1
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Peng D, Cahan P. OneSC: A computational platform for recapitulating cell state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596831. [PMID: 38895453 PMCID: PMC11185539 DOI: 10.1101/2024.05.31.596831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Computational modelling of cell state transitions has been a great interest of many in the field of developmental biology, cancer biology and cell fate engineering because it enables performing perturbation experiments in silico more rapidly and cheaply than could be achieved in a wet lab. Recent advancements in single-cell RNA sequencing (scRNA-seq) allow the capture of high-resolution snapshots of cell states as they transition along temporal trajectories. Using these high-throughput datasets, we can train computational models to generate in silico 'synthetic' cells that faithfully mimic the temporal trajectories. Here we present OneSC, a platform that can simulate synthetic cells across developmental trajectories using systems of stochastic differential equations govern by a core transcription factors (TFs) regulatory network. Different from the current network inference methods, OneSC prioritizes on generating Boolean network that produces faithful cell state transitions and steady cell states that mimic real biological systems. Applying OneSC to real data, we inferred a core TF network using a mouse myeloid progenitor scRNA-seq dataset and showed that the dynamical simulations of that network generate synthetic single-cell expression profiles that faithfully recapitulate the four myeloid differentiation trajectories going into differentiated cell states (erythrocytes, megakaryocytes, granulocytes and monocytes). Finally, through the in-silico perturbations of the mouse myeloid progenitor core network, we showed that OneSC can accurately predict cell fate decision biases of TF perturbations that closely match with previous experimental observations.
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Affiliation(s)
- Da Peng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, 21205, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, 21205, USA
- Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, 21205, USA
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2
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Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: a robust and accurate method to identify feature gene sets and annotate cells. Nucleic Acids Res 2024; 52:e46. [PMID: 38647069 PMCID: PMC11109959 DOI: 10.1093/nar/gkae307] [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: 08/10/2023] [Revised: 03/25/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024] Open
Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.
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Affiliation(s)
- Qi Gao
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Jichun Xie
- Department of Biostatistics and Bioinformatics, Duke University, USA
- Department of Mathematics, Duke University, USA
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3
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Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: A robust and accurate method to identify feature gene sets and annotate cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.24.541352. [PMID: 37577619 PMCID: PMC10418061 DOI: 10.1101/2023.05.24.541352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multiomic cellular profiles. It is conveniently available as an open-source R package.
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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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Differential Etv2 threshold requirement for endothelial and erythropoietic development. Cell Rep 2022; 39:110881. [PMID: 35649376 PMCID: PMC9203129 DOI: 10.1016/j.celrep.2022.110881] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/23/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022] Open
Abstract
Endothelial and erythropoietic lineages arise from a common developmental progenitor. Etv2 is a master transcriptional regulator required for the development of both lineages. However, the mechanisms through which Etv2 initiates the gene-regulatory networks (GRNs) for endothelial and erythropoietic specification and how the two GRNs diverge downstream of Etv2 remain incompletely understood. Here, by analyzing a hypomorphic Etv2 mutant, we demonstrate different threshold requirements for initiation of the downstream GRNs for endothelial and erythropoietic development. We show that Etv2 functions directly in a coherent feedforward transcriptional network for vascular endothelial development, and a low level of Etv2 expression is sufficient to induce and sustain the endothelial GRN. In contrast, Etv2 induces the erythropoietic GRN indirectly via activation of Tal1, which requires a significantly higher threshold of Etv2 to initiate and sustain erythropoietic development. These results provide important mechanistic insight into the divergence of the endothelial and erythropoietic lineages.
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6
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Caulier AL, Sankaran VG. Molecular and cellular mechanisms that regulate human erythropoiesis. Blood 2022; 139:2450-2459. [PMID: 34936695 PMCID: PMC9029096 DOI: 10.1182/blood.2021011044] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
To enable effective oxygen transport, ∼200 billion red blood cells (RBCs) need to be produced every day in the bone marrow through the fine-tuned process of erythropoiesis. Erythropoiesis is regulated at multiple levels to ensure that defective RBC maturation or overproduction can be avoided. Here, we provide an overview of different layers of this control, ranging from cytokine signaling mechanisms that enable extrinsic regulation of RBC production to intrinsic transcriptional pathways necessary for effective erythropoiesis. Recent studies have also elucidated the importance of posttranscriptional regulation and highlighted additional gatekeeping mechanisms necessary for effective erythropoiesis. We additionally discuss the insights gained by studying human genetic variation affecting erythropoiesis and highlight the discovery of BCL11A as a regulator of hemoglobin switching through genetic studies. Finally, we provide an outlook of how our ability to measure multiple facets of this process at single-cell resolution, while accounting for the impact of human variation, will continue to refine our knowledge of erythropoiesis and how this process is perturbed in disease. As we learn more about this intricate and important process, additional opportunities to modulate erythropoiesis for therapeutic purposes will undoubtedly emerge.
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Affiliation(s)
- Alexis L Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; and
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; and
- Broad Institute of MIT and Harvard, Cambridge, MA
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7
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Shmukler BE, Rivera A, Nishimura K, Hsu A, Wohlgemuth JG, Dlott JS, Michael Snyder L, Brugnara C, Alper SL. Erythroid-specific inactivation of Slc12a6/Kcc3 by EpoR promoter-driven Cre expression reduces K-Cl cotransport activity in mouse erythrocytes. Physiol Rep 2022; 10:e15186. [PMID: 35274823 PMCID: PMC8915159 DOI: 10.14814/phy2.15186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Investigation of erythrocytes from spontaneous or engineered germ‐line mutant mice has been instrumental in characterizing the physiological functions of components of the red cell cytoskeleton and membrane. However, the red blood cell expresses some proteins whose germline loss‐of‐function is embryonic‐lethal, perinatal‐lethal, or confers reduced post‐weaning viability. Promoter regions of erythroid‐specific genes have been used to engineer erythroid‐specific expression of Cre recombinase. Through breeding with mice carrying appropriately spaced insertions of loxP sequences, generation of erythroid‐specific knockouts has been carried out for signaling enzymes, transcription factors, peptide hormones, and single transmembrane span signaling receptors. We report here the use of Cre recombinase expression driven by the erythropoietin receptor (EpoR) promoter to generate EpoR‐Cre;Kcc3f/f mice, designed to express erythroid‐specific knockout of the KCC3 K‐Cl cotransporter encoded by Kcc3/Slc12A6. We confirm KCC3 as the predominant K‐Cl cotransporter of adult mouse red cells in mice with better viability than previously exhibited by Kcc3−/− germline knockouts. We demonstrate roughly proportionate preservation of K‐Cl stimulation by hypotonicity, staurosporine, and urea in the context of reduced, but not abrogated, K‐Cl function in EpoR‐Cre;Kcc3f/f mice. We also report functional evidence suggesting incomplete recombinase‐mediated excision of the Kcc3 gene in adult erythroid tissues.
