1
|
Daigle N, Duan S, Song H, Lima N, Sontz R, Merchant JL, Sawyer TW. Wide field-of-view fluorescence imaging for organ-level lineage tracing of rare intestinal stem cell populations. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:096004. [PMID: 37711357 PMCID: PMC10499363 DOI: 10.1117/1.jbo.28.9.096004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Significance Lineage tracing using fluorescent reporters is a common tool for monitoring the expression of genes and transcription factors in stem cell populations and their progeny. The zinc-binding protein 89 (ZBP-89/Zfp148 mouse gene) is a transcription factor that plays a role in gastrointestinal (GI) stem cell maintenance and cellular differentiation and has been linked to the progression of colon cancer. While lineage tracing is a useful tool, it is commonly performed with high-magnification microscopy on a small field of view within tissue sections, thereby limiting the ability to resolve reporter expression at the organ level. Furthermore, this technique requires extensive tissue processing, which is time consuming and requires euthanizing the animal. Further knowledge could be elucidated by measuring the expression of fluorescent reporters across entire organs with minimal tissue processing. Aim We present the application of wide-field fluorescence imaging for whole-organ lineage tracing of an inducible Zfp148-tdTomato-expressing transgenic mouse line to assess the expression of ZBP-89/Zfp148 in the GI tract. Approach We measured tdTomato fluorescence in ex vivo organs at time points between 24 h and 6 months post-induction. Fluctuations in tdTomato expression were validated by fluorescence microscopy of tissue sections. Results Quantification of the wide field-of-view images showed a statistically significant increase in fluorescent signal across the GI tract between transgenic mice and littermate controls. The results also showed a gradient of decreasing reporter expression from proximal to distal intestine, suggesting a higher abundance of ZBP-89 expressing stem cells, or higher expression of ZBP-89 within the stem cells, in the proximal intestine. Conclusions We demonstrate that wide-field fluorescence imaging is a valuable tool for monitoring whole-organ expression of fluorescent reporters. This technique could potentially be applied in vivo for longitudinal assessment of a single animal, further enhancing our ability to resolve rare stem cell lineages spatially and temporally.
Collapse
Affiliation(s)
- Noelle Daigle
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Suzann Duan
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Heyu Song
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Natzem Lima
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Ricky Sontz
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | | | - Travis W. Sawyer
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| |
Collapse
|
2
|
Zhao R, Xu Y, Chen Y, Zhang J, Teng F, Liao S, Chen S, Wu Q, Xiang C, Pang J, Shang Z, Zhao J, Bao H, Bao H, Shao Y, Lu S, Han Y. Clonal dynamics and Stereo-seq resolve origin and phenotypic plasticity of adenosquamous carcinoma. NPJ Precis Oncol 2023; 7:80. [PMID: 37634047 PMCID: PMC10460394 DOI: 10.1038/s41698-023-00430-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023] Open
Abstract
The genomic origin and development of the biphasic lung adenosquamous carcinoma (ASC) remain inconclusive. Here, we derived potential evolutionary trajectory of ASC through whole-exome sequencing, Stereo-seq, and patient-derived xenografts. We showed that EGFR and MET activating mutations were the main drivers in ASCs. Phylogenetically, these drivers and passenger mutations found in both components were trunk clonal events, confirming monoclonal origination. Comparison of multiple lesions also revealed closer genomic distance between lymph node metastases and the ASC component with the same phenotype. However, as mutational signatures of EGFR-positive lung squamous carcinomas (LUSCs) were more comparable to EGFR-positive ASCs than to wild-type LUSCs, we postulated different origination of these LUSCs, with ASC being the potential intermediate state of driver-positive LUSCs. Spatial transcriptomic profiling inferred transformation from adenocarcinoma to squamous cell carcinoma, which was then histologically captured in vivo. Together, our results explained the development of ASC and provided insights into future clinical decisions.
Collapse
Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Yunhua Xu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Yedan Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, PR China
| | - Jiajun Zhang
- BGI Research, Chongqing, 401329, PR China
- BGI Research, Shenzhen, 518083, PR China
| | - Fei Teng
- BGI Research, Shenzhen, 518083, PR China
| | - Sha Liao
- BGI Research, Chongqing, 401329, PR China
- BGI Research, Shenzhen, 518083, PR China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Qian Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, PR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Jiaohui Pang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, PR China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Hairong Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, PR China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, PR China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, PR China
- School of Public Health, Nanjing Medical University, Nanjing, 211166, PR China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China.
