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Liu K, Meng X, Liu Z, Tang M, Lv Z, Huang X, Jin H, Han X, Liu X, Pu W, Zhu H, Zhou B. Tracing the origin of alveolar stem cells in lung repair and regeneration. Cell 2024; 187:2428-2445.e20. [PMID: 38579712 DOI: 10.1016/j.cell.2024.03.010] [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: 09/15/2023] [Revised: 01/07/2024] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
Alveolar type 2 (AT2) cells are stem cells of the alveolar epithelia. Previous genetic lineage tracing studies reported multiple cellular origins for AT2 cells after injury. However, conventional lineage tracing based on Cre-loxP has the limitation of non-specific labeling. Here, we introduced a dual recombinase-mediated intersectional genetic lineage tracing approach, enabling precise investigation of AT2 cellular origins during lung homeostasis, injury, and repair. We found AT1 cells, being terminally differentiated, did not contribute to AT2 cells after lung injury and repair. Distinctive yet simultaneous labeling of club cells, bronchioalveolar stem cells (BASCs), and existing AT2 cells revealed the exact contribution of each to AT2 cells post-injury. Mechanistically, Notch signaling inhibition promotes BASCs but impairs club cells' ability to generate AT2 cells during lung repair. This intersectional genetic lineage tracing strategy with enhanced precision allowed us to elucidate the physiological role of various epithelial cell types in alveolar regeneration following injury.
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Affiliation(s)
- Kuo Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinfeng Meng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zixin Liu
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Muxue Tang
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zan Lv
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiuzhen Huang
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hengwei Jin
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ximeng Han
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiuxiu Liu
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenjuan Pu
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Zhu
- New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Zhou
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; New Cornerstone Investigator Institute, Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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2
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Deng S, Gong H, Zhang D, Zhang M, He X. A statistical method for quantifying progenitor cells reveals incipient cell fate commitments. Nat Methods 2024; 21:597-608. [PMID: 38379073 DOI: 10.1038/s41592-024-02189-7] [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: 03/04/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024]
Abstract
Quantifying the number of progenitor cells that found an organ, tissue or cell population is of fundamental importance for understanding the development and homeostasis of a multicellular organism. Previous efforts rely on marker genes that are specifically expressed in progenitors. This strategy is, however, often hindered by the lack of ideal markers. Here we propose a general statistical method to quantify the progenitors of any tissues or cell populations in an organism, even in the absence of progenitor-specific markers, by exploring the cell phylogenetic tree that records the cell division history during development. The method, termed targeting coalescent analysis (TarCA), computes the probability that two randomly sampled cells of a tissue coalesce within the tissue-specific monophyletic clades. The inverse of this probability then serves as a measure of the progenitor number of the tissue. Both mathematic modeling and computer simulations demonstrated the high accuracy of TarCA, which was then validated using real data from nematode, fruit fly and mouse, all with related cell phylogenetic trees. We further showed that TarCA can be used to identify lineage-specific upregulated genes during embryogenesis, revealing incipient cell fate commitments in mouse embryos.
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Affiliation(s)
- Shanjun Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Han Gong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Di Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mengdong Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xionglei He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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3
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Hall IF, Kishta F, Xu Y, Baker AH, Kovacic JC. Endothelial to mesenchymal transition: at the axis of cardiovascular health and disease. Cardiovasc Res 2024; 120:223-236. [PMID: 38385523 PMCID: PMC10939465 DOI: 10.1093/cvr/cvae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/01/2023] [Accepted: 08/25/2023] [Indexed: 02/23/2024] Open
Abstract
Endothelial cells (ECs) line the luminal surface of blood vessels and play a major role in vascular (patho)-physiology by acting as a barrier, sensing circulating factors and intrinsic/extrinsic signals. ECs have the capacity to undergo endothelial-to-mesenchymal transition (EndMT), a complex differentiation process with key roles both during embryonic development and in adulthood. EndMT can contribute to EC activation and dysfunctional alterations associated with maladaptive tissue responses in human disease. During EndMT, ECs progressively undergo changes leading to expression of mesenchymal markers while repressing EC lineage-specific traits. This phenotypic and functional switch is considered to largely exist in a continuum, being characterized by a gradation of transitioning stages. In this report, we discuss process plasticity and potential reversibility and the hypothesis that different EndMT-derived cell populations may play a different role in disease progression or resolution. In addition, we review advancements in the EndMT field, current technical challenges, as well as therapeutic options and opportunities in the context of cardiovascular biology.
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Affiliation(s)
- Ignacio Fernando Hall
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Franceska Kishta
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Yang Xu
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht 6229ER, The Netherlands
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010, Australia
- St. Vincent’s Clinical School and University of New South Wales, 390 Victoria St, Darlinghurst, NSW 2010, Australia
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4
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Zhong Y, Tan X, Wang X, Jiang J, Song K, Chen H, Zhang H, Wang Z, Zhang L, Guo C, Liang H, Yu W. Generation of Vgll4-DreER transgenic mouse for visualizing and manipulating VGLL4-expressing cells in vivo. J Biochem Mol Toxicol 2023; 37:e23435. [PMID: 37352117 DOI: 10.1002/jbt.23435] [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: 11/15/2022] [Revised: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
Vestigial like family member 4 (VGLL4), a member of the Hippo pathway, is a transcriptional cofactor involved in many biological processes, such as tumor progression, postnatal heart growth, and muscle regeneration. However, the VGLL4 expression pattern in vivo remains unclear. To detect and trace Vgll4-expressing cells and their progeny, we generated and characterized a new tamoxifen-inducible Dre knock-in mouse line, Vgll4-DreER. This mouse line expressed DreER (Dre recombinase fused to the estrogen receptor) under the control of the endogenous Vgll4 promoter. After crossing the Vgll4-DreER mouse line with the Dre-responsive reporter H11-rRFP, Dre-mediated recombination in the tissue was monitored on the basis of red fluorescent protein (RFP) signals, which indicated the distribution of VGLL4-positive cells in vivo. Our data revealed that VGLL4 is widely expressed in various cell types at embryonic and neonatal stages. After comparison with our previously reported Vgll4-GFP mouse, we found that the RFP signal profile was wider than the green fluorescent protein (GFP) pattern, indicating that Vgll4-DreER is more sensitive for labeling VGLL4-expressing cells. We next used a dual-recombination system to simultaneously label VGLL4- and keratin 5 (KRT5)-positive cell populations, and no crosstalk was observed in the Krt5-CreER;Vgll4-DreER;R26-rGlR mice. Taken together, the Vgll4-DreER mouse line is a valuable new tool for examining the precise VGLL4 expression profile and conditional manipulating of VGLL4-expressing cells and their progeny.
