: PMC9660366 DOI: 10.1369/00221554221130383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022] Open
Abstract
Spi-B, a member of the E26 transformation-specific (ETS) family of transcription factors, plays an important role in B cell differentiation. Spi-B also functions in development of diffuse large B-cell lymphoma; thus, we hypothesized that it may participate in leukemogenesis of B-cell acute lymphoblastic leukemia (B-ALL). To test this hypothesis, we first generated an anti-Spi-B monoclonal antibody that recognized Spi-B on formalin-fixed, paraffin-embedded tissue sections. This antibody, designated S28-5, selectively stained B cell nuclei at the pre-plasma cell stage (including centrocytes and centroblasts in germinal centers) and nuclei of plasmacytoid dendritic cells, but not fully differentiated plasma cells, T cells, macrophages, or follicular dendritic cells. Employing S28-5, we then performed immunohistochemical staining of bone marrow aspiration biopsy specimens obtained from B-ALL patients (n=62). Cases that showed stronger nuclear S28-5 signals than T-cell ALL were scored positive. In 26 (42%) of 62 specimens, leukemic cells showed nuclear Spi-B expression, and positivity was associated with patient age at diagnosis, and serum uric acid and creatinine levels. Moreover, Spi-B-positive patients demonstrated significantly shorter overall survival than did Spi-B-negative patients. These results suggest that Spi-B expression may serve as a prognostic indicator of B-ALL.
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Affiliation(s)
- Yuzuru Ariga
- Department of Tumor Pathology, Faculty of
Medical Sciences, University of Fukui, Eiheiji, Japan
- Department of Pediatrics, Faculty of Medical
Sciences, University of Fukui, Eiheiji, Japan
| | - Shulin Low
- Department of Tumor Pathology, Faculty of
Medical Sciences, University of Fukui, Eiheiji, Japan
| | - Hitomi Hoshino
- Department of Tumor Pathology, Faculty of
Medical Sciences, University of Fukui, Eiheiji, Japan
| | - Tsutomu Nakada
- Department of Instrumental Analysis, Research
Center for Advanced Science and Technology, Shinshu University, Matsumoto,
Japan
| | - Tomoya O. Akama
- Department of Pharmacology, Kansai Medical
University, Hirakata, Japan
| | - Akifumi Muramoto
- Department of Tumor Pathology, Faculty of
Medical Sciences, University of Fukui, Eiheiji, Japan
| | - Mana Fukushima
- Department of Tumor Pathology, Faculty of
Medical Sciences, University of Fukui, Eiheiji, Japan
| | - Takahiro Yamauchi
- Department of Hematology and Oncology, Faculty
of Medical Sciences, University of Fukui, Eiheiji, Japan
| | - Yusei Ohshima
- Department of Pediatrics, Faculty of Medical
Sciences, University of Fukui, Eiheiji, Japan
| | - Motohiro Kobayashi
- Department of Tumor Pathology, Faculty of
Medical Sciences, University of Fukui, Eiheiji, Japan
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10
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WhichTF is functionally important in your open chromatin data? PLoS Comput Biol 2022; 18:e1010378. [PMID: 36040971 PMCID: PMC9426921 DOI: 10.1371/journal.pcbi.1010378] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
We present WhichTF, a computational method to identify functionally important transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an ontology-guided functional approach to compute novel enrichment by integrating accessibility measurements, high-confidence pre-computed conservation-aware TF binding sites, and putative gene-regulatory models. Comparison with prior sheer abundance-based methods reveals the unique ability of WhichTF to identify context-specific TFs with functional relevance, including NF-κB family members in lymphocytes and GATA factors in cardiac cells. To distinguish the transcriptional regulatory landscape in closely related samples, we apply differential analysis and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We find suggestive, under-characterized TFs, such as RUNX3 in mesoderm development and GLI1 in systemic lupus erythematosus. We also find TFs known for stress response, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated cells. Transcription factors (TFs), a class of DNA binding proteins, regulate tissue- and cell-type-specific expression of genes. Identifying the critical TFs in a given cellular context leads to investigating molecular regulatory mechanisms in development, differentiation, and disease. Because there are more than 1,500 human TFs, experimental measurements of genome-wide occupancy across all TFs have been challenging. While computational approaches play pivotal roles, most existing methods rely on statistical enrichment, focusing either on sequence motif similarity recognized by TFs or the similarity of the genomic region of interest with the previously characterized TF occupancy profile. Here we propose WhichTF as an alternative, incorporating curated biomedical knowledge from ontology and integrating it with the high-confidence prediction of conserved TF binding sites in user-provided genomic regions of interest. We develop a new WhichTF score to rank TFs and demonstrate its applicability across human and mouse cell types, cellular differentiation trajectories, and disease-associated cells.
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11
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Jin J, Du X, Zhou L, Yao D, Zou Q. SPI1-related protein inhibits cervical cancer cell progression and prevents macrophage cell migration. J Obstet Gynaecol Res 2022; 48:2419-2430. [PMID: 35770729 DOI: 10.1111/jog.15336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022]
Abstract
AIM The functions and molecular mechanisms of SPI1-related protein (SPIB) were examined in cervical cancer (CC) cells. METHODS Genes related to miscarriage and prognosis in CC were identified by Kaplan-Meier and differential expression analysis, respectively. Cell proliferation, apoptosis, migration, and invasion were examined by cell counting kit-8, flow cytometry, transwell migration, and transwell invasion assays, respectively. The potential functions and molecular mechanisms of SPIB in CC were speculated by gene set enrichment analysis (GSEA) analysis. The mRNA and protein levels of genes were examined by RT-qPCR and western blot assays, respectively. The effect of SPIB on macrophage cells was tested by macrophage recruitment assay and bioinformatics analysis. RESULTS A total of 753 dysregulated genes were identified in 88 TCGA CC samples with a history of one or more miscarriages versus 208 CC samples with no miscarriage history. Also, 91 genes related to CC prognosis were identified. SPIB, a gene related to both miscarriage and CC prognosis, inhibited Hela cell proliferation, migration, and invasion, and facilitated Hela cell apoptosis. GSEA analysis disclosed that SPIB might play vital roles in immunity, chemokine signaling pathway, and macrophage chemotaxis/activation in CC. Moreover, SPIB inhibited C-X-C motif chemokine ligand 8 (CXCL8), C-C motif chemokine ligand 17 (CCL17), and C-C motif chemokine ligand 25 (CCL25) expression in Hela cells, and SPIB overexpression in Hela cells hampered THP-1 cell migration. Higher SPIB expression was associated with less M2 macrophage infiltration in CC. CONCLUSIONS SPIB inhibited CC-cell progression and hindered macrophage cell migration in CC.