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China.
| |
Collapse
|
3
|
Exploiting somatic mutations to decipher human blood production: a natural lineage-tracing strategy. Exp Hematol 2023; 121:2-5. [PMID: 36736573 DOI: 10.1016/j.exphem.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Lineage tracing using fluorescent proteins, genetic barcodes, and various other strategies has provided critical insights into the dynamics of both fetal and adult hematopoiesis in model organisms. However, these technologies cannot be readily used to study hematopoiesis in human beings. Therefore, there is a critical need to develop strategies to assess cellular dynamics within human hematopoietic tissues in vivo. Recently, researchers have used naturally acquired somatic mutations, coupled with other single-cell technologies, to retrospectively analyze clonal cellular dynamics. In summer 2022, the International Society for Experimental Hematology's New Investigator Committee hosted a webinar focused on novel approaches to dissect fetal and adult hematopoiesis, with presentations from Drs. Ana Cvejic and Vijay Sankaran. Here, we provide an overview of these exciting technological advances and some of the novel insights they have already provided in studying human hematopoiesis.
Collapse
|
4
|
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J. Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations. Nat Biotechnol 2023; 41:44-49. [PMID: 36065022 PMCID: PMC7614077 DOI: 10.1038/s41587-022-01427-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/12/2022] [Indexed: 01/19/2023]
Abstract
We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8% of cell lineages spanning 1 h, as compared to 31.8% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.
Collapse
Affiliation(s)
| | - Peter Hirsch
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leo Guignard
- HHMI Janelia, Ashburn, VA, USA
- CNRS, UTLN, LIS 7020, Turing Centre for Living Systems, Aix Marseille University, Marseille, France
| | - Katie McDole
- HHMI Janelia, Ashburn, VA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yinan Wan
- HHMI Janelia, Ashburn, VA, USA
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Dagmar Kainmueller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | | |
Collapse
|
5
|
Hadj Abed L, Tak T, Cosgrove J, Perié L. CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data. Front Med (Lausanne) 2022; 9:919345. [PMID: 36275810 PMCID: PMC9581332 DOI: 10.3389/fmed.2022.919345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.
Collapse
Affiliation(s)
- Louisa Hadj Abed
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Centre de Bio-Informatique, MINES ParisTech, Institut Curie, PSL University, Paris, France
| | - Tamar Tak
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,*Correspondence: Jason Cosgrove,
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Leïla Perié,
| |
Collapse
|
6
|
Lyne AM, Perie L. Comparing Phylogenetic Approaches to Reconstructing Cell Lineage From Microsatellites With Missing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2291-2301. [PMID: 32386163 DOI: 10.1109/tcbb.2020.2992813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Due to the imperfect fidelity of DNA replication, somatic cells acquire DNA mutations at each division which record their lineage history. Microsatellites, tandem repeats of DNA nucleotide motifs, mutate more frequently than other genomic regions and by observing microsatellite lengths in single cells and implementing suitable inference procedures, the cell lineage tree of an organism can be reconstructed. Due to recent advances in single cell Next Generation Sequencing (NGS) and the phylogenetic methods used to infer lineage trees, this work investigates which computational approaches best exploit the lineage information found in single cell NGS data. We simulated trees representing cell division with mutating microsatellites, and tested a range of available phylogenetic algorithms to reconstruct cell lineage. We found that distance-based approaches are fast and accurate with fully observed data. However, Maximum Parsimony and the computationally intensive probabilistic methods are more robust to missing data and therefore better suited to reconstructing cell lineage from NGS datasets. We also investigated how robust reconstruction algorithms are to different tree topologies and mutation generation models. Our results show that the flexibility of Maximum Parsimony and the probabilistic approaches mean they can be adapted to allow good reconstruction across a range of biologically relevant scenarios.
Collapse
|
7
|
Winkley KM, Reeves WM, Veeman MT. Single-cell analysis of cell fate bifurcation in the chordate Ciona. BMC Biol 2021; 19:180. [PMID: 34465302 PMCID: PMC8408944 DOI: 10.1186/s12915-021-01122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. RESULTS AND CONCLUSIONS We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a "broad-hourglass" model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.