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Affiliation(s)
- Yazhu Zhong
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Xixi Tan
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Xiaodong Wang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Jun Jiang
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Kai Song
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Haiyuan Chen
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Hao Zhang
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Zuoyun Wang
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Zhang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Chunming Guo
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Hongfeng Liang
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Wei Yu
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
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5
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Lotto J, Cullum R, Drissler S, Arostegui M, Garside VC, Fuglerud BM, Clement-Ranney M, Thakur A, Underhill TM, Hoodless PA. Cell diversity and plasticity during atrioventricular heart valve EMTs. Nat Commun 2023; 14:5567. [PMID: 37689753 PMCID: PMC10492828 DOI: 10.1038/s41467-023-41279-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
Epithelial-to-mesenchymal transitions (EMTs) of both endocardium and epicardium guide atrioventricular heart valve formation, but the cellular complexity and small scale of this tissue have restricted analyses. To circumvent these issues, we analyzed over 50,000 murine single-cell transcriptomes from embryonic day (E)7.75 hearts to E12.5 atrioventricular canals. We delineate mesenchymal and endocardial bifurcation during endocardial EMT, identify a distinct, transdifferentiating epicardial population during epicardial EMT, and reveal the activation of epithelial-mesenchymal plasticity during both processes. In Sox9-deficient valves, we observe increased epithelial-mesenchymal plasticity, indicating a role for SOX9 in promoting endothelial and mesenchymal cell fate decisions. Lastly, we deconvolve cell interactions guiding the initiation and progression of cardiac valve EMTs. Overall, these data reveal mechanisms of emergence of mesenchyme from endocardium or epicardium at single-cell resolution and will serve as an atlas of EMT initiation and progression with broad implications in regenerative medicine and cancer biology.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | | | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Martin Arostegui
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Victoria C Garside
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - T Michael Underhill
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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6
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Lotto J, Stephan TL, Hoodless PA. Fetal liver development and implications for liver disease pathogenesis. Nat Rev Gastroenterol Hepatol 2023; 20:561-581. [PMID: 37208503 DOI: 10.1038/s41575-023-00775-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/21/2023]
Abstract
The metabolic, digestive and homeostatic roles of the liver are dependent on proper crosstalk and organization of hepatic cell lineages. These hepatic cell lineages are derived from their respective progenitors early in organogenesis in a spatiotemporally controlled manner, contributing to the liver's specialized and diverse microarchitecture. Advances in genomics, lineage tracing and microscopy have led to seminal discoveries in the past decade that have elucidated liver cell lineage hierarchies. In particular, single-cell genomics has enabled researchers to explore diversity within the liver, especially early in development when the application of bulk genomics was previously constrained due to the organ's small scale, resulting in low cell numbers. These discoveries have substantially advanced our understanding of cell differentiation trajectories, cell fate decisions, cell lineage plasticity and the signalling microenvironment underlying the formation of the liver. In addition, they have provided insights into the pathogenesis of liver disease and cancer, in which developmental processes participate in disease emergence and regeneration. Future work will focus on the translation of this knowledge to optimize in vitro models of liver development and fine-tune regenerative medicine strategies to treat liver disease. In this Review, we discuss the emergence of hepatic parenchymal and non-parenchymal cells, advances that have been made in in vitro modelling of liver development and draw parallels between developmental and pathological processes.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
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7
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Liu K, Jin H, Zhang S, Tang M, Meng X, Li Y, Pu W, Lui KO, Zhou B. Intercellular genetic tracing of cardiac endothelium in the developing heart. Dev Cell 2023; 58:1502-1512.e3. [PMID: 37348503 DOI: 10.1016/j.devcel.2023.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/23/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023]
Abstract
Cardiac resident macrophages play vital roles in heart development, homeostasis, repair, and regeneration. Recent studies documented the hematopoietic potential of cardiac endothelium that supports the generation of cardiac macrophages and peripheral blood cells in mice. However, the conclusion was not strongly supported by previous genetic tracing studies, given the non-specific nature of conventional Cre-loxP tracing tools. Here, we develop an intercellular genetic labeling system that can permanently trace heart-specific endothelial cells based on cell-cell interaction in mice. Results from cell-cell contact-mediated genetic fate mapping demonstrate that cardiac endothelial cells do not exhibit hemogenic potential and do not contribute to cardiac macrophages or other circulating blood cells. This Matters Arising paper is in response to Shigeta et al. (2019), published in Developmental Cell. See also the response by Liu and Nakano (2023), published in this issue.