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Affiliation(s)
- Jing Jin
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Xin Du
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Limin Zhou
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Dongmei Yao
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
| | - Qian Zou
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan City, PR China
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12
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Maity AK, Hu X, Zhu T, Teschendorff AE. Inference of age-associated transcription factor regulatory activity changes in single cells. NATURE AGING 2022; 2:548-561. [PMID: 37118452 DOI: 10.1038/s43587-022-00233-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/03/2022] [Indexed: 04/30/2023]
Abstract
Transcription factors (TFs) control cell identity and function. How their activity is altered during healthy aging is critical for an improved understanding of aging and disease risk, yet relatively little is known about such changes at cell-type resolution. Here we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs. This revealed an age-associated signature of macrophage dedifferentiation, which is shared across tissue types, and aggravated in tumor-associated macrophages. By extending the analysis to all major cell types, we reveal cell-type and tissue-type-independent age-associated alterations to regulatory factors controlling antigen processing, inflammation, collagen processing and circadian rhythm, that are implicated in age-related diseases. Finally, our study highlights the limitations of using TF expression to infer age-associated changes, underscoring the need to use regulatory activity inference methods.
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Affiliation(s)
- Alok K Maity
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xue Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, UK.
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13
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Zhao X, Li L, Yuan S, Zhang Q, Jiang X, Luo T. SPIB acts as a tumor suppressor by activating the NFkB and JNK signaling pathways through MAP4K1 in colorectal cancer cells. Cell Signal 2021; 88:110148. [PMID: 34530056 DOI: 10.1016/j.cellsig.2021.110148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 01/03/2023]
Abstract
Spi-B transcription factor (SPIB) is a member of the E-twenty-six (ETS) transcription factor family. Previous studies have shown that the expression of SPIB is downregulated in human colorectal cancer tissues. The purpose of our study was to explore the biological function and related mechanism of SPIB in colorectal cancer cells. Our study found that SPIB could inhibit the proliferation, migration and invasion of CRC cells; inhibit angiogenesis; and induce CRC cells cycle arrest in G2/M phase and promote the apoptosis of CRC cells. We also found that compared with the control group, the 50% inhibitory concentration (IC50) values of oxaliplatin and 5-FU in the SPIB overexpression group were significantly reduced. Western blot results showed that the overexpression of SPIB upregulated cleaved-PARP(c-PARP), nuclear factor kB p65 (NFkB p65), phospho-NFkB p65 (p-NFkB P65), JNK1, and C-Jun protein expression levels compared with the control group. The silence of SPIB downregulated c-PARP, NFκB p65, p-NFκB p65, JNK1, and C-Jun protein expression levels. A dual-luciferase reporter assay showed that SPIB could activate the promoter of MAP4K1 and enhance the expression of MAP4K1. After silencing MAP4K1, the protein expression levels of c-PARP, NFkB P65, p-NFkB P65, JNK1, and C-Jun were downregulated. In summary, we found that SPIB is a tumor suppressor in colorectal cancer cells and that SPIB sensitizes colorectal cancer cells to oxaliplatin and 5-FU, SPIB exerts its anti-colorectal cancer effect by activating the NFkB and JNK signaling pathways through MAP4K1. The above findings may provide a reference for new molecular markers and therapeutic targets for CRC.
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Affiliation(s)
- Xunping Zhao
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Lin Li
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Shiyun Yuan
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Qia Zhang
- Department of Medical Oncology, Yongchuan Hospital of Chongqing Medical University, Chongqing 404000, People's Republic of China
| | - Xianyao Jiang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Tao Luo
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.
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14
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RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells through Activation of a SPIC-BCLAF1 Complex. Cell Rep 2020; 29:829-843.e5. [PMID: 31644907 PMCID: PMC6870970 DOI: 10.1016/j.celrep.2019.09.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/10/2019] [Accepted: 09/09/2019] [Indexed: 11/22/2022] Open
Abstract
Early B cell development is regulated by stage-specific transcription
factors. PU.1, an ETS-family transcription factor, is essential for coordination
of early B cell maturation and immunoglobulin gene (Ig)
rearrangement. Here we show that RAG DNA double-strand breaks (DSBs) generated
during Ig light chain gene (Igl) rearrangement
in pre-B cells induce global changes in PU.1 chromatin binding. RAG DSBs
activate a SPIC/BCLAF1 transcription factor complex that displaces PU.1
throughout the genome and regulates broad transcriptional changes. SPIC recruits
BCLAF1 to gene-regulatory elements that control expression of key B cell
developmental genes. The SPIC/BCLAF1 complex suppresses expression of the SYK
tyrosine kinase and enforces the transition from large to small pre-B cells.
These studies reveal that RAG DSBs direct genome-wide changes in ETS
transcription factor activity to promote early B cell development. ETS-family transcription factors are key regulators of early B cell
development. Soodgupta et al. show that RAG-induced DNA breaks generated during
antigen receptor gene recombination activate a SPIC/BCLAF1 transcription factor
complex that counters PU.1 activity and regulates gene expression changes to
promote transition from large to small pre-B cells.
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15
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Janus Kinase Mutations in Mice Lacking PU.1 and Spi-B Drive B Cell Leukemia through Reactive Oxygen Species-Induced DNA Damage. Mol Cell Biol 2020; 40:MCB.00189-20. [PMID: 32631903 DOI: 10.1128/mcb.00189-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022] Open
Abstract
Precursor B cell acute lymphoblastic leukemia (B-ALL) is caused by genetic lesions in developing B cells that function as drivers for the accumulation of additional mutations in an evolutionary selection process. We investigated secondary drivers of leukemogenesis in a mouse model of B-ALL driven by PU.1/Spi-B deletion (Mb1-CreΔPB). Whole-exome-sequencing analysis revealed recurrent mutations in Jak3 (encoding Janus kinase 3), Jak1, and Ikzf3 (encoding Aiolos). Mutations with a high variant-allele frequency (VAF) were dominated by C→T transition mutations that were compatible with activation-induced cytidine deaminase, whereas the majority of mutations, with a low VAF, were dominated by C→A transversions associated with 8-oxoguanine DNA damage caused by reactive oxygen species (ROS). The Janus kinase (JAK) inhibitor ruxolitinib delayed leukemia onset, reduced ROS and ROS-induced gene expression signatures, and altered ROS-induced mutational signatures. These results reveal that JAK mutations can alter the course of leukemia clonal evolution through ROS-induced DNA damage.
