1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Tiyaboonchai A, Wakefield L, Vonada A, May CL, Dorrell C, Enicks D, Sairavi A, Kaestner KH, Grompe M. In vivo tracing of the Cytokeratin 14 lineages using self-cleaving guide RNAs and CRISPR/Cas9. Dev Biol 2023; 504:120-127. [PMID: 37813160 DOI: 10.1016/j.ydbio.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023]
Abstract
The current gold-standard for genetic lineage tracing in transgenic mice is based on cell-type specific expression of Cre recombinase. As an alternative, we developed a cell-type specific CRISPR/spCas9 system for lineage tracing. This method relies on RNA polymerase II promoter driven self-cleaving guide RNAs (scgRNA) to achieve tissue-specificity. To demonstrate proof-of-principle for this approach a transgenic mouse was generated harbouring a knock-in of a scgRNA into the Cytokeratin 14 (Krt14) locus. Krt14 expression marks the stem cells of squamous epithelium in the skin and oral mucosa. The scgRNA targets a Stop cassette preceding a fluorescent reporter in the Ai9-tdtomato mouse. Ai9-tdtomato reporter mice harbouring this allele along with a spCas9 transgene demonstrated precise marking of the Krt14 lineage. We conclude that RNA polymerase II promoter driven scgRNAs enable the use of CRISPR/spCas9 for genetic lineage tracing.
Collapse
Affiliation(s)
- Amita Tiyaboonchai
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA.
| | - Leslie Wakefield
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Anne Vonada
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Catherine L May
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Genetics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Craig Dorrell
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - David Enicks
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Anusha Sairavi
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Klaus H Kaestner
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Genetics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
| |
Collapse
|
3
|
You Z, Wang L, He H, Wu Z, Zhang X, Xue S, Xu P, Hong Y, Xiong M, Wei W, Chen Y. Mapping of clonal lineages across developmental stages in human neural differentiation. Cell Stem Cell 2023; 30:473-487.e9. [PMID: 36933556 DOI: 10.1016/j.stem.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 03/19/2023]
Abstract
The cell lineages across developmental stages remain to be elucidated. Here, we developed single-cell split barcoding (SISBAR) that allows clonal tracking of single-cell transcriptomes across stages in an in vitro model of human ventral midbrain-hindbrain differentiation. We developed "potential-spective" and "origin-spective" analyses to investigate the cross-stage lineage relationships and mapped a multi-level clonal lineage landscape depicting the whole differentiation process. We uncovered many previously uncharacterized converging and diverging trajectories. Furthermore, we demonstrate that a transcriptome-defined cell type can arise from distinct lineages that leave molecular imprints on their progenies, and the multilineage fates of a progenitor cell-type represent the collective results of distinct rather than similar clonal fates of individual progenitors, each with distinct molecular signatures. Specifically, we uncovered a ventral midbrain progenitor cluster as the common clonal origin of midbrain dopaminergic (mDA) neurons, midbrain glutamatergic neurons, and vascular and leptomeningeal cells and identified a surface marker that can improve graft outcomes.
Collapse
Affiliation(s)
- Zhiwen You
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyue Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui He
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyan Wu
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyue Zhang
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuaixiang Xue
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peibo Xu
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanhong Hong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Man Xiong
- State Key Laboratory of Medical Neurobiology, Ministry of Education (MOE) Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; Lingang Laboratory, Shanghai 200031, China.
| | - Yuejun Chen
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China.