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Affiliation(s)
- Kuo Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Hengwei Jin
- New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shaohua Zhang
- New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Muxue Tang
- New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinfeng Meng
- New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Li
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjuan Pu
- New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Bin Zhou
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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8
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Liu X, Weng W, He L, Zhou B. Genetic recording of in vivo cell proliferation by ProTracer. Nat Protoc 2023:10.1038/s41596-023-00833-8. [PMID: 37268780 DOI: 10.1038/s41596-023-00833-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/17/2023] [Indexed: 06/04/2023]
Abstract
The ability to experimentally measure cell proliferation is the basis for understanding the sources of cells that drive organ development, tissue regeneration and repair. Recently, we generated a genetic approach to detect cell proliferation: we used genetic lineage-tracing technologies to achieve seamless recording of in vivo cell proliferation in a tissue-specific manner. We provide a detailed protocol (generation of mouse lines, characterization of mouse lines, mouse line crossing and cell-proliferation tracing) for using this genetic system to study cell proliferation. This cell-proliferation tracing system, which we term 'ProTracer' (Proliferation Tracer), permits lifelong noninvasive monitoring of cell proliferation of specific cell lineages in live animals. Compared with other short-term strategies that require execution of animals, ProTracer does not require sampling or animal sacrifice for tissue processing. To highlight these features, we used ProTracer to study the proliferation of hepatocytes during liver homeostasis and after tissue injury in mice. We show that the protocol is applicable to study any in vivo cell proliferation, which takes ~9 months to finish from mouse generation to data analysis. This protocol can easily be carried out by researchers skilled in mouse-related experiments.
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Affiliation(s)
- Xiuxiu Liu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wendong Weng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Lingjuan He
- School of Life Sciences, Westlake University, Hangzhou, China.
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
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9
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Li H, Weng W, Zhou B. Perfect duet: Dual recombinases improve genetic resolution. Cell Prolif 2023; 56:e13446. [PMID: 37060165 PMCID: PMC10212704 DOI: 10.1111/cpr.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 04/16/2023] Open
Abstract
As a powerful genetic tool, site-specific recombinases (SSRs) have been widely used in genomic manipulation to elucidate cell fate plasticity in vivo, advancing research in stem cell and regeneration medicine. However, the low resolution of conventional single-recombinase-mediated lineage tracing strategies, which rely heavily on the specificity of one marker gene, has led to controversial conclusions in many scientific questions. Therefore, different SSRs systems are combined to improve the accuracy of lineage tracing. Here we review the recent advances in dual-recombinase-mediated genetic approaches, including the development of novel genetic recombination technologies and their applications in cell differentiation, proliferation, and genetic manipulation. In comparison with the single-recombinase system, we also discuss the advantages of dual-genetic strategies in solving scientific issues as well as their technical limitations.
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Affiliation(s)
- Hongxin Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Wendong Weng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of SciencesHangzhouChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- New Cornerstone Science LaboratoryShenzhenChina
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10
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Gromowski T, Lukacs-Kornek V, Cisowski J. Current view of liver cancer cell-of-origin and proposed mechanisms precluding its proper determination. Cancer Cell Int 2023; 23:3. [PMID: 36609378 PMCID: PMC9824961 DOI: 10.1186/s12935-022-02843-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023] Open
Abstract
Hepatocellular carcinoma and intrahepatic cholangiocarcinoma are devastating primary liver cancers with increasing prevalence in many parts of the world. Despite intense investigation, many aspects of their biology are still largely obscure. For example, numerous studies have tackled the question of the cell-of-origin of primary liver cancers using different experimental approaches; they have not, however, provided a clear and undisputed answer. Here, we will review the evidence from animal models supporting the role of all major types of liver epithelial cells: hepatocytes, cholangiocytes, and their common progenitor as liver cancer cell-of-origin. Moreover, we will also propose mechanisms that promote liver cancer cell plasticity (dedifferentiation, transdifferentiation, and epithelial-to-mesenchymal transition) which may contribute to misinterpretation of the results and which make the issue of liver cancer cell-of-origin particularly complex.
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Affiliation(s)
- Tomasz Gromowski
- grid.5522.00000 0001 2162 9631Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Veronika Lukacs-Kornek
- grid.10388.320000 0001 2240 3300Institute of Experimental Immunology, University Hospital of the Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Jaroslaw Cisowski
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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11
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Chen C, Liao Y, Peng G. Connecting past and present: single-cell lineage tracing. Protein Cell 2022; 13:790-807. [PMID: 35441356 PMCID: PMC9237189 DOI: 10.1007/s13238-022-00913-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/06/2022] [Indexed: 01/16/2023] Open
Abstract
Central to the core principle of cell theory, depicting cells' history, state and fate is a fundamental goal in modern biology. By leveraging clonal analysis and single-cell RNA-seq technologies, single-cell lineage tracing provides new opportunities to interrogate both cell states and lineage histories. During the past few years, many strategies to achieve lineage tracing at single-cell resolution have been developed, and three of them (integration barcodes, polylox barcodes, and CRISPR barcodes) are noteworthy as they are amenable in experimentally tractable systems. Although the above strategies have been demonstrated in animal development and stem cell research, much care and effort are still required to implement these methods. Here we review the development of single-cell lineage tracing, major characteristics of the cell barcoding strategies, applications, as well as technical considerations and limitations, providing a guide to choose or improve the single-cell barcoding lineage tracing.
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Affiliation(s)
- Cheng Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yuanxin Liao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangdun Peng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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12
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Arias A, Manubens-Gil L, Dierssen M. Fluorescent transgenic mouse models for whole-brain imaging in health and disease. Front Mol Neurosci 2022; 15:958222. [PMID: 36211979 PMCID: PMC9538927 DOI: 10.3389/fnmol.2022.958222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.