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Affiliation(s)
- Boris E Shmukler
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Alicia Rivera
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Katherine Nishimura
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ann Hsu
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | | | | | | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seth L Alper
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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8
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Ali M, Ribeiro MM, Del Sol A. Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research. Methods Mol Biol 2022; 2471:83-109. [PMID: 35175592 DOI: 10.1007/978-1-0716-2193-6_4] [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] [Indexed: 06/14/2023]
Abstract
The large-scale development of high-throughput sequencing technologies has not only allowed the generation of reliable omics data related to various regulatory layers but also the development of novel computational models in the field of stem cell research. These computational approaches have enabled the disentangling of a complex interplay between these interrelated layers of regulation by interpreting large quantities of biomedical data in a systematic way. In the context of stem cell research, network modeling of complex gene-gene interactions has been successfully used for understanding the mechanisms underlying stem cell differentiation and cellular conversion. Notably, it has proven helpful for predicting cell-fate determinants and signaling molecules controlling such processes. This chapter will provide an overview of various computational approaches that rely on single-cell and/or bulk RNA sequencing data for elucidating the molecular underpinnings of cell subpopulation identities, lineage specification, and the process of cell-fate decisions. Furthermore, we discuss how these computational methods provide the right framework for computational modeling of biological systems in order to address long-standing challenges in the stem cell field by guiding experimental efforts in stem cell research and regenerative medicine.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Mariana Messias Ribeiro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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9
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Characterization of a genomic region 8 kb downstream of GFI1B associated with myeloproliferative neoplasms. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166259. [PMID: 34450246 DOI: 10.1016/j.bbadis.2021.166259] [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: 06/26/2021] [Revised: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022]
Abstract
A genomic locus 8 kb downstream of the transcription factor GFI1B (Growth Factor Independence 1B) predisposes to clonal hematopoiesis and myeloproliferative neoplasms. One of the most significantly associated polymorphisms in this region is rs621940-G. GFI1B auto-represses GFI1B, and altered GFI1B expression contributes to myeloid neoplasms. We studied whether rs621940-G affects GFI1B expression and growth of immature cells. GFI1B ChIP-seq showed clear binding to the rs621940 locus. Preferential binding of various hematopoietic transcription factors to either the rs621940-C or -G allele was observed, but GFI1B showed no preference. In gene reporter assays the rs621940 region inhibited GFI1B promoter activity with the G-allele having less suppressive effects compared to the C-allele. However, CRISPR-Cas9 mediated deletion of the locus in K562 cells did not alter GFI1B expression nor auto-repression. In healthy peripheral blood mononuclear cells GFI1B expression did not differ consistently between the rs621940 alleles. Long range and targeted deep sequencing did not detect consistent effects of rs621940-G on allelic GFI1B expression either. Finally, we observed that myeloid colony formation was not significantly affected by either rs621940 allele in 193 healthy donors. Together, these findings show no evidence that rs621940 or its locus affect GFI1B expression, auto-repression or growth of immature myeloid cells.
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Wang TF, Lin GL, Chu SC, Chen CC, Liou YS, Chang HH, Sun DS. AQP0 is a novel surface marker for deciphering abnormal erythropoiesis. Stem Cell Res Ther 2021; 12:274. [PMID: 33957977 PMCID: PMC8101103 DOI: 10.1186/s13287-021-02343-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background Hematopoiesis occurs in the bone marrow, producing a complete spectrum of blood cells to maintain homeostasis. In addition to light microscopy, chromosome analysis, and polymerase chain reaction, flow cytometry is a feasible and fast method for quantitatively analyzing hematological diseases. However, because sufficient specific cell markers are scarce, dyserythropoietic diseases are challenging to identify through flow cytometry. Methods Bone marrow samples from C57BL/B6 mice and one healthy donor were analyzed using traditional two-marker (CD71 and glycophorin A) flow cytometry analysis. After cell sorting, the gene expressions of membrane proteins in early and late erythropoiesis precursors and in nonerythroid cells were characterized using microarray analysis. Results Among characterized gene candidates, aquaporin 0 (AQP0) expressed as a surface protein in early- and late-stage erythropoiesis precursors and was not expressed on nonerythroid cells. With the help of AQP0 staining, we could define up to five stages of erythropoiesis in both mouse and human bone marrow using flow cytometry. In addition, because patients with dyserythropoiesis generally exhibited a reduced population of APQ0high cells relative to healthy participants, the analysis results also suggested that the levels of APQ0high cells in early erythropoiesis serve as a novel biomarker that distinguishes normal from dysregulated erythropoiesis. Conclusions AQP0 was successfully demonstrated to be a marker of erythroid differentiation. The expression levels of AQP0 are downregulated in patients with dyserythropoiesis, indicating a critical role of AQP0 in erythropoiesis. Accordingly, the level of AQP0high in early erythroid precursor cells may serve as a reference parameter for diagnosing diseases associated with dyserythropoiesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02343-4.
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Affiliation(s)
- Tso-Fu Wang
- Departments of Hematology and Oncology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan, Republic of China.,College of Medicine, Tzu-Chi University, Hualien, Taiwan, Republic of China
| | - Guan-Ling Lin
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, No. 701, Section 3, Zhong-Yang Road, Hualien, 97004, Taiwan, Republic of China
| | - Sung-Chao Chu
- Departments of Hematology and Oncology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan, Republic of China.,College of Medicine, Tzu-Chi University, Hualien, Taiwan, Republic of China
| | - Chang-Chin Chen
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, No. 701, Section 3, Zhong-Yang Road, Hualien, 97004, Taiwan, Republic of China.,Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan, Republic of China
| | - Yu-Shan Liou
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, No. 701, Section 3, Zhong-Yang Road, Hualien, 97004, Taiwan, Republic of China
| | - Hsin-Hou Chang
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, No. 701, Section 3, Zhong-Yang Road, Hualien, 97004, Taiwan, Republic of China
| | - Der-Shan Sun
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, No. 701, Section 3, Zhong-Yang Road, Hualien, 97004, Taiwan, Republic of China.
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11
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The transcription factors GFI1 and GFI1B as modulators of the innate and acquired immune response. Adv Immunol 2021; 149:35-94. [PMID: 33993920 DOI: 10.1016/bs.ai.2021.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GFI1 and GFI1B are small nuclear proteins of 45 and 37kDa, respectively, that have a simple two-domain structure: The first consists of a group of six c-terminal C2H2 zinc finger motifs that are almost identical in sequence and bind to very similar, specific DNA sites. The second is an N-terminal 20 amino acid SNAG domain that can bind to the pocket of the histone demethylase KDM1A (LSD1) near its active site. When bound to DNA, both proteins act as bridging factors that bring LSD1 and associated proteins into the vicinity of methylated substrates, in particular histone H3 or TP53. GFI1 can also bring methyl transferases such as PRMT1 together with its substrates that include the DNA repair proteins MRE11 and 53BP1, thereby enabling their methylation and activation. While GFI1B is expressed almost exclusively in the erythroid and megakaryocytic lineage, GFI1 has clear biological roles in the development and differentiation of lymphoid and myeloid immune cells. GFI1 is required for lymphoid/myeloid and monocyte/granulocyte lineage decision as well as the correct nuclear interpretation of a number of important immune-signaling pathways that are initiated by NOTCH1, interleukins such as IL2, IL4, IL5 or IL7, by the pre TCR or -BCR receptors during early lymphoid differentiation or by T and B cell receptors during activation of lymphoid cells. Myeloid cells also depend on GFI1 at both stages of early differentiation as well as later stages in the process of activation of macrophages through Toll-like receptors in response to pathogen-associated molecular patterns. The knowledge gathered on these factors over the last decades puts GFI1 and GFI1B at the center of many biological processes that are critical for both the innate and acquired immune system.
