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Li J, de Melo Jorge DM, Wang W, Sun S, Frum T, Hang YA, Liu Y, Zhou X, Xiao J, Wang X, Spence JR, Wobus CE, Zhu HJ. Differential Bioactivation Profiles of Different GS-441524 Prodrugs in Cell and Mouse Models: ProTide Prodrugs with High Cell Permeability and Susceptibility to Cathepsin A Are More Efficient in Delivering Antiviral Active Metabolites to the Lung. J Med Chem 2024. [PMID: 38690769 DOI: 10.1021/acs.jmedchem.4c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
We assessed factors that determine the tissue-specific bioactivation of ProTide prodrugs by comparing the disposition and activation of remdesivir (RDV), its methylpropyl and isopropyl ester analogues (MeRDV and IsoRDV, respectively), the oral prodrug GS-621763, and the parent nucleotide GS-441524 (Nuc). RDV and MeRDV yielded more active metabolite remdesivir-triphosphate (RDV-TP) than IsoRDV, GS-621763, and Nuc in human lung cell models due to superior cell permeability and higher susceptivity to cathepsin A. Intravenous administration to mice showed that RDV and MeRDV delivered significantly more RDV-TP to the lung than other compounds. Nevertheless, all four ester prodrugs exhibited very low oral bioavailability (<2%), with Nuc being the predominant metabolite in blood. In conclusion, ProTides prodrugs, such as RDV and MeRDV, are more efficient in delivering active metabolites to the lung than Nuc, driven by high cell permeability and susceptivity to cathepsin A. Optimizing ProTides' ester structures is an effective strategy for enhancing prodrug activation in the lung.
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Affiliation(s)
- Jiapeng Li
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Daniel Macedo de Melo Jorge
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Weiwen Wang
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Shuxin Sun
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yu-An Hang
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Yueting Liu
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Xingwu Zhou
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Jingcheng Xiao
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
| | - Xinwen Wang
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University College of Pharmacy, Rootstown, Ohio 44272, United States
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan 48109, United States
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan 48109, United States
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2
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Xue X, Kim YS, Ponce-Arias AI, O'Laughlin R, Yan RZ, Kobayashi N, Tshuva RY, Tsai YH, Sun S, Zheng Y, Liu Y, Wong FCK, Surani A, Spence JR, Song H, Ming GL, Reiner O, Fu J. A patterned human neural tube model using microfluidic gradients. Nature 2024; 628:391-399. [PMID: 38408487 PMCID: PMC11006583 DOI: 10.1038/s41586-024-07204-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/16/2024] [Indexed: 02/28/2024]
Abstract
The human nervous system is a highly complex but organized organ. The foundation of its complexity and organization is laid down during regional patterning of the neural tube, the embryonic precursor to the human nervous system. Historically, studies of neural tube patterning have relied on animal models to uncover underlying principles. Recently, models of neurodevelopment based on human pluripotent stem cells, including neural organoids1-5 and bioengineered neural tube development models6-10, have emerged. However, such models fail to recapitulate neural patterning along both rostral-caudal and dorsal-ventral axes in a three-dimensional tubular geometry, a hallmark of neural tube development. Here we report a human pluripotent stem cell-based, microfluidic neural tube-like structure, the development of which recapitulates several crucial aspects of neural patterning in brain and spinal cord regions and along rostral-caudal and dorsal-ventral axes. This structure was utilized for studying neuronal lineage development, which revealed pre-patterning of axial identities of neural crest progenitors and functional roles of neuromesodermal progenitors and the caudal gene CDX2 in spinal cord and trunk neural crest development. We further developed dorsal-ventral patterned microfluidic forebrain-like structures with spatially segregated dorsal and ventral regions and layered apicobasal cellular organizations that mimic development of the human forebrain pallium and subpallium, respectively. Together, these microfluidics-based neurodevelopment models provide three-dimensional lumenal tissue architectures with in vivo-like spatiotemporal cell differentiation and organization, which will facilitate the study of human neurodevelopment and disease.
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Affiliation(s)
- Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yung Su Kim
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Alfredo-Isaac Ponce-Arias
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Richard O'Laughlin
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Robin Zhexuan Yan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Norio Kobayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Rami Yair Tshuva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shiyu Sun
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yi Zheng
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yue Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Frederick C K Wong
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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3
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Eiken MK, Childs CJ, Brastrom LK, Frum T, Plaster EM, Shachaf O, Pfeiffer S, Levine JE, Alysandratos KD, Kotton DN, Spence JR, Loebel C. Nascent matrix deposition supports alveolar organoid formation from aggregates in synthetic hydrogels. bioRxiv 2024:2024.03.19.585720. [PMID: 38562781 PMCID: PMC10983987 DOI: 10.1101/2024.03.19.585720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Human induced pluripotent stem cell (iPSC) derived alveolar organoids have emerged as a system to model the alveolar epithelium in homeostasis and disease. However, alveolar organoids are typically grown in Matrigel, a mouse-sarcoma derived basement membrane matrix that offers poor control over matrix properties, prompting the development of synthetic hydrogels as a Matrigel alternative. Here, we develop a two-step culture method that involves pre-aggregation of organoids in hydrogel-based microwells followed by embedding in a synthetic hydrogel that supports alveolar organoid growth, while also offering considerable control over organoid and hydrogel properties. We find that the aggregated organoids secrete their own nascent extracellular matrix (ECM) both in the microwells and upon embedding in the synthetic hydrogels. Thus, the synthetic gels described here allow us to de-couple exogenous and nascent ECM in order to interrogate the role of ECM in organoid formation.
