1
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Conchola AS, Frum T, Xiao Z, Hsu PP, Kaur K, Downey MS, Hein RFC, Miller AJ, Tsai YH, Wu A, Holloway EM, Anand A, Murthy PKL, Glass I, Tata PR, Spence JR. Regionally distinct progenitor cells in the lower airway give rise to neuroendocrine and multiciliated cells in the developing human lung. Proc Natl Acad Sci U S A 2023; 120:e2210113120. [PMID: 37279279 PMCID: PMC10268599 DOI: 10.1073/pnas.2210113120] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 04/27/2023] [Indexed: 06/08/2023] Open
Abstract
Using scRNA-seq and microscopy, we describe a cell that is enriched in the lower airways of the developing human lung and identified by the unique coexpression of SCGB3A2/SFTPB/CFTR. To functionally interrogate these cells, we apply a single-cell barcode-based lineage tracing method, called CellTagging, to track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro. Lineage tracing reveals that these cells have a distinct differentiation potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. Lineage tracing results are supported by studies using organoids and isolated cells from the lower noncartilaginous airway. We conclude that SCGB3A2/SFTPB/CFTR cells are enriched in the lower airways of the developing human lung and contribute to the epithelial diversity and heterogeneity in this region.
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Affiliation(s)
- Ansley S. Conchola
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Tristan Frum
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Zhiwei Xiao
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Peggy P. Hsu
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
| | - Kamika Kaur
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Michael S. Downey
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
| | - Renee F. C. Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Alyssa J. Miller
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Angeline Wu
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Abhinav Anand
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
| | | | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA98195
| | | | - Jason R. Spence
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI48109
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI48109
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2
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Bouffi C, Wikenheiser-Brokamp KA, Chaturvedi P, Sundaram N, Goddard GR, Wunderlich M, Brown NE, Staab JF, Latanich R, Zachos NC, Holloway EM, Mahe MM, Poling HM, Vales S, Fisher GW, Spence JR, Mulloy JC, Zorn AM, Wells JM, Helmrath MA. In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Nat Biotechnol 2023; 41:824-831. [PMID: 36702898 PMCID: PMC10264243 DOI: 10.1038/s41587-022-01558-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/07/2022] [Indexed: 01/27/2023]
Abstract
Human intestinal organoids (HIOs) derived from pluripotent stem cells provide a valuable model for investigating human intestinal organogenesis and physiology, but they lack the immune components required to fully recapitulate the complexity of human intestinal biology and diseases. To address this issue and to begin to decipher human intestinal-immune crosstalk during development, we generated HIOs containing immune cells by transplanting HIOs under the kidney capsule of mice with a humanized immune system. We found that human immune cells temporally migrate to the mucosa and form cellular aggregates that resemble human intestinal lymphoid follicles. Moreover, after microbial exposure, epithelial microfold cells are increased in number, leading to immune cell activation determined by the secretion of IgA antibodies in the HIO lumen. This in vivo HIO system with human immune cells provides a framework for future studies on infection- or allergen-driven intestinal diseases.
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Affiliation(s)
- Carine Bouffi
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathryn A Wikenheiser-Brokamp
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gillian R Goddard
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nicole E Brown
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Janet F Staab
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Latanich
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily M Holloway
- Université de Nantes, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
| | - Maxime M Mahe
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Université de Nantes, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Holly M Poling
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Simon Vales
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Garrett W Fisher
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - James C Mulloy
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Helmrath
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
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3
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Childs CJ, Holloway EM, Sweet CW, Tsai YH, Wu A, Vallie A, Eiken MK, Capeling MM, Zwick RK, Palikuqi B, Trentesaux C, Wu JH, Pellón-Cardenas O, Zhang CJ, Glass I, Loebel C, Yu Q, Camp JG, Sexton JZ, Klein OD, Verzi MP, Spence JR. EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids. JCI Insight 2023; 8:e165566. [PMID: 36821371 PMCID: PMC10070114 DOI: 10.1172/jci.insight.165566] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Epithelial organoids derived from intestinal tissue, called enteroids, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Here, we interrogated the cell signaling environment within the developing human intestine to identify niche cues that may be important for epithelial development and homeostasis. We identified an EGF family member, EPIREGULIN (EREG), which is robustly expressed in the developing human crypt. Enteroids generated from the developing human intestine grown in standard culture conditions, which contain EGF, are dominated by stem and progenitor cells and feature little differentiation and no spatial organization. Our results demonstrate that EREG can replace EGF in vitro, and EREG leads to spatially resolved enteroids that feature budded and proliferative crypt domains and a differentiated villus-like central lumen. Multiomic (transcriptome plus epigenome) profiling of native crypts, EGF-grown enteroids, and EREG-grown enteroids showed that EGF enteroids have an altered chromatin landscape that is dependent on EGF concentration, downregulate the master intestinal transcription factor CDX2, and ectopically express stomach genes, a phenomenon that is reversible. This is in contrast to EREG-grown enteroids, which remain intestine like in culture. Thus, EREG creates a homeostatic intestinal niche in vitro, enabling interrogation of stem cell function, cellular differentiation, and disease modeling.