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Affiliation(s)
- Adrian Arias
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Mara Dierssen
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
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13
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Hirrlinger J, Nimmerjahn A. A perspective on astrocyte regulation of neural circuit function and animal behavior. Glia 2022; 70:1554-1580. [PMID: 35297525 PMCID: PMC9291267 DOI: 10.1002/glia.24168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/19/2022] [Accepted: 02/27/2022] [Indexed: 12/16/2022]
Abstract
Studies over the past two decades have demonstrated that astrocytes are tightly associated with neurons and play pivotal roles in neural circuit development, operation, and adaptation in health and disease. Nevertheless, precisely how astrocytes integrate diverse neuronal signals, modulate neural circuit structure and function at multiple temporal and spatial scales, and influence animal behavior or disease through aberrant excitation and molecular output remains unclear. This Perspective discusses how new and state-of-the-art approaches, including fluorescence indicators, opto- and chemogenetic actuators, genetic targeting tools, quantitative behavioral assays, and computational methods, might help resolve these longstanding questions. It also addresses complicating factors in interpreting astrocytes' role in neural circuit regulation and animal behavior, such as their heterogeneity, metabolism, and inter-glial communication. Research on these questions should provide a deeper mechanistic understanding of astrocyte-neuron assemblies' role in neural circuit function, complex behaviors, and disease.
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Affiliation(s)
- Johannes Hirrlinger
- Carl-Ludwig-Institute for Physiology, Medical Faculty,
University of Leipzig, Leipzig, Germany
- Department of Neurogenetics, Max-Planck-Institute for
Multidisciplinary Sciences, Göttingen, Germany
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, The Salk Institute for
Biological Studies, La Jolla, California
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14
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Liu K, Jin H, Tang M, Zhang S, Tian X, Zhang M, Han X, Liu X, Tang J, Pu W, Li Y, He L, Yang Z, Lui KO, Zhou B. Lineage tracing clarifies the cellular origin of tissue-resident macrophages in the developing heart. J Biophys Biochem Cytol 2022; 221:213182. [PMID: 35482005 DOI: 10.1083/jcb.202108093] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 11/22/2022] Open
Abstract
Tissue-resident macrophages play essential functions in the maintenance of tissue homeostasis and repair. Recently, the endocardium has been reported as a de novo hemogenic site for the contribution of hematopoietic cells, including cardiac macrophages, during embryogenesis. These observations challenge the current consensus that hematopoiesis originates from the hemogenic endothelium within the yolk sac and dorsal aorta. Whether the developing endocardium has such a hemogenic potential requires further investigation. Here, we generated new genetic tools to trace endocardial cells and reassessed their potential contribution to hematopoietic cells in the developing heart. Fate-mapping analyses revealed that the endocardium contributed minimally to cardiac macrophages and circulating blood cells. Instead, cardiac macrophages were mainly derived from the endothelium during primitive/transient definitive (yolk sac) and definitive (dorsal aorta) hematopoiesis. Our findings refute the concept of endocardial hematopoiesis, suggesting that the developing endocardium gives rise minimally to hematopoietic cells, including cardiac macrophages.
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Affiliation(s)
- Kuo Liu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.,State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hengwei Jin
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Muxue Tang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shaohua Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xueying Tian
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Mingjun Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ximeng Han
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiuxiu Liu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Tang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjuan Pu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lingjuan He
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Bin Zhou
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.,State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, College of Life Science and Technology, Jinan University, Guangzhou, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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15
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Xu Y, Schrank PR, Williams JW. Macrophage Fate Mapping. Curr Protoc 2022; 2:e456. [PMID: 35687806 PMCID: PMC9328150 DOI: 10.1002/cpz1.456] [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] [Indexed: 11/09/2022]
Abstract
Tissue-resident macrophages are present in all tissues where they perform homeostatic and immune surveillance functions. In many tissues, resident macrophages develop from embryonic progenitors, which mature into a self-maintaining population through local proliferation. However, tissue-resident macrophages can be supported by recruited monocyte-derived macrophages during scenarios such as tissue growth, infection, or sterile inflammation. Circulating blood monocytes arise from hematopoietic stem cell progenitors and possess unique gene profiles that support additional functions within the tissue. Determining cell origins (ontogeny) and cellular turnover within tissues has become important to understanding monocyte and macrophage contributions to tissue homeostasis and disease. Fate mapping, or lineage tracing, is a promising approach to tracking cells based on unique gene expression driving reporter systems, often downstream of a Cre-recombinase-mediated excision event, to express a fluorescent protein. This approach is typically deployed temporally with developmental stage, disease onset, or in association with key stages of inflammation resolution. Importantly, myeloid fate mapping can be combined with many emerging technologies, including single-cell RNA-sequencing and spatial imaging. The application of myeloid cell fate mapping approaches has allowed for impactful discoveries regarding myeloid ontogeny, tissue residency, and monocyte fate within disease models. This protocol outline will discuss a variety of myeloid fate mapping approaches, including constitutive and inducible labeling approaches in adult and embryo tissues. This article outlines basic approaches and models used in mice for fate mapping macrophages. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Adult Fate Mapping Basic Protocol 2: Embryonic Fate Mapping.
