1
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Iwata A, Maruyama J, Natsuki S, Nishiyama A, Tamura T, Tanaka M, Shichino S, Seki T, Komai T, Okamura T, Fujio K, Tanaka M, Asano K. Egr2 drives the differentiation of Ly6C hi monocytes into fibrosis-promoting macrophages in metabolic dysfunction-associated steatohepatitis in mice. Commun Biol 2024; 7:681. [PMID: 38831027 PMCID: PMC11148031 DOI: 10.1038/s42003-024-06357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Metabolic dysfunction-associated steatohepatitis (MASH), previously called non-alcoholic steatohepatitis (NASH), is a growing concern worldwide, with liver fibrosis being a critical determinant of its prognosis. Monocyte-derived macrophages have been implicated in MASH-associated liver fibrosis, yet their precise roles and the underlying differentiation mechanisms remain elusive. In this study, we unveil a key orchestrator of this process: long chain saturated fatty acid-Egr2 pathway. Our findings identify the transcription factor Egr2 as the driving force behind monocyte differentiation into hepatic lipid-associated macrophages (hLAMs) within MASH liver. Notably, Egr2-deficiency reroutes monocyte differentiation towards a macrophage subset resembling resident Kupffer cells, hampering hLAM formation. This shift has a profound impact, suppressing the transition from benign steatosis to liver fibrosis, demonstrating the critical pro-fibrotic role played by hLAMs in MASH pathogenesis. Long-chain saturated fatty acids that accumulate in MASH liver emerge as potent inducers of Egr2 expression in macrophages, a process counteracted by unsaturated fatty acids. Furthermore, oral oleic acid administration effectively reduces hLAMs in MASH mice. In conclusion, our work not only elucidates the intricate interplay between saturated fatty acids, Egr2, and monocyte-derived macrophages but also highlights the therapeutic promise of targeting the saturated fatty acid-Egr2 axis in monocytes for MASH management.
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Grants
- 22H05190 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H05064 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JPMXP0618217493, JPMXP0622717006, and JPMXP0723833149 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20H03473 Japan Society for the Promotion of Science London (JSPS London)
- 21K06877 Japan Society for the Promotion of Science London (JSPS London)
- JP18gm1210002 Japan Agency for Medical Research and Development (AMED)
- JP21gm6210025 Japan Agency for Medical Research and Development (AMED)
- Ono Medical Research Foundation
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Affiliation(s)
- Ayaka Iwata
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Juri Maruyama
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Shibata Natsuki
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Akira Nishiyama
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, 236-0004, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, 236-0004, Japan
- Advanced Medical Research Center, Yokohama City University, Kanagawa, 236-0004, Japan
| | - Minoru Tanaka
- Department of Regenerative Medicine, Research Institute National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, 278-0022, Japan
| | - Takao Seki
- Department of Biochemistry, Toho University School of Medicine, Tokyo, 143-8540, Japan
| | - Toshihiko Komai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Masato Tanaka
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan.
| | - Kenichi Asano
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan.
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2
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Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. Proc Natl Acad Sci U S A 2024; 121:e2318329121. [PMID: 38787881 PMCID: PMC11145184 DOI: 10.1073/pnas.2318329121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The Hill functions, [Formula: see text], have been widely used in biology for over a century but, with the exception of [Formula: see text], they have had no justification other than as a convenient fit to empirical data. Here, we show that they are the universal limit for the sharpness of any input-output response arising from a Markov process model at thermodynamic equilibrium. Models may represent arbitrary molecular complexity, with multiple ligands, internal states, conformations, coregulators, etc, under core assumptions that are detailed in the paper. The model output may be any linear combination of steady-state probabilities, with components other than the chosen input ligand held constant. This formulation generalizes most of the responses in the literature. We use a coarse-graining method in the graph-theoretic linear framework to show that two sharpness measures for input-output responses fall within an effectively bounded region of the positive quadrant, [Formula: see text], for any equilibrium model with [Formula: see text] input binding sites. [Formula: see text] exhibits a cusp which approaches, but never exceeds, the sharpness of [Formula: see text], but the region and the cusp can be exceeded when models are taken away from thermodynamic equilibrium. Such fundamental thermodynamic limits are called Hopfield barriers, and our results provide a biophysical justification for the Hill functions as the universal Hopfield barriers for sharpness. Our results also introduce an object, [Formula: see text], whose structure may be of mathematical interest, and suggest the importance of characterizing Hopfield barriers for other forms of cellular information processing.
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Affiliation(s)
| | - Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, MA02115
| | - Angela H. DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA02115
- HHMI, Boston, MA02115
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3
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Geng S, Liu SB, He W, Pan X, Sun Y, Xue T, Han S, Lou J, Chang Y, Zheng J, Shi X, Li Y, Song YH. Deletion of TECRL promotes skeletal muscle repair by up-regulating EGR2. Proc Natl Acad Sci U S A 2024; 121:e2317495121. [PMID: 38753506 PMCID: PMC11126978 DOI: 10.1073/pnas.2317495121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
Myogenic regeneration relies on the proliferation and differentiation of satellite cells. TECRL (trans-2,3-enoyl-CoA reductase like) is an endoplasmic reticulum protein only expressed in cardiac and skeletal muscle. However, its role in myogenesis remains unknown. We show that TECRL expression is increased in response to injury. Satellite cell-specific deletion of TECRL enhances muscle repair by increasing the expression of EGR2 through the activation of the ERK1/2 signaling pathway, which in turn promotes the expression of PAX7. We further show that TECRL deletion led to the upregulation of the histone acetyltransferase general control nonderepressible 5, which enhances the transcription of EGR2 through acetylation. Importantly, we showed that AAV9-mediated TECRL silencing improved muscle repair in mice. These findings shed light on myogenic regeneration and muscle repair.
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Affiliation(s)
- Sha Geng
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou215009, People’s Republic of China
| | - Wei He
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Xiangbin Pan
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, China and Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100037, People’s Republic of China
| | - Yi Sun
- Department of Cardiovascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Kunming650102, People’s Republic of China
| | - Ting Xue
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Shiyuan Han
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Jing Lou
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Ying Chang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Jiqing Zheng
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Xinghong Shi
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Yangxin Li
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou215123, People’s Republic of China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou215123, People’s Republic of China
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, SuzhouJiangsu215000, People’s Republic of China
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4
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Ochiai K, Shima H, Tamahara T, Sugie N, Funayama R, Nakayama K, Kurosaki T, Igarashi K. Accelerated plasma-cell differentiation in Bach2-deficient mouse B cells is caused by altered IRF4 functions. EMBO J 2024; 43:1947-1964. [PMID: 38605225 PMCID: PMC11099079 DOI: 10.1038/s44318-024-00077-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 04/13/2024] Open
Abstract
Transcription factors BACH2 and IRF4 are both essential for antibody class-switch recombination (CSR) in activated B lymphocytes, while they oppositely regulate the differentiation of plasma cells (PCs). Here, we investigated how BACH2 and IRF4 interact during CSR and plasma-cell differentiation. We found that BACH2 organizes heterochromatin formation of target gene loci in mouse splenic B cells, including targets of IRF4 activation such as Aicda, an inducer of CSR, and Prdm1, a master plasma-cell regulator. Release of these gene loci from heterochromatin in response to B-cell receptor stimulation was coupled to AKT-mTOR pathway activation. In Bach2-deficient B cells, PC genes' activation depended on IRF4 protein accumulation, without an increase in Irf4 mRNA. Mechanistically, a PU.1-IRF4 heterodimer in activated B cells promoted BACH2 function by inducing gene expression of Bach2 and Pten, a negative regulator of AKT signaling. Elevated AKT activity in Bach2-deficient B cells resulted in IRF4 protein accumulation. Thus, BACH2 and IRF4 mutually modulate the activity of each other, and BACH2 inhibits PC differentiation by both the repression of PC genes and the restriction of IRF4 protein accumulation.
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Affiliation(s)
- Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Toru Tamahara
- Division of Community Oral Health Science, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Sendai, 980-8573, Japan
| | - Nao Sugie
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan
- Laboratory for Lymhocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
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5
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Del Olmo M, Legewie S, Brunner M, Höfer T, Kramer A, Blüthgen N, Herzel H. Network switches and their role in circadian clocks. J Biol Chem 2024; 300:107220. [PMID: 38522517 PMCID: PMC11044057 DOI: 10.1016/j.jbc.2024.107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Circadian rhythms are generated by complex interactions among genes and proteins. Self-sustained ∼24 h oscillations require negative feedback loops and sufficiently strong nonlinearities that are the product of molecular and network switches. Here, we review common mechanisms to obtain switch-like behavior, including cooperativity, antagonistic enzymes, multisite phosphorylation, positive feedback, and sequestration. We discuss how network switches play a crucial role as essential components in cellular circadian clocks, serving as integral parts of transcription-translation feedback loops that form the basis of circadian rhythm generation. The design principles of network switches and circadian clocks are illustrated by representative mathematical models that include bistable systems and negative feedback loops combined with Hill functions. This work underscores the importance of negative feedback loops and network switches as essential design principles for biological oscillations, emphasizing how an understanding of theoretical concepts can provide insights into the mechanisms generating biological rhythms.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Michael Brunner
- Biochemistry Center, Universität Heidelberg, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Universität Heidelberg, Heidelberg, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
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6
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Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector CD8 T cells during chronic infection and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.579535. [PMID: 38659890 PMCID: PMC11042319 DOI: 10.1101/2024.04.18.579535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During chronic infections and tumor progression, CD8 T cells gradually lose their effector functions and become exhausted. These exhausted CD8 T cells are heterogeneous and comprised of different subsets, including self-renewing progenitors that give rise to Ly108 - CX3CR1 + effector-like cells. Generation of these effector-like cells is essential for the control of chronic infections and tumors, albeit limited. However, the precise cues and mechanisms directing the formation and maintenance of exhausted effector-like are incompletely understood. Using genetic mouse models challenged with LCMV Clone 13 or syngeneic tumors, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in exhausted CD8 T cells, which in turn regulates the formation of exhausted effector-like cells. Gfi1 deletion in T cells dysregulates the chromatin accessibility and transcriptomic programs associated with the differentiation of LCMV Clone 13-specific CD8 T cell exhaustion, preventing the formation of effector-like and terminally exhausted cells while maintaining progenitors and a newly identified Ly108 + CX3CR1 + state. These Ly108 + CX3CR1 + cells have a distinct chromatin profile and may represent an alternative target for therapeutic interventions to combat chronic infections and cancer. In sum, we show that Gfi1 is a critical regulator of the formation of exhausted effector-like cells.