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Affiliation(s)
- Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Caden W. Sweet
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Yu-Hwai Tsai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Angeline Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Abigail Vallie
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Meghan M. Capeling
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Rachel K. Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Brisa Palikuqi
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Coralie Trentesaux
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Joshua H. Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Oscar Pellón-Cardenas
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ian Glass
- Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
- Department of Materials Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Qianhui Yu
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - J. Gray Camp
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Jonathan Z. Sexton
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael P. Verzi
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
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4
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Ferrer-Torres D, Wu JH, Zhang CJ, Hammer MA, Dame MK, Wu A, Holloway EM, Karpoff K, McCarthy CL, Bohm MS, Cuttitta AJ, Tigani DJ, Huang S, Tsai YH, Miller AJ, Walker T, Bayer DE, Hogan SP, Turgeon DK, Lin J, Higgins PDR, Sexton J, Spence JR. Mapping the adult human esophagus in vivo and in vitro. Development 2022; 149:dev200614. [PMID: 36278875 PMCID: PMC9720751 DOI: 10.1242/dev.200614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/20/2022] [Indexed: 10/22/2023]
Abstract
Many esophageal diseases can arise during development or throughout life. Therefore, well-characterized in vitro models and detailed methods are essential for studying human esophageal development, homeostasis and disease. Here, we (1) create an atlas of the cell types observed in the normal adult human esophagus; (2) establish an ancestrally diverse biobank of in vitro esophagus tissue to interrogate homeostasis and injury; and (3) benchmark in vitro models using the adult human esophagus atlas. We created a single-cell RNA sequencing reference atlas using fresh adult esophagus biopsies and a continuously expanding biobank of patient-derived in vitro cultures (n=55 lines). We identify and validate several transcriptionally distinct cell classes in the native human adult esophagus, with four populations belonging to the epithelial layer, including basal, epibasal, early differentiating and terminally differentiated luminal cells. Benchmarking in vitro esophagus cultures to the in vivo reference using single-cell RNA sequencing shows that the basal stem cells are robustly maintained in vitro, and the diversity of epithelial cell types in culture is dependent on cell density. We also demonstrate that cultures can be grown in 2D or as 3D organoids, and these methods can be employed for modeling the complete epithelial layers, thereby enabling in vitro modeling of the human adult esophagus.
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Affiliation(s)
- Daysha Ferrer-Torres
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H. Wu
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charles J. Zhang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max A. Hammer
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael K. Dame
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kateryna Karpoff
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Caroline L. McCarthy
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Margaret S. Bohm
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ashley J. Cuttitta
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Dominic J. Tigani
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alyssa J. Miller
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Taylor Walker
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David E. Bayer
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Simon P. Hogan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Danielle Kim Turgeon
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jules Lin
- Department of Thoracic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter D. R. Higgins
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jonathan Sexton
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
- U-M Center for Drug Repurposing, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Hein RFC, Conchola AS, Fine AS, Xiao Z, Frum T, Brastrom LK, Akinwale MA, Childs CJ, Tsai YH, Holloway EM, Huang S, Mahoney J, Heemskerk I, Spence JR. Stable iPSC-derived NKX2-1+ lung bud tip progenitor organoids give rise to airway and alveolar cell types. Development 2022; 149:dev200693. [PMID: 36039869 PMCID: PMC9534489 DOI: 10.1242/dev.200693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022]
Abstract
Bud tip progenitors (BTPs) in the developing lung give rise to all epithelial cell types found in the airways and alveoli. This work aimed to develop an iPSC organoid model enriched with NKX2-1+ BTP-like cells. Building on previous studies, we optimized a directed differentiation paradigm to generate spheroids with more robust NKX2-1 expression. Spheroids were expanded into organoids that possessed NKX2-1+/CPM+ BTP-like cells, which increased in number over time. Single cell RNA-sequencing analysis revealed a high degree of transcriptional similarity between induced BTPs (iBTPs) and in vivo BTPs. Using FACS, iBTPs were purified and expanded as induced bud tip progenitor organoids (iBTOs), which maintained an enriched population of bud tip progenitors. When iBTOs were directed to differentiate into airway or alveolar cell types using well-established methods, they gave rise to organoids composed of organized airway or alveolar epithelium, respectively. Collectively, iBTOs are transcriptionally and functionally similar to in vivo BTPs, providing an important model for studying human lung development and differentiation.