Collapse
Affiliation(s)
- Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
8
|
Pang M, Bai L, Zong W, Wang X, Bu Y, Xiong C, Zheng J, Li J, Gao W, Feng Z, Chen L, Zhang J, Cheng H, Zhu X, Xiong JW. Light-sheet fluorescence imaging charts the gastrula origin of vascular endothelial cells in early zebrafish embryos. Cell Discov 2020; 6:74. [PMID: 33133634 PMCID: PMC7588447 DOI: 10.1038/s41421-020-00204-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/11/2020] [Indexed: 12/29/2022] Open
Abstract
It remains challenging to construct a complete cell lineage map of the origin of vascular endothelial cells in any vertebrate embryo. Here, we report the application of in toto light-sheet fluorescence imaging of embryos to trace the origin of vascular endothelial cells (ECs) at single-cell resolution in zebrafish. We first adapted a previously reported method to embryo mounting and light-sheet imaging, created an alignment, fusion, and extraction all-in-one software (AFEIO) for processing big data, and performed quantitative analysis of cell lineage relationships using commercially available Imaris software. Our data revealed that vascular ECs originated from broad regions of the gastrula along the dorsal–ventral and anterior–posterior axes, of which the dorsal–anterior cells contributed to cerebral ECs, the dorsal–lateral cells to anterior trunk ECs, and the ventral–lateral cells to posterior trunk and tail ECs. Therefore, this work, to our knowledge, charts the first comprehensive map of the gastrula origin of vascular ECs in zebrafish, and has potential applications for studying the origin of any embryonic organs in zebrafish and other model organisms.
Collapse
Affiliation(s)
- Meijun Pang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Linlu Bai
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weijian Zong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Xu Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Ye Bu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Connie Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jiyuan Zheng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jieyi Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Weizheng Gao
- School of Engineering, Peking University, Beijing 100871, China
| | - Zhiheng Feng
- School of Engineering, Peking University, Beijing 100871, China
| | - Liangyi Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jue Zhang
- School of Engineering, Peking University, Beijing 100871, China
| | - Heping Cheng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Xiaojun Zhu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jing-Wei Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| |
Collapse
|
9
|
Parasar B, Chang PV. Engineered Th17 Cell Differentiation Using a Photoactivatable Immune Modulator. J Am Chem Soc 2020; 142:18103-18108. [PMID: 32975936 PMCID: PMC11100974 DOI: 10.1021/jacs.0c07485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
T helper 17 (Th17) cells, an important subset of CD4+ T cells, help to eliminate extracellular infectious pathogens that have invaded our tissues. Despite the critical roles of Th17 cells in immunity, how the immune system regulates the production and maintenance of this cell type remains poorly understood. In particular, the plasticity of these cells or their dynamic ability to trans-differentiate into other CD4+ T cell subsets remains mostly uncharacterized. Here, we report a synthetic immunology approach using a photoactivatable immune modulator (PIM) to increase Th17 cell differentiation on demand with spatial and temporal precision to help elucidate this important and dynamic process. In this chemical strategy, we developed a latent agonist that upon photochemical activation releases a small-molecule ligand that targets the aryl hydrocarbon receptor (AhR) and ultimately induces Th17 cell differentiation. We used this chemical tool to control AhR activation with spatiotemporal precision within cells and to modulate Th17 cell differentiation on demand using UV light illumination. We envision that this approach will enable an understanding of the dynamic functions and behaviors of Th17 cells in vivo during immune responses and in mouse models of inflammatory disease.