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Affiliation(s)
- Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lindy K. Brastrom
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eleanor M. Plaster
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Orren Shachaf
- Department of Biomedical Engineering, University of Texas, Austin, TX, USA
| | - Suzanne Pfeiffer
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Justin E. Levine
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jason R. Spence
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
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4
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Jaiswal S, Wang F, Wu X, Chang TS, Shirazi A, Lee M, Dame MK, Spence JR, Wang TD. Near-Infrared In Vivo Imaging of Claudin-1 Expression by Orthotopically Implanted Patient-Derived Colonic Adenoma Organoids. Diagnostics (Basel) 2024; 14:273. [PMID: 38337789 PMCID: PMC10854921 DOI: 10.3390/diagnostics14030273] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Claudin-1 becomes overexpressed during the transformation of normal colonic mucosa to colorectal cancer (CRC). METHODS Patient-derived organoids expressed clinically relevant target levels and genetic heterogeneity, and were established from human adenoma and normal colons. Colonoids were implanted orthotopically in the colon of immunocompromised mice. This pre-clinical model of CRC provides an intact microenvironment and representative vasculature. Colonoid growth was monitored using white light endoscopy. A peptide specific for claudin-1 was fluorescently labeled for intravenous administration. NIR fluorescence images were collected using endoscopy and endomicroscopy. RESULTS NIR fluorescence images collected using wide-field endoscopy showed a significantly greater target-to-background (T/B) ratio for adenoma versus normal (1.89 ± 0.35 and 1.26 ± 0.06) colonoids at 1 h post-injection. These results were confirmed by optical sections collected using endomicroscopy. Optical sections were collected in vivo with sub-cellular resolution in vertical and horizontal planes. Greater claudin-1 expression by individual epithelial cells in adenomatous versus normal crypts was visualized. A human-specific cytokeratin stain ex vivo verified the presence of human tissues implanted adjacent to normal mouse colonic mucosa. CONCLUSIONS Increased claudin-1 expression was observed from adenoma versus normal colonoids in vivo using imaging with wide field endoscopy and endomicrosopy.
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Affiliation(s)
- Sangeeta Jaiswal
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fa Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoli Wu
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tse-Shao Chang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ahmad Shirazi
- Division of Integrative System and Design, University of Michigan, Ann Arbor, MI 48109, USA
| | - Miki Lee
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael K Dame
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas D Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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5
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Lee JH, LeCher JC, Parigoris E, Shinagawa N, Sentosa J, Manfredi C, Goh SL, De R, Tao S, Zandi K, Amblard F, Sorscher EJ, Spence JR, Tirouvanziam R, Schinazi RF, Takayama S. Stably-Inverted Apical-Out Human Upper Airway Organoids for SARS-CoV-2 Infection and Therapeutic Testing. bioRxiv 2024:2024.01.02.573939. [PMID: 38260306 PMCID: PMC10802305 DOI: 10.1101/2024.01.02.573939] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Apical-out organoids produced through eversion triggered by extra-organoid extracellular matrix (ECM) removal or degradation are generally small, structurally variable, and limited for viral infection and therapeutics testing. This work describes ECM-encapsulating, stably-inverted apical-out human upper airway organoids (AORBs) that are large (~500 μm diameter), consistently spherical, recapitulate in vivo-like cellular heterogeneity, and maintain their inverted morphology for over 60 days. Treatment of AORBs with IL-13 skews differentiation towards goblet cells and the apical-out geometry allows extra-organoid mucus collection. AORB maturation for 14 days induces strong co-expression of ACE2 and TMPRSS2 to allow high-yield infection with five SARS-CoV-2 variants. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds [remdesivir, bemnifosbuvir (AT-511), and nirmatrelvir] shows AORB antiviral assays to be comparable to gold-standard air-liquid interface cultures, but with higher throughput (~10-fold) and fewer cells (~100-fold). While this work focuses on SARS-CoV-2 applications, the consistent AORB shape and size, and one-organoid-per-well modularity broadly impacts in vitro human cell model standardization efforts in line with economic imperatives and recently updated FDA regulation on therapeutic testing.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA USA
| | - Julia C. LeCher
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA USA
| | - Noriyuki Shinagawa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Jason Sentosa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Candela Manfredi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Shu Ling Goh
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ramyani De
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sijia Tao
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Keivan Zandi
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Franck Amblard
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, 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
| | - Rabindra Tirouvanziam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Center for CF and Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Raymond F. Schinazi
- Center for Viroscience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA USA
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6
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Bragazzi Cunha J, Leix K, Sherman EJ, Mirabelli C, Frum T, Zhang CJ, Kennedy AA, Lauring AS, Tai AW, Sexton JZ, Spence JR, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in respiratory epithelial cells during SARS-CoV-2 infection. J Virol 2023; 97:e0127623. [PMID: 37975674 PMCID: PMC10734423 DOI: 10.1128/jvi.01276-23] [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: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain unclear. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top four genes identified in our screen encode components of the same type I interferon (IFN-I) signaling complex—IFNAR1, IFNAR2, JAK1, and TYK2. The fifth gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response in both Calu-3 cells and iPSC-derived type 2 alveolar epithelial cells. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
- Juliana Bragazzi Cunha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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7
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Ahmed DW, Eiken MK, DePalma SJ, Helms AS, Zemans RL, Spence JR, Baker BM, Loebel C. Integrating mechanical cues with engineered platforms to explore cardiopulmonary development and disease. iScience 2023; 26:108472. [PMID: 38077130 PMCID: PMC10698280 DOI: 10.1016/j.isci.2023.108472] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024] Open
Abstract
Mechanical forces provide critical biological signals to cells during healthy and aberrant organ development as well as during disease processes in adults. Within the cardiopulmonary system, mechanical forces, such as shear, compressive, and tensile forces, act across various length scales, and dysregulated forces are often a leading cause of disease initiation and progression such as in bronchopulmonary dysplasia and cardiomyopathies. Engineered in vitro models have supported studies of mechanical forces in a number of tissue and disease-specific contexts, thus enabling new mechanistic insights into cardiopulmonary development and disease. This review first provides fundamental examples where mechanical forces operate at multiple length scales to ensure precise lung and heart function. Next, we survey recent engineering platforms and tools that have provided new means to probe and modulate mechanical forces across in vitro and in vivo settings. Finally, the potential for interdisciplinary collaborations to inform novel therapeutic approaches for a number of cardiopulmonary diseases are discussed.