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12
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Beauchemin H, Möröy T. Multifaceted Actions of GFI1 and GFI1B in Hematopoietic Stem Cell Self-Renewal and Lineage Commitment. Front Genet 2020; 11:591099. [PMID: 33193732 PMCID: PMC7649360 DOI: 10.3389/fgene.2020.591099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
Growth factor independence 1 (GFI1) and the closely related protein GFI1B are small nuclear proteins that act as DNA binding transcriptional repressors. Both recognize the same consensus DNA binding motif via their C-terminal zinc finger domains and regulate the expression of their target genes by recruiting chromatin modifiers such as histone deacetylases (HDACs) and demethylases (LSD1) by using an N-terminal SNAG domain that comprises only 20 amino acids. The only region that is different between both proteins is the region that separates the zinc finger domains and the SNAG domain. Both proteins are co-expressed in hematopoietic stem cells (HSCs) and, to some extent, in multipotent progenitors (MPPs), but expression is specified as soon as early progenitors and show signs of lineage bias. While expression of GFI1 is maintained in lymphoid primed multipotent progenitors (LMPPs) that have the potential to differentiate into both myeloid and lymphoid cells, GFI1B expression is no longer detectable in these cells. By contrast, GFI1 expression is lost in megakaryocyte precursors (MKPs) and in megakaryocyte-erythrocyte progenitors (MEPs), which maintain a high level of GFI1B expression. Consequently, GFI1 drives myeloid and lymphoid differentiation and GFI1B drives the development of megakaryocytes, platelets, and erythrocytes. How such complementary cell type- and lineage-specific functions of GFI1 and GFI1B are maintained is still an unresolved question in particular since they share an almost identical structure and very similar biochemical modes of actions. The cell type-specific accessibility of GFI1/1B binding sites may explain the fact that very similar transcription factors can be responsible for very different transcriptional programming. An additional explanation comes from recent data showing that both proteins may have additional non-transcriptional functions. GFI1 interacts with a number of proteins involved in DNA repair and lack of GFI1 renders HSCs highly susceptible to DNA damage-induced death and restricts their proliferation. In contrast, GFI1B binds to proteins of the beta-catenin/Wnt signaling pathway and lack of GFI1B leads to an expansion of HSCs and MKPs, illustrating the different impact that GFI1 or GFI1B has on HSCs. In addition, GFI1 and GFI1B are required for endothelial cells to become the first blood cells during early murine development and are among those transcription factors needed to convert adult endothelial cells or fibroblasts into HSCs. This role of GFI1 and GFI1B bears high significance for the ongoing effort to generate hematopoietic stem and progenitor cells de novo for the autologous treatment of blood disorders such as leukemia and lymphoma.
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Affiliation(s)
| | - Tarik Möröy
- Institut de recherches cliniques de Montréal, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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13
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Beauchemin H, Shooshtharizadeh P, Pinder J, Dellaire G, Möröy T. Dominant negative Gfi1b mutations cause moderate thrombocytopenia and an impaired stress thrombopoiesis associated with mild erythropoietic abnormalities in mice. Haematologica 2020; 105:2457-2470. [PMID: 33054086 PMCID: PMC7556681 DOI: 10.3324/haematol.2019.222596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/21/2019] [Indexed: 11/30/2022] Open
Abstract
GFI1B-related thrombocytopenia (GFI1B-RT) is a rare bleeding disorder mainly caused by the presence of truncated GFI1B proteins with dominant-negative properties. The disease is characterized by low platelet counts, the presence of abnormal platelets, a megakaryocytic expansion and mild erythroid defects. However, no animal models faithfully reproducing the GFI1B-RT phenotype observed in patients exist. We had previously generated mice with floxed Gfi1b alleles that can be eliminated by Cre recombinase, but those animals developed a much more severe phenotype than GFI1B-RT patients and were of limited interest in assessing the disease. Using CRISPR/Cas9 technology, we have now established three independent mouse lines that carry mutated Gfi1b alleles producing proteins lacking DNA binding zinc fingers and thereby acting in a dominant negative (DN) manner. Mice heterozygous for these Gfi1b-DN alleles show reduced platelet counts and an expansion of megakaryocytes similar to features of human GFI1B-RT but lacking the distinctively large agranular platelets. In addition, Gfi1b-DN mice exhibit an expansion of erythroid precursors indicative of a mildly abnormal erythropoiesis but without noticeable red blood cell defects. When associated with megakaryocyte-specific ablation of the remaining allele, the Gfi1b-DN alleles triggered erythroid-specific deleterious defects. Gfi1b-DN mice also showed a delayed recovery from platelet depletion, indicating a defect in stress thrombopoiesis. However, injecting Gfi1b-DN mice with romiplostim, a thrombopoietin receptor super agonist, increased platelet numbers even beyond normal levels. Thus, our data support a causal link between DN mutations in GFI1B and thrombocytopenia and suggest that patients with GFI1B-RT could be treated successfully with thrombopoietin agonists.
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Affiliation(s)
- Hugues Beauchemin
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Quebec
| | | | - Jordan Pinder
- Departments of Pathology and Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia
| | - Graham Dellaire
- Departments of Pathology and Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Quebec
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Quebec
- Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada
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14
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Bao EL, Nandakumar SK, Liao X, Bick AG, Karjalainen J, Tabaka M, Gan OI, Havulinna AS, Kiiskinen TTJ, Lareau CA, de Lapuente Portilla AL, Li B, Emdin C, Codd V, Nelson CP, Walker CJ, Churchhouse C, de la Chapelle A, Klein DE, Nilsson B, Wilson PWF, Cho K, Pyarajan S, Gaziano JM, Samani NJ, Regev A, Palotie A, Neale BM, Dick JE, Natarajan P, O'Donnell CJ, Daly MJ, Milyavsky M, Kathiresan S, Sankaran VG. Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. Nature 2020; 586:769-775. [PMID: 33057200 PMCID: PMC7606745 DOI: 10.1038/s41586-020-2786-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Abstract
Myeloproliferative neoplasms (MPNs) are blood cancers that are characterized by the excessive production of mature myeloid cells and arise from the acquisition of somatic driver mutations in haematopoietic stem cells (HSCs). Epidemiological studies indicate a substantial heritable component of MPNs that is among the highest known for cancers1. However, only a limited number of genetic risk loci have been identified, and the underlying biological mechanisms that lead to the acquisition of MPNs remain unclear. Here, by conducting a large-scale genome-wide association study (3,797 cases and 1,152,977 controls), we identify 17 MPN risk loci (P < 5.0 × 10-8), 7 of which have not been previously reported. We find that there is a shared genetic architecture between MPN risk and several haematopoietic traits from distinct lineages; that there is an enrichment for MPN risk variants within accessible chromatin of HSCs; and that increased MPN risk is associated with longer telomere length in leukocytes and other clonal haematopoietic states-collectively suggesting that MPN risk is associated with the function and self-renewal of HSCs. We use gene mapping to identify modulators of HSC biology linked to MPN risk, and show through targeted variant-to-function assays that CHEK2 and GFI1B have roles in altering the function of HSCs to confer disease risk. Overall, our results reveal a previously unappreciated mechanism for inherited MPN risk through the modulation of HSC function.