Collapse
|
10
|
Zhang K, Chen S, Sun H, Wang L, Li H, Zhao J, Zhang C, Li N, Guo Z, Han Z, Han ZC, Zheng G, Chen X, Li Z. In vivo two-photon microscopy reveals the contribution of Sox9 + cell to kidney regeneration in a mouse model with extracellular vesicle treatment. J Biol Chem 2020; 295:12203-12213. [PMID: 32641493 PMCID: PMC7443503 DOI: 10.1074/jbc.ra120.012732] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 07/02/2020] [Indexed: 01/05/2023] Open
Abstract
Mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) have been shown to stimulate regeneration in the treatment of kidney injury. Renal regeneration is also thought to be stimulated by the activation of Sox9+ cells. However, whether and how the activation mechanisms underlying EV treatment and Sox9+ cell-dependent regeneration intersect is unclear. We reasoned that a high-resolution imaging platform in living animals could help to untangle this system. To test this idea, we first applied EVs derived from human placenta-derived MSCs (hP-MSCs) to a Sox9-CreERT2; R26mTmG transgenic mouse model of acute kidney injury (AKI). Then, we developed an abdominal imaging window in the mouse and tracked the Sox9+ cells in the inducible Sox9-Cre transgenic mice via in vivo lineage tracing with two-photon intravital microscopy. Our results demonstrated that EVs can travel to the injured kidneys post intravenous injection as visualized by Gaussia luciferase imaging and markedly increase the activation of Sox9+ cells. Moreover, the two-photon living imaging of lineage-labeled Sox9+ cells showed that the EVs promoted the expansion of Sox9+ cells in kidneys post AKI. Histological staining results confirmed that the descendants of Sox9+ cells contributed to nephric tubule regeneration which significantly ameliorated the renal function after AKI. In summary, intravital lineage tracing with two-photon microscopy through an embedded abdominal imaging window provides a practical strategy to investigate the beneficial functions and to clarify the mechanisms of regenerative therapies in AKI.
Collapse
Affiliation(s)
- Kaiyue Zhang
- Nankai University School of Medicine, Tianjin, China; The Key Laboratory of Bioactive Materials, Ministry of Education, the College of Life Sciences, Nankai University, Tianjin, China
| | - Shang Chen
- Nankai University School of Medicine, Tianjin, China; The Key Laboratory of Bioactive Materials, Ministry of Education, the College of Life Sciences, Nankai University, Tianjin, China
| | - Huimin Sun
- Nankai University School of Medicine, Tianjin, China
| | - Lina Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huifang Li
- Nankai University School of Medicine, Tianjin, China
| | - Jinglei Zhao
- Nankai University School of Medicine, Tianjin, China
| | - Chuyue Zhang
- State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China
| | - Nana Li
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, China
| | - Zhikun Guo
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, China
| | - Zhibo Han
- Jiangxi Engineering Research Center for Stem Cell, Shangrao, Jiangxi, China; Tianjin Key Laboratory of Engineering Technologies for Cell Pharmaceutical, National Engineering Research Center of Cell Products, AmCellGene Co., Ltd., Tianjin, China
| | - Zhong-Chao Han
- Jiangxi Engineering Research Center for Stem Cell, Shangrao, Jiangxi, China; Tianjin Key Laboratory of Engineering Technologies for Cell Pharmaceutical, National Engineering Research Center of Cell Products, AmCellGene Co., Ltd., Tianjin, China; Beijing Engineering Laboratory of Perinatal Stem Cells, Beijing Institute of Health and Stem Cells, Health & Biotech Co., Beijing, China
| | - Guoguang Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiangmei Chen
- State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China
| | - Zongjin Li
- Nankai University School of Medicine, Tianjin, China; The Key Laboratory of Bioactive Materials, Ministry of Education, the College of Life Sciences, Nankai University, Tianjin, China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China; Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, China.
| |
Collapse
|
11
|
Zafar H, Lin C, Bar-Joseph Z. Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. Nat Commun 2020; 11:3055. [PMID: 32546686 PMCID: PMC7298005 DOI: 10.1038/s41467-020-16821-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
Recent studies combine two novel technologies, single-cell RNA-sequencing and CRISPR-Cas9 barcode editing for elucidating developmental lineages at the whole organism level. While these studies provided several insights, they face several computational challenges. First, lineages are reconstructed based on noisy and often saturated random mutation data. Additionally, due to the randomness of the mutations, lineages from multiple experiments cannot be combined to reconstruct a species-invariant lineage tree. To address these issues we developed a statistical method, LinTIMaT, which reconstructs cell lineages using a maximum-likelihood framework by integrating mutation and expression data. Our analysis shows that expression data helps resolve the ambiguities arising in when lineages are inferred based on mutations alone, while also enabling the integration of different individual lineages for the reconstruction of an invariant lineage tree. LinTIMaT lineages have better cell type coherence, improve the functional significance of gene sets and provide new insights on progenitors and differentiation pathways.