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Affiliation(s)
- Donia W. Ahmed
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Samuel J. DePalma
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Adam S. Helms
- Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachel L. Zemans
- Department of Internal Medicine, Division of Pulmonary Sciences and Critical Care Medicine – Gastroenterology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Department of Internal Medicine – Gastroenterology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Brendon M. Baker
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
- Department of Materials Science & Engineering, University of Michigan, North Campus Research Complex, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
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8
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Marella S, Sharma A, Ganesan V, Ferrer-Torres D, Krempski JW, Idelman G, Clark S, Nasiri Z, Vanoni S, Zeng C, Dlugosz AA, Zhou H, Wang S, Doyle AD, Wright BL, Spence JR, Chehade M, Hogan SP. IL-13-induced STAT3-dependent signaling networks regulate esophageal epithelial proliferation in eosinophilic esophagitis. J Allergy Clin Immunol 2023; 152:1550-1568. [PMID: 37652141 PMCID: PMC11102758 DOI: 10.1016/j.jaci.2023.07.021] [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: 01/06/2023] [Revised: 07/11/2023] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Basal zone hyperplasia (BZH) and dilated intercellular spaces (DISs) are thought to contribute to the clinical manifestations of eosinophilic esophagitis (EoE); however, the molecular pathways that drive BZH remain largely unexplored. OBJECTIVE We sought to define the role of IL-13-induced transcriptional programs in esophageal epithelial proliferation in EoE. METHODS We performed RNA sequencing, bioinformatics, Western blot, reverse transcriptase quantitative PCR, and histologic analyses on esophageal biopsies from healthy control and patients with EoE, primary esophageal cells derived from patients with EoE, and IL-13-stimulated esophageal epithelial keratinocytes grown at the air-liquid interface (EPC2-ALI). Genetic (shRNA) and pharmacologic (proteolysis-targeting chimera degrader) approaches and in vivo model of IL-13-induced esophageal epithelial remodeling (Krt5-rtTA x tetO-IL-13Tg) were used to define the role of signal transducer and activator of transcription 3 (STAT3) and STAT6 and secreted frizzled-related protein 1 (SFRP1) in esophageal epithelial proliferation. RESULTS RNA-sequencing analysis of esophageal biopsies (healthy control vs EoE) and EPC2-ALI revealed 82 common differentially expressed genes that were enriched for putative STAT3 target genes. In vitro and in vivo analyses revealed a link between IL-13-induced STAT3 and STAT6 phosphorylation, SFRP1 mRNA expression, and esophageal epithelial proliferation. In vitro studies showed that IL-13-induced esophageal epithelial proliferation was STAT3-dependent and regulated by the STAT3 target SFRP1. SFRP1 mRNA is increased in esophageal biopsies from patients with active EoE compared with healthy controls or patients in remission and identifies an esophageal suprabasal epithelial cell subpopulation that uniquely expressed the core EoE proinflammatory transcriptome genes (CCL26, ALOX15, CAPN14, ANO1, and TNFAIP6). CONCLUSIONS These studies identify SFRP1 as a key regulator of IL-13-induced and STAT3-dependent esophageal proliferation and BZH in EoE and link SFRP1+ esophageal epithelial cells with the proinflammatory and epithelial remodeling response in EoE.
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Affiliation(s)
- Sahiti Marella
- Department of Pathology, University of Michigan, Ann Arbor, Mich
| | - Ankit Sharma
- Department of Pathology, University of Michigan, Ann Arbor, Mich; Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Mich
| | - Varsha Ganesan
- Department of Pathology, University of Michigan, Ann Arbor, Mich; Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Mich
| | | | - James W Krempski
- Department of Pathology, University of Michigan, Ann Arbor, Mich; Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Mich
| | - Gila Idelman
- Department of Pathology, University of Michigan, Ann Arbor, Mich; Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Mich
| | - Sydney Clark
- Department of Pathology, University of Michigan, Ann Arbor, Mich
| | - Zena Nasiri
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Mich
| | - Simone Vanoni
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chang Zeng
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andrej A Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | - Haibin Zhou
- Pharmacology and Medicinal Chemistry, University of Michigan, Ann Arbor, Mich
| | - Shaomeng Wang
- Pharmacology and Medicinal Chemistry, University of Michigan, Ann Arbor, Mich
| | - Alfred D Doyle
- Division of Allergy, Asthma and Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, Ariz
| | - Benjamin L Wright
- Division of Allergy, Asthma and Immunology, Department of Medicine, Mayo Clinic Arizona, Scottsdale, Ariz; Section of Allergy and Immunology, Division of Pulmonology, Phoenix Children's Hospital, Phoenix, Ariz
| | - Jason R Spence
- Internal Medicine, University of Michigan, Ann Arbor, Mich
| | - Mirna Chehade
- Mount Sinai Center for Eosinophilic Disorders, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Simon P Hogan
- Department of Pathology, University of Michigan, Ann Arbor, Mich; Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Mich.
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9
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Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP. TGFB1 induces fetal reprogramming and enhances intestinal regeneration. Cell Stem Cell 2023; 30:1520-1537.e8. [PMID: 37865088 PMCID: PMC10841757 DOI: 10.1016/j.stem.2023.09.015] [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: 01/11/2023] [Revised: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
The gut epithelium has a remarkable ability to recover from damage. We employed a combination of high-throughput sequencing approaches, mouse genetics, and murine and human organoids and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. The depletion of macrophages or genetic disruption of TGFB signaling significantly impaired the regenerative response. Intestinal regeneration is characterized by the induction of a fetal-like transcriptional signature during repair. In organoid culture, TGFB1 treatment was necessary and sufficient to induce the fetal-like/regenerative state. Mesenchymal cells were also responsive to TGFB1 and enhanced the regenerative response. Mechanistically, pro-regenerative factors, YAP/TEAD and SOX9, are activated in the epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Xiaojiao Fan
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Xiaoting Xu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Prateeksha Rout
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Katherine D Walton
- Department of Internal Medicine, Division of 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
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ruolan Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Wenxin Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Rachel Ofer
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Alexandra Logerfo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Gaetan Barbet
- Child Health Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA
| | - Yan Wang
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nan Gao
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Ansu O Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of 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
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA; Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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10
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Múnera JO, Kechele DO, Bouffi C, Qu N, Jing R, Maity P, Enriquez JR, Han L, Campbell I, Mahe MM, McCauley HA, Zhang X, Sundaram N, Hudson JR, Zarsozo-Lacoste A, Pradhan S, Tominaga K, Sanchez JG, Weiss AA, Chatuvedi P, Spence JR, Hachimi M, North T, Daley GQ, Mayhew CN, Hu YC, Takebe T, Helmrath MA, Wells JM. Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon. Cell Stem Cell 2023; 30:1434-1451.e9. [PMID: 37922878 PMCID: PMC10913028 DOI: 10.1016/j.stem.2023.10.002] [Citation(s) in RCA: 1] [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: 04/18/2023] [Revised: 07/31/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Most organs have tissue-resident immune cells. Human organoids lack these immune cells, which limits their utility in modeling many normal and disease processes. Here, we describe that pluripotent stem cell-derived human colonic organoids (HCOs) co-develop a diverse population of immune cells, including hemogenic endothelium (HE)-like cells and erythromyeloid progenitors that undergo stereotypical steps in differentiation, resulting in the generation of functional macrophages. HCO macrophages acquired a transcriptional signature resembling human fetal small and large intestine tissue-resident macrophages. HCO macrophages modulate cytokine secretion in response to pro- and anti-inflammatory signals and were able to phagocytose and mount a robust response to pathogenic bacteria. When transplanted into mice, HCO macrophages were maintained within the colonic organoid tissue, established a close association with the colonic epithelium, and were not displaced by the host bone-marrow-derived macrophages. These studies suggest that HE in HCOs gives rise to multipotent hematopoietic progenitors and functional tissue-resident macrophages.