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16
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Michida H, Imoto H, Shinohara H, Yumoto N, Seki M, Umeda M, Hayashi T, Nikaido I, Kasukawa T, Suzuki Y, Okada-Hatakeyama M. The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression. Cell Rep 2020; 31:107724. [DOI: 10.1016/j.celrep.2020.107724] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/24/2019] [Accepted: 05/13/2020] [Indexed: 12/15/2022] Open
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17
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Zhang B, Wang Q, Fu C, Jiang C, Ma S. Exploration of the immune-related signature and immune infiltration analysis for breast ductal and lobular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:730. [PMID: 32042746 DOI: 10.21037/atm.2019.11.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background In this study, we aimed to explore the tumour associated immune signature of breast cancer (BC) and conduct integrative analyses with immune infiltrates in BC. Methods We downloaded the transcriptome profiling and clinical data of BC from The Cancer Genome Atlas (TCGA) database. The list of immune-related signatures was from the Innate database. The limma package was utilized to conduct the normalization, and we screened the differential immune signatures in BC. A univariate Cox regression model and the LASSO method were used to find the hub prognostic immune genes. The TAIG risk model was calculated based on the multivariate Cox regression results, and a receiver operating characteristic (ROC) curve was generated to assess the predictive power of TAIG. Moreover, we also conducted a correlation analysis between TAIG and the clinical characteristics. Additionally, we utilized the METABRIC cohort as the validation data set. The TIMER database is a comprehensive resource for performing systematic analyses of immune infiltrates across various malignancies. We evaluated the associations of immune signatures with several immune cells based on TIMER. Furthermore, we used the CIBERSORT algorithm to determine the fractions of immune cells in each sample and compared the differential distributions of immune infiltrates between two TAIG groups using the Wilcoxon rank-sum test. Results A total of 1,178 samples were obtained from the TCGA-BRCA database, but only 1,045 breast tumour samples were matched with complete transcriptome expression data. Meanwhile, we collected a total of 1,094 BC patients from the METABRIC cohort. We found a list of 1,399 differential immune signatures associated with survival, and functional analysis revealed that these genes participated in cytokine-cytokine receptor interactions, Th1 and Th2 cell differentiation and the JAK-STAT signalling pathway. The TAIG risk model was established from the multivariate Cox analysis, and we observed that high TAIG levels correlated with poor survival outcomes based on Kaplan-Meier analysis. The Kruskal-Wallis test suggested that high TAIG levels correlated with high AJCC-TNM stages and advanced pathological stages (P<0.01). We validated the well robustness of TAIG in METABRIC cohort and 5-year AUC reached up to 0.829. Moreover, we further uncovered the associations of hub immune signatures with immune cells and calculated the immune cell fractions in specific tumour samples based on gene signature expression. Last, we used the Wilcoxon rank-sum test to compare the differential immune density in the two groups and found that several immune cells had a significantly lower infiltrating density in the high TAIG groups, including CD8+ T cells (P=0.031), memory resting CD4+ T cells (P=0.026), M0 macrophages (P=0.023), and M2 macrophages (P=0.048). Conclusions In summary, we explored the immune signature of BC and constructed a TAIG risk model to predict prognosis. Moreover, we integrated the identified immune signature with tumour-infiltrating immune cells and found adverse associations between the TAIG levels and immune cell infiltrating density.
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Affiliation(s)
- Bochuan Zhang
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang 110161, China
| | - Qingfeng Wang
- Basic Medical College Liaoning University of Traditional Chinese Medicine, Shenyang 110847, China
| | - Chenghao Fu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
| | - Chunying Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
| | - Shiliang Ma
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang 110161, China.,College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
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18
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Driver mutations in Janus kinases in a mouse model of B-cell leukemia induced by deletion of PU.1 and Spi-B. Blood Adv 2019; 2:2798-2810. [PMID: 30355579 DOI: 10.1182/bloodadvances.2018019950] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/02/2018] [Indexed: 01/13/2023] Open
Abstract
Precursor B-cell acute lymphoblastic leukemia (B-ALL) is associated with recurrent mutations that occur in cancer-initiating cells. There is a need to understand how driver mutations influence clonal evolution of leukemia. The E26-transformation-specific (ETS) transcription factors PU.1 and Spi-B (encoded by Spi1 and Spib) execute a critical role in B-cell development and serve as complementary tumor suppressors. Here, we used a mouse model to conditionally delete Spi1 and Spib genes in developing B cells. These mice developed B-ALL with a median time to euthanasia of 18 weeks. We performed RNA and whole-exome sequencing (WES) on leukemias isolated from Mb1-CreΔPB mice and identified single nucleotide variants (SNVs) in Jak1, Jak3, and Ikzf3 genes, resulting in amino acid sequence changes. Jak3 mutations resulted in amino acid substitutions located in the pseudo-kinase (R653H, V670A) and in the kinase (T844M) domains. Introduction of Jak3 T844M into Spi1/Spib-deficient precursor B cells was sufficient to promote proliferation in response to low IL-7 concentrations in culture, and to promote proliferation and leukemia-like disease in transplanted mice. We conclude that mutations in Janus kinases represent secondary drivers of leukemogenesis that cooperate with Spi1/Spib deletion. This mouse model represents a useful tool to study clonal evolution in B-ALL.
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19
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Willis SN, Nutt SL. New players in the gene regulatory network controlling late B cell differentiation. Curr Opin Immunol 2019; 58:68-74. [DOI: 10.1016/j.coi.2019.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
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20
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Xu LS, Francis A, Turkistany S, Shukla D, Wong A, Batista CR, DeKoter RP. ETV6-RUNX1 interacts with a region in SPIB intron 1 to regulate gene expression in pre-B-cell acute lymphoblastic leukemia. Exp Hematol 2019; 73:50-63.e2. [PMID: 30986496 DOI: 10.1016/j.exphem.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 03/28/2019] [Accepted: 03/30/2019] [Indexed: 11/19/2022]
Abstract
The most frequently occurring genetic abnormality in pediatric B-lymphocyte-lineage acute lymphoblastic leukemia is the t(12;21) chromosomal translocation that results in a ETV6-RUNX1 (also known as TEL-AML1) fusion gene. Expression of ETV6-RUNX1 induces a preleukemic condition leading to acquisition of secondary driver mutations, but the mechanism is poorly understood. SPI-B (encoded by SPIB) is an important transcriptional activator of B-cell development and differentiation. We hypothesized that SPIB is directly transcriptionally repressed by ETV6-RUNX1. Using chromatin immunoprecipitation, we identified a regulatory region in the first intron of SPIB that interacts with ETV6-RUNX1. Mutation of the RUNX1 binding site in SPIB intron 1 prevented transcriptional repression in transient transfection assays. Next, we sought to determine to what extent gene expression in REH cells can be altered by ectopic SPI-B expression. SPI-B expression was forced using CRISPR-mediated gene activation and also using a retroviral vector. Forced expression of SPI-B resulted in altered gene expression and, at high levels, impaired cell proliferation and induced apoptosis. Finally, we identified CARD11 and CDKN1A (encoding p21) as transcriptional targets of SPI-B involved in regulation of proliferation and apoptosis. Taken together, this study identifies SPIB as an important target of ETV6-RUNX1 in regulation of B-cell gene expression in t(12;21) leukemia.
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MESH Headings
- Apoptosis/genetics
- CARD Signaling Adaptor Proteins/biosynthesis
- CARD Signaling Adaptor Proteins/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 12/metabolism
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Cyclin-Dependent Kinase Inhibitor p21/biosynthesis
- Cyclin-Dependent Kinase Inhibitor p21/genetics
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Leukemic
- Guanylate Cyclase/biosynthesis
- Guanylate Cyclase/genetics
- Humans
- Introns
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Response Elements
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Translocation, Genetic
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Affiliation(s)
- Li S Xu
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, ON, Canada
| | - Alyssa Francis
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | | | - Devanshi Shukla
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Alison Wong
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Carolina R Batista
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, ON, Canada
| | - Rodney P DeKoter
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, ON, Canada.
