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Capdevila C, Trifas M, Miller J, Anderson T, Sims PA, Yan KS. Cellular origins and lineage relationships of the intestinal epithelium. Am J Physiol Gastrointest Liver Physiol 2021; 321:G413-G425. [PMID: 34431400 PMCID: PMC8560372 DOI: 10.1152/ajpgi.00188.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 01/31/2023]
Abstract
Knowledge of the development and hierarchical organization of tissues is key to understanding how they are perturbed in injury and disease, as well as how they may be therapeutically manipulated to restore homeostasis. The rapidly regenerating intestinal epithelium harbors diverse cell types and their lineage relationships have been studied using numerous approaches, from classical label-retaining and genetic lineage tracing methods to novel transcriptome-based annotations. Here, we describe the developmental trajectories that dictate differentiation and lineage specification in the intestinal epithelium. We focus on the most recent single-cell RNA-sequencing (scRNA-seq)-based strategies for understanding intestinal epithelial cell lineage relationships, underscoring how they have refined our view of the development of this tissue and highlighting their advantages and limitations. We emphasize how these technologies have been applied to understand the dynamics of intestinal epithelial cells in homeostatic and injury-induced regeneration models.
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Affiliation(s)
- Claudia Capdevila
- Columbia Stem Cell Initiative, Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York
| | - Maria Trifas
- Columbia Stem Cell Initiative, Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York
| | - Jonathan Miller
- Columbia Stem Cell Initiative, Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York
| | - Troy Anderson
- Columbia Stem Cell Initiative, Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, New York
| | - Kelley S Yan
- Columbia Stem Cell Initiative, Division of Digestive and Liver Diseases, Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York
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Hu WY, Hu DP, Xie L, Nonn L, Lu R, Abern M, Shioda T, Prins GS. Keratin Profiling by Single-Cell RNA-Sequencing Identifies Human Prostate Stem Cell Lineage Hierarchy and Cancer Stem-Like Cells. Int J Mol Sci 2021; 22:ijms22158109. [PMID: 34360875 PMCID: PMC8346986 DOI: 10.3390/ijms22158109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/10/2023] Open
Abstract
Single prostate stem cells can generate stem and progenitor cells to form prostaspheres in 3D culture. Using a prostasphere-based label retention assay, we recently identified keratin 13 (KRT13)-enriched prostate stem cells at single-cell resolution, distinguishing them from daughter progenitors. Herein, we characterized the epithelial cell lineage hierarchy in prostaspheres using single-cell RNA-seq analysis. Keratin profiling revealed three clusters of label-retaining prostate stem cells; cluster I represents quiescent stem cells (PSCA, CD36, SPINK1, and KRT13/23/80/78/4 enriched), while clusters II and III represent active stem and bipotent progenitor cells (KRT16/17/6 enriched). Gene set enrichment analysis revealed enrichment of stem and cancer-related pathways in cluster I. In non-label-retaining daughter progenitor cells, three clusters were identified; cluster IV represents basal progenitors (KRT5/14/6/16 enriched), while clusters V and VI represent early and late-stage luminal progenitors, respectively (KRT8/18/10 enriched). Furthermore, MetaCore analysis showed enrichment of the “cytoskeleton remodeling–keratin filaments” pathway in cancer stem-like cells from human prostate cancer specimens. Along with common keratins (KRT13/23/80/78/4) in normal stem cells, unique keratins (KRT10/19/6C/16) were enriched in cancer stem-like cells. Clarification of these keratin profiles in human prostate stem cell lineage hierarchy and cancer stem-like cells can facilitate the identification and therapeutic targeting of prostate cancer stem-like cells.
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Affiliation(s)
- Wen-Yang Hu
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.-P.H.); (L.X.); (R.L.); (M.A.); (G.S.P.)
- Correspondence:
| | - Dan-Ping Hu
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.-P.H.); (L.X.); (R.L.); (M.A.); (G.S.P.)
| | - Lishi Xie
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.-P.H.); (L.X.); (R.L.); (M.A.); (G.S.P.)
| | - Larisa Nonn
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Ranli Lu
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.-P.H.); (L.X.); (R.L.); (M.A.); (G.S.P.)
| | - Michael Abern
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.-P.H.); (L.X.); (R.L.); (M.A.); (G.S.P.)
| | - Toshihiro Shioda
- Massachusetts General Hospital Center for Cancer Research and Harvard Medical School, Charlestown, MA 02129, USA;
| | - Gail S. Prins
- Department of Urology, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.-P.H.); (L.X.); (R.L.); (M.A.); (G.S.P.)