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Affiliation(s)
- Renee F. C. Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ansley S. Conchola
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexis S. Fine
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhiwei Xiao
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lindy K. Brastrom
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mayowa A. Akinwale
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John Mahoney
- Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | - Idse Heemskerk
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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6
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Hein RFC, Wu JH, Holloway EM, Frum T, Conchola AS, Tsai YH, Wu A, Fine AS, Miller AJ, Szenker-Ravi E, Yan KS, Kuo CJ, Glass I, Reversade B, Spence JR. R-SPONDIN2 + mesenchymal cells form the bud tip progenitor niche during human lung development. Dev Cell 2022; 57:1598-1614.e8. [PMID: 35679862 PMCID: PMC9283295 DOI: 10.1016/j.devcel.2022.05.010] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 01/23/2023]
Abstract
The human respiratory epithelium is derived from a progenitor cell in the distal buds of the developing lung. These "bud tip progenitors" are regulated by reciprocal signaling with surrounding mesenchyme; however, mesenchymal heterogeneity and function in the developing human lung are poorly understood. We interrogated single-cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonist RSPO2, and we found that the adjacent bud tip progenitors are enriched for the RSPO2 receptor LGR5. Functional experiments using organoid models, explant cultures, and FACS-isolated RSPO2+ mesenchyme show that RSPO2 is a critical niche cue that potentiates WNT signaling in bud tip progenitors to support their maintenance and multipotency.
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Affiliation(s)
- Renee F C Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ansley S Conchola
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexis S Fine
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alyssa J Miller
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emmanuelle Szenker-Ravi
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore 138648, Singapore
| | - Kelley S Yan
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Departments of Medicine and Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore 138648, Singapore; Laboratory of Human Genetics & Therapeutics, Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore; Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
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7
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Tsai YH, Wu A, Wu JH, Capeling MM, Holloway EM, Huang S, Czerwinkski M, Glass I, Higgins PDR, Spence JR. Acquisition of NOTCH dependence is a hallmark of human intestinal stem cell maturation. Stem Cell Reports 2022; 17:1138-1153. [PMID: 35395175 PMCID: PMC9133587 DOI: 10.1016/j.stemcr.2022.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/28/2022] Open
Abstract
NOTCH signaling is a key regulator involved in maintaining intestinal stem cell (ISC) homeostasis and for balancing differentiation. Using single-cell transcriptomics, we observed that OLFM4, a NOTCH target gene present in ISCs, is first expressed at 13 weeks post-conception in the developing human intestine and increases over time. This led us to hypothesize that the requirement for NOTCH signaling is acquired across human development. To test this, we established a series of epithelium-only organoids (enteroids) from different developmental stages and used γ-secretase inhibitors (dibenzazepine [DBZ] or DAPT) to functionally block NOTCH signaling. Using quantitative enteroid-forming assays, we observed a decrease in enteroid forming efficiency in response to γ-secretase inhibition as development progress. When DBZ was added to cultures and maintained during routine passaging, enteroids isolated from tissue before 20 weeks had higher recovery rates following single-cell serial passaging. Finally, bulk RNA sequencing (RNA-seq) analysis 1 day and 3 days after DBZ treatment showed major differences in the transcriptional changes between developing or adult enteroids. Collectively, these data suggest that ISC dependence on NOTCH signaling increases as the human intestine matures.