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7
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Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587054. [PMID: 38585761 PMCID: PMC10996692 DOI: 10.1101/2024.03.27.587054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The Hill functions, ℋ h ( x ) = x h / 1 + x h , have been widely used in biology for over a century but, with the exception of ℋ 1 , they have had no justification other than as a convenient fit to empirical data. Here, we show that they are the universal limit for the sharpness of any input-output response arising from a Markov process model at thermodynamic equilibrium. Models may represent arbitrary molecular complexity, with multiple ligands, internal states, conformations, co-regulators, etc, under core assumptions that are detailed in the paper. The model output may be any linear combination of steady-state probabilities, with components other than the chosen input ligand held constant. This formulation generalises most of the responses in the literature. We use a coarse-graining method in the graph-theoretic linear framework to show that two sharpness measures for input-output responses fall within an effectively bounded region of the positive quadrant, Ω m ⊂ ℝ + 2 , for any equilibrium model with m input binding sites. Ω m exhibits a cusp which approaches, but never exceeds, the sharpness of ℋ m but the region and the cusp can be exceeded when models are taken away from thermodynamic equilibrium. Such fundamental thermodynamic limits are called Hopfield barriers and our results provide a biophysical justification for the Hill functions as the universal Hopfield barriers for sharpness. Our results also introduce an object, Ω m , whose structure may be of mathematical interest, and suggest the importance of characterising Hopfield barriers for other forms of cellular information processing.
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Affiliation(s)
| | - Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H. DePace
- Howard Hughes Medical Institute, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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8
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Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024; 20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Precision in the establishment and maintenance of cellular identities is crucial for the development of multicellular organisms and requires tight regulation of gene expression. While extensive research has focused on understanding cell type-specific gene activation, the complex mechanisms underlying the transcriptional repression of alternative fates are not fully understood. Here, we provide an overview of the repressive mechanisms involved in cell fate regulation. We discuss the molecular machinery responsible for suppressing alternative fates and highlight the crucial role of sequence-specific transcription factors (TFs) in this process. Depletion of these TFs can result in unwanted gene expression and increased cellular plasticity. We suggest that these TFs recruit cell type-specific repressive complexes to their cis-regulatory elements, enabling them to modulate chromatin accessibility in a context-dependent manner. This modulation effectively suppresses master regulators of alternative fate programs and their downstream targets. The modularity and dynamic behavior of these repressive complexes enables a limited number of repressors to canalize and maintain major and minor cell fate decisions at different stages of development.
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Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany.
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9
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Zolotarev N, Wang Y, Du M, Bayer M, Grosschedl A, Cisse I, Grosschedl R. Regularly spaced tyrosines in EBF1 mediate BRG1 recruitment and formation of nuclear subdiffractive clusters. Genes Dev 2024; 38:4-10. [PMID: 38233109 PMCID: PMC10903943 DOI: 10.1101/gad.350828.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
B lineage priming by pioneer transcription factor EBF1 requires the function of an intrinsically disordered region (IDR). Here, we examine the role of regularly spaced tyrosines in the IDR as potential determinants of IDR function and activity of EBF1. We found that four Y > A mutations in EBF1 reduced the formation of condensates in vitro and subdiffractive clusters in vivo. Notably, Y > A mutant EBF1 was inefficient in promoting B cell differentiation and showed impaired chromatin binding, recruitment of BRG1, and activation of specific target genes. Thus, regularly spaced tyrosines in the IDR contribute to the biophysical and functional properties of EBF1.
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Affiliation(s)
- Nikolay Zolotarev
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Yuanting Wang
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Manyu Du
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Marc Bayer
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Anna Grosschedl
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Ibrahim Cisse
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany;
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10
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
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11
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Nakamura YT, Himeoka Y, Saito N, Furusawa C. Evolution of hierarchy and irreversibility in theoretical cell differentiation model. PNAS NEXUS 2024; 3:pgad454. [PMID: 38205032 PMCID: PMC10776358 DOI: 10.1093/pnasnexus/pgad454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
The process of cell differentiation in multicellular organisms is characterized by hierarchy and irreversibility in many cases. However, the conditions and selection pressures that give rise to these characteristics remain poorly understood. By using a mathematical model, here we show that the network of differentiation potency (differentiation diagram) becomes necessarily hierarchical and irreversible by increasing the number of terminally differentiated states under certain conditions. The mechanisms generating these characteristics are clarified using geometry in the cell state space. The results demonstrate that the hierarchical organization and irreversibility can manifest independently of direct selection pressures associated with these characteristics, instead they appear to evolve as byproducts of selective forces favoring a diversity of differentiated cell types. The study also provides a new perspective on the structure of gene regulatory networks that produce hierarchical and irreversible differentiation diagrams. These results indicate some constraints on cell differentiation, which are expected to provide a starting point for theoretical discussion of the implicit limits and directions of evolution in multicellular organisms.
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Affiliation(s)
- Yoshiyuki T Nakamura
- Department of Physics, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Center for Biosystems Dynamics Research, RIKEN, Suita 565-0874, Japan
| | - Yusuke Himeoka
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku 113-0033, Japan
| | - Nen Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8526, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Chikara Furusawa
- Department of Physics, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Center for Biosystems Dynamics Research, RIKEN, Suita 565-0874, Japan
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12
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Kim H, Choi H, Lee D, Kim J. A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing. Genes Genomics 2024; 46:1-11. [PMID: 38032470 DOI: 10.1007/s13258-023-01473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Understanding gene regulatory networks (GRNs) is essential for unraveling the molecular mechanisms governing cellular behavior. With the advent of high-throughput transcriptome measurement technology, researchers have aimed to reverse engineer the biological systems, extracting gene regulatory rules from their outputs, which represented by gene expression data. Bulk RNA sequencing, a widely used method for measuring gene expression, has been employed for GRN reconstruction. However, it falls short in capturing dynamic changes in gene expression at the level of individual cells since it averages gene expression across mixed cell populations. OBJECTIVE In this review, we provide an overview of 15 GRN reconstruction tools and discuss their respective strengths and limitations, particularly in the context of single cell RNA sequencing (scRNA-seq). METHODS Recent advancements in scRNA-seq break new ground of GRN reconstruction. They offer snapshots of the individual cell transcriptomes and capturing dynamic changes. We emphasize how these technological breakthroughs have enhanced GRN reconstruction. CONCLUSION GRN reconstructors can be classified based on their requirement for cellular trajectory, which represents a dynamical cellular process including differentiation, aging, or disease progression. Benchmarking studies support the superiority of GRN reconstructors that do not require trajectory analysis in identifying regulator-target relationships. However, methods equipped with trajectory analysis demonstrate better performance in identifying key regulatory factors. In conclusion, researchers should select a suitable GRN reconstructor based on their specific research objectives.
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Affiliation(s)
- Hyeonkyu Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Hwisoo Choi
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Daewon Lee
- School of Art and Technology, Chung-Ang University, 4726 Seodong-Daero, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea.
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
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13
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Leary JR, Bacher R. Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572477. [PMID: 38187622 PMCID: PMC10769309 DOI: 10.1101/2023.12.19.572477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to determine which genes exhibit changes in expression that are significantly associated with progression through the biological trajectory. While a few techniques for performing trajectory differential expression exist, most rely on the flexibility of generalized additive models in order to account for the inherent nonlinearity of changes in gene expression. As such, the results can be difficult to interpret, and biological conclusions often rest on subjective visual inspections of the most dynamic genes. To address this challenge, we propose scLANE testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several different simulation scenarios, we apply it to a set of diverse biological datasets and display its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods.
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Affiliation(s)
- Jack R. Leary
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
| | - Rhonda Bacher
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
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14
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Eram N, Sachan S, Singh J, Shreya, Dwivedi U, Das D, Rai G, Rajan M. Growth Factor Independence-1 (GFI-1) Gene Expression in Hematopoietic Stem Cell Lineage Differentiation in Low Birth Weight Newborns Compared With Normal Birth Weight Newborns at Term Pregnancy. Cureus 2023; 15:e50696. [PMID: 38239528 PMCID: PMC10796131 DOI: 10.7759/cureus.50696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction Low birth weight (LBW), which is a risk factor for noncommunicable diseases throughout life, is a significant public health concern. In addition to regulating myeloid cell differentiation and proliferation, a transcriptional repressor identified as growth factor independence-1 (GFI-1) is essential for hematopoietic stem cell maintenance and self-renewal. The current study was designed to compare the expression of the GFI-1 gene in the differentiation of hematopoietic stem cells in newborns with LBW and those with normal birth weight (NBW). Methods A prospective comparative analytical study was carried out from September 2019 to September 2021 after obtaining Institute Ethical Committee approval at a tertiary care center in north India. The GFI-1 gene expression levels in 50 cord blood samples from women with term gestation and LBW newborns (<2500 grams) were measured using quantitative real-time polymerase chain reaction (RT-PCR) and compared to gene expression levels in 50 cord blood samples from women with term gestation and NBW newborns (≥2500 grams). The data were analyzed using IBM SPSS statistics software version 24.0 (IBM Corp., Armonk, NY). Results The median GFI-1 expression in LBW newborns is 3.1, whereas among NBW newborns it is 9.39. The difference is significant (P <0.001). The level of GFI-1 gene expression in LBW newborns was correlated with their birth weight. The coefficient of correlation was found to be weakly positive (r = 0.223). The birth weight of NBW newborns was correlated to the level of expression of the GFI-1 gene, which was found to be positively correlated (r = 0.332). Conclusion The levels of the GFI-1 gene and newborn birth weight were compared in LBW infants, which were weakly positively correlated. The level of GFI-1 gene expression at birth was compared to the birth weight of NBW newborns, which was positively correlated.