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Affiliation(s)
- Jorge O Múnera
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Daniel O Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Carine Bouffi
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Na Qu
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ran Jing
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Pritiprasanna Maity
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jacob R Enriquez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Lu Han
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Ian Campbell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Maxime M Mahe
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Heather A McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Xinghao Zhang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jonathan R Hudson
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Adrian Zarsozo-Lacoste
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Suman Pradhan
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Kentaro Tominaga
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - J Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Alison A Weiss
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Praneet Chatuvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Jason R Spence
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mariam Hachimi
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Trista North
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Pluripotent Stem Cell Facility, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Pluripotent Stem Cell Facility, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Takanori Takebe
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, 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
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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11
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Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics 2023; 24:641. [PMID: 37884859 PMCID: PMC10601309 DOI: 10.1186/s12864-023-09743-1] [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: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. RESULTS We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. CONCLUSION The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Meghan Capeling
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan W Villanueva
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Vera D Rinaldi
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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12
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Wu X, Chen CW, Jaiswal S, Chang TS, Zhang R, Dame MK, Duan Y, Jiang H, Spence JR, Hsieh SY, Wang TD. Near-Infrared Imaging of Colonic Adenomas In Vivo Using Orthotopic Human Organoids for Early Cancer Detection. Cancers (Basel) 2023; 15:4795. [PMID: 37835489 PMCID: PMC10571995 DOI: 10.3390/cancers15194795] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Colorectal cancer is a leading cause of cancer-related morbidity and mortality worldwide. Premalignant lesions that are flat and subtle in morphology are often missed in conventional colonoscopies. Patient-derived adenoma colonoids with high and low cMet expression and normal colonoids were implanted orthotopically in the colon of immunocompromised mice to serve as a preclinical model system. A peptide specific for cMet was labeled with IRDye800, a near-infrared (NIR) fluorophore. This peptide was administered intravenously, and in vivo imaging was performed using a small animal fluorescence endoscope. Quantified intensities showed a peak target-to-background ratio at ~1 h after intravenous peptide injection, and the signal cleared by ~24 h. The peptide was stable in serum with a half-life of 3.6 h. Co-staining of adenoma and normal colonoids showed a high correlation between peptide and anti-cMet antibody. A human-specific cytokeratin stain verified the presence of human tissues implanted among surrounding normal mouse colonic mucosa. Peptide biodistribution was consistent with rapid renal clearance. No signs of acute toxicity were found on either animal necropsy or serum hematology and chemistries. Human colonoids provide a clinically relevant preclinical model to evaluate the specific uptake of a NIR peptide to detect premalignant colonic lesions in vivo.
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Affiliation(s)
- Xiaoli Wu
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (X.W.); (S.J.); (M.K.D.); (J.R.S.)
| | - Chun-Wei Chen
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
| | - Sangeeta Jaiswal
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (X.W.); (S.J.); (M.K.D.); (J.R.S.)
| | - Tse-Shao Chang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Ruoliu Zhang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Michael K. Dame
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (X.W.); (S.J.); (M.K.D.); (J.R.S.)
| | - Yuting Duan
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (Y.D.); (H.J.)
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (Y.D.); (H.J.)
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (X.W.); (S.J.); (M.K.D.); (J.R.S.)
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
| | - Thomas D. Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (X.W.); (S.J.); (M.K.D.); (J.R.S.)
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
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13
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Frum T, Hsu PP, Hein RFC, Conchola AS, Zhang CJ, Utter OR, Anand A, Zhang Y, Clark SG, Glass I, Sexton JZ, Spence JR. Opposing roles for TGFβ- and BMP-signaling during nascent alveolar differentiation in the developing human lung. NPJ Regen Med 2023; 8:48. [PMID: 37689780 PMCID: PMC10492838 DOI: 10.1038/s41536-023-00325-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 08/31/2023] [Indexed: 09/11/2023] Open
Abstract
Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in repair after injury. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development. Using lung explant and organoid models, we identified opposing effects of TGFβ- and BMP-signaling, where inhibition of TGFβ- and activation of BMP-signaling in the context of high WNT- and FGF-signaling efficiently differentiated early lung progenitors into AT2-like cells in vitro. AT2-like cells differentiated in this manner exhibit surfactant processing and secretion capabilities, and long-term commitment to a mature AT2 phenotype when expanded in media optimized for primary AT2 culture. Comparing AT2-like cells differentiated with TGFβ-inhibition and BMP-activation to alternative differentiation approaches revealed improved specificity to the AT2 lineage and reduced off-target cell types. These findings reveal opposing roles for TGFβ- and BMP-signaling in AT2 differentiation and provide a new strategy to generate a therapeutically relevant cell type in vitro.
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Affiliation(s)
- Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Peggy P Hsu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Renee F C Hein
- Department of Cell and Developmental Biology, 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
| | - Charles J Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Olivia R Utter
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abhinav Anand
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yi Zhang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sydney G Clark
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, 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
- Center for Drug Repurposing, University of Michigan, Ann Arbor, MI, 48109, USA
- Michigan Institute for Clinical and Health Research, University of Michigan, 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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14
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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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15
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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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16
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Frum T, Hsu PP, Hein RFC, Conchola AS, Zhang CJ, Utter OR, Anand A, Zhang Y, Clark SG, Glass I, Sexton JZ, Spence JR. Opposing roles for TGFβ- and BMP-signaling during nascent alveolar differentiation in the developing human lung. bioRxiv 2023:2023.05.05.539573. [PMID: 37205521 PMCID: PMC10187311 DOI: 10.1101/2023.05.05.539573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in repair after injury. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development. Using lung explant and organoid models, we identified opposing effects of TGFβ- and BMP-signaling, where inhibition of TGFβ- and activation of BMP-signaling in the context of high WNT- and FGF-signaling efficiently differentiated early lung progenitors into AT2-like cells in vitro . AT2-like cells differentiated in this manner exhibit surfactant processing and secretion capabilities, and long-term commitment to a mature AT2 phenotype when expanded in media optimized for primary AT2 culture. Comparing AT2-like cells differentiated with TGFβ-inhibition and BMP-activation to alternative differentiation approaches revealed improved specificity to the AT2 lineage and reduced off-target cell types. These findings reveal opposing roles for TGFβ- and BMP-signaling in AT2 differentiation and provide a new strategy to generate a therapeutically relevant cell type in vitro .