| |
Collapse
|
4
|
Das RN, Tevet Y, Safriel S, Han Y, Moshe N, Lambiase G, Bassi I, Nicenboim J, Brückner M, Hirsch D, Eilam-Altstadter R, Herzog W, Avraham R, Poss KD, Yaniv K. Generation of specialized blood vessels via lymphatic transdifferentiation. Nature 2022; 606:570-575. [PMID: 35614218 PMCID: PMC9875863 DOI: 10.1038/s41586-022-04766-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/14/2022] [Indexed: 01/27/2023]
Abstract
The lineage and developmental trajectory of a cell are key determinants of cellular identity. In the vascular system, endothelial cells (ECs) of blood and lymphatic vessels differentiate and specialize to cater to the unique physiological demands of each organ1,2. Although lymphatic vessels were shown to derive from multiple cellular origins, lymphatic ECs (LECs) are not known to generate other cell types3,4. Here we use recurrent imaging and lineage-tracing of ECs in zebrafish anal fins, from early development to adulthood, to uncover a mechanism of specialized blood vessel formation through the transdifferentiation of LECs. Moreover, we demonstrate that deriving anal-fin vessels from lymphatic versus blood ECs results in functional differences in the adult organism, uncovering a link between cell ontogeny and functionality. We further use single-cell RNA-sequencing analysis to characterize the different cellular populations and transition states involved in the transdifferentiation process. Finally, we show that, similar to normal development, the vasculature is rederived from lymphatics during anal-fin regeneration, demonstrating that LECs in adult fish retain both potency and plasticity for generating blood ECs. Overall, our research highlights an innate mechanism of blood vessel formation through LEC transdifferentiation, and provides in vivo evidence for a link between cell ontogeny and functionality in ECs.
Collapse
Affiliation(s)
- Rudra N. Das
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel, Corresponding Authors Karina Yaniv Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel, , Rudra N. Das Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel,
| | - Yaara Tevet
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Stav Safriel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yanchao Han
- Duke Regeneration Center, Department of Cell Biology, Duke University School of Medicine, Durham, United States, Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Noga Moshe
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Giuseppina Lambiase
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ivan Bassi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julian Nicenboim
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias Brückner
- University of Muenster and Max Plank Institute for Molecular Biomedicine, Muenster, Germany
| | - Dana Hirsch
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | | | - Wiebke Herzog
- University of Muenster and Max Plank Institute for Molecular Biomedicine, Muenster, Germany
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University School of Medicine, Durham, United States
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel, Corresponding Authors Karina Yaniv Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel, , Rudra N. Das Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel,
| |
Collapse
|
5
|
Jafree DJ, Long DA, Scambler PJ, Ruhrberg C. Mechanisms and cell lineages in lymphatic vascular development. Angiogenesis 2021; 24:271-288. [PMID: 33825109 PMCID: PMC8205918 DOI: 10.1007/s10456-021-09784-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Lymphatic vessels have critical roles in both health and disease and their study is a rapidly evolving area of vascular biology. The consensus on how the first lymphatic vessels arise in the developing embryo has recently shifted. Originally, they were thought to solely derive by sprouting from veins. Since then, several studies have uncovered novel cellular mechanisms and a diversity of contributing cell lineages in the formation of organ lymphatic vasculature. Here, we review the key mechanisms and cell lineages contributing to lymphatic development, discuss the advantages and limitations of experimental techniques used for their study and highlight remaining knowledge gaps that require urgent attention. Emerging technologies should accelerate our understanding of how lymphatic vessels develop normally and how they contribute to disease.
Collapse
Affiliation(s)
- Daniyal J Jafree
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
- Faculty of Medical Sciences, University College London, London, UK
| | - David A Long
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Peter J Scambler
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Christiana Ruhrberg
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| |
Collapse
|
6
|
Greenspan LJ, Weinstein BM. To be or not to be: endothelial cell plasticity in development, repair, and disease. Angiogenesis 2021; 24:251-269. [PMID: 33449300 PMCID: PMC8205957 DOI: 10.1007/s10456-020-09761-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023]
Abstract
Endothelial cells display an extraordinary plasticity both during development and throughout adult life. During early development, endothelial cells assume arterial, venous, or lymphatic identity, while selected endothelial cells undergo additional fate changes to become hematopoietic progenitor, cardiac valve, and other cell types. Adult endothelial cells are some of the longest-lived cells in the body and their participation as stable components of the vascular wall is critical for the proper function of both the circulatory and lymphatic systems, yet these cells also display a remarkable capacity to undergo changes in their differentiated identity during injury, disease, and even normal physiological changes in the vasculature. Here, we discuss how endothelial cells become specified during development as arterial, venous, or lymphatic endothelial cells or convert into hematopoietic stem and progenitor cells or cardiac valve cells. We compare findings from in vitro and in vivo studies with a focus on the zebrafish as a valuable model for exploring the signaling pathways and environmental cues that drive these transitions. We also discuss how endothelial plasticity can aid in revascularization and repair of tissue after damage- but may have detrimental consequences under disease conditions. By better understanding endothelial plasticity and the mechanisms underlying endothelial fate transitions, we can begin to explore new therapeutic avenues.