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21
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Pang SHM, de Graaf CA, Hilton DJ, Huntington ND, Carotta S, Wu L, Nutt SL. PU.1 Is Required for the Developmental Progression of Multipotent Progenitors to Common Lymphoid Progenitors. Front Immunol 2018; 9:1264. [PMID: 29942304 PMCID: PMC6005176 DOI: 10.3389/fimmu.2018.01264] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/22/2018] [Indexed: 01/27/2023] Open
Abstract
The transcription factor PU.1 is required for the development of mature myeloid and lymphoid cells. Due to this essential role and the importance of PU.1 in regulating several signature markers of lymphoid progenitors, its precise function in early lymphopoiesis has been difficult to define. Here, we demonstrate that PU.1 was required for efficient generation of lymphoid-primed multipotent progenitors (LMPPs) from hematopoietic stem cells and was essential for the subsequent formation of common lymphoid progenitors (CLPs). By contrast, further differentiation into the B-cell lineage was independent of PU.1. Examination of the transcriptional changes in conditional progenitors revealed that PU.1 activates lymphoid genes in LMPPs, while repressing genes normally expressed in neutrophils. These data identify PU.1 as a critical regulator of lymphoid priming and the transition between LMPPs and CLPs.
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Affiliation(s)
- Swee Heng Milon Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Carolyn A de Graaf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Oncology Research, Boehringer Ingelheim, Vienna, Austria
| | - Li Wu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Institute for Immunology, Tsinghua University School of Medicine, Beijing, China
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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22
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Ji MM, Huang YH, Huang JY, Wang ZF, Fu D, Liu H, Liu F, Leboeuf C, Wang L, Ye J, Lu YM, Janin A, Cheng S, Zhao WL. Histone modifier gene mutations in peripheral T-cell lymphoma not otherwise specified. Haematologica 2018; 103:679-687. [PMID: 29305415 PMCID: PMC5865443 DOI: 10.3324/haematol.2017.182444] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/03/2018] [Indexed: 01/03/2023] Open
Abstract
Due to heterogeneous morphological and immunophenotypic features, approximately 50% of peripheral T-cell lymphomas are unclassifiable and categorized as peripheral T-cell lymphomas, not otherwise specified. These conditions have an aggressive course and poor clinical outcome. Identification of actionable biomarkers is urgently needed to develop better therapeutic strategies. Epigenetic alterations play a crucial role in tumor progression. Histone modifications, particularly methylation and acetylation, are generally involved in chromatin state regulation. Here we screened the core set of genes related to histone methylation (KMT2D, SETD2, KMT2A, KDM6A) and acetylation (EP300, CREBBP) and identified 59 somatic mutations in 45 of 125 (36.0%) patients with peripheral T-cell lymphomas, not otherwise specified. Histone modifier gene mutations were associated with inferior progression-free survival time of the patients, irrespective of chemotherapy regimens, but an increased response to the histone deacetylase inhibitor chidamide. In vitro, chidamide significantly inhibited the growth of EP300-mutated T-lymphoma cells and KMT2D-mutated T-lymphoma cells when combined with the hypomethylating agent decitabine. Mechanistically, decitabine acted synergistically with chidamide to enhance the interaction of KMT2D with transcription factor PU.1, regulated H3K4me-associated signaling pathways, and sensitized T-lymphoma cells to chidamide. In a xenograft KMT2D-mutated T-lymphoma model, dual treatment with chidamide and decitabine significantly retarded tumor growth and induced cell apoptosis through modulation of the KMT2D/H3K4me axis. Our work thus contributes to the understanding of aberrant histone modification in peripheral T-cell lymphomas, not otherwise specified and the stratification of a biological subset that can benefit from epigenetic treatment.
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Affiliation(s)
- Meng-Meng Ji
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Yao-Hui Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Jin-Yan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Zhao-Fu Wang
- Department of Pathology, Shanghai Rui Jin Hospital; Shanghai Jiao Tong University School of Medicine, China
| | - Di Fu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Han Liu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Feng Liu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Christophe Leboeuf
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China.,U1165 Inserm/Université Paris 7, Hôpital Saint Louis, Paris, France
| | - Li Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China.,Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
| | - Jing Ye
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
| | - Yi-Ming Lu
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
| | - Anne Janin
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China.,U1165 Inserm/Université Paris 7, Hôpital Saint Louis, Paris, France
| | - Shu Cheng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Wei-Li Zhao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology; Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China .,Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
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23
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Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB. Nat Commun 2017; 8:1426. [PMID: 29127283 PMCID: PMC5681560 DOI: 10.1038/s41467-017-01605-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/03/2017] [Indexed: 01/04/2023] Open
Abstract
Humoral immunity requires B cells to respond to multiple stimuli, including antigen, membrane and soluble ligands, and microbial products. Ets family transcription factors regulate many aspects of haematopoiesis, although their functions in humoral immunity are difficult to decipher as a result of redundancy between the family members. Here we show that mice lacking both PU.1 and SpiB in mature B cells do not generate germinal centers and high-affinity antibody after protein immunization. PU.1 and SpiB double-deficient B cells have a survival defect after engagement of CD40 or Toll-like receptors (TLR), despite paradoxically enhanced plasma cell differentiation. PU.1 and SpiB regulate the expression of many components of the B cell receptor signaling pathway and the receptors for CD40L, BAFF and TLR ligands. Thus, PU.1 and SpiB enable B cells to appropriately respond to environmental cues.
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24
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Liu J, Kumar S, Dolzhenko E, Alvarado GF, Guo J, Lu C, Chen Y, Li M, Dessing MC, Parvez RK, Cippà PE, Krautzberger AM, Saribekyan G, Smith AD, McMahon AP. Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion. JCI Insight 2017; 2:94716. [PMID: 28931758 PMCID: PMC5612583 DOI: 10.1172/jci.insight.94716] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/10/2017] [Indexed: 12/16/2022] Open
Abstract
Though an acute kidney injury (AKI) episode is associated with an increased risk of chronic kidney disease (CKD), the mechanisms determining the transition from acute to irreversible chronic injury are not well understood. To extend our understanding of renal repair, and its limits, we performed a detailed molecular characterization of a murine ischemia/reperfusion injury (IRI) model for 12 months after injury. Together, the data comprising RNA-sequencing (RNA-seq) analysis at multiple time points, histological studies, and molecular and cellular characterization of targeted gene activity provide a comprehensive profile of injury, repair, and long-term maladaptive responses following IRI. Tubular atrophy, interstitial fibrosis, inflammation, and development of multiple renal cysts were major long-term outcomes of IRI. Progressive proximal tubular injury tracks with de novo activation of multiple Krt genes, including Krt20, a biomarker of renal tubule injury. RNA-seq analysis highlights a cascade of temporal-specific gene expression patterns related to tubular injury/repair, fibrosis, and innate and adaptive immunity. Intersection of these data with human kidney transplant expression profiles identified overlapping gene expression signatures correlating with different stages of the murine IRI response. The comprehensive characterization of incomplete recovery after ischemic AKI provides a valuable resource for determining the underlying pathophysiology of human CKD.