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17
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Singh A, Poling HM, Chaturvedi P, Thorner K, Sundaram N, Kechele DO, Childs CJ, McCauley HA, Fisher GW, Brown NE, Spence JR, Wells JM, Helmrath MA. Transplanted human intestinal organoids: a resource for modeling human intestinal development. Development 2023; 150:dev201416. [PMID: 37070767 PMCID: PMC10259511 DOI: 10.1242/dev.201416] [Citation(s) in RCA: 1] [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: 11/04/2022] [Accepted: 03/28/2023] [Indexed: 04/19/2023]
Abstract
The in vitro differentiation of pluripotent stem cells into human intestinal organoids (HIOs) has served as a powerful means for creating complex three-dimensional intestinal structures. Owing to their diverse cell populations, transplantation into an animal host is supported with this system and allows the temporal formation of fully laminated structures, including crypt-villus architecture and smooth muscle layers that resemble native human intestine. Although the endpoint of HIO engraftment has been well described, here we aim to elucidate the developmental stages of HIO engraftment and establish whether it parallels fetal human intestinal development. We analyzed a time course of transplanted HIOs histologically at 2, 4, 6 and 8 weeks post-transplantation, and demonstrated that HIO maturation closely resembles key stages of fetal human intestinal development. We also utilized single-nuclear RNA sequencing to determine and track the emergence of distinct cell populations over time, and validated our transcriptomic data through in situ protein expression. These observations suggest that transplanted HIOs do indeed recapitulate early intestinal development, solidifying their value as a human intestinal model system.
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Affiliation(s)
- Akaljot Singh
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Holly M. Poling
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Konrad Thorner
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Daniel O. Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Heather A. McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Garrett W. Fisher
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nicole E. Brown
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - James M. Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael A. Helmrath
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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18
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Kim H, Villareal LB, Liu Z, Haneef M, Falcon DM, Martin DR, Lee H, Dame MK, Attili D, Chen Y, Varani J, Spence JR, Kovbasnjuk O, Colacino JA, Lyssiotis CA, Lin HC, Shah YM, Xue X. Transferrin Receptor-Mediated Iron Uptake Promotes Colon Tumorigenesis. Adv Sci (Weinh) 2023; 10:e2207693. [PMID: 36703617 PMCID: PMC10074045 DOI: 10.1002/advs.202207693] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Indexed: 05/17/2023]
Abstract
Transferrin receptor (TFRC) is the major mediator for iron entry into a cell. Under excessive iron conditions, TFRC is expected to be reduced to lower iron uptake and toxicity. However, the mechanism whereby TFRC expression is maintained at high levels in iron-enriched cancer cells and the contribution of TFRC to cancer development are enigmatic. Here the work shows TFRC is induced by adenomatous polyposis coli (APC) gene loss-driven β-catenin activation in colorectal cancer, whereas TFRC-mediated intratumoral iron accumulation potentiates β-catenin signaling by directly enhancing the activity of tankyrase. Disruption of TFRC leads to a reduction of colonic iron levels and iron-dependent tankyrase activity, which caused stabilization of axis inhibition protein 2 (AXIN2) and subsequent repression of the β-catenin/c-Myc/E2F Transcription Factor 1/DNA polymerase delta1 (POLD1) axis. POLD1 knockdown, iron chelation, and TFRC disruption increase DNA replication stress, DNA damage response, apoptosis, and reduce colon tumor growth. Importantly, a combination of iron chelators and DNA damaging agents increases DNA damage response and reduces colon tumor cell growth. TFRC-mediated iron import is at the center of a novel feed-forward loop that facilitates colonic epithelial cell survival. This discovery may provide novel strategies for colorectal cancer therapy.
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Affiliation(s)
- Hyeoncheol Kim
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Luke B Villareal
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Zhaoli Liu
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Mohammad Haneef
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Daniel M Falcon
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - David R Martin
- Department of PathologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Ho‐Joon Lee
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Michael K Dame
- Department of Internal MedicineDivision of GastroenterologyUniversity of MichiganAnn ArborMI48109USA
| | - Durga Attili
- Department of PathologyThe University of Michigan Medical SchoolAnn ArborMI48109USA
| | - Ying Chen
- Center for clinical research and translational medicineYangpu hospitalTongji University School of MedicineShanghai200090China
| | - James Varani
- Department of PathologyThe University of Michigan Medical SchoolAnn ArborMI48109USA
| | - Jason R. Spence
- Department of Internal MedicineDivision of GastroenterologyUniversity of MichiganAnn ArborMI48109USA
| | - Olga Kovbasnjuk
- Division of Gastroenterology and HepatologyDepartment of Medicinethe University of New MexicoAlbuquerqueNM87131USA
| | - Justin A Colacino
- Department of Environmental Health SciencesUniversity of MichiganAnn ArborMI48109USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Henry C Lin
- Section of GastroenterologyMedicine ServiceNew Mexico VA Health Care SystemAlbuquerqueNM87108USA
| | - Yatrik M Shah
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Xiang Xue
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
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19
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Danopoulos S, Belgacemi R, Hein RFC, Miller AJ, Deutsch GH, Glass I, Spence JR, Al Alam D. FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells. Am J Physiol Lung Cell Mol Physiol 2023; 324:L433-L444. [PMID: 36791060 PMCID: PMC10027085 DOI: 10.1152/ajplung.00316.2022] [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: 09/23/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Fibroblast growth factor (FGF) signaling is known to play an important role in lung organogenesis. However, we recently demonstrated that FGF10 fails to induce branching in human fetal lungs as is observed in mouse. Our previous human fetal lung RNA sequencing data exhibited increased FGF18 during the pseudoglandular stage of development, suggestive of its importance in human lung branching morphogenesis. Whereas it has been previously reported that FGF18 is critical during alveologenesis, few studies have described its implication in lung branching, specifically in human. Therefore, we aimed to determine the role of FGF18 in human lung branching morphogenesis. Human fetal lung explants within the pseudoglandular stage of development were treated with recombinant human FGF18 in air-liquid interface culture. Explants were analyzed grossly to assess differences in branching pattern, as well as at the cellular and molecular levels. FGF18 treatment promoted branching in explant cultures and demonstrated increased epithelial proliferation as well as maintenance of the double positive SOX2/SOX9 distal bud progenitor cells, confirming its role in human lung branching morphogenesis. In addition, FGF18 treated explants displayed increased expression of SOX9, FN1, and COL2A1 within the mesenchyme, all factors that are important to chondrocyte differentiation. In humans, cartilaginous airways extend deep into the lung up to the 12th generation of branching whereas in mouse these are restricted to the trachea and main bronchi. Therefore, our data suggest that FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells.