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Affiliation(s)
- Najma Eram
- Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Shikha Sachan
- Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Jigyasa Singh
- Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Shreya
- Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Utkarsh Dwivedi
- Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Doli Das
- Molecular and Human Genetics, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Geeta Rai
- Molecular and Human Genetics, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
| | - Mamta Rajan
- Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, IND
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15
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Mulet-Lazaro R, Delwel R. From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis. Hemasphere 2023; 7:e969. [PMID: 37953829 PMCID: PMC10635615 DOI: 10.1097/hs9.0000000000000969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
Blood comprises a wide array of specialized cells, all of which share the same genetic information and ultimately derive from the same precursor, the hematopoietic stem cell (HSC). This diversity of phenotypes is underpinned by unique transcriptional programs gradually acquired in the process known as hematopoiesis. Spatiotemporal regulation of gene expression depends on many factors, but critical among them are enhancers-sequences of DNA that bind transcription factors and increase transcription of genes under their control. Thus, hematopoiesis involves the activation of specific enhancer repertoires in HSCs and their progeny, driving the expression of sets of genes that collectively determine morphology and function. Disruption of this tightly regulated process can have catastrophic consequences: in hematopoietic malignancies, dysregulation of transcriptional control by enhancers leads to misexpression of oncogenes that ultimately drive transformation. This review attempts to provide a basic understanding of enhancers and their role in transcriptional regulation, with a focus on normal and malignant hematopoiesis. We present examples of enhancers controlling master regulators of hematopoiesis and discuss the main mechanisms leading to enhancer dysregulation in leukemia and lymphoma.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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16
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Nooti S, Naylor M, Long T, Groll B, Manu. LucFlow: A method to measure Luciferase reporter expression in single cells. PLoS One 2023; 18:e0292317. [PMID: 37792708 PMCID: PMC10550117 DOI: 10.1371/journal.pone.0292317] [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: 06/28/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Reporter assays, in which the expression of an inert protein is driven by gene regulatory elements such as promoters and enhancers, are a workhorse for investigating gene regulation. Techniques for measuring reporter gene expression vary from single-cell or single-molecule approaches having low throughput to bulk Luciferase assays that have high throughput. We developed a Luciferase Reporter Assay using Flow-Cytometry (LucFlow), which measures reporter expression in single cells immunostained for Luciferase. We optimized and tested LucFlow with a murine cell line that can be differentiated into neutrophils, into which promoter-reporter and enhancer-promoter-reporter constructs have been integrated in a site-specific manner. The single-cell measurements are comparable to bulk ones but we found that dead cells have no detectable Luciferase protein, so that bulk assays underestimate reporter expression. LucFlow is able to achieve a higher accuracy than bulk methods by excluding dead cells during flow cytometry. Prior to fixation and staining, the samples are spiked with stained cells that can be discriminated during flow cytometry and control for tube-to-tube variation in experimental conditions. Computing fold change relative to control cells allows LucFlow to achieve a high level of precision. LucFlow, therefore, enables the accurate and precise measurement of reporter expression in a high throughput manner.
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Affiliation(s)
- Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Brayden Groll
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
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17
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Zhao Y, Zhao C, Guo H, Zhang Z, Xu H, Shi M, Xu Y, Wei D, Zhao Y. mTORC2 orchestrates monocytic and granulocytic lineage commitment by an ATF5-mediated pathway. iScience 2023; 26:107540. [PMID: 37649699 PMCID: PMC10462862 DOI: 10.1016/j.isci.2023.107540] [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: 02/07/2023] [Revised: 06/12/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023] Open
Abstract
Myeloid hematopoiesis is a finely controlled consecutive developmental process, which is essential to maintain peripheral innate immune homeostasis. Herein, we found that Rictor deletion caused the remarkable reduction of granulocyte-monocyte progenitors (GMPs), monocytes, and macrophages, while the levels of neutrophils were unaffected. Adoptive transfer of Rictor-deleted GMPs or common myeloid progenitors (CMPs) in syngeneic mice showed poor re-constitution of monocytes compared to wild-type GMPs or CMPs. In addition to decreasing the proliferation of CMPs/GMPs, Rictor deletion preferentially inhibited Ly6C+ monocyte differentiation, while enhancing neutrophil differentiation, as determined by colony formation assays. mTORC2 promotes monocyte development by downregulation of the AKT-Foxo4-activating transcription factor 5 (ATF5)-mitochondrial unfolded protein response (mtUPR) pathway. Genetic overexpression of ATF5 or exposure to ethidium bromide significantly rescued monocyte/macrophage differentiation defects of Rictor-deficient myeloid progenitors. Therefore, Rictor is required for CMP/GMP proliferation and acts as an important switch to balance monocytic and granulocytic lineage commitment in bone marrow.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxu Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huawen Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingpu Shi
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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18
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Olson WJ, Derudder E. The miR-142 miRNAs: Shaping the naïve immune system. Immunol Lett 2023; 261:37-46. [PMID: 37459958 DOI: 10.1016/j.imlet.2023.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Immunity in a naïve organism is tightly controlled. Adequate proportions of the many immune cell subsets must be produced to mount efficient responses to eventual challenges. In addition, a functioning immune system is highly dynamic at steady state. Mature immune cells must be positioned properly and/or circulate to facilitate the detection of dangers. They must also be poised to promptly react to unusual encounters, while ignoring innocuous germs and self. Numerous regulatory mechanisms act at the molecular level to generate such an exquisite structure, including miRNA-mediated repression of protein synthesis. Notably, the miRNAs from the miR-142 locus are preferentially expressed in hematopoietic cells. Their importance is underscored by the deeply disturbed immune system seen upon inactivation of the locus in mice. In this review, we explore reported roles for the miR-142 miRNAs in the shaping of immunity in vertebrates, discussing in particular their contributions to the generation, migration and survival of hematopoietic cells.
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Affiliation(s)
- William J Olson
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Emmanuel Derudder
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria.
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19
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Sigvardsson M. Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia. Genes Dev 2023; 37:703-723. [PMID: 37673459 PMCID: PMC10546977 DOI: 10.1101/gad.349879.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
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20
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Zhao J, Perkins ML, Norstad M, Garcia HG. A bistable autoregulatory module in the developing embryo commits cells to binary expression fates. Curr Biol 2023; 33:2851-2864.e11. [PMID: 37453424 PMCID: PMC10428078 DOI: 10.1016/j.cub.2023.06.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/13/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Bistable autoactivation has been proposed as a mechanism for cells to adopt binary fates during embryonic development. However, it is unclear whether the autoactivating modules found within developmental gene regulatory networks are bistable, unless their parameters are quantitatively determined. Here, we combine in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of the fruit fly pair-rule gene fushi tarazu (ftz), which is regulated by two known enhancers: the early (non-autoregulating) element and the autoregulatory element. Live imaging of transcription and protein concentration in the blastoderm revealed that binary Ftz fates are achieved as Ftz expression rapidly transitions from being dictated by the early element to the autoregulatory element. Moreover, we discovered that Ftz concentration alone is insufficient to activate the autoregulatory element, and that this element only becomes responsive to Ftz at a prescribed developmental time. Based on these observations, we developed a dynamical systems model and quantitated its kinetic parameters directly from experimental measurements. Our model demonstrated that the ftz autoregulatory module is indeed bistable and that the early element transiently establishes the content of the binary cell fate decision to which the autoregulatory module then commits. Further in silico analysis revealed that the autoregulatory element locks the Ftz fate quickly, within 35 min of exposure to the transient signal of the early element. Overall, our work confirms the widely held hypothesis that autoregulation can establish developmental fates through bistability and, most importantly, provides a framework for the quantitative dissection of cellular decision-making.
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Affiliation(s)
- Jiaxi Zhao
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Matthew Norstad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hernan G Garcia
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA.
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21
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Benyoucef A, Haigh JJ, Brand M. Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies. Front Oncol 2023; 13:1151343. [PMID: 37441426 PMCID: PMC10333584 DOI: 10.3389/fonc.2023.1151343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The functionality and longevity of hematopoietic tissue is ensured by a tightly controlled balance between self-renewal, quiescence, and differentiation of hematopoietic stem cells (HSCs) into the many different blood lineages. Cell fate determination in HSCs is influenced by signals from extrinsic factors (e.g., cytokines, irradiation, reactive oxygen species, O2 concentration) that are translated and integrated by intrinsic factors such as Transcription Factors (TFs) to establish specific gene regulatory programs. TFs also play a central role in the establishment and/or maintenance of hematological malignancies, highlighting the need to understand their functions in multiple contexts. TFs bind to specific DNA sequences and interact with each other to form transcriptional complexes that directly or indirectly control the expression of multiple genes. Over the past decades, significant research efforts have unraveled molecular programs that control HSC function. This, in turn, led to the identification of more than 50 TF proteins that influence HSC fate. However, much remains to be learned about how these proteins interact to form molecular networks in combination with cofactors (e.g. epigenetics factors) and how they control differentiation, expansion, and maintenance of cellular identity. Understanding these processes is critical for future applications particularly in the field of cell therapy, as this would allow for manipulation of cell fate and induction of expansion, differentiation, or reprogramming of HSCs using specific cocktails of TFs. Here, we review recent findings that have unraveled the complexity of molecular networks controlled by TFs in HSCs and point towards possible applications to obtain functional HSCs ex vivo for therapeutic purposes including hematological malignancies. Furthermore, we discuss the challenges and prospects for the derivation and expansion of functional adult HSCs in the near future.