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Affiliation(s)
- Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Sanjeev Kumar
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Egor Dolzhenko
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Gregory F Alvarado
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Can Lu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Yibu Chen
- Norris Medical Library, University of Southern California, Los Angeles, California
| | - Meng Li
- Norris Medical Library, University of Southern California, Los Angeles, California
| | - Mark C Dessing
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Pietro E Cippà
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - A Michaela Krautzberger
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Gohar Saribekyan
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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25
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Batista CR, Li SKH, Xu LS, Solomon LA, DeKoter RP. PU.1 Regulates Ig Light Chain Transcription and Rearrangement in Pre-B Cells during B Cell Development. THE JOURNAL OF IMMUNOLOGY 2017; 198:1565-1574. [PMID: 28062693 DOI: 10.4049/jimmunol.1601709] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/12/2016] [Indexed: 12/27/2022]
Abstract
B cell development and Ig rearrangement are governed by cell type- and developmental stage-specific transcription factors. PU.1 and Spi-B are E26-transformation-specific transcription factors that are critical for B cell differentiation. To determine whether PU.1 and Spi-B are required for B cell development in the bone marrow, Spi1 (encoding PU.1) was conditionally deleted in B cells by Cre recombinase under control of the Mb1 gene in Spib (encoding Spi-B)-deficient mice. Combined deletion of Spi1 and Spib resulted in a lack of mature B cells in the spleen and a block in B cell development in the bone marrow at the small pre-B cell stage. To determine target genes of PU.1 that could explain this block, we applied a gain-of-function approach using a PU.1/Spi-B-deficient pro-B cell line in which PU.1 can be induced by doxycycline. PU.1-induced genes were identified by integration of chromatin immunoprecipitation-sequencing and RNA-sequencing data. We found that PU.1 interacted with multiple sites in the Igκ locus, including Vκ promoters and regions located downstream of Vκ second exons. Induction of PU.1 induced Igκ transcription and rearrangement. Upregulation of Igκ transcription was impaired in small pre-B cells from PU.1/Spi-B-deficient bone marrow. These studies reveal an important role for PU.1 in the regulation of Igκ transcription and rearrangement and a requirement for PU.1 and Spi-B in B cell development.
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Affiliation(s)
- Carolina R Batista
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada.,The Centre for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; and.,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2R5, Canada
| | - Stephen K H Li
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada.,The Centre for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; and
| | - Li S Xu
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada.,The Centre for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; and.,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2R5, Canada
| | - Lauren A Solomon
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada.,The Centre for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; and.,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2R5, Canada
| | - Rodney P DeKoter
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; .,The Centre for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; and.,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2R5, Canada
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26
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Yu M, Al-Dallal S, Al-Haj L, Panjwani S, McCartney AS, Edwards SM, Manjunath P, Walker C, Awgulewitsch A, Hentges KE. Transcriptional regulation of the proto-oncogene Zfp521 by SPI1 (PU.1) and HOXC13. Genesis 2016; 54:519-533. [PMID: 27506447 PMCID: PMC5073027 DOI: 10.1002/dvg.22963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/08/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
Abstract
The mouse zinc‐finger gene Zfp521 (also known as ecotropic viral insertion site 3; Evi3; and ZNF521 in humans) has been identified as a B‐cell proto‐oncogene, causing leukemia in mice following retroviral insertions in its promoter region that drive Zfp521 over‐expression. Furthermore, ZNF521 is expressed in human hematopoietic cells, and translocations between ZNF521 and PAX5 are associated with pediatric acute lymphoblastic leukemia. However, the regulatory factors that control Zfp521 expression directly have not been characterized. Here we demonstrate that the transcription factors SPI1 (PU.1) and HOXC13 synergistically regulate Zfp521 expression, and identify the regions of the Zfp521 promoter required for this transcriptional activity. We also show that SPI1 and HOXC13 activate Zfp521 in a dose‐dependent manner. Our data support a role for this regulatory mechanism in vivo, as transgenic mice over‐expressing Hoxc13 in the fetal liver show a strong correlation between Hoxc13 expression levels and Zfp521 expression. Overall these experiments provide insights into the regulation of Zfp521 expression in a nononcogenic context. The identification of transcription factors capable of activating Zfp521 provides a foundation for further investigation of the regulatory mechanisms involved in ZFP521‐driven cell differentiation processes and diseases linked to Zfp521 mis‐expression.
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Affiliation(s)
- Ming Yu
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.,The Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Salma Al-Dallal
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Latifa Al-Haj
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.,Molecular Biomedicine Program, Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Shiraj Panjwani
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Akina S McCartney
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Sarah M Edwards
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Pooja Manjunath
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Catherine Walker
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | | | - Kathryn E Hentges
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.
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27
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Pang SHM, Minnich M, Gangatirkar P, Zheng Z, Ebert A, Song G, Dickins RA, Corcoran LM, Mullighan CG, Busslinger M, Huntington ND, Nutt SL, Carotta S. PU.1 cooperates with IRF4 and IRF8 to suppress pre-B-cell leukemia. Leukemia 2016; 30:1375-87. [PMID: 26932576 PMCID: PMC5179358 DOI: 10.1038/leu.2016.27] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 11/14/2015] [Accepted: 01/08/2016] [Indexed: 12/22/2022]
Abstract
The Ets family transcription factor PU.1 and the interferon regulatory factor (IRF)4 and IRF8 regulate gene expression by binding to composite DNA sequences known as Ets/interferon consensus elements. Although all three factors are expressed from the onset of B-cell development, single deficiency of these factors in B-cell progenitors only mildly impacts on bone marrow B lymphopoiesis. Here we tested whether PU.1 cooperates with IRF factors in regulating early B-cell development. Lack of PU.1 and IRF4 resulted in a partial block in development the pre-B-cell stage. The combined deletion of PU.1 and IRF8 reduced recirculating B-cell numbers. Strikingly, all PU.1/IRF4 and ~50% of PU.1/IRF8 double deficient mice developed pre-B-cell acute lymphoblastic leukemia (B-ALL) associated with reduced expression of the established B-lineage tumor suppressor genes, Ikaros and Spi-B. These genes are directly regulated by PU.1/IRF4/IRF8, and restoration of Ikaros or Spi-B expression inhibited leukemic cell growth. In summary, we demonstrate that PU.1, IRF4 and IRF8 cooperate to regulate early B-cell development and to prevent pre-B-ALL formation.
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Affiliation(s)
- Swee Heng Milon Pang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Martina Minnich
- The Institute of Molecular Pathology, Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Pradnya Gangatirkar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhiqiang Zheng
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Anja Ebert
- The Institute of Molecular Pathology, Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Guangchun Song
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678, USA
| | - Ross A Dickins
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lynn M Corcoran
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678, USA
| | - Meinrad Busslinger
- The Institute of Molecular Pathology, Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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28
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Transcription factor networks in B-cell differentiation link development to acute lymphoid leukemia. Blood 2015; 126:144-52. [PMID: 25990863 DOI: 10.1182/blood-2014-12-575688] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 05/12/2015] [Indexed: 12/26/2022] Open
Abstract
B-lymphocyte development in the bone marrow is controlled by the coordinated action of transcription factors creating regulatory networks ensuring activation of the B-lymphoid program and silencing of alternative cell fates. This process is tightly connected to malignant transformation because B-lineage acute lymphoblastic leukemia cells display a pronounced block in differentiation resulting in the expansion of immature progenitor cells. Over the last few years, high-resolution analysis of genetic changes in leukemia has revealed that several key regulators of normal B-cell development, including IKZF1, TCF3, EBF1, and PAX5, are genetically altered in a large portion of the human B-lineage acute leukemias. This opens the possibility of directly linking the disrupted development as well as aberrant gene expression patterns in leukemic cells to molecular functions of defined transcription factors in normal cell differentiation. This review article focuses on the roles of transcription factors in early B-cell development and their involvement in the formation of human leukemia.