Collapse
Affiliation(s)
- Hamim Zafar
- Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, India
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chieh Lin
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| |
Collapse
|
12
|
Kabadi A, McDonnell E, Frank CL, Drowley L. Applications of Functional Genomics for Drug Discovery. SLAS DISCOVERY 2020; 25:823-842. [PMID: 32026742 DOI: 10.1177/2472555220902092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many diseases, such as diabetes, autoimmune diseases, cancer, and neurological disorders, are caused by a dysregulation of a complex interplay of genes. Genome-wide association studies have identified thousands of disease-linked polymorphisms in the human population. However, detailing the causative gene expression or functional changes underlying those associations has been elusive in many cases. Functional genomics is an emerging field of research that aims to deconvolute the link between genotype and phenotype by making use of large -omic data sets and next-generation gene and epigenome editing tools to perturb genes of interest. Here we review how functional genomic tools can be used to better understand the biological interplay between genes, improve disease modeling, and identify novel drug targets. Incorporation of functional genomic capabilities into conventional drug development pipelines is predicted to expedite the development of first-in-class therapeutics.
Collapse
Affiliation(s)
- Ami Kabadi
- Element Genomics, a UCB company, Durham, NC, USA
| | | | | | | |
Collapse
|
13
|
He S, Tian Y, Feng S, Wu Y, Shen X, Chen K, He Y, Sun Q, Li X, Xu J, Wen Z, Qu JY. In vivo single-cell lineage tracing in zebrafish using high-resolution infrared laser-mediated gene induction microscopy. eLife 2020; 9:52024. [PMID: 31904340 PMCID: PMC7018510 DOI: 10.7554/elife.52024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/04/2020] [Indexed: 12/15/2022] Open
Abstract
Heterogeneity broadly exists in various cell types both during development and at homeostasis. Investigating heterogeneity is crucial for comprehensively understanding the complexity of ontogeny, dynamics, and function of specific cell types. Traditional bulk-labeling techniques are incompetent to dissect heterogeneity within cell population, while the new single-cell lineage tracing methodologies invented in the last decade can hardly achieve high-fidelity single-cell labeling and long-term in-vivo observation simultaneously. In this work, we developed a high-precision infrared laser-evoked gene operator heat-shock system, which uses laser-induced CreERT2 combined with loxP-DsRedx-loxP-GFP reporter to achieve precise single-cell labeling and tracing. In vivo study indicated that this system can precisely label single cell in brain, muscle and hematopoietic system in zebrafish embryo. Using this system, we traced the hematopoietic potential of hemogenic endothelium (HE) in the posterior blood island (PBI) of zebrafish embryo and found that HEs in the PBI are heterogeneous, which contains at least myeloid unipotent and myeloid-lymphoid bipotent subtypes. Animals begin life as a single cell that then divides to become a complex organism with many different types of cells. Every time a cell divides, each of its two daughter cells can either stay the same type as their parent or adopt a different identity. Once a cell acquires an identity, it usually cannot ‘go back’ and choose another. Eventually, this process will produce daughter cells with the identity of a specific tissue or organ and that cannot divide further. Multipotent cells are cells that can produce daughter cells with different identities, including other multipotent cells. These cells can usually give rise to different cell types in a specific organ, and generate more cells to replace any cells that die in that organ. Tracking the cells descended from a multipotent cell in a specific tissue can provide information about how the tissue develops. Hemogenic endothelium cells produce the multipotent cells that give rise to two types of white blood cells: myeloid cells and lymphoid cells. Myeloid cells include innate immune cells that protect the body from infection non-specifically; while lymphoid cells include T cells and B cells with receptors that detect specific bacteria or viruses. It remains unclear whether each of these two cell types originate from a single population of hemogenic endothelium cells or from two distinct subpopulations. He et al. have now developed a new optical technique to label a single hemogenic endothelium cell in a zebrafish and track the cell and its descendants. This method revealed that there are at least two distinct populations of hemogenic endothelium cells. One of them can give rise to both lymphoid and myeloid cells, while the other can only give rise to myeloid cells. These findings shed light on the mechanisms of blood formation, and potentially could provide useful tools to study the development of diseases such as leukemia. Additionally, the single-cell labeling technology He et al. have developed could be applied to study the development of other tissues and organs.