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Affiliation(s)
- Aissa Benyoucef
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Jody J. Haigh
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
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22
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Bernasek SM, Hur SSJ, Peláez-Restrepo N, Boisclair Lachance JF, Bakker R, Navarro HT, Sanchez-Luege N, Amaral LAN, Bagheri N, Rebay I, Carthew RW. Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila. Development 2023; 150:dev201467. [PMID: 36942737 PMCID: PMC10163347 DOI: 10.1242/dev.201467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
Cell state transitions are often triggered by large changes in the concentrations of transcription factors and therefore large differences in their stoichiometric ratios. Whether cells can elicit transitions using modest changes in the ratios of co-expressed factors is unclear. Here, we investigate how cells in the Drosophila eye resolve state transitions by quantifying the expression dynamics of the ETS transcription factors Pnt and Yan. Eye progenitor cells maintain a relatively constant ratio of Pnt/Yan protein, despite expressing both proteins with pulsatile dynamics. A rapid and sustained twofold increase in the Pnt/Yan ratio accompanies transitions to photoreceptor fates. Genetic perturbations that modestly disrupt the Pnt/Yan ratio produce fate transition defects consistent with the hypothesis that transitions are normally driven by a twofold shift in the ratio. A biophysical model based on cooperative Yan-DNA binding coupled with non-cooperative Pnt-DNA binding illustrates how twofold ratio changes could generate ultrasensitive changes in target gene transcription to drive fate transitions. Thus, coupling cell state transitions to the Pnt/Yan ratio sensitizes the system to modest fold-changes, conferring robustness and ultrasensitivity to the developmental program.
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Affiliation(s)
- Sebastian M. Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Suzy S. J. Hur
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Nicolás Peláez-Restrepo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute (HHMI), Hanna H. Gray Fellows Program
| | | | - Rachael Bakker
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | | | - Nicelio Sanchez-Luege
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Luís A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes, Northwestern University, Evanston, IL 60208, USA
| | - Ilaria Rebay
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Richard W. Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL 60611, USA
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23
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
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24
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In Vitro Human Haematopoietic Stem Cell Expansion and Differentiation. Cells 2023; 12:cells12060896. [PMID: 36980237 PMCID: PMC10046976 DOI: 10.3390/cells12060896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
The haematopoietic system plays an essential role in our health and survival. It is comprised of a range of mature blood and immune cell types, including oxygen-carrying erythrocytes, platelet-producing megakaryocytes and infection-fighting myeloid and lymphoid cells. Self-renewing multipotent haematopoietic stem cells (HSCs) and a range of intermediate haematopoietic progenitor cell types differentiate into these mature cell types to continuously support haematopoietic system homeostasis throughout life. This process of haematopoiesis is tightly regulated in vivo and primarily takes place in the bone marrow. Over the years, a range of in vitro culture systems have been developed, either to expand haematopoietic stem and progenitor cells or to differentiate them into the various haematopoietic lineages, based on the use of recombinant cytokines, co-culture systems and/or small molecules. These approaches provide important tractable models to study human haematopoiesis in vitro. Additionally, haematopoietic cell culture systems are being developed and clinical tested as a source of cell products for transplantation and transfusion medicine. This review discusses the in vitro culture protocols for human HSC expansion and differentiation, and summarises the key factors involved in these biological processes.
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25
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Tu X, Gomez HM, Kim RY, Brown AC, de Jong E, Galvao I, Faiz A, Bosco A, Horvat JC, Hansbro P, Donovan C. Airway and parenchyma transcriptomics in a house dust mite model of experimental asthma. Respir Res 2023; 24:32. [PMID: 36698141 PMCID: PMC9878882 DOI: 10.1186/s12931-022-02298-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023] Open
Abstract
Lung transcriptomics studies in asthma have provided valuable information in the whole lung context, however, deciphering the individual contributions of the airway and parenchyma in disease pathogenesis may expedite the development of novel targeted treatment strategies. In this study, we performed transcriptomics on the airway and parenchyma using a house dust mite (HDM)-induced model of experimental asthma that replicates key features of the human disease. HDM exposure increased the expression of 3,255 genes, of which 212 were uniquely increased in the airways, 856 uniquely increased in the parenchyma, and 2187 commonly increased in both compartments. Further interrogation of these genes using a combination of network and transcription factor enrichment analyses identified several transcription factors that regulate airway and/or parenchymal gene expression, including transcription factor EC (TFEC), transcription factor PU.1 (SPI1), H2.0-like homeobox (HLX), metal response element binding transcription factor-1 (MTF1) and E74-like factor 4 (ets domain transcription factor, ELF4) involved in controlling innate immune responses. We next assessed the effects of inhibiting lung SPI1 responses using commercially available DB1976 and DB2313 on key disease outcomes. We found that both compounds had no protective effects on airway inflammation, however DB2313 (8 mg/kg) decreased mucus secreting cell number, and both DB2313 (1 mg/kg) and DB1976 (2.5 mg/kg and 1 mg/kg) reduced small airway collagen deposition. Significantly, both compounds decreased airway hyperresponsiveness. This study demonstrates that SPI1 is important in HDM-induced experimental asthma and that its pharmacological inhibition reduces HDM-induced airway collagen deposition and hyperresponsiveness.
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Affiliation(s)
- Xiaofan Tu
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Henry M. Gomez
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Richard Y. Kim
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia ,grid.117476.20000 0004 1936 7611Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW Australia
| | - Alexandra C. Brown
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Emma de Jong
- Centre for Health Research, Telethon Kids Institute, The University of Western Australia, Nedlands, WA Australia
| | - Izabela Galvao
- grid.117476.20000 0004 1936 7611Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Alen Faiz
- grid.117476.20000 0004 1936 7611Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW Australia
| | - Anthony Bosco
- grid.134563.60000 0001 2168 186XAsthma and Airway Disease Research Center, University of Arizona, Arizona, USA
| | - Jay C. Horvat
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Philip Hansbro
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia ,grid.117476.20000 0004 1936 7611Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Chantal Donovan
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia ,grid.117476.20000 0004 1936 7611Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW Australia
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26
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The ENL YEATS epigenetic reader domain critically links MLL-ENL to leukemic stem cell frequency in t(11;19) Leukemia. Leukemia 2023; 37:190-201. [PMID: 36435883 DOI: 10.1038/s41375-022-01765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
MLL (KMT2a) translocations are found in ~10% of acute leukemia patients, giving rise to oncogenic MLL-fusion proteins. A common MLL translocation partner is ENL and associated with a poor prognosis in t(11;19) patients. ENL contains a highly conserved N-terminal YEATS domain that binds acetylated histones and interacts with the PAF1c, an epigenetic regulator protein complex essential for MLL-fusion leukemogenesis. Recently, wild-type ENL, and specifically the YEATS domain, was shown to be essential for leukemic cell growth. However, the inclusion and importance of the YEATS domain in MLL-ENL-mediated leukemogenesis remains unexplored. We found the YEATS domain is retained in 84.1% of MLL-ENL patients and crucial for MLL-ENL-mediated leukemogenesis in mouse models. Mechanistically, deletion of the YEATS domain impaired MLL-ENL fusion protein binding and decreased expression of pro-leukemic genes like Eya1 and Meis1. Point mutations that disrupt YEATS domain binding to acetylated histones decreased stem cell frequency and increased MLL-ENL-mediated leukemia latency. Therapeutically, YEATS containing MLL-ENL leukemic cells display increased sensitivity to the YEATS inhibitor SGC-iMLLT compared to control AML cells. Our results demonstrate that the YEATS domain is important for MLL-ENL fusion protein-mediated leukemogenesis and exposes an "Achilles heel" that may be therapeutically targeted for treating t(11;19) patients.
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27
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Lenaerts A, Kucinski I, Deboutte W, Derecka M, Cauchy P, Manke T, Göttgens B, Grosschedl R. EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine multipotent progenitors. J Exp Med 2022; 219:213432. [PMID: 36048017 PMCID: PMC9437269 DOI: 10.1084/jem.20212437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/23/2022] [Accepted: 08/03/2022] [Indexed: 11/04/2022] Open
Abstract
Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) generate all cells of the blood system. Despite their multipotency, MPPs display poorly understood lineage bias. Here, we examine whether lineage-specifying transcription factors, such as the B-lineage determinant EBF1, regulate lineage preference in early progenitors. We detect low-level EBF1 expression in myeloid-biased MPP3 and lymphoid-biased MPP4 cells, coinciding with expression of the myeloid determinant C/EBPα. Hematopoietic deletion of Ebf1 results in enhanced myelopoiesis and reduced HSC repopulation capacity. Ebf1-deficient MPP3 and MPP4 cells exhibit an augmented myeloid differentiation potential and a transcriptome with an enriched C/EBPα signature. Correspondingly, EBF1 binds the Cebpa enhancer, and the deficiency and overexpression of Ebf1 in MPP3 and MPP4 cells lead to an up- and downregulation of Cebpa expression, respectively. In addition, EBF1 primes the chromatin of B-lymphoid enhancers specifically in MPP3 cells. Thus, our study implicates EBF1 in regulating myeloid/lymphoid fate bias in MPPs by constraining C/EBPα-driven myelopoiesis and priming the B-lymphoid fate.