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29
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Li SKH, Solomon LA, Fulkerson PC, DeKoter RP. Identification of a negative regulatory role for spi-C in the murine B cell lineage. THE JOURNAL OF IMMUNOLOGY 2015; 194:3798-807. [PMID: 25769919 DOI: 10.4049/jimmunol.1402432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/09/2015] [Indexed: 11/19/2022]
Abstract
Spi-C is an E26 transformation-specific family transcription factor that is highly related to PU.1 and Spi-B. Spi-C is expressed in developing B cells, but its function in B cell development and function is not well characterized. To determine whether Spi-C functions as a negative regulator of Spi-B (encoded by Spib), mice were generated that were germline knockout for Spib and heterozygous for Spic (Spib(-/-)Spic(+/-)). Interestingly, loss of one Spic allele substantially rescued B cell frequencies and absolute numbers in Spib(-/-) mouse spleens. Spib(-/-)Spic(+/-) B cells had restored proliferation compared with Spib(-/-) B cells in response to anti-IgM or LPS stimulation. Investigation of a potential mechanism for the Spib(-/-)Spic(+/-) phenotype revealed that steady-state levels of Nfkb1, encoding p50, were elevated in Spib(-/-)Spic(+/-) B cells compared with Spib(-/-) B cells. Spi-B was shown to directly activate the Nfkb1 gene, whereas Spi-C was shown to repress this gene. These results indicate a novel role for Spi-C as a negative regulator of B cell development and function.
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Affiliation(s)
- Stephen K H Li
- Department of Microbiology and Immunology, Centre for Human Immunology, Schulich School of Medicine and Dentistry, Collaborative Graduate Program in Developmental Biology, Western University, London, Ontario N6A 5C1, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2V5, Canada; and
| | - Lauren A Solomon
- Department of Microbiology and Immunology, Centre for Human Immunology, Schulich School of Medicine and Dentistry, Collaborative Graduate Program in Developmental Biology, Western University, London, Ontario N6A 5C1, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2V5, Canada; and
| | - Patricia C Fulkerson
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Rodney P DeKoter
- Department of Microbiology and Immunology, Centre for Human Immunology, Schulich School of Medicine and Dentistry, Collaborative Graduate Program in Developmental Biology, Western University, London, Ontario N6A 5C1, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2V5, Canada; and
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30
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The RUNX1–PU.1 axis in the control of hematopoiesis. Int J Hematol 2015; 101:319-29. [DOI: 10.1007/s12185-015-1762-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 02/23/2015] [Indexed: 01/16/2023]
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31
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Nfkb1 activation by the E26 transformation-specific transcription factors PU.1 and Spi-B promotes Toll-like receptor-mediated splenic B cell proliferation. Mol Cell Biol 2015; 35:1619-32. [PMID: 25733685 DOI: 10.1128/mcb.00117-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/23/2015] [Indexed: 12/31/2022] Open
Abstract
Generation of antibodies against T-independent and T-dependent antigens requires Toll-like receptor (TLR) engagement on B cells for efficient responses. However, the regulation of TLR expression and responses in B cells is not well understood. PU.1 and Spi-B (encoded by Sfpi1 and Spib, respectively) are transcription factors of the E26 transformation-specific (ETS) family and are important for B cell development and function. It was found that B cells from mice knocked out for Spi-B and heterozygous for PU.1 (Sfpi1(+/-) Spib(-/-) [PUB] mice) proliferated poorly in response to TLR ligands compared to wild-type (WT) B cells. The NF-κB family member p50 (encoded by Nfkb1) is required for lipopolysaccharide (LPS) responsiveness in mice. PUB B cells expressed reduced Nfkb1 mRNA transcripts and p50 protein. The Nfkb1 promoter was regulated directly by PU.1 and Spi-B, as shown by reporter assays and chromatin immunoprecipitation analysis. Occupancy of the Nfkb1 promoter by PU.1 was reduced in PUB B cells compared to that in WT B cells. Finally, infection of PUB B cells with a retroviral vector encoding p50 substantially restored proliferation in response to LPS. We conclude that Nfkb1 transcriptional activation by PU.1 and Spi-B promotes TLR-mediated B cell proliferation.
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32
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Solomon LA, Li SKH, Piskorz J, Xu LS, DeKoter RP. Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line. BMC Genomics 2015; 16:76. [PMID: 25765478 PMCID: PMC4334403 DOI: 10.1186/s12864-015-1303-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both expressed in B cells, and have been demonstrated to redundantly activate transcription of genes required for B cell differentiation and function. It was hypothesized that Spi-B and PU.1 occupy a similar set of regions within the genome of a B lymphoma cell line. Results To compare binding regions of Spi-B and PU.1, murine WEHI-279 lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) was performed. Analysis for high-stringency enriched genomic regions demonstrated that PU.1 occupied 4528 regions and Spi-B occupied 3360 regions. The majority of regions occupied by Spi-B were also occupied by PU.1. Regions bound by Spi-B and PU.1 were frequently located immediately upstream of genes associated with immune response and activation of B cells. Motif-finding revealed that both transcription factors were predominantly located at the ETS core domain (GGAA), however, other unique motifs were identified when examining regions associated with only one of the two factors. Motifs associated with unique PU.1 binding included POU2F2, while unique motifs in the Spi-B regions contained a combined ETS-IRF motif. Conclusions Our results suggest that complementary biological functions of PU.1 and Spi-B may be explained by their interaction with a similar set of regions in the genome of B cells. However, sites uniquely occupied by PU.1 or Spi-B provide insight into their unique functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1303-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lauren A Solomon
- Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada.
| | - Stephen K H Li
- Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada.
| | - Jan Piskorz
- Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada.
| | - Li S Xu
- Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada.
| | - Rodney P DeKoter
- Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada. .,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Canada. .,Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, ON, N6A 5C1, Canada.
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33
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Christie DA, Xu LS, Turkistany SA, Solomon LA, Li SKH, Yim E, Welch I, Bell GI, Hess DA, DeKoter RP. PU.1 opposes IL-7-dependent proliferation of developing B cells with involvement of the direct target gene bruton tyrosine kinase. THE JOURNAL OF IMMUNOLOGY 2014; 194:595-605. [PMID: 25505273 DOI: 10.4049/jimmunol.1401569] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Deletion of genes encoding the E26 transformation-specific transcription factors PU.1 and Spi-B in B cells (CD19-CreΔPB mice) leads to impaired B cell development, followed by B cell acute lymphoblastic leukemia at 100% incidence and with a median survival of 21 wk. However, little is known about the target genes that explain leukemogenesis in these mice. In this study we found that immature B cells were altered in frequency in the bone marrow of preleukemic CD19-CreΔPB mice. Enriched pro-B cells from CD19-CreΔPB mice induced disease upon transplantation, suggesting that these were leukemia-initiating cells. Bone marrow cells from preleukemic CD19-CreΔPB mice had increased responsiveness to IL-7 and could proliferate indefinitely in response to this cytokine. Bruton tyrosine kinase (BTK), a negative regulator of IL-7 signaling, was reduced in preleukemic and leukemic CD19-CreΔPB cells compared with controls. Induction of PU.1 expression in cultured CD19-CreΔPB pro-B cell lines induced Btk expression, followed by reduced STAT5 phosphorylation and early apoptosis. PU.1 and Spi-B regulated Btk directly as shown by chromatin immunoprecipitation analysis. Ectopic expression of BTK was sufficient to induce apoptosis in cultured pro-B cells. In summary, these results suggest that PU.1 and Spi-B activate Btk to oppose IL-7 responsiveness in developing B cells.