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Affiliation(s)
- Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
- Division of Neonatology, Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, California, United States
| | - Randa Belgacemi
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
| | - Renee F C Hein
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Alyssa J Miller
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Gail H Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, Washington, United States
| | - Ian Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States
| | - Jason R Spence
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
- Division of Neonatology, Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, California, United States
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20
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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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21
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Lotakis DM, Dheer R, Dame MK, Cuttitta AJ, Tigani DJ, Spence JR, Young VB, Ralls MW. A Pilot Study: Transcriptional Profiling, Functional Analysis, and Organoid Modeling of Intestinal Mucosa in Hirschsprung Disease. J Pediatr Surg 2023; 58:1164-1169. [PMID: 36922279 DOI: 10.1016/j.jpedsurg.2023.02.020] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital colonic aganglionosis. Many HSCR patients develop enterocolitis despite surgical resection. The pathophysiology of this inflammatory process is poorly understood. We compared transcriptional profiles and function of ganglionic and aganglionic tissue in HSCR patients. METHODS RNA sequencing was performed on mucosal tissues from HSCR patients (n = 6) and controls (n = 3). Function of matched ganglionic and aganglionic regions were investigated utilizing organoids generated from these tissues. RESULTS Transcriptional differences observed in ganglionic and aganglionic regions of HSCR patients included upregulation of genes involving inflammation, cell differentiation and proliferation as well as decreased expression of genes encoding mucins compared to controls. Organoids derived from ganglionic and aganglionic regions of HSCR patients were similar in epithelial cell differentiation, epithelial barrier formation and response to stimulation with bacterial metabolites and pro-inflammatory cytokines. CONCLUSIONS Despite normal ganglionic structure, the section of colon adjacent to the aganglionic region in HSCR patients has perturbed gene expression which resembles the aganglionic segment. Transcriptional and functional changes in colonic epithelium are persevered in the ganglionic colon used for pull-through surgery. This may explain persistence of enterocolitis despite surgical excision of aganglionic colon and subsequent endorectal pull-through performed with ganglionic colon during correction of HSCR. LEVEL OF EVIDENCE N/A.
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Affiliation(s)
- Dimitra M Lotakis
- University of Michigan, Department of Surgery, Division of Pediatric Surgery, 1540 East Hospital Drive, Ann Arbor, MI, 48109-4211, USA.
| | - Rishu Dheer
- University of Michigan, Department of Internal Medicine, Division of Infectious Disease, Ann Arbor, MI, 48109, USA
| | - Michael K Dame
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA
| | - Ashley J Cuttitta
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA
| | - Dominic J Tigani
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA
| | - Jason R Spence
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA; University of Michigan Medical School, Department of Cell and Developmental Biology, Ann Arbor, MI, 48109, USA; University of Michigan Medical School, Department of Biomedical Engineering Medicine, Ann Arbor, MI, 48109, USA
| | - Vincent B Young
- University of Michigan, Department of Internal Medicine, Division of Infectious Disease, Ann Arbor, MI, 48109, USA; University of Michigan, Department of Microbiology & Immunology, Ann Arbor, MI, 48109, USA
| | - Matthew W Ralls
- University of Michigan, Department of Surgery, Division of Pediatric Surgery, 1540 East Hospital Drive, Ann Arbor, MI, 48109-4211, USA
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22
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Zhang CJ, Meyer SR, O'Meara MJ, Huang S, Capeling MM, Ferrer-Torres D, Childs CJ, Spence JR, Fontana RJ, Sexton JZ. A human liver organoid screening platform for DILI risk prediction. J Hepatol 2023; 78:998-1006. [PMID: 36738840 DOI: 10.1016/j.jhep.2023.01.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Drug-induced liver injury (DILI), both intrinsic and idiosyncratic, causes frequent morbidity, mortality, clinical trial failures and post-approval withdrawal. This suggests an unmet need for improved in vitro models for DILI risk prediction that can account for diverse host genetics and other clinical factors. In this study, we evaluated the utility of human liver organoids (HLOs) for high-throughput DILI risk prediction and in an organ-on-chip system. METHODS HLOs were derived from three separate iPSC lines and benchmarked on two platforms for their ability to model in vitro liver function and identify hepatotoxic compounds using biochemical assays for albumin, ALT, AST, microscopy-based morphological profiling, and single-cell transcriptomics: i) HLOs dispersed in 384-well-formatted plates and exposed to a library of compounds; ii) HLOs adapted to a liver-on-chip system. RESULTS Dispersed HLOs derived from the three iPSC lines had similar DILI predictive capacity as intact HLOs in a high-throughput screening format, allowing for measurable IC50 values of compound cytotoxicity. Distinct morphological differences were observed in cells treated with drugs exerting differing mechanisms of toxicity. On-chip HLOs significantly increased albumin production, CYP450 expression, and ALT/AST release when treated with known hepatoxic drugs compared to dispersed HLOs and primary human hepatocytes. On-chip HLOs were able to predict the synergistic hepatotoxicity of tenofovir-inarigivir and displayed steatosis and mitochondrial perturbation, via phenotypic and transcriptomic analysis, on exposure to fialuridine and acetaminophen, respectively. CONCLUSIONS The high-throughput and liver-on-chip systems exhibit enhanced in vivo-like functions and demonstrate the potential utility of these platforms for DILI risk assessment. Tenofovir-inarigivr-associated hepatotoxicity was observed and correlates with the clinical manifestation of DILI observed in patients. IMPACT AND IMPLICATIONS Idiosyncratic (spontaneous, patient-specific) drug-induced liver injury (DILI) is difficult to study due to the lack of liver models that function as human liver tissue and are adaptable for large-scale drug screening. Human liver organoids grown from patient stem cells respond to known DILI-causing drugs in both a high-throughput and on a physiological "chip" culture system. These platforms show promise for researchers in their use as predictive models for novel drugs before entering clinical trials and as a potential in vitro diagnostic tool. Our findings support further development of patient-derived liver organoid lines and their use in the context of DILI research.
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Affiliation(s)
- Charles J Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sophia R Meyer
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meghan M Capeling
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, 48109, USA
| | - Daysha Ferrer-Torres
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, 48109, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Robert J Fontana
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, 48109, USA; U-M Center for Drug Repurposing, University of Michigan, Ann Arbor, MI, 48109, USA.