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Affiliation(s)
- Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinkski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
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8
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Kong W, Fu YC, Holloway EM, Garipler G, Yang X, Mazzoni EO, Morris SA. Capybara: A computational tool to measure cell identity and fate transitions. Cell Stem Cell 2022; 29:635-649.e11. [PMID: 35354062 PMCID: PMC9040453 DOI: 10.1016/j.stem.2022.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 01/14/2023]
Abstract
Measuring cell identity in development, disease, and reprogramming is challenging as cell types and states are in continual transition. Here, we present Capybara, a computational tool to classify discrete cell identity and intermediate "hybrid" cell states, supporting a metric to quantify cell fate transition dynamics. We validate hybrid cells using experimental lineage tracing data to demonstrate the multi-lineage potential of these intermediate cell states. We apply Capybara to diagnose shortcomings in several cell engineering protocols, identifying hybrid states in cardiac reprogramming and off-target identities in motor neuron programming, which we alleviate by adding exogenous signaling factors. Further, we establish a putative in vivo correlate for induced endoderm progenitors. Together, these results showcase the utility of Capybara to dissect cell identity and fate transitions, prioritizing interventions to enhance the efficiency and fidelity of stem cell engineering.
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Affiliation(s)
- Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Yuheng C Fu
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Emily M Holloway
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY 10003, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | | | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA.
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9
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Capeling MM, Huang S, Childs CJ, Wu JH, Tsai YH, Wu A, Garg N, Holloway EM, Sundaram N, Bouffi C, Helmrath M, Spence JR. Suspension culture promotes serosal mesothelial development in human intestinal organoids. Cell Rep 2022; 38:110379. [PMID: 35172130 PMCID: PMC9002973 DOI: 10.1016/j.celrep.2022.110379] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 09/08/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Pluripotent-stem-cell-derived human intestinal organoids (HIOs) model some aspects of intestinal development and disease, but current culture methods do not fully recapitulate the diverse cell types and complex organization of the human intestine and are reliant on 3D extracellular matrix or hydrogel systems, which limit experimental control and translational potential for regenerative medicine. We describe suspension culture as a simple, low-maintenance method for culturing HIOs and for promoting in vitro differentiation of an organized serosal mesothelial layer that is similar to primary human intestinal serosal mesothelium based on single-cell RNA sequencing and histological analysis. Functionally, HIO serosal mesothelium has the capacity to differentiate into smooth-muscle-like cells and exhibits fibrinolytic activity. An inhibitor screen identifies Hedgehog and WNT signaling as regulators of human serosal mesothelial differentiation. Collectively, suspension HIOs represent a three-dimensional model to study the human serosal mesothelium.
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Affiliation(s)
- Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Neil Garg
- School of Kinesiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Carine Bouffi
- Division of Pediatric General and Thoracic Surgery Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Michael Helmrath
- Division of Pediatric General and Thoracic Surgery Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Jason R Spence
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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10
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Yu Q, Kilik U, Holloway EM, Tsai YH, Harmel C, Wu A, Wu JH, Czerwinski M, Childs CJ, He Z, Capeling MM, Huang S, Glass IA, Higgins PDR, Treutlein B, Spence JR, Camp JG. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 2021; 184:3281-3298.e22. [PMID: 34019796 PMCID: PMC8208823 DOI: 10.1016/j.cell.2021.04.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022]
Abstract
Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity during human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract. We illuminate cell states, transcription factors, and organ-specific epithelial stem cell and mesenchyme interactions across lineages. We implement the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions. We show that HIOs recapitulate reference cell states and use HIOs to reconstruct the molecular dynamics of intestinal epithelium and mesenchyme emergence. We show that the mesenchyme-derived niche cue NRG1 enhances intestinal stem cell maturation in vitro and that the homeobox transcription factor CDX2 is required for regionalization of intestinal epithelium and mesenchyme in humans. This work combines cell atlases and organoid technologies to understand how human organ development is orchestrated.
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Affiliation(s)
- Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Umut Kilik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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11
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Howden SE, Wilson SB, Groenewegen E, Starks L, Forbes TA, Tan KS, Vanslambrouck JM, Holloway EM, Chen YH, Jain S, Spence JR, Little MH. Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk. Cell Stem Cell 2021; 28:671-684.e6. [PMID: 33378647 PMCID: PMC8026527 DOI: 10.1016/j.stem.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 10/05/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
During development, distinct progenitors contribute to the nephrons versus the ureteric epithelium of the kidney. Indeed, previous human pluripotent stem-cell-derived models of kidney tissue either contain nephrons or pattern specifically to the ureteric epithelium. By re-analyzing the transcriptional distinction between distal nephron and ureteric epithelium in human fetal kidney, we show here that, while existing nephron-containing kidney organoids contain distal nephron epithelium and no ureteric epithelium, this distal nephron segment alone displays significant in vitro plasticity and can adopt a ureteric epithelial tip identity when isolated and cultured in defined conditions. "Induced" ureteric epithelium cultures can be cryopreserved, serially passaged without loss of identity, and transitioned toward a collecting duct fate. Cultures harboring loss-of-function mutations in PKHD1 also recapitulate the cystic phenotype associated with autosomal recessive polycystic kidney disease.