Collapse
Affiliation(s)
- Leah J Greenspan
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
7
|
Gutierrez-Miranda L, Yaniv K. Cellular Origins of the Lymphatic Endothelium: Implications for Cancer Lymphangiogenesis. Front Physiol 2020; 11:577584. [PMID: 33071831 PMCID: PMC7541848 DOI: 10.3389/fphys.2020.577584] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The lymphatic system plays important roles in physiological and pathological conditions. During cancer progression in particular, lymphangiogenesis can exert both positive and negative effects. While the formation of tumor associated lymphatic vessels correlates with metastatic dissemination, increased severity and poor patient prognosis, the presence of functional lymphatics is regarded as beneficial for anti-tumor immunity and cancer immunotherapy delivery. Therefore, a profound understanding of the cellular origins of tumor lymphatics and the molecular mechanisms controlling their formation is required in order to improve current strategies to control malignant spread. Data accumulated over the last decades have led to a controversy regarding the cellular sources of tumor-associated lymphatic vessels and the putative contribution of non-endothelial cells to this process. Although it is widely accepted that lymphatic endothelial cells (LECs) arise mainly from pre-existing lymphatic vessels, additional contribution from bone marrow-derived cells, myeloid precursors and terminally differentiated macrophages, has also been claimed. Here, we review recent findings describing new origins of LECs during embryonic development and discuss their relevance to cancer lymphangiogenesis.
Collapse
Affiliation(s)
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
8
|
Alison MR. The cellular origins of cancer with particular reference to the gastrointestinal tract. Int J Exp Pathol 2020; 101:132-151. [PMID: 32794627 DOI: 10.1111/iep.12364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 12/18/2022] Open
Abstract
Stem cells or their closely related committed progenitor cells are the likely founder cells of most neoplasms. In the continually renewing and hierarchically organized epithelia of the oesophagus, stomach and intestine, homeostatic stem cells are located at the beginning of the cell flux, in the basal layer of the oesophagus, the isthmic region of gastric oxyntic glands and at the bottom of gastric pyloric-antral glands and colonic crypts. The introduction of mutant oncogenes such as KrasG12D or loss of Tp53 or Apc to specific cell types expressing the likes of Lgr5 and Mist1 can be readily accomplished in genetically engineered mouse models to initiate tumorigenesis. Other origins of cancer are discussed including 'reserve' stem cells that may be activated by damage or through disruption of morphogen gradients along the crypt axis. In the liver and pancreas, with little cell turnover and no obvious stem cell markers, the importance of regenerative hyperplasia associated with chronic inflammation to tumour initiation is vividly apparent, though inflammatory conditions in the renewing populations are also permissive for tumour induction. In the liver, hepatocytes, biliary epithelial cells and hepatic progenitor cells are embryologically related, and all can give rise to hepatocellular carcinoma and cholangiocarcinoma. In the exocrine pancreas, both acinar and ductal cells can give rise to pancreatic ductal adenocarcinoma (PDAC), although the preceding preneoplastic states are quite different: acinar-ductal metaplasia gives rise to pancreatic intraepithelial neoplasia culminating in PDAC, while ducts give rise to PDAC via. mucinous cell metaplasia that may have a polyclonal origin.
Collapse
Affiliation(s)
- Malcolm R Alison
- Centre for Tumour Biology, Barts Cancer Institute, Charterhouse Square, Barts and The London School of Medicine and Dentistry, London, UK
| |
Collapse
|