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Affiliation(s)
- Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaotian Liao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander G Bick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- VA Boston Healthcare, Section of Cardiology, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marcin Tabaka
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tuomo T J Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Bo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Connor Emdin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Veryan Codd
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Christopher J Walker
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Albert de la Chapelle
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Daryl E Klein
- Department of Pharmacology, Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, USA
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Peter W F Wilson
- Atlanta VA Medical Center, Atlanta, GA, USA
- Emory Clinical Cardiovascular Research Institute, Atlanta, GA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biology, Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aarno Palotie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare, Section of Cardiology, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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15
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He B, Gao P, Ding YY, Chen CH, Chen G, Chen C, Kim H, Tasian SK, Hunger SP, Tan K. Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. SCIENCE ADVANCES 2020; 6:eaba3064. [PMID: 32832663 PMCID: PMC7439310 DOI: 10.1126/sciadv.aba3064] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/10/2020] [Indexed: 05/14/2023]
Abstract
Interpreting the function of noncoding mutations in cancer genomes remains a major challenge. Here, we developed a computational framework to identify putative causal noncoding mutations of all classes by joint analysis of mutation and gene expression data. We identified thousands of SNVs/small indels and structural variants as putative causal mutations in five major pediatric cancers. We experimentally validated the oncogenic role of CHD4 overexpression via enhancer hijacking in B-ALL. We observed a general exclusivity of coding and noncoding mutations affecting the same genes and pathways. We showed that integrated mutation profiles can help define novel patient subtypes with different clinical outcomes. Our study introduces a general strategy to systematically identify and characterize the full spectrum of noncoding mutations in cancers.
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Affiliation(s)
- Bing He
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yang-Yang Ding
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chia-Hui Chen
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gregory Chen
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Changya Chen
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hannah Kim
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah K. Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen P. Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author.
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16
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Delic D, Wunderlich F, Al-Quraishy S, Abdel-Baki AAS, Dkhil MA, Araúzo-Bravo MJ. Vaccination accelerates hepatic erythroblastosis induced by blood-stage malaria. Malar J 2020; 19:49. [PMID: 31996238 PMCID: PMC6988251 DOI: 10.1186/s12936-020-3130-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/18/2020] [Indexed: 02/06/2023] Open
Abstract
Background Vaccination induces survival of otherwise lethal blood-stage infections of the experimental malaria Plasmodium chabaudi. Blood-stage malaria induces extramedullary erythropoiesis in the liver. This study investigates how vaccination affects the course of malaria-induced expression of erythrocytic genes in the liver. Methods Female Balb/c mice were vaccinated at week 3 and week 1 before challenging with 106P. chabaudi-parasitized erythrocytes. The non-infectious vaccine consisted of erythrocyte ghosts isolated from P. chabaudi-infected erythrocytes. Gene expression microarrays and quantitative real-time PCR were used to compare mRNA expression of different erythrocytic genes in the liver of vaccination-protected and non-protected mice during infections on days 0, 1, 4, 8, and 11 p.i. Results Global transcriptomics analyses reveal vaccination-induced modifications of malaria-induced increases in hepatic gene expression on days 4 and 11 p.i. On these days, vaccination also alters hepatic expression of the erythropoiesis-involved genes Ermap, Kel, Rhd, Rhag, Slc4a1, Gypa, Add2, Ank1, Epb4.1, Epb4.2, Epb4.9, Spta1, Sptb, Tmod1, Ahsp, Acyp1, Gata1, Gfi1b, Tal1, Klf1, Epor, and Cldn13. In vaccination-protected mice, expression of these genes, except Epb4.1, is significantly higher on day 4 p.i. than in un-protected non-vaccinated mice, reaches maximal expression at peak parasitaemia on day 8 p.i., and is slowed down or even decreased towards the end of crisis phase on day 11 p.i.. After day 1 p.i., Epor expression takes about the same course as that of the other erythroid genes. Hepatic expression of Epo, however, is delayed in both vaccinated and non-vaccinated mice for the first 4 days p.i. and is maximal at significantly higher levels in vaccinated mice on day 8 p.i., before declining towards the end of crisis phase on day 11 p.i. Conclusion The present data indicate that vaccination accelerates malaria-induced erythroblastosis in the liver for 1–2 days. This may contribute to earlier replenishment of peripheral red blood cells by liver-derived reticulocytes, which may favour final survival of otherwise lethal blood-stage malaria, since reticulocytes are not preferred as host cells by P. chabaudi.
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Affiliation(s)
- Denis Delic
- Department of Biology, Heinrich-Heine-University, Duesseldorf, Germany. .,Boehringer Ingelheim Pharma, Biberach, Germany.
| | - Frank Wunderlich
- Department of Biology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Saleh Al-Quraishy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdel-Azeem S Abdel-Baki
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Zoology, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Mohamed A Dkhil
- Boehringer Ingelheim Pharma, Biberach, Germany.,Department of Zoology and Entomology, Faculty of Science, Helwan University, Cairo, Egypt
| | - Marcos J Araúzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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17
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Möröy T, Khandanpour C. Role of GFI1 in Epigenetic Regulation of MDS and AML Pathogenesis: Mechanisms and Therapeutic Implications. Front Oncol 2019; 9:824. [PMID: 31508375 PMCID: PMC6718700 DOI: 10.3389/fonc.2019.00824] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023] Open
Abstract
Growth factor independence 1 (GFI1) is a DNA binding zinc finger protein, which can mediate transcriptional repression mainly by recruiting histone-modifying enzymes to its target genes. GFI1 plays important roles in hematopoiesis, in particular by regulating both the function of hematopoietic stem- and precursor cells and differentiation along myeloid and lymphoid lineages. In recent years, a number of publications have provided evidence that GFI1 is involved in the pathogenesis of acute myeloid leukemia (AML), its proposed precursor, myelodysplastic syndrome (MDS), and possibly also in the progression from MDS to AML. For instance, expression levels of the GFI1 gene correlate with patient survival and treatment response in both AML and MDS and can influence disease progression and maintenance in experimental animal models. Also, a non-synonymous single nucleotide polymorphism (SNP) of GFI1, GFI1-36N, which encodes a variant GFI1 protein with a decreased efficiency to act as a transcriptional repressor, was found to be a prognostic factor for the development of AML and MDS. Both the GFI1-36N variant as well as reduced expression of the GFI1 gene lead to genome-wide epigenetic changes at sites where GFI1 occupies target gene promoters and enhancers. These epigenetic changes alter the response of leukemic cells to epigenetic drugs such as HDAC- or HAT inhibitors, indicating that GFI1 expression levels and genetic variants of GFI1 are of clinical relevance. Based on these and other findings, specific therapeutic approaches have been proposed to treat AML by targeting some of the epigenetic changes that occur as a consequence of GFI1 expression. Here, we will review the well-known role of Gfi1 as a transcription factor and describe the more recently discovered functions of GFI1 that are independent of DNA binding and how these might affect disease progression and the choice of epigenetic drugs for therapeutic regimens of AML and MDS.