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Affiliation(s)
- Yingzheng Xu
- Center for Immunology Department of Integrative Biology & Physiology University of Minnesota Minneapolis Minnesota
| | - Patricia R. Schrank
- Center for Immunology Department of Integrative Biology & Physiology University of Minnesota Minneapolis Minnesota
| | - Jesse W. Williams
- Center for Immunology Department of Integrative Biology & Physiology University of Minnesota Minneapolis Minnesota
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16
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Li X, Zhang Z, Han M, Li Y, He L, Zhou B. Generation of Piezo1-CreER transgenic mice for visualization and lineage tracing of mechanical force responsive cells in vivo. Genesis 2022; 60:e23476. [PMID: 35500107 DOI: 10.1002/dvg.23476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 01/21/2023]
Abstract
Cells and tissues are exposed to a wide range of mechanical stimuli during development, tissue homeostasis, repair, and regeneration. Over the past few decades, mechanosensitive ion channels (MSCs), as force-sensing integral membrane proteins, have attracted great attention with regard to their structural dynamics and mechanics at the molecular level and functions in various cells. Piezo-type MSC component 1 (Piezo1) is a newly discovered MSC; it is inherently mechanosensitive. However, which type of cells express Piezo1 in vivo remains unclear. To detect and trace Piezo1-expressing cells, we generated and characterized a novel tamoxifen-inducible Cre knock-in mouse line, Piezo1-CreER, which expresses CreER recombinase under the control of the endogenous Piezo1 promoter. Using this genetic tool, we detected the expression of Piezo1 in various cell types at the embryonic, neonatal, and adult stages. Our data showed that Piezo1 was highly expressed in endothelial cells in all the three stages, while the Piezo1 expression in epithelial cells was dynamic during development and growth. In summary, we established a new genetic tool, Piezo1-CreER, to study Piezo1-expressing cells in vivo during development, injury response, and tissue repair and regeneration.
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Affiliation(s)
- Xufeng Li
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Zhenqian Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Maoying Han
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yang Li
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Lingjuan He
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Bin Zhou
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.,State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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17
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Ganji C, Farran B. Current clinical trials for epigenetic targets and therapeutic inhibitors for pancreatic cancer therapy. Drug Discov Today 2022; 27:1404-1410. [PMID: 34952224 DOI: 10.1016/j.drudis.2021.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/17/2021] [Indexed: 02/06/2023]
Abstract
Pancreatic cancer (PC) is an aggressive disease characterized by high mortality. Diagnosis at advanced stage, resistance, and recurrence are major hurdles for PC therapy and contribute to poor survival rate. Mutations in tumor-promoting kinases and epigenetic dysregulation in tumor suppressor genes are hallmarks of PC and can be used for diagnosis and therapy. In this review, we highlight dysregulated genes associated with epigenetic mechanisms, including DNA methylation and histone acetylation, involved in PC progression and resistance. We also explore epigenetic drugs currently in clinical trials. Combining epigenetic drugs and targeted therapies might represent a promising approach for PC.
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Affiliation(s)
| | - Batoul Farran
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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18
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Yoshihara M, Nishino T, Sambe N, Nayakama T, Radtke F, Mizuno S, Takahashi S. Generation of a Gal4-dependent gene recombination and illuminating mouse. Exp Anim 2022; 71:385-390. [PMID: 35444103 PMCID: PMC9388339 DOI: 10.1538/expanim.21-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cell labeling technologies, including the Cre/loxP system, are powerful tools in developmental biology. Although the conventional Cre/loxP system has been extensively used to label the
expression of specific genes, it is less frequently used for labeling protein-protein interactions owing to technical difficulties. In the present study, we generated a new Gal4-dependent
transgenic reporter mouse line that expressed Cre recombinase and a near-infrared fluorescent protein, miRFP670. To examine whether this newly generated transgenic mouse line is applicable
in labeling of protein-protein interaction, we used a previously reported transgenic mouse lines that express Notch1 receptor with its intracellular domain replaced with a yeast
transcription factor, Gal4. Upon the binding of this artificial Notch1 receptor and endogenous Notch1 ligands, Gal4 would be cleaved from the cell membrane to induce expression of Cre
recombinase and miRFP670. Indeed, we observed miRFP670 signal in the mouse embryos (embryonic day 14.5). In addition, we examined whether our Cre recombinase was functional by using another
transgenic mouse line that express dsRed after Cre-mediated recombination. We observed dsRed signal in small intestine epithelial cells where Notch1 signal was suggested to be involved in
the crypt stem cell maintenance, suggesting that our Cre recombinase was functional. As our newly generated mouse line required only the functioning of Gal4, it could be useful for labeling
several types of molecular activities in vivo.
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Affiliation(s)
- Masaharu Yoshihara
- Ph.D. Program in Humanics, School of Integrative and Global Majors, University of Tsukuba
| | - Teppei Nishino
- College of Medicine, School of Medicine and Health Sciences, University of Tsukuba
| | - Naoto Sambe
- College of Medicine, School of Medicine and Health Sciences, University of Tsukuba
| | - Takahiro Nayakama
- College of Medicine, School of Medicine and Health Sciences, University of Tsukuba
| | - Freddy Radtke
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC)
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba
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19
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Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression. Proc Natl Acad Sci U S A 2022; 119:2117451119. [PMID: 35027456 PMCID: PMC8784106 DOI: 10.1073/pnas.2117451119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2021] [Indexed: 12/15/2022] Open
Abstract
Tools that afford spatiotemporal control of gene expression are crucial for studying genes and processes in multicellular organisms. Stop cassettes consist of exogenous sequences that interrupt gene expression and flanking site-specific recombinase sites to allow for tissue-specific excision and restoration of function by expression of the cognate recombinase. We describe a stop cassette called a flexon, composed of an artificial exon flanked by artificial introns that can be flexibly positioned in a gene. We demonstrate its efficacy in Caenorhabditis elegans for lineage-specific control of gene expression and for tissue-specific RNA interference and discuss other potential uses. The Flexon approach should be feasible in any system amenable to site-specific recombination-based methods and applicable to diverse areas including development, neuroscience, and metabolism. Conditional gene expression is a powerful tool for genetic analysis of biological phenomena. In the widely used “lox-stop-lox” approach, insertion of a stop cassette consisting of a series of stop codons and polyadenylation signals flanked by lox sites into the 5′ untranslated region (UTR) of a gene prevents expression until the cassette is excised by tissue-specific expression of Cre recombinase. Although lox-stop-lox and similar approaches using other site-specific recombinases have been successfully used in many experimental systems, this design has certain limitations. Here, we describe the Floxed exon (Flexon) approach, which uses a stop cassette composed of an artificial exon flanked by artificial introns, designed to cause premature termination of translation and nonsense-mediated decay of the mRNA and allowing for flexible placement into a gene. We demonstrate its efficacy in Caenorhabditis elegans by showing that, when promoters that cause weak and/or transient cell-specific expression are used to drive Cre in combination with a gfp(flexon) transgene, strong and sustained expression of green fluorescent protein (GFP) is obtained in specific lineages. We also demonstrate its efficacy in an endogenous gene context: we inserted a flexon into the Argonaute gene rde-1 to abrogate RNA interference (RNAi), and restored RNAi tissue specifically by expression of Cre. Finally, we describe several potential additional applications of the Flexon approach, including more precise control of gene expression using intersectional methods, tissue-specific protein degradation, and generation of genetic mosaics. The Flexon approach should be feasible in any system where a site-specific recombination-based method may be applied.