Collapse
Affiliation(s)
- Sicong He
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China
| | - Ye Tian
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Shachuan Feng
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Yi Wu
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Xinwei Shen
- Department of Mathematics, The Hong Kong University of Science and Technology, Kowloon, China
| | - Kani Chen
- Department of Mathematics, The Hong Kong University of Science and Technology, Kowloon, China
| | - Yingzhu He
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China
| | - Qiqi Sun
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China
| | - Xuesong Li
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China
| | - Jin Xu
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Jianan Y Qu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, China.,Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, China
| |
Collapse
|
14
|
Zhao H, Zhou B. Dual genetic approaches for deciphering cell fate plasticity in vivo: more than double. Curr Opin Cell Biol 2019; 61:101-109. [DOI: 10.1016/j.ceb.2019.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/16/2022]
|
15
|
Abstract
Cancer arises from a single cell through a series of acquired mutations and epigenetic alterations. Tumors gradually develop into a complex tissue comprised of phenotypically heterogeneous cancer cell populations, as well as noncancer cells that make up the tumor microenvironment. The phenotype, or state, of each cancer and stromal cell is influenced by a plethora of cell-intrinsic and cell-extrinsic factors. The diversity of these cellular states promotes tumor progression, enables metastasis, and poses a challenge for effective cancer treatments. Thus, the identification of strategies for the therapeutic manipulation of tumor heterogeneity would have significant clinical implications. A major barrier in the field is the difficulty in functionally investigating heterogeneity in tumors in cancer patients. Here we review how mouse models of human cancer can be leveraged to interrogate tumor heterogeneity and to help design better therapeutic strategies.
Collapse
Affiliation(s)
- Tuomas Tammela
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julien Sage
- Department of Pediatrics and Department of Genetics, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
16
|
Drake KA, Fessler AR, Carroll TJ. Methods for renal lineage tracing: In vivo and beyond. Methods Cell Biol 2019; 154:121-143. [PMID: 31493814 DOI: 10.1016/bs.mcb.2019.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lineage tracing has resulted in fundamental discoveries in kidney development and disease and remains a powerful technique to study mechanisms of organogenesis, homeostasis, and repair/regeneration. Following decades of research on the cellular and molecular regulation of renal organogenesis, the kidney has become one of the most well-characterized organs, resulting in exciting advancements in pluripotent stem cell differentiation, tissue bioengineering, and the potential for developing novel regenerative therapies for kidney disease. Lineage tracing, or the labeling of progeny cells arising from a single cell or group of cells, allows for spatial and temporal analyses of dynamic in vivo and in vitro processes. As lineage tracing techniques expand across disciplines of developmental biology, stem cell biology, and regenerative medicine, careful experimental design and interpretation, along with an understanding of the basic principles and technical limitations, are essential for utilizing genetically complex lineage tracing models to further understand kidney development and disease.
Collapse
Affiliation(s)
- Keri A Drake
- Division of Pediatric Nephrology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Alicia R Fessler
- Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Thomas J Carroll
- Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| |
Collapse
|
17
|
Abstract
The function of the mammalian heart depends on the interplay between different cardiac cell types. The deployment of these cells, with precise spatiotemporal regulation, is also important during development to establish the heart structure. In this Review, we discuss the diverse origins of cardiac cell types and the lineage relationships between cells of a given type that contribute to different parts of the heart. The emerging lineage tree shows the progression of cell fate diversification, with patterning cues preceding cell type segregation, as well as points of convergence, with overlapping lineages contributing to a given tissue. Several cell lineage markers have been identified. However, caution is required with genetic-tracing experiments in comparison with clonal analyses. Genetic studies on cell populations provided insights into the mechanisms for lineage decisions. In the past 3 years, results of single-cell transcriptomics are beginning to reveal cell heterogeneity and early developmental trajectories. Equating this information with the in vivo location of cells and their lineage history is a current challenge. Characterization of the progenitor cells that form the heart and of the gene regulatory networks that control their deployment is of major importance for understanding the origin of congenital heart malformations and for producing cardiac tissue for use in regenerative medicine.