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23
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Chen L, Dupre A, Qiu X, Pellon-Cardenas O, Walton KD, Wang J, Perekatt AO, Hu W, Spence JR, Verzi MP. TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration. bioRxiv 2023:2023.01.13.523825. [PMID: 36711781 PMCID: PMC9882197 DOI: 10.1101/2023.01.13.523825] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The adult gut epithelium has a remarkable ability to recover from damage. To achieve cellular therapies aimed at restoring and/or replacing defective gastrointestinal tissue, it is important to understand the natural mechanisms of tissue regeneration. We employed a combination of high throughput sequencing approaches, mouse genetic models, and murine and human organoid models, and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. Depletion of macrophages or genetic disruption of TGFB-signaling significantly impaired the regenerative response following irradiation. Murine intestinal regeneration is also characterized by a process where a fetal transcriptional signature is induced during repair. In organoid culture, TGFB1-treatment was necessary and sufficient to induce a transcriptomic shift to the fetal-like/regenerative state. The regenerative response was enhanced by the function of mesenchymal cells, which are also primed for regeneration by TGFB1. Mechanistically, integration of ATAC-seq, scRNA-seq, and ChIP-seq suggest that a regenerative YAP-SOX9 transcriptional circuit is activated in epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for the application of the TGFB-induced regenerative circuit in cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Katherine D. Walton
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Ansu O. Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Jason R. Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- 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
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ, USA
- Member of the NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ, USA
- Lead Contact
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24
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Cable J, Lutolf MP, Fu J, Park SE, Apostolou A, Chen S, Song CJ, Spence JR, Liberali P, Lancaster M, Meier AB, Pek NMQ, Wells JM, Capeling MM, Uzquiano A, Musah S, Huch M, Gouti M, Hombrink P, Quadrato G, Urenda JP. Organoids as tools for fundamental discovery and translation-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1518:196-208. [PMID: 36177906 DOI: 10.1111/nyas.14874] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complex three-dimensional in vitro organ-like models, or organoids, offer a unique biological tool with distinct advantages over two-dimensional cell culture systems, which can be too simplistic, and animal models, which can be too complex and may fail to recapitulate human physiology and pathology. Significant progress has been made in driving stem cells to differentiate into different organoid types, though several challenges remain. For example, many organoid models suffer from high heterogeneity, and it can be difficult to fully incorporate the complexity of in vivo tissue and organ development to faithfully reproduce human biology. Successfully addressing such limitations would increase the viability of organoids as models for drug development and preclinical testing. On April 3-6, 2022, experts in organoid development and biology convened at the Keystone Symposium "Organoids as Tools for Fundamental Discovery and Translation" to discuss recent advances and insights from this relatively new model system into human development and disease.
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Affiliation(s)
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Lausanne, Switzerland
- Institute of Chemical Sciences and Engineering, School of Basic Science (SB), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Roche Institute for Translational Bioengineering (ITB), Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sunghee Estelle Park
- Department of Bioengineering and NSF Science and Technology Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Athanasia Apostolou
- Emulate Inc, Boston, Massachusetts, USA
- Department of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York City, New York, USA
| | - Cheng Jack Song
- Keck Medicine of University of Southern California, Los Angeles, California, USA
| | - Jason R Spence
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI) and University of Basel, Basel, Switzerland
| | | | - Anna B Meier
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Nicole Min Qian Pek
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - James M Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Developmental Biology and Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samira Musah
- Developmental and Stem Cell Biology Program and Division of Nephrology, Department of Medicine and Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Center for Biomolecular and Tissue Engineering, Durham, North Carolina, USA
- Department of Biomedical Engineering, Pratt School of Engineering, Durham, North Carolina, USA
- Duke Regeneration Center, Duke University, Durham, North Carolina, USA
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mina Gouti
- Stem Cell Modelling of Development & Disease Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pleun Hombrink
- University Medical Center Utrecht and HUB Organoids, Utrecht, Netherlands
| | - Giorgia Quadrato
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
| | - Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
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25
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Dye BR, Decker JT, Hein RF, Miller AJ, Huang S, Spence JR, Shea LD. Human Lung Organoid Culture in Alginate With and Without Matrigel to Model Development and Disease. Tissue Eng Part A 2022; 28:893-906. [PMID: 36029210 PMCID: PMC9805886 DOI: 10.1089/ten.tea.2022.0054] [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: 03/08/2022] [Accepted: 07/12/2022] [Indexed: 01/13/2023] Open
Abstract
Human lung organoids (HLOs) are enabling the study of human lung development and disease by modeling native organ tissue structure, cellular composition, and cellular organization. In this report, we demonstrate that HLOs derived from human pluripotent stem cells cultured in alginate, a fully defined nonanimal product substrate, exhibit enhanced cellular differentiation compared with HLOs cultured in the commercially available Matrigel. More specifically, we observed an earlier onset and increase in the number of multiciliated cells, along with mucus producing MUC5AC+ goblet-like cells that were not observed in HLOs cultured in Matrigel. The epithelium in alginate-grown HLOs was organized in a pseudostratified epithelium with airway basal cells lining the basal lamina, but with the apical surface of cells on the exterior of the organoid. We further observed that HLOs cultured in Matrigel exhibited mesenchymal overgrowth that was not present in alginate cultures. The containment of the mesenchyme within HLOs in alginate enabled modeling of key features of idiopathic pulmonary fibrosis (IPF) by treatment with transforming growth factor β (TGFβ). TGFβ treatment resulted in morphological changes including an increase in mesenchymal growth, increased expression of IPF markers, and decreased numbers of alveolar-like cells. This culture system provides a model to study the interaction of the mesenchyme with the epithelium during lung development and diseased states such as IPF.
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Affiliation(s)
- Briana R. Dye
- Department of Biomedical Engineering, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph T. Decker
- Department of Biomedical Engineering, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Renee F.C. Hein
- Department of Internal Medicine, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyssa J. Miller
- Department of Internal Medicine, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lonnie D. Shea
- Department of Biomedical Engineering, Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
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26
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Abstract
In vitro human models, such as gastruloids and organoids, are complex three-dimensional (3D) structures often consist of cells from multiple germ layers that possess some attributes of a developing embryo or organ. To use these models to interrogate human development and organogenesis, these 3D models must accurately recapitulate aspects of their in vivo counterparts. Recent advances in single-cell technologies, including sequencing and spatial approaches, have enabled efforts to better understand and directly compare organoids with native tissues. For example, single-cell genomic efforts have created cell and organ atlases that enable benchmarking of in vitro models and can also be leveraged to gain novel biological insights that can be used to further improve in vitro models. This Spotlight discusses the state of current in vitro model systems, the efforts to create large publicly available atlases of the developing human and how these data are being used to improve organoids. Limitations and perspectives on future efforts are also discussed.