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20
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Muto Y, Humphreys BD. Recent advances in lineage tracing for the kidney. Kidney Int 2021; 100:1179-1184. [PMID: 34217781 PMCID: PMC8608712 DOI: 10.1016/j.kint.2021.05.040] [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: 04/12/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/19/2022]
Abstract
Lineage tracing was originally developed by developmental biologists to identify all progeny of a single cell during morphogenesis. More recently this approach has been applied to other fields, including organ homeostasis and recovery from injury. Modern lineage tracing techniques typically rely on reporter gene expression induced by cell-specific DNA recombination. There have been important scientific advances in the last 10 years that have impacted lineage tracing approaches, including intersectional genetics, optical clearing techniques, and the use of sequencing-based genomic lineage tracing. The latter combines CRISPR-Cas9-based genetic scarring with single-cell RNA-sequencing that, in theory, could allow comprehensive reconstruction of a lineage tree for an entire organism. This review summarizes recent advances in lineage tracing technologies and outlines potential applications for kidney research.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.
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21
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Harnessing orthogonal recombinases to decipher cell fate with enhanced precision. Trends Cell Biol 2021; 32:324-337. [PMID: 34657762 DOI: 10.1016/j.tcb.2021.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Precisely deciphering the cellular plasticity in vivo is essential in understanding many key biological processes. Site-specific recombinases are genetic tools used for in vivo lineage tracing and gene manipulation. Conventional Cre-loxP, Dre-rox, and Flp-frt technologies form the orthogonal recombination systems that can also be used in combination to increase the precision. As such, more than one marker gene can be targeted for lineage tracing, studying cellular heterogeneity, recording cellular activities, or even genome editing. Their combinatory use has recently resolved some controversies in defining cellular fate plasticity. Focusing on cell fate studies, we introduce the design principles of orthogonal recombinases-based strategies, describe some working examples in resolving cell fate-related controversies, and discuss some of their technical strengths and limits.
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22
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Peterson JC, Kelder TP, Goumans MJTH, Jongbloed MRM, DeRuiter MC. The Role of Cell Tracing and Fate Mapping Experiments in Cardiac Outflow Tract Development, New Opportunities through Emerging Technologies. J Cardiovasc Dev Dis 2021; 8:47. [PMID: 33925811 PMCID: PMC8146276 DOI: 10.3390/jcdd8050047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Whilst knowledge regarding the pathophysiology of congenital heart disease (CHDs) has advanced greatly in recent years, the underlying developmental processes affecting the cardiac outflow tract (OFT) such as bicuspid aortic valve, tetralogy of Fallot and transposition of the great arteries remain poorly understood. Common among CHDs affecting the OFT, is a large variation in disease phenotypes. Even though the different cell lineages contributing to OFT development have been studied for many decades, it remains challenging to relate cell lineage dynamics to the morphologic variation observed in OFT pathologies. We postulate that the variation observed in cellular contribution in these congenital heart diseases might be related to underlying cell lineage dynamics of which little is known. We believe this gap in knowledge is mainly the result of technical limitations in experimental methods used for cell lineage analysis. The aim of this review is to provide an overview of historical fate mapping and cell tracing techniques used to study OFT development and introduce emerging technologies which provide new opportunities that will aid our understanding of the cellular dynamics underlying OFT pathology.
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Affiliation(s)
- Joshua C. Peterson
- Department Anatomy & Embryology, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (J.C.P.); (T.P.K.); (M.R.M.J.)
| | - Tim P. Kelder
- Department Anatomy & Embryology, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (J.C.P.); (T.P.K.); (M.R.M.J.)
| | - Marie José T. H. Goumans
- Department Cellular and Chemical Biology, Leiden University Medical Center, 2300RC Leiden, The Netherlands;
| | - Monique R. M. Jongbloed
- Department Anatomy & Embryology, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (J.C.P.); (T.P.K.); (M.R.M.J.)
- Department of Cardiology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Marco C. DeRuiter
- Department Anatomy & Embryology, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (J.C.P.); (T.P.K.); (M.R.M.J.)
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23
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Chenouard V, Remy S, Tesson L, Ménoret S, Ouisse LH, Cherifi Y, Anegon I. Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models. Front Genet 2021; 12:615491. [PMID: 33959146 PMCID: PMC8093876 DOI: 10.3389/fgene.2021.615491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.