Collapse
|
18
|
Chessel A, Carazo Salas RE. From observing to predicting single-cell structure and function with high-throughput/high-content microscopy. Essays Biochem 2019; 63:197-208. [PMID: 31243141 PMCID: PMC6610450 DOI: 10.1042/ebc20180044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
In the past 15 years, cell-based microscopy has evolved its focus from observing cell function to aiming to predict it. In particular-powered by breakthroughs in computer vision, large-scale image analysis and machine learning-high-throughput and high-content microscopy imaging have enabled to uniquely harness single-cell information to systematically discover and annotate genes and regulatory pathways, uncover systems-level interactions and causal links between cellular processes, and begin to clarify and predict causal cellular behaviour and decision making. Here we review these developments, discuss emerging trends in the field, and describe how single-cell 'omics and single-cell microscopy are imminently in an intersecting trajectory. The marriage of these two fields will make possible an unprecedented understanding of cell and tissue behaviour and function.
Collapse
Affiliation(s)
- Anatole Chessel
- École polytechnique, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | | |
Collapse
|
19
|
Pei W, Wang X, Rössler J, Feyerabend TB, Höfer T, Rodewald HR. Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nat Protoc 2019; 14:1820-1840. [PMID: 31110297 DOI: 10.1038/s41596-019-0163-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/12/2019] [Indexed: 01/02/2023]
Abstract
Fate mapping is a powerful genetic tool for linking stem or progenitor cells with their progeny, and hence for defining cell lineages in vivo. The resolution of fate mapping depends on the numbers of distinct markers that are introduced in the beginning into stem or progenitor cells; ideally, numbers should be sufficiently large to allow the tracing of output from individual cells. Highly diverse genetic barcodes can serve this purpose. We recently developed an endogenous genetic barcoding system, termed Polylox. In Polylox, random DNA recombination can be induced by transient activity of Cre recombinase in a 2.1-kb-long artificial recombination substrate that has been introduced into a defined locus in mice (Rosa26Polylox reporter mice). Here, we provide a step-by-step protocol for the use of Polylox, including barcode induction and estimation of induction efficiency, barcode retrieval with single-molecule real-time (SMRT) DNA sequencing followed by computational barcode identification, and the calculation of barcode-generation probabilities, which is key for estimations of single-cell labeling for a given number of stem cells. Thus, Polylox barcoding enables high-resolution fate mapping in essentially all tissues in mice for which inducible Cre driver lines are available. Alternative methods include ex vivo cell barcoding, inducible transposon insertion and CRISPR-Cas9-based barcoding; Polylox currently allows combining non-invasive and cell-type-specific labeling with high label diversity. The execution time of this protocol is ~2-3 weeks for experimental data generation and typically <2 d for computational Polylox decoding and downstream analysis.
Collapse
Affiliation(s)
- Weike Pei
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Xi Wang
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Jens Rössler
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany. .,Bioquant Center, University of Heidelberg, Heidelberg, Germany.
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
20
|
Abstract
Systemic Salmonella enterica infections are a major cause of mortality worldwide and are becoming increasingly untreatable. Recent single-cell data from a mouse model of typhoid fever show that the host immune system actually eradicates many Salmonella cells, while other Salmonella organisms thrive at the same time in the same tissue, causing lethal disease progression. The surviving Salmonella cells have highly heterogeneous metabolism, growth rates, and exposure to various stresses. Emerging evidence suggests that similarly heterogeneous host-pathogen encounters might be a key feature of many infectious diseases. This heterogeneity offers fascinating opportunities for research and application. If we understand the mechanisms that determine the disparate local outcomes, we might be able to develop entirely novel strategies for infection control by broadening successful host antimicrobial attacks and closing permissive niches in which pathogens can thrive. This review describes suitable technologies, a current working model of heterogeneous host-Salmonella interactions, the impact of diverse Salmonella subsets on antimicrobial chemotherapy, and major open questions and challenges.