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA;
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Karlsson G, Sommarin MNE, Böiers C. Defining the Emerging Blood System During Development at Single-Cell Resolution. Front Cell Dev Biol 2021; 9:660350. [PMID: 34055791 PMCID: PMC8158578 DOI: 10.3389/fcell.2021.660350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/26/2021] [Indexed: 12/20/2022] Open
Abstract
Developmental hematopoiesis differs from adult and is far less described. In the developing embryo, waves of lineage-restricted blood precede the ultimate emergence of definitive hematopoietic stem cells (dHSCs) capable of maintaining hematopoiesis throughout life. During the last two decades, the advent of single-cell genomics has provided tools to circumvent previously impeding characteristics of embryonic hematopoiesis, such as cell heterogeneity and rare cell states, allowing for definition of lineage trajectories, cellular hierarchies, and cell-type specification. The field has rapidly advanced from microfluidic platforms and targeted gene expression analysis, to high throughput unbiased single-cell transcriptomic profiling, single-cell chromatin analysis, and cell tracing-offering a plethora of tools to resolve important questions within hematopoietic development. Here, we describe how these technologies have been implemented to address a wide range of aspects of embryonic hematopoiesis ranging from the gene regulatory network of dHSC formation via endothelial to hematopoietic transition (EHT) and how EHT can be recapitulated in vitro, to hematopoietic trajectories and cell fate decisions. Together, these studies have important relevance for regenerative medicine and for our understanding of genetic blood disorders and childhood leukemias.
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Affiliation(s)
| | | | - Charlotta Böiers
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
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Abstract
INTRODUCTION Lifelong maintenance of a healthy lung requires resident stem cells to proliferate according to tissue requirements. Once thought to be a quiescent tissue, evolving views of the complex differentiation landscape of lung stem and progenitor cells have broad implications for our understanding of how the lung is maintained, as well as the development of new therapies for promoting endogenous regeneration in lung disease. AREAS COVERED This review collates a large body of research relating to the hierarchical organization of epithelial stem cells in the adult lung and their role in tissue homeostasis and regeneration after injury. To identify relevant studies, PubMed was queried using one or a combination of the terms 'lung', 'airway', 'alveoli', 'stem cells', 'progenitor', 'repair' and 'regeneration'. EXPERT OPINION This review discusses how new technologies and injury models have challenged the demarcations between stem and progenitor cell populations.
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Affiliation(s)
- Jonathan L McQualter
- a School of Health and Biomedical Sciences , RMIT University , Melbourne , Australia
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Wu B, An C, Li Y, Yin Z, Gong L, Li Z, Liu Y, Heng BC, Zhang D, Ouyang H, Zou X. Reconstructing Lineage Hierarchies of Mouse Uterus Epithelial Development Using Single-Cell Analysis. Stem Cell Reports 2017. [PMID: 28625536 PMCID: PMC5511104 DOI: 10.1016/j.stemcr.2017.05.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The endometrial layer comprises luminal and glandular epithelia that both develop from the same simple layer of fetal uterine epithelium. Mechanisms of uterine epithelial progenitor self-renewal and differentiation are unclear. This study aims to systematically analyze the molecular and cellular mechanisms of uterine epithelial development by single-cell analysis. An integrated set of single-cell transcriptomic data of uterine epithelial progenitors and their differentiated progenies is provided. Additionally the unique molecular signatures of these cells, characterized by sequential upregulation of specific epigenetic and metabolic activities, and activation of unique signaling pathways and transcription factors, were also investigated. Finally a unique subpopulation of early progenitor, as well as differentiated luminal and glandular lineages, were identified. A complex cellular hierarchy of uterine epithelial development was thus delineated. Our study therefore systematically decoded molecular markers and a cellular program of uterine epithelial development that sheds light on uterine developmental biology. Single-cell transcriptome of mouse uterine epithelial development is provided Epithelial progenitors during early development of uterine epithelia is identified Molecular cascades orchestrating uterine epithelial development are dissected Cellular hierarchical map of uterine epithelial development is reconstructed
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Affiliation(s)
- Bingbing Wu
- Department of Gynecology, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, Zhejiang 310003, PR China; Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China
| | - Chengrui An
- Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China
| | - Yu Li
- Department of Gynecology, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, Zhejiang 310003, PR China; Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China
| | - Zi Yin
- Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China
| | - Lin Gong
- Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China
| | - Zhenli Li
- Department of Pathology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Yixiao Liu
- Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China
| | - Boon Chin Heng
- Department of Endodontology, Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Dandan Zhang
- Department of Pathology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Hongwei Ouyang
- Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, PR China.
| | - Xiaohui Zou
- Department of Gynecology, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, Zhejiang 310003, PR China; Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, Zhejiang 310058, PR China; Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, PR China.