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Affiliation(s)
- Tarik Möröy
- Department of Hematopoiesis and Cancer, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
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18
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Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40. Nat Immunol 2019; 20:1322-1334. [PMID: 31427773 DOI: 10.1038/s41590-019-0464-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
Abstract
We report a new immunodeficiency disorder in mice caused by a viable hypomorphic mutation of Snrnp40, an essential gene encoding a subunit of the U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome. Snrnp40 is ubiquitous but strongly expressed in lymphoid tissue. Homozygous mutant mice showed hypersusceptibility to infection by murine cytomegalovirus and multiple defects of lymphoid development, stability and function. Cell-intrinsic defects of hematopoietic stem cell differentiation also affected homozygous mutants. SNRNP40 deficiency in primary hematopoietic stem cells or T cells or the EL4 cell line increased the frequency of splicing errors, mostly intron retention, in several hundred messenger RNAs. Altered expression of proteins associated with immune cell function was also observed in Snrnp40-mutant cells. The immunological consequences of SNRNP40 deficiency presumably result from cumulative, moderate effects on processing of many different mRNA molecules and secondary reductions in the expression of critical immune proteins, yielding a syndromic immune disorder.
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19
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Growth Factor Independence 1B-Mediated Transcriptional Repression and Lineage Allocation Require Lysine-Specific Demethylase 1-Dependent Recruitment of the BHC Complex. Mol Cell Biol 2019; 39:MCB.00020-19. [PMID: 30988160 DOI: 10.1128/mcb.00020-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/09/2019] [Indexed: 12/16/2022] Open
Abstract
Growth factor independence 1B (GFI1B) coordinates assembly of transcriptional repressor complexes comprised of corepressors and histone-modifying enzymes to control gene expression programs governing lineage allocation in hematopoiesis. Enforced expression of GFI1B in K562 erythroleukemia cells favors erythroid over megakaryocytic differentiation, providing a platform to define molecular determinants of binary fate decisions triggered by GFI1B. We deployed proteome-wide proximity labeling to identify factors whose inclusion in GFI1B complexes depends upon GFI1B's obligate effector, lysine-specific demethylase 1 (LSD1). We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin-remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1, ZMYM2, and ZNF217) in an LSD1-dependent manner to control acquisition of erythroid traits by K562 cells. Among these elements, depletion of both HMG20A and HMG20B or of GSE1 blocks GFI1B-mediated erythroid differentiation, phenocopying impaired differentiation brought on by LSD1 depletion or disruption of GFI1B-LSD1 binding. These findings demonstrate the central role of the GFI1B-LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.
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20
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Gfi1b regulates the level of Wnt/β-catenin signaling in hematopoietic stem cells and megakaryocytes. Nat Commun 2019; 10:1270. [PMID: 30894540 PMCID: PMC6426870 DOI: 10.1038/s41467-019-09273-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 02/25/2019] [Indexed: 01/06/2023] Open
Abstract
Gfi1b is a transcriptional repressor expressed in hematopoietic stem cells (HSCs) and megakaryocytes (MKs). Gfi1b deficiency leads to expansion of both cell types and abrogates the ability of MKs to respond to integrin. Here we show that Gfi1b forms complexes with β-catenin, its co-factors Pontin52, CHD8, TLE3 and CtBP1 and regulates Wnt/β-catenin-dependent gene expression. In reporter assays, Gfi1b can activate TCF-dependent transcription and Wnt3a treatment enhances this activation. This requires interaction between Gfi1b and LSD1 and suggests that a tripartite β-catenin/Gfi1b/LSD1 complex exists, which regulates Wnt/β-catenin target genes. Consistently, numerous canonical Wnt/β-catenin target genes, co-occupied by Gfi1b, β-catenin and LSD1, have their expression deregulated in Gfi1b-deficient cells. When Gfi1b-deficient cells are treated with Wnt3a, their normal cellularity is restored and Gfi1b-deficient MKs regained their ability to spread on integrin substrates. This indicates that Gfi1b controls both the cellularity and functional integrity of HSCs and MKs by regulating Wnt/β-catenin signaling pathway. Gfi1b regulates cellularity of haematopoietic stem cells (HSCs) and megakaryocytes (MKs) as well as spreading of MKs on matrix. Here the authors show that Gfi1b regulates this behaviour by recruiting LSD1 and β-catenin to Wnt/β-catenin signalling targets.
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21
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Zhang K, Wang M, Zhao Y, Wang W. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. SCIENCE ADVANCES 2019; 5:eaav3262. [PMID: 30944857 PMCID: PMC6436936 DOI: 10.1126/sciadv.aav3262] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/30/2019] [Indexed: 05/20/2023]
Abstract
Transcriptional regulation is pivotal to the specification of distinct cell types during embryonic development. However, it still lacks a systematic way to identify key transcription factors (TFs) orchestrating the temporal and tissue specificity of gene expression. Here, we integrated epigenomic and transcriptomic data to reveal key regulators from two cells to postnatal day 0 in mouse embryogenesis. We predicted three-dimensional chromatin interactions in 12 tissues across eight developmental stages, which facilitates linking TFs to their target genes for constructing transcriptional regulatory networks. To identify driver TFs, we developed a new algorithm, dubbed Taiji, to assess the global influence of each TF and systematically uncovered TFs critical for lineage-specific and stage-dependent tissue specification. We have also identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress. Furthermore, lacking stage-specific TF combinations suggests a distributed timing strategy to orchestrate the coordination between tissues during embryonic development.
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Affiliation(s)
- Kai Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Ying Zhao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Corresponding author.
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22
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Moore C, Richens JL, Hough Y, Ucanok D, Malla S, Sang F, Chen Y, Elworthy S, Wilkinson RN, Gering M. Gfi1aa and Gfi1b set the pace for primitive erythroblast differentiation from hemangioblasts in the zebrafish embryo. Blood Adv 2018; 2:2589-2606. [PMID: 30309860 PMCID: PMC6199651 DOI: 10.1182/bloodadvances.2018020156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
The transcriptional repressors Gfi1(a) and Gfi1b are epigenetic regulators with unique and overlapping roles in hematopoiesis. In different contexts, Gfi1 and Gfi1b restrict or promote cell proliferation, prevent apoptosis, influence cell fate decisions, and are essential for terminal differentiation. Here, we show in primitive red blood cells (prRBCs) that they can also set the pace for cellular differentiation. In zebrafish, prRBCs express 2 of 3 zebrafish Gfi1/1b paralogs, Gfi1aa and Gfi1b. The recently identified zebrafish gfi1aa gene trap allele qmc551 drives erythroid green fluorescent protein (GFP) instead of Gfi1aa expression, yet homozygous carriers have normal prRBCs. prRBCs display a maturation defect only after splice morpholino-mediated knockdown of Gfi1b in gfi1aa qmc551 homozygous embryos. To study the transcriptome of the Gfi1aa/1b double-depleted cells, we performed an RNA-Seq experiment on GFP-positive prRBCs sorted from 20-hour-old embryos that were heterozygous or homozygous for gfi1aa qmc551 , as well as wt or morphant for gfi1b We subsequently confirmed and extended these data in whole-mount in situ hybridization experiments on newly generated single- and double-mutant embryos. Combined, the data showed that in the absence of Gfi1aa, the synchronously developing prRBCs were delayed in activating late erythroid differentiation, as they struggled to suppress early erythroid and endothelial transcription programs. The latter highlighted the bipotent nature of the progenitors from which prRBCs arise. In the absence of Gfi1aa, Gfi1b promoted erythroid differentiation as stepwise loss of wt gfi1b copies progressively delayed Gfi1aa-depleted prRBCs even further, showing that Gfi1aa and Gfi1b together set the pace for prRBC differentiation from hemangioblasts.