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Affiliation(s)
- Darah A Christie
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Li S Xu
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Shereen A Turkistany
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Lauren A Solomon
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Stephen K H Li
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Edmund Yim
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ian Welch
- Department of Animal Care and Veterinary Services, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gillian I Bell
- Robarts Research Institute, University of Western Ontario, London, Ontario N6A 5C1, Canada; Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario N6A 5C1, Canada; and
| | - David A Hess
- Robarts Research Institute, University of Western Ontario, London, Ontario N6A 5C1, Canada; Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario N6A 5C1, Canada; and Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2R5, Canada
| | - Rodney P DeKoter
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario N6C 2R5, Canada
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Abstract
The hematopoietically expressed homeobox gene, Hhex, is a transcription factor that is important for development of definitive hematopoietic stem cells (HSCs) and B cells, and that causes T-cell leukemia when overexpressed. Here, we have used an Hhex inducible knockout mouse model to study the role of Hhex in adult hematopoiesis. We found that loss of Hhex was tolerated in HSCs and myeloid lineages, but resulted in a progressive loss of B lymphocytes in the circulation. This was accompanied by a complete loss of B-cell progenitors in the bone marrow and of transitional B-cell subsets in the spleen. In addition, transplantation and in vitro culture experiments demonstrated an almost complete failure of Hhex-null HSCs to contribute to lymphoid lineages beyond the common lymphoid precursor stage, including T cells, B cells, NK cells, and dendritic cells. Gene expression analysis of Hhex-deleted progenitors demonstrated deregulated expression of a number of cell cycle regulators. Overexpression of one of these, cyclin D1, could rescue the B-cell developmental potential of Hhex-null lymphoid precursors. Thus, Hhex is a key regulator of early lymphoid development, functioning, at least in part, via regulation of the cell cycle.
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35
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Carotta S, Willis SN, Hasbold J, Inouye M, Pang SHM, Emslie D, Light A, Chopin M, Shi W, Wang H, Morse HC, Tarlinton DM, Corcoran LM, Hodgkin PD, Nutt SL. The transcription factors IRF8 and PU.1 negatively regulate plasma cell differentiation. ACTA ACUST UNITED AC 2014; 211:2169-81. [PMID: 25288399 PMCID: PMC4203955 DOI: 10.1084/jem.20140425] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Activated B cells undergo immunoglobulin class-switch recombination (CSR) and differentiate into antibody-secreting plasma cells. The distinct transcriptomes of B cells and plasma cells are maintained by the antagonistic influences of two groups of transcription factors: those that maintain the B cell program, including BCL6 and PAX5, and plasma cell-promoting factors, such as IRF4 and BLIMP-1. We show that the complex of IRF8 and PU.1 controls the propensity of B cells to undergo CSR and plasma cell differentiation by concurrently promoting the expression of BCL6 and PAX5 and repressing AID and BLIMP-1. As the PU.1-IRF8 complex functions in a reciprocal manner to IRF4, we propose that concentration-dependent competition between these factors controls B cell terminal differentiation.
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Affiliation(s)
- Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Simon N Willis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jhagvaral Hasbold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael Inouye
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Swee Heng Milon Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dianne Emslie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Amanda Light
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Michael Chopin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hongsheng Wang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Herbert C Morse
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - David M Tarlinton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lynn M Corcoran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Philip D Hodgkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia Department of Medical Biology, Department of Pathology, Department of Microbiology and Immunology, and Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
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Nakano H, Yanagita A, Takahashi S. The differentiation effect of low-dose cytosine arabinoside is disturbed in PU.1-knockdown K562 cells. Biomed Rep 2014; 2:564-568. [PMID: 24944809 DOI: 10.3892/br.2014.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 03/25/2014] [Indexed: 11/06/2022] Open
Abstract
We recently demonstrated by using PU.1-knockdown K562 (K562 PU.1KD) cells stably expressing PU.1 short inhibitory RNAs and PU.1-overexpressing K562 (K562 PU.1OE) cells, that therapeutic concentrations of 5-aza-2'-deoxycytidine (5-azadC) induce erythroid differentiation of these cells and that the PU.1 expression level is closely associated with the differentiating and apoptotic effects of 5-azadC on K562 cells. In this study, we investigated whether the effects of low-dose cytosine arabinoside (Ara-C), which is another erythroid differentiation inducer in K562 cells, is associated with the expression level of PU.1 in these cells. As a result, we demonstrated that the effect of Ara-C on cell viability and differentiation, as determined by the WST-8 assay and β-globin mRNA expression analysis, respectively, was suppressed in K562 PU.1KD cells compared to their controls. Collectively, these findings suggest that sufficient expression of PU.1 is indispensable for the erythroid differentiation of K562 cells.
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Affiliation(s)
- Hiroko Nakano
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa 252-0373, Japan
| | - Akane Yanagita
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa 252-0373, Japan
| | - Shinichiro Takahashi
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa 252-0373, Japan ; Division of Molecular Hematology, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa 252-0373, Japan
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Pang SHM, Carotta S, Nutt SL. Transcriptional control of pre-B cell development and leukemia prevention. Curr Top Microbiol Immunol 2014; 381:189-213. [PMID: 24831348 DOI: 10.1007/82_2014_377] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The differentiation of early B cell progenitors is controlled by multiple transcriptional regulators and growth-factor receptors. The triad of DNA-binding proteins, E2A, EBF1, and PAX5 is critical for both the early specification and commitment of B cell progenitors, while a larger number of secondary determinants, such as members of the Ikaros, ETS, Runx, and IRF families have more direct roles in promoting stage-specific pre-B gene-expression program. Importantly, it is now apparent that mutations in many of these transcription factors are associated with the progression to acute lymphoblastic leukemia. In this review, we focus on recent studies that have shed light on the transcriptional hierarchy that controls efficient B cell commitment and differentiation as well as focus on the oncogenic consequences of the loss of many of the same factors.
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Affiliation(s)
- Swee Heng Milon Pang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
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38
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Zhong S, He X, Bar-Joseph Z. Predicting tissue specific transcription factor binding sites. BMC Genomics 2013; 14:796. [PMID: 24238150 PMCID: PMC3898213 DOI: 10.1186/1471-2164-14-796] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/06/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding, including ChIP-chip and ChIP-seq, can only study one transcription factor in a single cell type and under a specific condition in each experiment, and therefore cannot scale to determine the full set of regulatory interactions in mammalian transcriptional regulatory networks. RESULTS We developed a new computational approach, PIPES, for predicting tissue-specific TF binding. PIPES integrates in vitro protein binding microarrays (PBMs), sequence conservation and tissue-specific epigenetic (DNase I hypersensitivity) information. We demonstrate that PIPES improves over existing methods on distinguishing between in vivo bound and unbound sequences using ChIP-seq data for 11 mouse TFs. In addition, our predictions are in good agreement with current knowledge of tissue-specific TF regulation. CONCLUSIONS We provide a systematic map of computationally predicted tissue-specific binding targets for 284 mouse TFs across 55 tissue/cell types. Such comprehensive resource is useful for researchers studying gene regulation.