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Affiliation(s)
- Aurelie Lenaerts
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,International Max Planck Research School for Molecular and Cellular Biology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Marta Derecka
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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28
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Toh K, Saunders D, Verd B, Steventon B. Zebrafish neuromesodermal progenitors undergo a critical state transition in vivo. iScience 2022; 25:105216. [PMID: 36274939 PMCID: PMC9579027 DOI: 10.1016/j.isci.2022.105216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
The transition state model of cell differentiation proposes that a transient window of gene expression stochasticity precedes entry into a differentiated state. Here, we assess this theoretical model in zebrafish neuromesodermal progenitors (NMps) in vivo during late somitogenesis stages. We observed an increase in gene expression variability at the 24 somite stage (24ss) before their differentiation into spinal cord and paraxial mesoderm. Analysis of a published 18ss scRNA-seq dataset showed that the NMp population is noisier than its derivatives. By building in silico composite gene expression maps from image data, we assigned an 'NM index' to in silico NMps based on the expression of neural and mesodermal markers and demonstrated that cell population heterogeneity peaked at 24ss. Further examination revealed cells with gene expression profiles incongruent with their prospective fate. Taken together, our work supports the transition state model within an endogenous cell fate decision making event.
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Affiliation(s)
- Kane Toh
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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29
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Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19. Proc Natl Acad Sci U S A 2022; 119:e2120680119. [PMID: 35998224 PMCID: PMC9457492 DOI: 10.1073/pnas.2120680119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
SARS-CoV-2–infected patients often display characteristic changes in the production of immune mediators that trigger life-threatening courses of COVID-19. The underlying molecular mechanisms are not yet fully understood. Here, we used single-cell RNA sequencing to investigate the involvement of the emerging class of long regulatory RNA in COVID-19. Our data reveal that a previously unknown regulatory RNA in the nucleus of immune cells is altered after SARS-CoV-2 infection. The degradation of this RNA removes a natural brake on the production of critical immune mediators that can promote the development of severe COVID-19. We believe that therapeutic intervention in this nuclear RNA circuit could counteract the overproduction of disease-causing immune mediators and protect against severe COVID-19. The systemic immune response to viral infection is shaped by master transcription factors, such as NF-κB, STAT1, or PU.1. Although long noncoding RNAs (lncRNAs) have been suggested as important regulators of transcription factor activity, their contributions to the systemic immunopathologies observed during SARS-CoV-2 infection have remained unknown. Here, we employed a targeted single-cell RNA sequencing approach to reveal lncRNAs differentially expressed in blood leukocytes during severe COVID-19. Our results uncover the lncRNA PIRAT (PU.1-induced regulator of alarmin transcription) as a major PU.1 feedback-regulator in monocytes, governing the production of the alarmins S100A8/A9, key drivers of COVID-19 pathogenesis. Knockout and transgene expression, combined with chromatin-occupancy profiling, characterized PIRAT as a nuclear decoy RNA, keeping PU.1 from binding to alarmin promoters and promoting its binding to pseudogenes in naïve monocytes. NF-κB–dependent PIRAT down-regulation during COVID-19 consequently releases a transcriptional brake, fueling alarmin production. Alarmin expression is additionally enhanced by the up-regulation of the lncRNA LUCAT1, which promotes NF-κB–dependent gene expression at the expense of targets of the JAK-STAT pathway. Our results suggest a major role of nuclear noncoding RNA networks in systemic antiviral responses to SARS-CoV-2 in humans.
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30
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Yan M, Komatsu N, Muro R, Huynh NCN, Tomofuji Y, Okada Y, Suzuki HI, Takaba H, Kitazawa R, Kitazawa S, Pluemsakunthai W, Mitsui Y, Satoh T, Okamura T, Nitta T, Im SH, Kim CJ, Kollias G, Tanaka S, Okamoto K, Tsukasaki M, Takayanagi H. ETS1 governs pathological tissue-remodeling programs in disease-associated fibroblasts. Nat Immunol 2022; 23:1330-1341. [PMID: 35999392 DOI: 10.1038/s41590-022-01285-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/08/2022] [Indexed: 02/04/2023]
Abstract
Fibroblasts, the most abundant structural cells, exert homeostatic functions but also drive disease pathogenesis. Single-cell technologies have illuminated the shared characteristics of pathogenic fibroblasts in multiple diseases including autoimmune arthritis, cancer and inflammatory colitis. However, the molecular mechanisms underlying the disease-associated fibroblast phenotypes remain largely unclear. Here, we identify ETS1 as the key transcription factor governing the pathological tissue-remodeling programs in fibroblasts. In arthritis, ETS1 drives polarization toward tissue-destructive fibroblasts by orchestrating hitherto undescribed regulatory elements of the osteoclast differentiation factor receptor activator of nuclear factor-κB ligand (RANKL) as well as matrix metalloproteinases. Fibroblast-specific ETS1 deletion resulted in ameliorated bone and cartilage damage under arthritic conditions without affecting the inflammation level. Cross-tissue fibroblast single-cell data analyses and genetic loss-of-function experiments lent support to the notion that ETS1 defines the perturbation-specific fibroblasts shared among various disease settings. These findings provide a mechanistic basis for pathogenic fibroblast polarization and have important therapeutic implications.
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Affiliation(s)
- Minglu Yan
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Komatsu
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryunosuke Muro
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nam Cong-Nhat Huynh
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory of Oral-Maxillofacial Biology, Faculty of Odonto-Stomatology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University, Graduate School of Medicine, Osaka, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University, Graduate School of Medicine, Osaka, Japan.,Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Hiroshi I Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Hiroyuki Takaba
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital, Toon City, Japan
| | - Sohei Kitazawa
- Department of Molecular Pathology, Graduate School of Medicine, Ehime University, Toon City, Japan
| | - Warunee Pluemsakunthai
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuichi Mitsui
- Department of Immune Regulation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Innate Cell Therapy, Osaka, Japan
| | - Takashi Satoh
- Department of Immune Regulation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Innate Cell Therapy, Osaka, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takeshi Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), POSTECH Biotech Center, Pohang, Republic of Korea.,ImmunoBiome, Pohang, Republic of Korea.,Institute of Convergence Science, Yonsei University, Seoul, Republic of Korea
| | - Chan Johng Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), POSTECH Biotech Center, Pohang, Republic of Korea
| | - George Kollias
- Institute for Bioinnovation, Biomedical Sciences Research Center (BSRC) 'Alexander Fleming,' Vari, Attika, Greece.,Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Sakae Tanaka
- Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuo Okamoto
- Department of Osteoimmunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masayuki Tsukasaki
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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31
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Bain CC, Louwe PA, Steers NJ, Bravo‐Blas A, Hegarty LM, Pridans C, Milling SW, MacDonald AS, Rückerl D, Jenkins SJ. CD11c identifies microbiota and EGR2-dependent MHCII + serous cavity macrophages with sexually dimorphic fate in mice. Eur J Immunol 2022; 52:1243-1257. [PMID: 35568024 PMCID: PMC7613339 DOI: 10.1002/eji.202149756] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/11/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022]
Abstract
The murine serous cavities contain a rare and enigmatic population of short-lived F4/80lo MHCII+ macrophages but what regulates their development, survival, and fate is unclear. Here, we show that mature F4/80lo MHCII+ peritoneal macrophages arise after birth, but that this occurs largely independently of colonization by microbiota. Rather, microbiota specifically regulate development of a subpopulation of CD11c+ cells that express the immunoregulatory cytokine RELM-α, are reliant on the transcription factor EGR2, and develop independently of the growth factor CSF1. Furthermore, we demonstrate that intrinsic expression of RELM-α, a signature marker shared by CD11c+ and CD11c- F4/80lo MHCII+ cavity macrophages, regulates survival and differentiation of these cells in the peritoneal cavity in a sex-specific manner. Thus, we identify a previously unappreciated diversity in serous cavity F4/80lo MHCII+ macrophages that is regulated by microbiota, and describe a novel sex and site-specific function for RELM-α in regulating macrophage endurance that reveals the unique survival challenge presented to monocyte-derived macrophages by the female peritoneal environment.
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Affiliation(s)
- Calum C. Bain
- Queens Medical Research InstituteUniversity of Edinburgh Centre for Inflammation ResearchEdinburghUK
| | - Pieter A. Louwe
- Queens Medical Research InstituteUniversity of Edinburgh Centre for Inflammation ResearchEdinburghUK
| | | | - Alberto Bravo‐Blas
- Institute of Infection, Immunity, and InflammationUniversity of GlasgowGlasgowUK
| | - Lizi M. Hegarty
- Queens Medical Research InstituteUniversity of Edinburgh Centre for Inflammation ResearchEdinburghUK
| | - Clare Pridans
- Queens Medical Research InstituteUniversity of Edinburgh Centre for Inflammation ResearchEdinburghUK
- Simons Initiative for the Developing Brain, Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
| | - Simon W.F. Milling
- Institute of Infection, Immunity, and InflammationUniversity of GlasgowGlasgowUK
| | - Andrew S. MacDonald
- Lydia Becker Institute for Immunology and Infection, School of Biological Sciences, Faculty of Biology, Medicine & HealthUniversity of ManchesterManchesterUK
| | - Dominik Rückerl
- Lydia Becker Institute for Immunology and Infection, School of Biological Sciences, Faculty of Biology, Medicine & HealthUniversity of ManchesterManchesterUK
| | - Stephen J. Jenkins
- Queens Medical Research InstituteUniversity of Edinburgh Centre for Inflammation ResearchEdinburghUK
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32
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Kulkarni R. Early Growth Response Factor 1 in Aging Hematopoietic Stem Cells and Leukemia. Front Cell Dev Biol 2022; 10:925761. [PMID: 35923847 PMCID: PMC9340249 DOI: 10.3389/fcell.2022.925761] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is associated with various hematological disorders and a higher risk of myeloproliferative disorders. An aged hematopoietic system can be characterized by decreased immune function and increased myeloid cell production. Hematopoietic stem cells (HSCs) regulate the production of blood cells throughout life. The self-renewal and regenerative potential of HSCs determine the quality and quantity of the peripheral blood cells. External signals from the microenvironment under different conditions determine the fate of the HSCs to proliferate, self-renew, differentiate, or remain quiescent. HSCs respond impromptu to a vast array of extracellular signaling cascades such as cytokines, growth factors, or nutrients, which are crucial in the regulation of HSCs. Early growth response factor 1 (EGR1) is one of the key transcription factors controlling HSC proliferation and their localization in the bone marrow (BM) niche. Downregulation of Egr1 activates and recruits HSCs for their proliferation and differentiation to produce mature blood cells. Increased expression of Egr1 is implicated in immuno-aging of HSCs. However, dysregulation of Egr1 is associated with hematological malignancies such as acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and chronic myelogenous leukemia (CML). Here, we summarize the current understanding of the role of EGR1 in the regulation of HSC functionality and the manifestation of leukemia. We also discuss the alternative strategies to rejuvenate the aged HSCs by targeting EGR1 in different settings.