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Abstract
The pathway to generate T cells from hematopoietic stem cells guides progenitors through a succession of fate choices while balancing differentiation progression against proliferation, stage to stage. Many elements of the regulatory system that controls this process are known, but the requirement for multiple, functionally distinct transcription factors needs clarification in terms of gene network architecture. Here, we compare the features of the T-cell specification system with the rule sets underlying two other influential types of gene network models: first, the combinatorial, hierarchical regulatory systems that generate the orderly, synchronized increases in complexity in most invertebrate embryos; second, the dueling 'master regulator' systems that are commonly used to explain bistability in microbial systems and in many fate choices in terminal differentiation. The T-cell specification process shares certain features with each of these prevalent models but differs from both of them in central respects. The T-cell system is highly combinatorial but also highly dose-sensitive in its use of crucial regulatory factors. The roles of these factors are not always T-lineage-specific, but they balance and modulate each other's activities long before any mutually exclusive silencing occurs. T-cell specification may provide a new hybrid model for gene networks in vertebrate developmental systems.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Yuan Kueh
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mary A Yui
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jingli A Zhang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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Kwon OJ, Xin L. Prostate epithelial stem and progenitor cells. Am J Clin Exp Urol 2014; 2:209-218. [PMID: 25374923 PMCID: PMC4219311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/30/2014] [Indexed: 06/04/2023]
Abstract
The classic androgen ablation and replacement experiment demonstrates that prostate epithelia possess extensive regenerative capacities and implies the existence of the prostate stem/progenitor cells. These cells may serve as the cells of origin for prostate cancer and their intrinsic property may dictate the clinical behaviors of the resulting diseases. Therefore, detailed characterization of these cells will potentially benefit disease prevention, diagnosis and prognosis. In this review, we describe several major in vitro and in vivo approaches that have been employed in the studies of the prostate stem cell activities, summarize the major progress that has been made during the last two decades regarding the identity of prostate stem/progenitor cells and their niches, and discuss some remaining outstanding questions in the field.
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Affiliation(s)
- Oh-Joon Kwon
- Department of Molecular and Cellular Biology, Baylor College of MedicineUSA
| | - Li Xin
- Department of Molecular and Cellular Biology, Baylor College of MedicineUSA
- Department of Pathology and Immunology, Baylor College of MedicineUSA
- Dan L. Duncan Cancer Center, Baylor College of MedicineUSA
- Baylor College of MedicineOne Baylor Plaza, Houston, TX 77030, USA
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Choi N, Zhang B, Zhang L, Ittmann M, Xin L. Adult murine prostate basal and luminal cells are self-sustained lineages that can both serve as targets for prostate cancer initiation. Cancer Cell 2012; 21:253-65. [PMID: 22340597 PMCID: PMC3285423 DOI: 10.1016/j.ccr.2012.01.005] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/02/2012] [Accepted: 01/06/2012] [Indexed: 12/21/2022]
Abstract
The prostate epithelial lineage hierarchy and the cellular origin for prostate cancer remain inadequately defined. Using a lineage-tracing approach, we show that adult rodent prostate basal and luminal cells are independently self-sustained in vivo. Disrupting the tumor suppressor Pten in either lineage led to prostate cancer initiation. However, the cellular composition and onset dynamics of the resulting tumors are distinctive. Prostate luminal cells are more responsive to Pten null-induced mitogenic signaling. In contrast, basal cells are resistant to direct transformation. Instead, loss of Pten activity induces the capability of basal cells to differentiate into transformation-competent luminal cells. Our study suggests that deregulation of epithelial differentiation is a critical step for the initiation of prostate cancers of basal cell origin.
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Affiliation(s)
- Nahyun Choi
- Department of Molecular and Cellular Biology
| | - Boyu Zhang
- Department of Molecular and Cellular Biology
| | - Li Zhang
- Department of Molecular and Cellular Biology
| | - Michael Ittmann
- Department of Pathology and Immunology
- Dan L. Duncan Cancer Center
| | - Li Xin
- Department of Molecular and Cellular Biology
- Department of Pathology and Immunology
- Dan L. Duncan Cancer Center
- Corresponding author: Li Xin, Ph.D., Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, Phone: 713-798-1650, FAX: 713-798-3017,
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