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Affiliation(s)
| | | | | | | | - Sunir Malla
- Deep Seq, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Fei Sang
- Deep Seq, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Yan Chen
- Department of Infection, Immunity & Cardiovascular Disease, Medical School, and
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Stone Elworthy
- Department of Infection, Immunity & Cardiovascular Disease, Medical School, and
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Robert N Wilkinson
- Department of Infection, Immunity & Cardiovascular Disease, Medical School, and
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
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23
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Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift. Nat Commun 2018; 9:2595. [PMID: 29968757 PMCID: PMC6030214 DOI: 10.1038/s41467-018-05016-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 06/06/2018] [Indexed: 11/08/2022] Open
Abstract
Single-cell RNA sequencing allows defining molecularly distinct cell subpopulations. However, the identification of specific sets of transcription factors (TFs) that define the identity of these subpopulations remains a challenge. Here we propose that subpopulation identity emerges from the synergistic activity of multiple TFs. Based on this concept, we develop a computational platform (TransSyn) for identifying synergistic transcriptional cores that determine cell subpopulation identities. TransSyn leverages single-cell RNA-seq data, and performs a dynamic search for an optimal synergistic transcriptional core using an information theoretic measure of synergy. A large-scale TransSyn analysis identifies transcriptional cores for 186 subpopulations, and predicts identity conversion TFs between 3786 pairs of cell subpopulations. Finally, TransSyn predictions enable experimental conversion of human hindbrain neuroepithelial cells into medial floor plate midbrain progenitors, capable of rapidly differentiating into dopaminergic neurons. Thus, TransSyn can facilitate designing strategies for conversion of cell subpopulation identities with potential applications in regenerative medicine.
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24
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Thivakaran A, Botezatu L, Hönes JM, Schütte J, Vassen L, Al-Matary YS, Patnana P, Zeller A, Heuser M, Thol F, Gabdoulline R, Olberding N, Frank D, Suslo M, Köster R, Lennartz K, Görgens A, Giebel B, Opalka B, Dührsen U, Khandanpour C. Gfi1b: a key player in the genesis and maintenance of acute myeloid leukemia and myelodysplastic syndrome. Haematologica 2018; 103:614-625. [PMID: 29326122 PMCID: PMC5865438 DOI: 10.3324/haematol.2017.167288] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
Differentiation of hematopoietic stem cells is regulated by a concert of different transcription factors. Disturbed transcription factor function can be the basis of (pre)malignancies such as myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Growth factor independence 1b (Gfi1b) is a repressing transcription factor regulating quiescence of hematopoietic stem cells and differentiation of erythrocytes and platelets. Here, we show that low expression of Gfi1b in blast cells is associated with an inferior prognosis of MDS and AML patients. Using different models of human MDS or AML, we demonstrate that AML development was accelerated with heterozygous loss of Gfi1b, and latency was further decreased when Gfi1b was conditionally deleted. Loss of Gfi1b significantly increased the number of leukemic stem cells with upregulation of genes involved in leukemia development. On a molecular level, we found that loss of Gfi1b led to epigenetic changes, increased levels of reactive oxygen species, as well as alteration in the p38/Akt/FoXO pathways. These results demonstrate that Gfi1b functions as an oncosuppressor in MDS and AML development.
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Affiliation(s)
- Aniththa Thivakaran
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lacramioara Botezatu
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Judith M Hönes
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Judith Schütte
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lothar Vassen
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Yahya S Al-Matary
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Pradeep Patnana
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Amos Zeller
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Heuser
- Department of Haematology, Haemostaseology, Oncology, and Stem Cell Transplantation, Medical University of Hannover, Germany
| | - Felicitas Thol
- Department of Haematology, Haemostaseology, Oncology, and Stem Cell Transplantation, Medical University of Hannover, Germany
| | - Razif Gabdoulline
- Department of Haematology, Haemostaseology, Oncology, and Stem Cell Transplantation, Medical University of Hannover, Germany
| | - Nadine Olberding
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daria Frank
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Marina Suslo
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Renata Köster
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Klaus Lennartz
- Institute for Cell Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andre Görgens
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Bertram Opalka
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Dührsen
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Cyrus Khandanpour
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany .,Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Germany
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25
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Léon C, Dupuis A, Gachet C, Lanza F. The contribution of mouse models to the understanding of constitutional thrombocytopenia. Haematologica 2017; 101:896-908. [PMID: 27478199 DOI: 10.3324/haematol.2015.139394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/04/2016] [Indexed: 11/09/2022] Open
Abstract
Constitutional thrombocytopenias result from platelet production abnormalities of hereditary origin. Long misdiagnosed and poorly studied, knowledge about these rare diseases has increased considerably over the last twenty years due to improved technology for the identification of mutations, as well as an improvement in obtaining megakaryocyte culture from patient hematopoietic stem cells. Simultaneously, the manipulation of mouse genes (transgenesis, total or conditional inactivation, introduction of point mutations, random chemical mutagenesis) have helped to generate disease models that have contributed greatly to deciphering patient clinical and laboratory features. Most of the thrombocytopenias for which the mutated genes have been identified now have a murine model counterpart. This review focuses on the contribution that these mouse models have brought to the understanding of hereditary thrombocytopenias with respect to what was known in humans. Animal models have either i) provided novel information on the molecular and cellular pathways that were missing from the patient studies; ii) improved our understanding of the mechanisms of thrombocytopoiesis; iii) been instrumental in structure-function studies of the mutated gene products; and iv) been an invaluable tool as preclinical models to test new drugs or develop gene therapies. At present, the genetic determinants of thrombocytopenia remain unknown in almost half of all cases. Currently available high-speed sequencing techniques will identify new candidate genes, which will in turn allow the generation of murine models to confirm and further study the abnormal phenotype. In a complementary manner, programs of random mutagenesis in mice should also identify new candidate genes involved in thrombocytopenia.