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33
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Capp JP, Thomas F. From developmental to atavistic bet-hedging: How cancer cells pervert the exploitation of random single-cell phenotypic fluctuations. Bioessays 2022; 44:e2200048. [PMID: 35839471 DOI: 10.1002/bies.202200048] [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: 02/28/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/08/2022]
Abstract
Stochastic gene expression plays a leading developmental role through its contribution to cell differentiation. It is also proposed to promote phenotypic diversification in malignant cells. However, it remains unclear if these two forms of cellular bet-hedging are identical or rather display distinct features. Here we argue that bet-hedging phenomena in cancer cells are more similar to those occurring in unicellular organisms than to those of normal metazoan cells. We further propose that the atavistic bet-hedging strategies in cancer originate from a hijacking of the normal developmental bet-hedging of metazoans. Finally, we discuss the constraints that may shape the atavistic bet-hedging strategies of cancer cells.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA / University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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34
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Alata Jimenez N, Strobl-Mazzulla PH. Folate Carrier Deficiency Drives Differential Methylation and Enhanced Cellular Potency in the Neural Plate Border. Front Cell Dev Biol 2022; 10:834625. [PMID: 35912103 PMCID: PMC9326018 DOI: 10.3389/fcell.2022.834625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
The neural plate border (NPB) of vertebrate embryos segregates from the neural and epidermal regions, and it is comprised of an intermingled group of multipotent progenitor cells. Folate is the precursor of S-adenosylmethionine, the main methyl donor for DNA methylation, and it is critical for embryonic development, including the specification of progenitors which reside in the NPB. Despite the fact that several intersecting signals involved in the specification and territorial restriction of NPB cells are known, the role of epigenetics, particularly DNA methylation, has been a matter of debate. Here, we examined the temporal and spatial distribution of the methyl source and analyzed the abundance of 5mC/5 hmC and their epigenetic writers throughout the segregation of the neural and NPB territories. Reduced representation bisulfite sequencing (RRBS) on Reduced Folate Carrier 1 (RFC1)-deficient embryos leads to the identification of differentially methylated regions (DMRs). In the RFC1-deficient embryos, we identified several DMRs in the Notch1 locus, and the spatiotemporal expression of Notch1 and its downstream target gene Bmp4 were expanded in the NPB. Cell fate analysis on folate deficient embryos revealed a significant increase in the number of cells coexpressing both neural (SOX2) and NPB (PAX7) markers, which may represent an enhancing effect in the cellular potential of those progenitors. Taken together, our findings propose a model where the RFC1 deficiency drives methylation changes in specific genomic regions that are correlated with a dysregulation of pathways involved in early development such as Notch1 and BMP4 signaling. These changes affect the potency of the progenitors residing in the juncture of the neural plate and NPB territories, thus driving them to a primed state.
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35
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Akula S, Lara S, Olsson AK, Hellman L. Quantitative Analysis of the Transcriptome of Two Commonly Used Human Monocytic Cell Lines—THP-1 and Mono Mac 6—Reveals Their Arrest during Early Monocyte/Neutrophil Differentiation. Int J Mol Sci 2022; 23:ijms23105818. [PMID: 35628628 PMCID: PMC9145822 DOI: 10.3390/ijms23105818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/10/2022] Open
Abstract
Cell lines of monocyte/macrophage origin are often used as model systems to study monocyte/macrophage biology. A relevant question is how similar these cell lines are to their in vivo counterparts? To address this issue, we performed a detailed analysis of the transcriptome of two commonly used human monocyte/macrophage cell lines, Mono Mac 6 and THP-1. Both of these cell lines originate from leukemic cells with myelo-monocytic characteristics. We found that both Mono Mac 6 and THP-1 represent cells of very immature origin. Their transcriptomes show more similarities to immature neutrophils than cells of the monocyte/macrophage lineage. They express significant levels of N-elastase, proteinase 3, cathepsin G, and azurocidin but very low levels of CD14, ficolin, and complement factor P. All major MHC class II genes are also expressed at low levels. They show high levels of lysozyme and low levels of one of the immunoglobulin Fc receptors, FCGRIIA, which is characteristic of both neutrophils and monocytes. THP-1, but not Mono Mac 6, also expresses the high-affinity receptor for IgG, FCGRIA. Both cell lines lack the expression of the connective tissue components fibronectin, proteoglycan 4, and syndecan 3, which are characteristics of tissue macrophages but are absent in blood monocytes, indicating that they originate from bone marrow precursors and not yolk sac-derived hematopoietic cells. Both of these cell lines seem, therefore, to represent cells arrested during early myelo-monocytic development, at a branch point between neutrophil and monocyte differentiation. Their very immature phenotype indicates that great care should be taken when using these cell lines as models for normal monocyte/macrophage biology.
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Affiliation(s)
- Srinivas Akula
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, P.O. Box 596, SE-75124 Uppsala, Sweden
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, SE-75007 Uppsala, Sweden
| | - Sandra Lara
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, P.O. Box 596, SE-75124 Uppsala, Sweden
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123 Uppsala, Sweden
| | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, P.O. Box 596, SE-75124 Uppsala, Sweden
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36
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Biswas K, Jolly MK, Ghosh A. Mean residence times of TF-TF and TF-miRNA toggle switches. J Biosci 2022. [DOI: 10.1007/s12038-022-00261-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Overbeeke C, Tak T, Koenderman L. The journey of neutropoiesis: how complex landscapes in bone marrow guide continuous neutrophil lineage determination. Blood 2022; 139:2285-2293. [PMID: 34986245 PMCID: PMC11022826 DOI: 10.1182/blood.2021012835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/31/2021] [Indexed: 12/16/2022] Open
Abstract
Neutrophils are the most abundant white blood cell, and they differentiate in homeostasis in the bone marrow from hematopoietic stem cells (HSCs) via multiple intermediate progenitor cells into mature cells that enter the circulation. Recent findings support a continuous model of differentiation in the bone marrow of heterogeneous HSCs and progenitor populations. Cell fate decisions at the levels of proliferation and differentiation are enforced through expression of lineage-determining transcription factors and their interactions, which are influenced by intrinsic (intracellular) and extrinsic (extracellular) mechanisms. Neutrophil homeostasis is subjected to positive-feedback loops, stemming from the gut microbiome, as well as negative-feedback loops resulting from the clearance of apoptotic neutrophils by mature macrophages. Finally, the cellular kinetics regarding the replenishing of the mature neutrophil pool is discussed in light of recent contradictory data.
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Affiliation(s)
- Celine Overbeeke
- Department of Respiratory Medicine and Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tamar Tak
- Department of Parasitology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Leo Koenderman
- Department of Respiratory Medicine and Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
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38
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Werle SD, Ikonomi N, Schwab JD, Kraus JM, Weidner FM, Lenhard Rudolph K, Pfister AS, Schuler R, Kühl M, Kestler HA. Identification of dynamic driver sets controlling phenotypical landscapes. Comput Struct Biotechnol J 2022; 20:1603-1617. [PMID: 35465155 PMCID: PMC9010550 DOI: 10.1016/j.csbj.2022.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/03/2022] Open
Abstract
Controlling phenotypical landscapes is of vital interest to modern biology. This task becomes highly demanding because cellular decisions involve complex networks engaging in crosstalk interactions. Previous work on control theory indicates that small sets of compounds can control single phenotypes. However, a dynamic approach is missing to determine the drivers of the whole network dynamics. By analyzing 35 biologically motivated Boolean networks, we developed a method to identify small sets of compounds sufficient to decide on the entire phenotypical landscape. These compounds do not strictly prefer highly related compounds and show a smaller impact on the stability of the attractor landscape. The dynamic driver sets include many intervention targets and cellular reprogramming drivers in human networks. Finally, by using a new comprehensive model of colorectal cancer, we provide a complete workflow on how to implement our approach to shift from in silico to in vitro guided experiments.
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39
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Abstract
The inflammation is an important biological response induced by various harmful stimuli, like viruses, bacterial infections, toxins, toxic compounds, tissue injury. During inflammation inflammatory cytokines and reactive oxygen species are produced. Inflammatory cytokines act on various receptors present on the plasma membrane of target cells. To initiate signaling cascade, and activate transcription factors, receptors should be internalized and enter the early endosomes, where the members of the signaling cascade can meet. The further cytoplasmic fate of the receptor plays crucial role in the progression and the course of inflammation. Usually acute inflammation removes injurious stimuli and helps to regain the normal healthy status of the organism. In contrast to this the uncontrolled chronic inflammation—stimulating other than immune cells, inducing transdifferentiation—can provide base of various serious diseases. This paper draws the attention of the long-lasting consequence of chronic inflammation, pointing out that one of the most important step in medication is to identify in time the factors initiating and maintaining inflammation.