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Affiliation(s)
- Vanessa Chenouard
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- genOway, Lyon, France
| | - Séverine Remy
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Laurent Tesson
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Séverine Ménoret
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes Université, Nantes, France
| | - Laure-Hélène Ouisse
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | | | - Ignacio Anegon
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
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24
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Dual recombinases-based genetic lineage tracing for stem cell research with enhanced precision. SCIENCE CHINA-LIFE SCIENCES 2021; 64:2060-2072. [PMID: 33847909 DOI: 10.1007/s11427-020-1889-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Stem cell research has become a hot topic in biology, as the understanding of stem cell biology can provide new insights for both regenerative medicine and clinical treatment of diseases. Accurately deciphering the fate of stem cells is the basis for understanding the mechanism and function of stem cells during tissue repair and regeneration. Cre-loxP-mediated recombination has been widely applied in fate mapping of stem cells for many years. However, nonspecific labeling by conventional cell lineage tracing strategies has led to discrepancies or even controversies in multiple fields. Recently, dual recombinase-mediated lineage tracing strategies have been developed to improve both the resolution and precision of stem cell fate mapping. These new genetic strategies also expand the application of lineage tracing in studying cell origin and fate. Here, we review cell lineage tracing methods, especially dual genetic approaches, and then provide examples to describe how they are used to study stem cell fate plasticity and function in vivo.
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25
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Tian X, Zhou B. Strategies for site-specific recombination with high efficiency and precise spatiotemporal resolution. J Biol Chem 2021; 296:100509. [PMID: 33676891 PMCID: PMC8050033 DOI: 10.1016/j.jbc.2021.100509] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
Site-specific recombinases (SSRs) are invaluable genome engineering tools that have enormously boosted our understanding of gene functions and cell lineage relationships in developmental biology, stem cell biology, regenerative medicine, and multiple diseases. However, the ever-increasing complexity of biomedical research requires the development of novel site-specific genetic recombination technologies that can manipulate genomic DNA with high efficiency and fine spatiotemporal control. Here, we review the latest innovative strategies of the commonly used Cre-loxP recombination system and its combinatorial strategies with other site-specific recombinase systems. We also highlight recent progress with a focus on the new generation of chemical- and light-inducible genetic systems and discuss the merits and limitations of each new and established system. Finally, we provide the future perspectives of combining various recombination systems or improving well-established site-specific genetic tools to achieve more efficient and precise spatiotemporal genetic manipulation.
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Affiliation(s)
- Xueying Tian
- Key Laboratory of Regenerative Medicine of Ministry of Education, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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26
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A suite of new Dre recombinase drivers markedly expands the ability to perform intersectional genetic targeting. Cell Stem Cell 2021; 28:1160-1176.e7. [PMID: 33567267 DOI: 10.1016/j.stem.2021.01.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/06/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
The use of the dual recombinase-mediated intersectional genetic approach involving Cre-loxP and Dre-rox has significantly enhanced the precision of in vivo lineage tracing, as well as gene manipulation. However, this approach is limited by the small number of Dre recombinase driver constructs available. Here, we developed more than 70 new intersectional drivers to better target diverse cell lineages. To highlight their applicability, we used these new tools to study the in vivo adipogenic fate of perivascular progenitors, which revealed that PDGFRa+ but not PDGFRa-PDGFRb+ perivascular cells are the endogenous progenitors of adult adipocytes. In addition to lineage tracing, we used members of this new suite of drivers to more specifically knock out genes in complex tissues, such as white adipocytes and lymphatic vessels, that heretofore cannot be selectively targeted by conventional Cre drivers alone. In summary, these new transgenic tools expand the intersectional genetic approach while enhancing its precision.
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27
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New Insights into Development of Female Reproductive Tract-Hedgehog-Signal Response in Wolffian Tissues Directly Contributes to Uterus Development. Int J Mol Sci 2021; 22:ijms22031211. [PMID: 33530552 PMCID: PMC7865753 DOI: 10.3390/ijms22031211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The reproductive tract in mammals emerges from two ductal systems during embryogenesis: Wolffian ducts (WDs) and Mullerian ducts (MDs). Most of the female reproductive tract (FRT) including the oviducts, uterine horn and cervix, originate from MDs. It is widely accepted that the formation of MDs depends on the preformed WDs within the urogenital primordia. Here, we found that the WD mesenchyme under the regulation of Hedgehog (Hh) signaling is closely related to the developmental processes of the FRT during embryonic and postnatal periods. Deficiency of Sonic hedgehog (Shh), the only Hh ligand expressed exclusively in WDs, prevents the MD mesenchyme from affecting uterine growth along the radial axis. The in vivo cell tracking approach revealed that after WD regression, distinct cells responding to WD-derived Hh signal continue to exist in the developing FRT and gradually contribute to the formation of various tissues such as smooth muscle, endometrial stroma and vascular vessel, in the mouse uterus. Our study thus provides a novel developmental mechanism of FRT relying on WD.
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28
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Almeida MP, Welker JM, Siddiqui S, Luiken J, Ekker SC, Clark KJ, Essner JJ, McGrail M. Endogenous zebrafish proneural Cre drivers generated by CRISPR/Cas9 short homology directed targeted integration. Sci Rep 2021; 11:1732. [PMID: 33462297 PMCID: PMC7813866 DOI: 10.1038/s41598-021-81239-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/04/2021] [Indexed: 01/04/2023] Open
Abstract
We previously reported efficient precision targeted integration of reporter DNA in zebrafish and human cells using CRISPR/Cas9 and short regions of homology. Here, we apply this strategy to isolate zebrafish Cre recombinase drivers whose spatial and temporal restricted expression mimics endogenous genes. A 2A-Cre recombinase transgene with 48 bp homology arms was targeted into proneural genes ascl1b, olig2 and neurod1. We observed high rates of germline transmission ranging from 10 to 100% (2/20 olig2; 1/5 neurod1; 3/3 ascl1b). The transgenic lines Tg(ascl1b-2A-Cre)is75, Tg(olig2-2A-Cre)is76, and Tg(neurod1-2A-Cre)is77 expressed functional Cre recombinase in the expected proneural cell populations. Somatic targeting of 2A-CreERT2 into neurod1 resulted in tamoxifen responsive recombination in the nervous system. The results demonstrate Cre recombinase expression is driven by the native promoter and regulatory elements of the targeted genes. This approach provides a straightforward, efficient, and cost-effective method to generate cell type specific zebrafish Cre and CreERT2 drivers, overcoming challenges associated with promoter-BAC and transposon mediated transgenics.