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Affiliation(s)
- Catherine Léon
- UMR_S949, INSERM, Strasbourg, France Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France Université de Strasbourg, France Fédération de Médecine Translationnelle de Strasbourg (FMTS), France
| | - Arnaud Dupuis
- UMR_S949, INSERM, Strasbourg, France Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France Université de Strasbourg, France Fédération de Médecine Translationnelle de Strasbourg (FMTS), France
| | - Christian Gachet
- UMR_S949, INSERM, Strasbourg, France Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France Université de Strasbourg, France Fédération de Médecine Translationnelle de Strasbourg (FMTS), France
| | - François Lanza
- UMR_S949, INSERM, Strasbourg, France Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France Université de Strasbourg, France Fédération de Médecine Translationnelle de Strasbourg (FMTS), France
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26
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Schulze H, Schlagenhauf A, Manukjan G, Beham-Schmid C, Andres O, Klopocki E, König EM, Haidl H, Panzer S, Althaus K, Muntean WE, Schwinger W, Urban C, Greinacher A, Bakchoul T, Seidel MG. Recessive grey platelet-like syndrome with unaffected erythropoiesis in the absence of the splice isoform GFI1B-p37. Haematologica 2017; 102:e375-e378. [PMID: 28550182 DOI: 10.3324/haematol.2017.167957] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Harald Schulze
- Chair of Experimental Biomedicine I, University Hospital Würzburg, Germany
| | - Axel Schlagenhauf
- Department of Pediatrics and Adolescent Medicine, Medical University Graz, Austria
| | - Georgi Manukjan
- Chair of Experimental Biomedicine I, University Hospital Würzburg, Germany
| | | | - Oliver Andres
- University Children's Hospital, University Hospital Würzburg, Germany
| | - Eva Klopocki
- Institute of Human Genetics, Biocenter, University of Würzburg, Germany
| | - Eva-Maria König
- Institute of Human Genetics, Biocenter, University of Würzburg, Germany
| | - Harald Haidl
- Department of Pediatrics and Adolescent Medicine, Medical University Graz, Austria
| | - Simon Panzer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Austria
| | - Karina Althaus
- Institute of Immunology and Transfusion Medicine, Universitätsmedizin Greifswald, Germany
| | - Wolfgang E Muntean
- Department of Pediatrics and Adolescent Medicine, Medical University Graz, Austria
| | - Wolfgang Schwinger
- Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Austria
| | - Christian Urban
- Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Austria
| | - Andreas Greinacher
- Institute of Immunology and Transfusion Medicine, Universitätsmedizin Greifswald, Germany
| | - Tamam Bakchoul
- Institute of Immunology and Transfusion Medicine, Universitätsmedizin Greifswald, Germany
| | - Markus G Seidel
- Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Austria.,Research Unit Pediatric Hematology and Immunology, Medical University Graz, Austria
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27
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Ferreira CR, Chen D, Abraham SM, Adams DR, Simon KL, Malicdan MC, Markello TC, Gunay-Aygun M, Gahl WA. Combined alpha-delta platelet storage pool deficiency is associated with mutations in GFI1B. Mol Genet Metab 2017; 120:288-294. [PMID: 28041820 PMCID: PMC5346474 DOI: 10.1016/j.ymgme.2016.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/09/2016] [Accepted: 12/09/2016] [Indexed: 01/25/2023]
Abstract
Combined alpha-delta platelet storage pool deficiency is characterized by the absence or reduction in the number of both alpha granules and dense bodies. This disorder can have variable severity as well as a variable inheritance pattern. We describe two patients from unrelated families with combined alpha-delta storage pool deficiency due to mutations in GFI1B, a zinc finger protein known to act as a transcriptional repressor of various genes. We demonstrate that this disease is associated with either a heterozygous mutation (de novo or familial) abrogating the binding of the zinc fingers with the promoter of its target genes, or by hypomorphic biallelic mutations in GFI1B leading to autosomal recessive inheritance.
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Affiliation(s)
- Carlos R Ferreira
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Division of Genetics and Metabolism, Children's National Health System, Washington, DC, United States.
| | - Dong Chen
- Special Coagulation Laboratory, Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, United States
| | - Shirley M Abraham
- Division of Hematology and Oncology, Department of Pediatrics, University of New Mexico, Albuquerque, NM, United States
| | - David R Adams
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; NIH Undiagnosed Diseases Program, NIH Common Fund, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karen L Simon
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - May C Malicdan
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; NIH Undiagnosed Diseases Program, NIH Common Fund, National Institutes of Health, Bethesda, MD, United States
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, NIH Common Fund, National Institutes of Health, Bethesda, MD, United States
| | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Johns Hopkins University School of Medicine, Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD, United States
| | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; NIH Undiagnosed Diseases Program, NIH Common Fund, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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28
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Beauchemin H, Shooshtarizadeh P, Vadnais C, Vassen L, Pastore YD, Möröy T. Gfi1b controls integrin signaling-dependent cytoskeleton dynamics and organization in megakaryocytes. Haematologica 2017; 102:484-497. [PMID: 28082345 PMCID: PMC5394960 DOI: 10.3324/haematol.2016.150375] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
Mutations in GFI1B are associated with inherited bleeding disorders called GFI1B-related thrombocytopenias. We show here that mice with a megakaryocyte-specific Gfi1b deletion exhibit a macrothrombocytopenic phenotype along a megakaryocytic dysplasia reminiscent of GFI1B-related thrombocytopenia. GFI1B deficiency increases megakaryocyte proliferation and affects their ploidy, but also abrogates their responsiveness towards integrin signaling and their ability to spread and reorganize their cytoskeleton. Gfi1b-null megakaryocytes are also unable to form proplatelets, a process independent of integrin signaling. GFI1B-deficient megakaryocytes exhibit aberrant expression of several components of both the actin and microtubule cytoskeleton, with a dramatic reduction of α-tubulin. Inhibition of FAK or ROCK, both important for actin cytoskeleton organization and integrin signaling, only partially restored their response to integrin ligands, but the inhibition of PAK, a regulator of the actin cytoskeleton, completely rescued the responsiveness of Gfi1b-null megakaryocytes to ligands, but not their ability to form proplatelets. We conclude that Gfi1b controls major functions of megakaryocytes such as integrin-dependent cytoskeleton organization, spreading and migration through the regulation of PAK activity whereas the proplatelet formation defect in GFI1B-deficient megakaryocytes is due, at least partially, to an insufficient α-tubulin content.
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Affiliation(s)
| | | | - Charles Vadnais
- Institut de Recherches Cliniques de Montréal, IRCM, QC, Canada
| | - Lothar Vassen
- Institut de Recherches Cliniques de Montréal, IRCM, QC, Canada
| | - Yves D Pastore
- Département de Pédiatrie, Service d'Hématologie et Oncologie, CHU Ste-Justine, Montréal, QC, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, IRCM, QC, Canada .,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, QC, Canada.,Division of Experimental Medicine, McGill University, Montréal, QC, Canada
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29
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Bariana TK, Ouwehand WH, Guerrero JA, Gomez K. Dawning of the age of genomics for platelet granule disorders: improving insight, diagnosis and management. Br J Haematol 2016; 176:705-720. [PMID: 27984638 DOI: 10.1111/bjh.14471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inherited disorders of platelet granules are clinically heterogeneous and their prevalence is underestimated because most patients do not undergo a complete diagnostic work-up. The lack of a genetic diagnosis limits the ability to tailor management, screen family members, aid with family planning, predict clinical progression and detect serious consequences, such as myelofibrosis, lung fibrosis and malignancy, in a timely manner. This is set to change with the introduction of high throughput sequencing (HTS) as a routine clinical diagnostic test. HTS diagnostic tests are now available, affordable and allow parallel screening of DNA samples for variants in all of the 80 known bleeding, thrombotic and platelet genes. Increased genetic diagnosis and curation of variants is, in turn, improving our understanding of the pathobiology and clinical course of inherited platelet disorders. Our understanding of the genetic causes of platelet granule disorders and the regulation of granule biogenesis is a work in progress and has been significantly enhanced by recent genomic discoveries from high-powered genome-wide association studies and genome sequencing projects. In the era of whole genome and epigenome sequencing, new strategies are required to integrate multiple sources of big data in the search for elusive, novel genes underlying granule disorders.