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Affiliation(s)
- Anna L Kiss
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
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40
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Tsuda S, Pipkin ME. Transcriptional Control of Cell Fate Determination in Antigen-Experienced CD8 T Cells. Cold Spring Harb Perspect Biol 2022; 14:a037945. [PMID: 34127445 PMCID: PMC8805646 DOI: 10.1101/cshperspect.a037945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Robust immunity to intracellular infections is mediated by antigen-specific naive CD8 T cells that become activated and differentiate into phenotypically and functionally diverse subsets of effector cells, some of which terminally differentiate and others that give rise to memory cells that provide long-lived protection. This developmental system is an outstanding model with which to elucidate how regulation of chromatin structure and transcriptional control establish gene expression programs that govern cell fate determination, insights from which are likely to be useful for informing the design of immunotherapeutic approaches to engineer durable immunity to infections and tumors. A unifying framework that describes how naive CD8 T cells develop into memory cells is still outstanding. We propose a model that incorporates a common early linear path followed by divergent paths that slowly lose capacity to interconvert and discuss classical and contemporary observations that support these notions, focusing on insights from transcriptional control and chromatin regulation.
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Affiliation(s)
- Shanel Tsuda
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
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41
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Zhu R, Del Rio-Salgado JM, Garcia-Ojalvo J, Elowitz MB. Synthetic multistability in mammalian cells. Science 2022; 375:eabg9765. [PMID: 35050677 DOI: 10.1126/science.abg9765] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In multicellular organisms, gene regulatory circuits generate thousands of molecularly distinct, mitotically heritable states through the property of multistability. Designing synthetic multistable circuits would provide insight into natural cell fate control circuit architectures and would allow engineering of multicellular programs that require interactions among distinct cell types. We created MultiFate, a naturally inspired, synthetic circuit that supports long-term, controllable, and expandable multistability in mammalian cells. MultiFate uses engineered zinc finger transcription factors that transcriptionally self-activate as homodimers and mutually inhibit one another through heterodimerization. Using a model-based design, we engineered MultiFate circuits that generate as many as seven states, each stable for at least 18 days. MultiFate permits controlled state switching and modulation of state stability through external inputs and can be expanded with additional transcription factors. These results provide a foundation for engineering multicellular behaviors in mammalian cells.
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Affiliation(s)
- Ronghui Zhu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jesus M Del Rio-Salgado
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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42
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Ramos RN, Couto SCF, Oliveira TGM, Klinger P, Braga TT, Rego EM, Barbuto JAM, Rocha V. Myeloid Immune Cells CARrying a New Weapon Against Cancer. Front Cell Dev Biol 2022; 9:784421. [PMID: 34977027 PMCID: PMC8716000 DOI: 10.3389/fcell.2021.784421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/22/2021] [Indexed: 12/20/2022] Open
Abstract
Chimeric antigen receptor (CAR) engineering for T cells and natural killer cells (NK) are now under clinical evaluation for the treatment of hematologic cancers. Although encouraging clinical results have been reported for hematologic diseases, pre-clinical studies in solid tumors have failed to prove the same effectiveness. Thus, there is a growing interest of the scientific community to find other immune cell candidate to express CAR for the treatment of solid tumors and other diseases. Mononuclear phagocytes may be the most adapted group of cells with potential to overcome the dense barrier imposed by solid tumors. In addition, intrinsic features of these cells, such as migration, phagocytic capability, release of soluble factors and adaptive immunity activation, could be further explored along with gene therapy approaches. Here, we discuss the elements that constitute the tumor microenvironment, the features and advantages of these cell subtypes and the latest studies using CAR-myeloid immune cells in solid tumor models.
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Affiliation(s)
- Rodrigo Nalio Ramos
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil
| | - Samuel Campanelli Freitas Couto
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
| | - Theo Gremen M Oliveira
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
| | - Paulo Klinger
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | - Tarcio Teodoro Braga
- Department of Pathology, Federal University of Parana, Curitiba, Brazil.,Graduate Program in Biosciences and Biotechnology, Instituto Carlos Chagas, Fiocruz-Parana, Curitiba, Brazil
| | - Eduardo Magalhães Rego
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil
| | - José Alexandre M Barbuto
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Departamento de Imunologia, Instituto de CienciasBiomedicas, Universidade de Sao Paulo, São Paulo, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil.,Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil.,Churchill Hospital, Department of Hematology, University of Oxford, Oxford, United Kingdom
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43
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Ahmed N, Etzrodt M, Dettinger P, Kull T, Loeffler D, Hoppe PS, Chavez JS, Zhang Y, Camargo Ortega G, Hilsenbeck O, Nakajima H, Pietras EM, Schroeder T. Blood stem cell PU.1 upregulation is a consequence of differentiation without fast autoregulation. J Exp Med 2022; 219:e20202490. [PMID: 34817548 PMCID: PMC8624737 DOI: 10.1084/jem.20202490] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 11/12/2022] Open
Abstract
Transcription factors (TFs) regulate cell fates, and their expression must be tightly regulated. Autoregulation is assumed to regulate many TFs' own expression to control cell fates. Here, we manipulate and quantify the (auto)regulation of PU.1, a TF controlling hematopoietic stem and progenitor cells (HSPCs), and correlate it to their future fates. We generate transgenic mice allowing both inducible activation of PU.1 and noninvasive quantification of endogenous PU.1 protein expression. The quantified HSPC PU.1 dynamics show that PU.1 up-regulation occurs as a consequence of hematopoietic differentiation independently of direct fast autoregulation. In contrast, inflammatory signaling induces fast PU.1 up-regulation, which does not require PU.1 expression or its binding to its own autoregulatory enhancer. However, the increased PU.1 levels induced by inflammatory signaling cannot be sustained via autoregulation after removal of the signaling stimulus. We conclude that PU.1 overexpression induces HSC differentiation before PU.1 up-regulation, only later generating cell types with intrinsically higher PU.1.
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Affiliation(s)
- Nouraiz Ahmed
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Martin Etzrodt
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Philip Dettinger
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Tobias Kull
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Philipp S. Hoppe
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - James S. Chavez
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Yang Zhang
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Germán Camargo Ortega
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Oliver Hilsenbeck
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eric M. Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Timm Schroeder
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
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44
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Handzlik JE. Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors. PLoS Comput Biol 2022; 18:e1009779. [PMID: 35030198 PMCID: PMC8794271 DOI: 10.1371/journal.pcbi.1009779] [Citation(s) in RCA: 3] [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: 06/10/2021] [Revised: 01/27/2022] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Cellular differentiation during hematopoiesis is guided by gene regulatory networks (GRNs) comprising transcription factors (TFs) and the effectors of cytokine signaling. Based largely on analyses conducted at steady state, these GRNs are thought to be organized as a hierarchy of bistable switches, with antagonism between Gata1 and PU.1 driving red- and white-blood cell differentiation. Here, we utilize transient gene expression patterns to infer the genetic architecture—the type and strength of regulatory interconnections—and dynamics of a twelve-gene GRN including key TFs and cytokine receptors. We trained gene circuits, dynamical models that learn genetic architecture, on high temporal-resolution gene-expression data from the differentiation of an inducible cell line into erythrocytes and neutrophils. The model is able to predict the consequences of gene knockout, knockdown, and overexpression experiments and the inferred interconnections are largely consistent with prior empirical evidence. The inferred genetic architecture is densely interconnected rather than hierarchical, featuring extensive cross-antagonism between genes from alternative lineages and positive feedback from cytokine receptors. The analysis of the dynamics of gene regulation in the model reveals that PU.1 is one of the last genes to be upregulated in neutrophil conditions and that the upregulation of PU.1 and other neutrophil genes is driven by Cebpa and Gfi1 instead. This model inference is confirmed in an independent single-cell RNA-Seq dataset from mouse bone marrow in which Cebpa and Gfi1 expression precedes the neutrophil-specific upregulation of PU.1 during differentiation. These results demonstrate that full PU.1 upregulation during neutrophil development involves regulatory influences extrinsic to the Gata1-PU.1 bistable switch. Furthermore, although there is extensive cross-antagonism between erythroid and neutrophil genes, it does not have a hierarchical structure. More generally, we show that the combination of high-resolution time series data and data-driven dynamical modeling can uncover the dynamics and causality of developmental events that might otherwise be obscured. The supply of blood cells is replenished by the maturation of hematopoietic progenitor cells into different cell types. Which cell type a progenitor cell develops into is determined by a complex network of genes whose protein products directly or indirectly regulate each others’ expression and that of downstream genes characteristic of the cell type. We inferred the nature and causality of the regulatory connections in a 12-gene network known to affect the decision between erythrocyte and neutrophil cell fates using a predictive machine-learning approach. Our analysis showed that the overall architecture of the network is densely interconnected and not hierarchical. Furthermore, the model inferred that PU.1, considered a master regulator of all white-blood cell lineages, is upregulated during neutrophil development by two other proteins, Cebpa and Gfi1. We validated this prediction by showing that Cebpa and Gfi1 expression precedes that of PU.1 in single-cell gene expression data from mouse bone marrow. These results revise the architecture of the gene network and the causality of regulatory events guiding hematopoiesis. The results also show that combining machine learning approaches with time course data can help resolve causality during development.
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Affiliation(s)
- Joanna E Handzlik
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America
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45
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Glauche I, Marr C. Mechanistic models of blood cell fate decisions in the era of single-cell data. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:None. [PMID: 34950807 PMCID: PMC8660645 DOI: 10.1016/j.coisb.2021.100355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Billions of functionally distinct blood cells emerge from a pool of hematopoietic stem cells in our bodies every day. This progressive differentiation process is hierarchically structured and remarkably robust. We provide an introductory review to mathematical approaches addressing the functional aspects of how lineage choice is potentially implemented on a molecular level. Emerging from studies on the mutual repression of key transcription factors, we illustrate how those simple concepts have been challenged in recent years and subsequently extended. Especially, the analysis of omics data on the single-cell level with computational tools provides descriptive insights on a yet unknown level, while their embedding into a consistent mechanistic and mathematical framework is still incomplete.