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Affiliation(s)
| | | | - Ziv Bar-Joseph
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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39
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Abstract
The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. This study revealed 2 critical functions of Runx1: (1) to promote survival and development of progenitors specified to the B-cell lineage, a function that can be substituted by ectopic Bcl2 expression, and (2) to enable the developmental transition through the pre-B stage triggered by the pre-B-cell antigen receptor (pre-BCR). Gene expression analysis and genomewide Runx1 occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network governing early B-cell survival and development and specifically regulates genes encoding members of the Lyn kinase subfamily (key integrators of interleukin-7 and pre-BCR signaling) and the stage-specific transcription factors SpiB and Aiolos (critical downstream effectors of pre-BCR signaling). Interrogation of expression databases of 257 ALL samples demonstrated the specific down-regulation of the SPIB and IKZF3 genes (the latter encoding AIOLOS) in t(12;21) ALL, providing novel insight into the mechanism by which the translocation blocks B-cell development and promotes leukemia.
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Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res 2013; 22:1711-22. [PMID: 22955983 PMCID: PMC3431488 DOI: 10.1101/gr.135129.111] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Complex patterns of cell-type-specific gene expression are thought to be achieved by combinatorial binding of transcription factors (TFs) to sequence elements in regulatory regions. Predicting cell-type-specific expression in mammals has been hindered by the oftentimes unknown location of distal regulatory regions. To alleviate this bottleneck, we used DNase-seq data from 19 diverse human cell types to identify proximal and distal regulatory elements at genome-wide scale. Matched expression data allowed us to separate genes into classes of cell-type-specific up-regulated, down-regulated, and constitutively expressed genes. CG dinucleotide content and DNA accessibility in the promoters of these three classes of genes displayed substantial differences, highlighting the importance of including these aspects in modeling gene expression. We associated DNase I hypersensitive sites (DHSs) with genes, and trained classifiers for different expression patterns. TF sequence motif matches in DHSs provided a strong performance improvement in predicting gene expression over the typical baseline approach of using proximal promoter sequences. In particular, we achieved competitive performance when discriminating up-regulated genes from different cell types or genes up- and down-regulated under the same conditions. We identified previously known and new candidate cell-type-specific regulators. The models generated testable predictions of activating or repressive functions of regulators. DNase I footprints for these regulators were indicative of their direct binding to DNA. In summary, we successfully used information of open chromatin obtained by a single assay, DNase-seq, to address the problem of predicting cell-type-specific gene expression in mammalian organisms directly from regulatory sequence.
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Affiliation(s)
- Anirudh Natarajan
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
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41
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Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2013; 22:1798-812. [PMID: 22955990 PMCID: PMC3431495 DOI: 10.1101/gr.139105.112] [Citation(s) in RCA: 601] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion. We frequently detected secondary motifs in addition to the canonical motifs of the TFs, indicating tethered binding and cobinding between multiple TFs. We observed significant position and orientation preferences between many cobinding TFs. Genes specifically expressed in a cell line are often associated with a greater occurrence of nearby TF binding in that cell line. We observed cell-line-specific secondary motifs that mediate the binding of the histone deacetylase HDAC2 and the enhancer-binding protein EP300. TF binding sites are located in GC-rich, nucleosome-depleted, and DNase I sensitive regions, flanked by well-positioned nucleosomes, and many of these features show cell type specificity. The GC-richness may be beneficial for regulating TF binding because, when unoccupied by a TF, these regions are occupied by nucleosomes in vivo. We present the results of our analysis in a TF-centric web repository Factorbook (http://factorbook.org) and will continually update this repository as more ENCODE data are generated.
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Affiliation(s)
- Jie Wang
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Xu LS, Sokalski KM, Hotke K, Christie DA, Zarnett O, Piskorz J, Thillainadesan G, Torchia J, DeKoter RP. Regulation of B Cell Linker Protein Transcription by PU.1 and Spi-B in Murine B Cell Acute Lymphoblastic Leukemia. THE JOURNAL OF IMMUNOLOGY 2012; 189:3347-54. [DOI: 10.4049/jimmunol.1201267] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Hume DA. Plenary perspective: the complexity of constitutive and inducible gene expression in mononuclear phagocytes. J Leukoc Biol 2012; 92:433-44. [PMID: 22773680 DOI: 10.1189/jlb.0312166] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Monocytes and macrophages differentiate from progenitor cells under the influence of colony-stimulating factors. Genome-scale data have enabled the identification of the set of genes that distinguishes macrophages from other cell types and the ways in which thousands of genes are regulated in response to pathogen challenge. Although there has been a focus on a small subset of lineage-enriched transcription factors, such as PU.1, more than one-half of the transcription factors in the genome can be expressed in macrophage lineage cells under some state of activation, and they interact in a complex network. The network architecture is conserved across species, but many of the target genes evolve rapidly and differ between mouse and human. The data and publication deluge related to macrophage biology require the development of new analytical tools and ways of presenting information in an accessible form.
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Affiliation(s)
- David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom.
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44
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Ilan L, Katzav S. Human Vav1 expression in hematopoietic and cancer cell lines is regulated by c-Myb and by CpG methylation. PLoS One 2012; 7:e29939. [PMID: 22253833 PMCID: PMC3256210 DOI: 10.1371/journal.pone.0029939] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/07/2011] [Indexed: 01/09/2023] Open
Abstract
Vav1 is a signal transducer protein that functions as a guanine nucleotide exchange factor for the Rho/Rac GTPases in the hematopoietic system where it is exclusively expressed. Recently, Vav1 was shown to be involved in several human malignancies including neuroblastoma, lung cancer, and pancreatic ductal adenocarcinoma (PDA). Although some factors that affect vav1 expression are known, neither the physiological nor pathological regulation of vav1 expression is completely understood. We demonstrate herein that mutations in putative transcription factor binding sites at the vav1 promoter affect its transcription in cells of different histological origin. Among these sites is a consensus site for c-Myb, a hematopoietic-specific transcription factor that is also found in Vav1-expressing lung cancer cell lines. Depletion of c-Myb using siRNA led to a dramatic reduction in vav1 expression in these cells. Consistent with this, co-transfection of c-Myb activated transcription of a vav1 promoter-luciferase reporter gene construct in lung cancer cells devoid of Vav1 expression. Together, these results indicate that c-Myb is involved in vav1 expression in lung cancer cells. We also explored the methylation status of the vav1 promoter. Bisulfite sequencing revealed that the vav1 promoter was completely unmethylated in human lymphocytes, but methylated to various degrees in tissues that do not normally express vav1. The vav1 promoter does not contain CpG islands in proximity to the transcription start site; however, we demonstrated that methylation of a CpG dinucleotide at a consensus Sp1 binding site in the vav1 promoter interferes with protein binding in vitro. Our data identify two regulatory mechanisms for vav1 expression: binding of c-Myb and CpG methylation of 5′ regulatory sequences. Mutation of other putative transcription factor binding sites suggests that additional factors regulate vav1 expression as well.
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Affiliation(s)
- Lena Ilan
- Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Shulamit Katzav
- Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University, Jerusalem, Israel
- * E-mail:
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