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Affiliation(s)
- Tadbir K Bariana
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK.,Department of Haematology, University College London Cancer Institute, London, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.,Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Keith Gomez
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
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30
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Liu L, Pertsemlidis A, Ding LH, Story MD, Steinberg MH, Sebastiani P, Hoppe C, Ballas SK, Pace BS. Original Research: A case-control genome-wide association study identifies genetic modifiers of fetal hemoglobin in sickle cell disease. Exp Biol Med (Maywood) 2016; 241:706-18. [PMID: 27022141 DOI: 10.1177/1535370216642047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sickle cell disease (SCD) is a group of inherited blood disorders that have in common a mutation in the sixth codon of the β-globin (HBB) gene on chromosome 11. However, people with the same genetic mutation display a wide range of clinical phenotypes. Fetal hemoglobin (HbF) expression is an important genetic modifier of SCD complications leading to milder symptoms and improved long-term survival. Therefore, we performed a genome-wide association study (GWAS) using a case-control experimental design in 244 African Americans with SCD to discover genetic factors associated with HbF expression. The case group consisted of subjects with HbF≥8.6% (133 samples) and control group subjects with HbF≤£3.1% (111 samples). Our GWAS results replicated SNPs previously identified in an erythroid-specific enhancer region located in the second intron of the BCL11A gene associated with HbF expression. In addition, we identified SNPs in the SPARC, GJC1, EFTUD2 and JAZF1 genes as novel candidates associated with HbF levels. To gain insights into mechanisms of globin gene regulation in the HBB locus, linkage disequilibrium (LD) and haplotype analyses were conducted. We observed strong LD in the low HbF group in contrast to a loss of LD and greater number of haplotypes in the high HbF group. A search of known HBB locus regulatory elements identified SNPs 5' of δ-globin located in an HbF silencing region. In particular, SNP rs4910736 created a binding site for a known transcription repressor GFi1 which is a candidate protein for further investigation. Another HbF-associated SNP, rs2855122 in the cAMP response element upstream of Gγ-globin, was analyzed for functional relevance. Studies performed with siRNA-mediated CREB binding protein (CBP) knockdown in primary erythroid cells demonstrated γ-globin activation and HbF induction, supporting a repressor role for CBP. This study identifies possible molecular determinants of HbF production.
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Affiliation(s)
- Li Liu
- Department of Biological Sciences, University of Texas at Dallas, Dallas, TX 75083, USA
| | - Alexander Pertsemlidis
- Departments of Pediatrics and Cellular & Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Liang-Hao Ding
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael D Story
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Martin H Steinberg
- Center of Excellence in Sickle Cell Disease Boston Medical Center, Pediatrics, Pathology and Laboratory Medicine, Boston University, Boston, MA 02215, USA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02215, USA
| | - Carolyn Hoppe
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Samir K Ballas
- Cardeza Foundation for Hematologic Research, Department of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, GA 30912, USA
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31
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Selective and reversible suppression of intestinal stem cell differentiation by pharmacological inhibition of BET bromodomains. Sci Rep 2016; 6:20390. [PMID: 26856877 PMCID: PMC4746593 DOI: 10.1038/srep20390] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/31/2015] [Indexed: 12/13/2022] Open
Abstract
Absorptive and secretory cells of the small intestine are derived from a single population of Lgr5-expressing stem cells. While key genetic pathways required for differentiation into specific lineages have been defined, epigenetic programs contributing to this process remain poorly characterized. Members of the BET family of chromatin adaptors contain tandem bromodomains that mediate binding to acetylated lysines on target proteins to regulate gene expression. In this study, we demonstrate that mice treated with a small molecule inhibitor of BET bromodomains, CPI203, exhibit greater than 90% decrease in tuft and enteroendocrine cells in both crypts and villi of the small intestine, with no changes observed in goblet or Paneth cells. BET bromodomain inhibition did not alter the abundance of Lgr5-expressing stem cells in crypts, but rather exerted its effects on intermediate progenitors, in part through regulation of Ngn3 expression. When BET bromodomain inhibition was combined with the chemotherapeutic gemcitabine, pervasive apoptosis was observed in intestinal crypts, revealing an important role for BET bromodomain activity in intestinal homeostasis. Pharmacological targeting of BET bromodomains defines a novel pathway required for tuft and enteroendocrine differentiation and provides an important tool to further dissect the progression from stem cell to terminally differentiated secretory cell.
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32
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Anguita E, Gupta R, Olariu V, Valk PJ, Peterson C, Delwel R, Enver T. A somatic mutation of GFI1B identified in leukemia alters cell fate via a SPI1 (PU.1) centered genetic regulatory network. Dev Biol 2016; 411:277-286. [PMID: 26851695 DOI: 10.1016/j.ydbio.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 01/22/2023]
Abstract
We identify a mutation (D262N) in the erythroid-affiliated transcriptional repressor GFI1B, in an acute myeloid leukemia (AML) patient with antecedent myelodysplastic syndrome (MDS). The GFI1B-D262N mutant functionally antagonizes the transcriptional activity of wild-type GFI1B. GFI1B-D262N promoted myelomonocytic versus erythroid output from primary human hematopoietic precursors and enhanced cell survival of both normal and MDS derived precursors. Re-analysis of AML transcriptome data identifies a distinct group of patients in whom expression of wild-type GFI1B and SPI1 (PU.1) have an inverse pattern. In delineating this GFI1B-SPI1 relationship we show that (i) SPI1 is a direct target of GFI1B, (ii) expression of GFI1B-D262N produces elevated expression of SPI1, and (iii) SPI1-knockdown restores balanced lineage output from GFI1B-D262N-expressing precursors. These results table the SPI1-GFI1B transcriptional network as an important regulatory axis in AML as well as in the development of erythroid versus myelomonocytic cell fate.
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Affiliation(s)
- Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos (IdISSC), Prof. Martín Lagos s/n, 28040 Madrid, Spain.
| | - Rajeev Gupta
- UCL Cancer Institute, Paul O'Gorman Building 72 Huntley St., London WC1E6BT, United Kingdom.
| | - Victor Olariu
- Computational Biology and Biological Physics Division, Lund University, Lund, Sweden.
| | - Peter J Valk
- Department of Hematology Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Carsten Peterson
- Computational Biology and Biological Physics Division, Lund University, Lund, Sweden.
| | - Ruud Delwel
- Department of Hematology Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Tariq Enver
- UCL Cancer Institute, Paul O'Gorman Building 72 Huntley St., London WC1E6BT, United Kingdom.
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From cytopenia to leukemia: the role of Gfi1 and Gfi1b in blood formation. Blood 2015; 126:2561-9. [PMID: 26447191 DOI: 10.1182/blood-2015-06-655043] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/06/2015] [Indexed: 12/24/2022] Open
Abstract
The DNA-binding zinc finger transcription factors Gfi1 and Gfi1b were discovered more than 20 years ago and are recognized today as major regulators of both early hematopoiesis and hematopoietic stem cells. Both proteins function as transcriptional repressors by recruiting histone-modifying enzymes to promoters and enhancers of target genes. The establishment of Gfi1 and Gfi1b reporter mice made it possible to visualize their cell type-specific expression and to understand their function in hematopoietic lineages. We now know that Gfi1 is primarily important in myeloid and lymphoid differentiation, whereas Gfi1b is crucial for the generation of red blood cells and platelets. Several rare hematologic diseases are associated with acquired or inheritable mutations in the GFI1 and GFI1B genes. Certain patients with severe congenital neutropenia carry mutations in the GFI1 gene that lead to the disruption of the C-terminal zinc finger domains. Other mutations have been found in the GFI1B gene in families with inherited bleeding disorders. In addition, the Gfi1 locus is frequently found to be a proviral integration site in retrovirus-induced lymphomagenesis, and new, emerging data suggest a role of Gfi1 in human leukemia and lymphoma, underlining the role of both factors not only in normal hematopoiesis, but also in a wide spectrum of human blood diseases.
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