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Affiliation(s)
- Ingmar Glauche
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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46
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Guilberteau J, Pouchol C, Pouradier Duteil N. Monostability and bistability of biological switches. J Math Biol 2021; 83:65. [PMID: 34800197 DOI: 10.1007/s00285-021-01687-y] [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: 04/02/2021] [Revised: 09/10/2021] [Accepted: 10/21/2021] [Indexed: 12/01/2022]
Abstract
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological trait'). In this paper, we focus on simple ODE systems modeling two molecules which each negatively (or positively) regulate the other. It is well-known that such models may lead to monostability or multistability, depending on the selected parameters. However, extensive numerical simulations have led systems biologists to conjecture that in the vast majority of cases, there cannot be more than two stable points. Our main result is a proof of this conjecture. More specifically, we provide a criterion ensuring at most bistability, which is indeed satisfied by most commonly used functions. This includes Hill functions, but also a wide family of convex and sigmoid functions. We also determine which parameters lead to monostability, and which lead to bistability, by developing a more general framework encompassing all our results.
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Affiliation(s)
- Jules Guilberteau
- Laboratoire Jacques-Louis Lions (LJLL), CNRS, Inria, Sorbonne Université and Université de Paris, 75005, Paris, France.
| | - Camille Pouchol
- FP2M, CNRS FR 2036, MAP5 UMR 8145, Université de Paris, 75006, Paris, France
| | - Nastassia Pouradier Duteil
- Laboratoire Jacques-Louis Lions (LJLL), CNRS, Inria, Sorbonne Université and Université de Paris, 75005, Paris, France
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47
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Dey A, Barik D. Emergent Bistable Switches from the Incoherent Feed-Forward Signaling of a Positive Feedback Loop. ACS Synth Biol 2021; 10:3117-3128. [PMID: 34694110 DOI: 10.1021/acssynbio.1c00373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bistability is intrinsically connected to various decision making processes in living systems. The operating principles of a bistable switch, generated from a positive feedback loop, are well understood both in natural and synthetic settings. However, the fate of dynamic modularity of a positive feedback loop is unknown when it is connected to another dynamically modular signaling motif. In order to address this, here we investigate feed-forward signaling of a positive feedback loop to determine the fate of a bistable switch under such signaling. Using the potential energy based high-throughput bifurcation analysis method, we uncover that in addition to the conventional bistability the hybrid motifs generate various emergent bistable switches, namely mushroom and isola switches, which are not produced by the individual motifs. Using random parameter sampling, network perturbation, and phase plane analysis, we establish the design principles of such emergent behaviors. Incoherent feed-forward signaling of a positive feedback loop with distinct regulatory thresholds of the two arms of the feed-forward loop are the key requirements for such emergent behaviors. Our calculations show that the specific types of atypical bistable responses depend on the logic gate configuration of the signals. However, the emergent bistable behaviors of the hybrid networks do not depend on the nature of the positive feedback loop.
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Affiliation(s)
- Anupam Dey
- School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, 500046, Telangana, India
| | - Debashis Barik
- School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, 500046, Telangana, India
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48
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McCowan J, Fercoq F, Kirkwood PM, T’Jonck W, Hegarty LM, Mawer CM, Cunningham R, Mirchandani AS, Hoy A, Humphries DC, Jones GR, Hansen CG, Hirani N, Jenkins SJ, Henri S, Malissen B, Walmsley SR, Dockrell DH, Saunders PTK, Carlin LM, Bain CC. The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair. Sci Immunol 2021; 6:eabj2132. [PMID: 34797692 PMCID: PMC7612216 DOI: 10.1126/sciimmunol.abj2132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alveolar macrophages are the most abundant macrophages in the healthy lung where they play key roles in homeostasis and immune surveillance against airborne pathogens. Tissue-specific differentiation and survival of alveolar macrophages rely on niche-derived factors, such as granulocyte-macrophage colony-stimulating factor (GM-CSF) and transforming growth factor–β (TGF-β). However, the nature of the downstream molecular pathways that regulate the identity and function of alveolar macrophages and their response to injury remain poorly understood. Here, we identify that the transcription factor EGR2 is an evolutionarily conserved feature of lung alveolar macrophages and show that cell-intrinsic EGR2 is indispensable for the tissue-specific identity of alveolar macrophages. Mechanistically, we show that EGR2 is driven by TGF-β and GM-CSF in a PPAR-γ–dependent manner to control alveolar macrophage differentiation. Functionally, EGR2 was dispensable for the regulation of lipids in the airways but crucial for the effective handling of the respiratory pathogen Streptococcus pneumoniae. Last, we show that EGR2 is required for repopulation of the alveolar niche after sterile, bleomycin-induced lung injury and demonstrate that EGR2-dependent, monocyte-derived alveolar macrophages are vital for effective tissue repair after injury. Collectively, we demonstrate that EGR2 is an indispensable component of the transcriptional network controlling the identity and function of alveolar macrophages in health and disease.
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Affiliation(s)
- Jack McCowan
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | | | - Phoebe M. Kirkwood
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Wouter T’Jonck
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Lizi M. Hegarty
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Connar M. Mawer
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
| | - Richard Cunningham
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Ananda S. Mirchandani
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Anna Hoy
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
| | - Duncan C. Humphries
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Gareth-Rhys Jones
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Carsten G. Hansen
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Nik Hirani
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Stephen J. Jenkins
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Sarah R. Walmsley
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - David H. Dockrell
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Philippa T. K. Saunders
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Leo M. Carlin
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Calum C. Bain
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
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49
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Kelsh RN, Camargo Sosa K, Farjami S, Makeev V, Dawes JHP, Rocco A. Cyclical fate restriction: a new view of neural crest cell fate specification. Development 2021; 148:273451. [PMID: 35020872 DOI: 10.1242/dev.176057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neural crest cells are crucial in development, not least because of their remarkable multipotency. Early findings stimulated two hypotheses for how fate specification and commitment from fully multipotent neural crest cells might occur, progressive fate restriction (PFR) and direct fate restriction, differing in whether partially restricted intermediates were involved. Initially hotly debated, they remain unreconciled, although PFR has become favoured. However, testing of a PFR hypothesis of zebrafish pigment cell development refutes this view. We propose a novel 'cyclical fate restriction' hypothesis, based upon a more dynamic view of transcriptional states, reconciling the experimental evidence underpinning the traditional hypotheses.
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Affiliation(s)
- Robert N Kelsh
- Department of Biology & Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Karen Camargo Sosa
- Department of Biology & Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Saeed Farjami
- Department of Microbial Sciences, FHMS, University of Surrey, Guildford, GU2 7XH, UK
| | - Vsevolod Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Jonathan H P Dawes
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Andrea Rocco
- Department of Microbial Sciences, FHMS, University of Surrey, Guildford, GU2 7XH, UK.,Department of Physics, FEPS, University of Surrey, Guildford, GU2 7XH, UK
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50
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Yu L, Myers G, Ku CJ, Schneider E, Wang Y, Singh SA, Jearawiriyapaisarn N, White A, Moriguchi T, Khoriaty R, Yamamoto M, Rosenfeld MG, Pedron J, Bushweller JH, Lim KC, Engel JD. An erythroid-to-myeloid cell fate conversion is elicited by LSD1 inactivation. Blood 2021; 138:1691-1704. [PMID: 34324630 PMCID: PMC8569417 DOI: 10.1182/blood.2021011682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/18/2021] [Indexed: 01/28/2023] Open
Abstract
Histone H3 lysine 4 methylation (H3K4Me) is most often associated with chromatin activation, and removing H3K4 methyl groups has been shown to be coincident with gene repression. H3K4Me demethylase KDM1a/LSD1 is a therapeutic target for multiple diseases, including for the potential treatment of β-globinopathies (sickle cell disease and β-thalassemia), because it is a component of γ-globin repressor complexes, and LSD1 inactivation leads to robust induction of the fetal globin genes. The effects of LSD1 inhibition in definitive erythropoiesis are not well characterized, so we examined the consequences of conditional inactivation of Lsd1 in adult red blood cells using a new Gata1creERT2 bacterial artificial chromosome transgene. Erythroid-specific loss of Lsd1 activity in mice led to a block in erythroid progenitor differentiation and to the expansion of granulocyte-monocyte progenitor-like cells, converting hematopoietic differentiation potential from an erythroid fate to a myeloid fate. The analogous phenotype was also observed in human hematopoietic stem and progenitor cells, coincident with the induction of myeloid transcription factors (eg, PU.1 and CEBPα). Finally, blocking the activity of the transcription factor PU.1 or RUNX1 at the same time as LSD1 inhibition rescued myeloid lineage conversion to an erythroid phenotype. These data show that LSD1 promotes erythropoiesis by repressing myeloid cell fate in adult erythroid progenitors and that inhibition of the myeloid-differentiation pathway reverses the lineage switch induced by LSD1 inactivation.
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Affiliation(s)
- Lei Yu
- Department of Cell and Developmental Biology
| | - Greggory Myers
- Department of Cell and Developmental Biology
- Department of Internal Medicine, and
| | - Chia-Jui Ku
- Department of Cell and Developmental Biology
| | | | - Yu Wang
- Department of Cell and Developmental Biology
| | - Sharon A Singh
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI
| | - Natee Jearawiriyapaisarn
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Andrew White
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, MI
| | - Takashi Moriguchi
- Division of Medical Chemistry, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Rami Khoriaty
- Department of Cell and Developmental Biology
- Department of Internal Medicine, and
| | - Masayuki Yamamoto
- Department of Cell and Developmental Biology
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA; and
| | - Julien Pedron
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville , VA
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville , VA
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