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Affiliation(s)
- Sara E Howden
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, 3052 VIC, Australia.
| | - Sean B Wilson
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Ella Groenewegen
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia
| | - Lakshi Starks
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia
| | - Thomas A Forbes
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, 3052 VIC, Australia; Department of Nephrology, Royal Children's Hospital, Flemington Rd, Parkville, Melbourne, 3052 VIC, Australia
| | - Ker Sin Tan
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia
| | | | | | | | | | - Jason R Spence
- University of Michigan Medical School, Ann Arbor, MI, USA
| | - Melissa H Little
- Murdoch Children's Research Institute, Parkville, Melbourne, 3052 VIC, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, 3052 VIC, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC, Australia.
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12
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Holloway EM, Czerwinski M, Tsai YH, Wu JH, Wu A, Childs CJ, Walton KD, Sweet CW, Yu Q, Glass I, Treutlein B, Camp JG, Spence JR. Mapping Development of the Human Intestinal Niche at Single-Cell Resolution. Cell Stem Cell 2021; 28:568-580.e4. [PMID: 33278341 PMCID: PMC7935765 DOI: 10.1016/j.stem.2020.11.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/27/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
The human intestinal stem cell niche supports self-renewal and epithelial function, but little is known about its development. We used single-cell mRNA sequencing with in situ validation approaches to interrogate human intestinal development from 7-21 weeks post conception, assigning molecular identities and spatial locations to cells and factors that comprise the niche. Smooth muscle cells of the muscularis mucosa, in close proximity to proliferative crypts, are a source of WNT and RSPONDIN ligands, whereas EGF is expressed far from crypts in the villus epithelium. Instead, an PDGFRAHI/F3HI/DLL1HI mesenchymal population lines the crypt-villus axis and is the source of the epidermal growth factor (EGF) family member NEUREGULIN1 (NRG1). In developing intestine enteroid cultures, NRG1, but not EGF, permitted increased cellular diversity via differentiation of secretory lineages. This work highlights the complexities of intestinal EGF/ERBB signaling and delineates key niche cells and signals of the developing intestine.
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Affiliation(s)
- Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Katherine D Walton
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Caden W Sweet
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA.
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13
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Miller AJ, Yu Q, Czerwinski M, Tsai YH, Conway RF, Wu A, Holloway EM, Walker T, Glass IA, Treutlein B, Camp JG, Spence JR. In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. Dev Cell 2020; 54:818. [PMID: 32991836 PMCID: PMC7540720 DOI: 10.1016/j.devcel.2020.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Holloway EM, Wu JH, Czerwinski M, Sweet CW, Wu A, Tsai YH, Huang S, Stoddard AE, Capeling MM, Glass I, Spence JR. Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells. Dev Cell 2020; 54:516-528.e7. [PMID: 32841595 PMCID: PMC7480827 DOI: 10.1016/j.devcel.2020.07.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 12/17/2022]
Abstract
Human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) lack some cellular populations found in the native organ, including vasculature. Using single-cell RNA sequencing (scRNA-seq), we have identified a population of endothelial cells (ECs) present early in HIO differentiation that declines over time in culture. Here, we developed a method to expand and maintain this endogenous population of ECs within HIOs (vHIOs). Given that ECs possess organ-specific gene expression, morphology, and function, we used bulk RNA-seq and scRNA-seq to interrogate the developing human intestine, lung, and kidney in order to identify organ-enriched EC gene signatures. By comparing these gene signatures and validated markers to HIO ECs, we find that HIO ECs grown in vitro share the highest similarity with native intestinal ECs relative to kidney and lung. Together, these data demonstrate that HIOs can co-differentiate a native EC population that is properly patterned with an intestine-specific EC transcriptional signature in vitro.