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Affiliation(s)
- Maira P Almeida
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA
| | - Jordan M Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA.,Department III - Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sahiba Siddiqui
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA
| | - Jon Luiken
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. .,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA.
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29
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The art of lineage tracing: From worm to human. Prog Neurobiol 2020; 199:101966. [PMID: 33249090 DOI: 10.1016/j.pneurobio.2020.101966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022]
Abstract
Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.
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30
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Redpath AN, Smart N. Recapturing embryonic potential in the adult epicardium: Prospects for cardiac repair. Stem Cells Transl Med 2020; 10:511-521. [PMID: 33222384 PMCID: PMC7980211 DOI: 10.1002/sctm.20-0352] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/07/2020] [Accepted: 10/25/2020] [Indexed: 12/12/2022] Open
Abstract
Research into potential targets for cardiac repair encompasses recognition of tissue‐resident cells with intrinsic regenerative properties. The adult vertebrate heart is covered by mesothelium, named the epicardium, which becomes active in response to injury and contributes to repair, albeit suboptimally. Motivation to manipulate the epicardium for treatment of myocardial infarction is deeply rooted in its central role in cardiac formation and vasculogenesis during development. Moreover, the epicardium is vital to cardiac muscle regeneration in lower vertebrate and neonatal mammalian‐injured hearts. In this review, we discuss our current understanding of the biology of the mammalian epicardium in development and injury. Considering present challenges in the field, we further contemplate prospects for reinstating full embryonic potential in the adult epicardium to facilitate cardiac regeneration.
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Affiliation(s)
- Andia N Redpath
- Department of Physiology, Anatomy and Genetics, British Heart Foundation Centre of Regenerative Medicine, Burdon Sanderson Cardiac Science Centre, University of Oxford, Oxford, UK
| | - Nicola Smart
- Department of Physiology, Anatomy and Genetics, British Heart Foundation Centre of Regenerative Medicine, Burdon Sanderson Cardiac Science Centre, University of Oxford, Oxford, UK
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31
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Al Khabouri S, Gerlach C. T cell fate mapping and lineage tracing technologies probing clonal aspects underlying the generation of CD8 T cell subsets. Scand J Immunol 2020; 92:e12983. [PMID: 33037653 PMCID: PMC7757170 DOI: 10.1111/sji.12983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022]
Abstract
T cells responding to acute infections generally provide two key functions to protect the host: (1) active contribution to pathogen elimination and (2) providing long‐lived cells that are poised to rapidly respond to renewed infection, thus ensuring long‐lasting protection against the particular pathogen. Extensive work has established an astonishing amount of additional diversity among T cells actively contributing to pathogen elimination, as well as among resting, long‐lived antigen‐experienced T cells. This led to the description of a variety of functionally distinct T cell ‘subsets’. Understanding how this heterogeneity develops among T cells responding to the same antigen is currently an active area of research, since knowledge of such mechanisms may have implications for the development of vaccines and immunotherapy. The number of naïve T cells specific to a given antigen span a great range. Considering this, one mechanistic angle focusses on how individual naïve T cells contribute to the development of the distinct T cell subsets. In this review, we highlight the current technologies that enable one to address the contributions of individual naïve T cells to different T cell subsets, with a focus on CD8 T cell subsets generated in the context of acute infections. Moreover, we discuss the requirements of new technologies to further our understanding of the mechanisms that help generate long‐lasting immunity.
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Affiliation(s)
- Shaima Al Khabouri
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Carmen Gerlach
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
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32
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Abstract
The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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33
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Pek NMQ, Liu KJ, Nichane M, Ang LT. Controversies Surrounding the Origin of Hepatocytes in Adult Livers and the in Vitro Generation or Propagation of Hepatocytes. Cell Mol Gastroenterol Hepatol 2020; 11:273-290. [PMID: 32992051 PMCID: PMC7695885 DOI: 10.1016/j.jcmgh.2020.09.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
Epithelial cells in the liver (known as hepatocytes) are high-performance engines of myriad metabolic functions and versatile responders to liver injury. As hepatocytes metabolize amino acids, alcohol, drugs, and other substrates, they produce and are exposed to a milieu of toxins and harmful byproducts that can damage themselves. In the healthy liver, hepatocytes generally divide slowly. However, after liver injury, hepatocytes can ramp up proliferation to regenerate the liver. Yet, on extensive injury, regeneration falters, and liver failure ensues. It is therefore critical to understand the mechanisms underlying liver regeneration and, in particular, which liver cells are mobilized during liver maintenance and repair. Controversies continue to surround the very existence of hepatic stem cells and, if they exist, their spatial location, multipotency, degree of contribution to regeneration, ploidy, and susceptibility to tumorigenesis. This review discusses these controversies. Finally, we highlight how insights into hepatocyte regeneration and biology in vivo can inform in vitro studies to propagate primary hepatocytes with liver regeneration-associated signals and to generate hepatocytes de novo from pluripotent stem cells.
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Affiliation(s)
| | | | | | - Lay Teng Ang
- Correspondence Address correspondence to: Lay Teng Ang, PhD, Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California 94305.
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