Collapse
|
21
|
Nef S, Stévant I, Greenfield A. Characterizing the bipotential mammalian gonad. Curr Top Dev Biol 2019; 134:167-194. [DOI: 10.1016/bs.ctdb.2019.01.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
22
|
Raj B, Gagnon JA, Schier AF. Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT. Nat Protoc 2018; 13:2685-2713. [PMID: 30353175 PMCID: PMC6279253 DOI: 10.1038/s41596-018-0058-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lineage relationships among the large number of heterogeneous cell types generated during development are difficult to reconstruct in a high-throughput manner. We recently established a method, scGESTALT, that combines cumulative editing of a lineage barcode array by CRISPR-Cas9 with large-scale transcriptional profiling using droplet-based single-cell RNA sequencing (scRNA-seq). The technique generates edits in the barcode array over multiple timepoints using Cas9 and pools of single-guide RNAs (sgRNAs) introduced during early and late zebrafish embryonic development, which distinguishes it from similar Cas9 lineage-tracing methods. The recorded lineages are captured, along with thousands of cellular transcriptomes, to build lineage trees with hundreds of branches representing relationships among profiled cell types. Here, we provide details for (i) generating transgenic zebrafish; (ii) performing multi-timepoint barcode editing; (iii) building scRNA-seq libraries from brain tissue; and (iv) concurrently amplifying lineage barcodes from captured single cells. Generating transgenic lines takes 6 months, and performing barcode editing and generating single-cell libraries involve 7 d of hands-on time. scGESTALT provides a scalable platform to map lineage relationships between cell types in any system that permits genome editing during development, regeneration, or disease.
Collapse
Affiliation(s)
- Bushra Raj
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
| | - James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Biozentrum, University of Basel, Basel, Switzerland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| |
Collapse
|
23
|
Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P, Janjuha S, Ninov N, Junker JP. Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 2018; 36:469-473. [PMID: 29644996 PMCID: PMC5942543 DOI: 10.1038/nbt.4124] [Citation(s) in RCA: 319] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022]
Abstract
A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ1. However, organizing the resulting taxonomy of cell types into lineage trees to understand developmental origin of cells remains challenging. Here we present LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)—a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
Collapse
Affiliation(s)
- Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bo Hu
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nina Mitic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sharan Janjuha
- DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Nikolay Ninov
- DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| |
Collapse
|
24
|
Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A. Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. eLife 2018; 7:34410. [PMID: 29595475 PMCID: PMC5929908 DOI: 10.7554/elife.34410] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic. During early life, animals develop from a single fertilized egg cell to hundreds, millions or even trillions of cells. These cells specialize to do different tasks; forming different tissues and organs like muscle, skin, lungs and liver. For more than a century, scientists have strived to understand the details of how animal cells become different and specialize, and have created many new techniques and technologies to help them achieve this goal. Limbs – such as arms, legs and wings – form from small lumps of cells called limb buds. Scientists use the shrimp-like crustacean, Parhyale hawaiensis, to study development, including limb growth. This species is useful because it is easy to grow, manipulate and observe its developing young in the laboratory. Understanding how its limbs develop offers important new insights into how limbs develop in other animals too. Wolff, Tinevez, Pietzsch et al. have now combined advanced microscopy with custom computer software, called Massive Multi-view Tracker (MaMuT) to investigate this. As limbs develop in Parhyale, the MaMuT software tracks how cells behave, and how they are organized. This analysis revealed that for cells to produce a limb bud, they need to split at an early stage into separate groups. These groups are organized along two body axes, one that goes from head to tail, and one that runs from back to belly. The limb grows perpendicular to these main body axes, along a new ‘proximal-distal’ axis that goes from nearest to furthest from the body. Wolff et al. found that the cells that contribute to the extremities of the limb divide faster than the ones that stay closer to the body. Finally, the results show that when cells in a limb divide, they mostly divide along the proximal-distal axis, producing one cell that is further from the body than the other. These cell activities may help limbs to get longer as they grow. Notably, the groups of cells seen by Wolff et al. were expressing genes that had previously been identified in developing limbs. This helps to validate the new results and to identify which active genes control the behaviors of the analyzed cells. These findings reveal new ways to study animal development. This approach could have many research uses and may help to link the mechanisms of cell biology to their effects. It could also contribute to new understanding of developmental and genetic conditions that affect human health.
Collapse
Affiliation(s)
- Carsten Wolff
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Tobias Pietzsch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Benjamin Harich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Léo Guignard
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | |
Collapse
|