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Affiliation(s)
- Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Caden W Sweet
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Amy E Stoddard
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
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15
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Miller AJ, Yu Q, Czerwinski M, Tsai YH, Conway RF, Wu A, Holloway EM, Walker T, Glass IA, Treutlein B, Camp JG, Spence JR. In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. Dev Cell 2020; 53:117-128.e6. [PMID: 32109386 PMCID: PMC7396815 DOI: 10.1016/j.devcel.2020.01.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
Bud tip progenitor cells give rise to all murine lung epithelial lineages and have been described in the developing human lung; however, the mechanisms controlling human bud tip differentiation into specific lineages are unclear. Here, we used homogeneous human bud tip organoid cultures and identified SMAD signaling as a key regulator of the bud tip-to-airway transition. SMAD induction led to the differentiation of airway-like organoids possessing functional basal cells capable of clonal expansion and multilineage differentiation. To benchmark in vitro-derived organoids, we developed a single-cell mRNA sequencing atlas of the human lung from 11.5 to 21 weeks of development, which revealed high degrees of similarity between the in vitro-derived and in vivo airway. Together, this work sheds light on human airway differentiation in vitro and provides a single-cell atlas of the developing human lung.
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Affiliation(s)
- Alyssa J Miller
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; University of Basel, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Renee F Conway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Taylor Walker
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; University of Basel, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Jason R Spence
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
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16
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Abstract
Organoids are complex three-dimensional in vitro organ-like model systems. Human organoids, which are derived from human pluripotent stem cells or primary human donor tissue, have been used to address fundamental questions about human development, stem cell biology and organ regeneration. Focus has now shifted towards implementation of organoids for biological discovery and advancing existing systems to more faithfully recapitulate the native organ. This work has highlighted significant unknowns in human biology and has invigorated new exploration into the cellular makeup of human organs during development and in the adult - work that is crucial for providing appropriate benchmarks for organoid systems. In this Review, we discuss efforts to characterize human organ cellular complexity and attempts to make organoid models more realistic through co-culture, transplantation and bioengineering approaches.
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Affiliation(s)
- Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Masterton G, Holloway EM, Timbury GC. Role of local authority homes in the care of the dependent elderly: a prospective study. Br Med J (Clin Res Ed) 1981; 283:523-4. [PMID: 6455180 PMCID: PMC1507955 DOI: 10.1136/bmj.283.6290.523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A two-year prospective study of 11 local authority homes showed no increase in the degrees of behavioural disabilities or the prevalence of dependency or dementia among the residents. This finding, which differed from trends reported in other studies, was unlikely to be due to the design of the study and occurred in the absence of a co-ordinated service for the elderly. It was probably the effect of changes in the admission policy of the social-work services and suggests that, in some parts of Britain at least, residential homes are no longer absorbing additional numbers of dependent or demented old people in need of institutional care.
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18
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Masterton G, Holloway EM, Timbury GC. The behavioural characteristics of local authority home residents referred to a geriatric psychiatry service. J Epidemiol Community Health 1980; 34:102-5. [PMID: 7400721 PMCID: PMC1052052 DOI: 10.1136/jech.34.2.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
With increasing demands upon a geriatric psychiatry service, the priorities for day care and long-term hospital care have had to be re-examined. As a result, old people already in local authority residential care are receiving lower priority than those still in the community. In this study we suggest that certain behavioural characteristics and, in particular, incontinence, may present the caring staff of residential homes with special difficulties. We conclude that adequate assessment is essential to ensure that residents are suited to the level of facilities supplied.
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19
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Masterton G, Holloway EM, Timbury GC. The prevalence of incontinence in local authority homes for the elderly. Health Bull (Edinb) 1980; 38:62-4. [PMID: 7380652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Masterton G, Holloway EM, Timburg GC. The prevalence of organic cerebral impairment and behavioural problems within local authority homes for the elderly. Age Ageing 1979; 8:226-30. [PMID: 517315 DOI: 10.1093/ageing/8.4.226] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ninety-six per cent of the residents occupying the 11 Local Authority Homes within the catchment area of one Scottish district psychiatric hospital were surveyed to estimate current levels of organic cerebral impairment and behavioural problems in the Homes. Clear evidence of dementia was shown by 27.1% of the residents but the actual prevalence of organic cerebral impairment could be as high as 66.4%. An excessively high level of socially disruptive behaviour was discovered. This study suggests that Local Authority Homes, with their present staffing levels, are having to cope with large numbers of dependent and behaviourally disturbed old people. Four possible solutions are outlined. Irrespective of what is adopted, it is essential that Health and Social Service developments are fully co-ordinated.
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