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Affiliation(s)
- Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Madeline K. Eiken
- 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, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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27
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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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28
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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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29
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Lawrence ALE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Sule GJ, Knight JS, Wobus CE, Spence JR, Young VB, O’Riordan MX, Abuaita BH. Human neutrophil IL1β directs intestinal epithelial cell extrusion during Salmonella infection. PLoS Pathog 2022; 18:e1010855. [PMID: 36191054 PMCID: PMC9578578 DOI: 10.1371/journal.ppat.1010855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/18/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Infection of the human gut by Salmonella enterica Typhimurium (STM) results in a localized inflammatory disease that is not mimicked in murine infections. To determine mechanisms by which neutrophils, as early responders to bacterial challenge, direct inflammatory programming of human intestinal epithelium, we established a multi-component human intestinal organoid (HIO) model of STM infection. HIOs were micro-injected with STM and seeded with primary human polymorphonuclear leukocytes (PMN-HIOs). PMNs did not significantly alter luminal colonization of Salmonella, but their presence reduced intraepithelial bacterial burden. Adding PMNs to infected HIOs resulted in substantial accumulation of shed TUNEL+ epithelial cells that was driven by PMN Caspase-1 activity. Inhibition of Caspases-1, -3 or -4 abrogated epithelial cell death and extrusion in the infected PMN-HIOs but only Caspase-1 inhibition significantly increased bacterial burden in the PMN-HIO epithelium. Thus, PMNs promote cell death in human intestinal epithelial cells through multiple caspases as a protective response to infection. IL-1β was necessary and sufficient to induce cell shedding in the infected HIOs. These data support a critical innate immune function for human neutrophils in amplifying cell death and extrusion of human epithelial cells from the Salmonella-infected intestinal monolayer. Neutrophils are early responders to Salmonella intestinal infection, but how they influence infection progression and outcome is unknown. Here we use a co-culture model of human intestinal organoids and human primary neutrophils to study the contribution of human neutrophils to Salmonella infection of the intestinal epithelium. We found that neutrophils markedly enhanced epithelial defenses, including enhancing cell extrusion to reduce intraepithelial burden of Salmonella and close association with the epithelium. These findings reveal an early role for neutrophils in the gut in shaping the gut environment to control epithelial infection.
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Affiliation(s)
- Anna-Lisa E. Lawrence
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan P. Berger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Veda K. Yadagiri
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brooke Bons
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Courtney Fields
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Gautam J. Sule
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason S. Knight
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Vincent B. Young
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (MXO); (BHA)
| | - Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (MXO); (BHA)
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30
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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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31
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Loebel C, Weiner AI, Eiken MK, Katzen JB, Morley MP, Bala V, Cardenas-Diaz FL, Davidson MD, Shiraishi K, Basil MC, Ferguson LT, Spence JR, Ochs M, Beers MF, Morrisey EE, Vaughan AE, Burdick JA. Microstructured Hydrogels to Guide Self-Assembly and Function of Lung Alveolospheres. Adv Mater 2022; 34:e2202992. [PMID: 35522531 PMCID: PMC9283320 DOI: 10.1002/adma.202202992] [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] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/02/2022] [Indexed: 06/01/2023]
Abstract
Epithelial cell organoids have increased opportunities to probe questions on tissue development and disease in vitro and for therapeutic cell transplantation. Despite their potential, current protocols to grow these organoids almost exclusively depend on culture within 3D Matrigel, which limits defined culture conditions, introduces animal components, and results in heterogenous organoids (i.e., shape, size, composition). Here, a method is described that relies on hyaluronic acid hydrogels for the generation and expansion of lung alveolar organoids (alveolospheres). Using synthetic hydrogels with defined chemical and physical properties, human-induced pluripotent stem cell (iPSC)-derived alveolar type 2 cells (iAT2s) self-assemble into alveolospheres and propagate in Matrigel-free conditions. By engineering predefined microcavities within these hydrogels, the heterogeneity of alveolosphere size and structure is reduced when compared to 3D culture, while maintaining the alveolar type 2 cell fate of human iAT2-derived progenitor cells. This hydrogel system is a facile and accessible system for the culture of iPSC-derived lung progenitors and the method can be expanded to the culture of primary mouse tissue derived AT2 and other epithelial progenitor and stem cell aggregates.
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Affiliation(s)
- Claudia Loebel
- Department of Materials Science & Engineering, University of Michigan, North Campus Research Complex, 2800 Plymouth Rd, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Carl A. Gerstacker Building, 2200 Bonisteel Blvd, Ann Arbor, MI, 48109, USA
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall 210 S. 33rd Street, Philadelphia, PA, 19104, USA
| | - Aaron I Weiner
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Madeline K Eiken
- Department of Biomedical Engineering, University of Michigan, Carl A. Gerstacker Building, 2200 Bonisteel Blvd, Ann Arbor, MI, 48109, USA
| | - Jeremy B Katzen
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Michael P Morley
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Vikram Bala
- Department of Biomedical Engineering, University of Michigan, Carl A. Gerstacker Building, 2200 Bonisteel Blvd, Ann Arbor, MI, 48109, USA
| | - Fabian L Cardenas-Diaz
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Matthew D Davidson
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall 210 S. 33rd Street, Philadelphia, PA, 19104, USA
- BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, 596 UCB, Boulder, CO, 80309, USA
| | - Kazushige Shiraishi
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Maria C Basil
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Laura T Ferguson
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Jason R Spence
- Department of Biomedical Engineering, University of Michigan, Carl A. Gerstacker Building, 2200 Bonisteel Blvd, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine - Gastroenterology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA
| | - Matthias Ochs
- Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, Campus Charité Mitte, Philippstraße 12, 10115, Berlin, Germany
| | - Michael F Beers
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Edward E Morrisey
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
| | - Andrew E Vaughan
- Department of Medicine, Lung Biology Institute, University of Pennsylvania, 3450 Hamilton Walk, Stemmler Hall, Philadelphia, PA, 19104, USA
- School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St, Philadelphia, PA, 19104, USA
| | - Jason A Burdick
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall 210 S. 33rd Street, Philadelphia, PA, 19104, USA
- BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, 596 UCB, Boulder, CO, 80309, USA
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32
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Kim KS, Peck BC, Hung YH, Koch-Laskowski K, Wood L, Dedhia PH, Spence JR, Seeley RJ, Sethupathy P, Sandoval DA. Vertical sleeve gastrectomy induces enteroendocrine cell differentiation of intestinal stem cells through bile acid signaling. JCI Insight 2022; 7:154302. [PMID: 35503251 PMCID: PMC9220851 DOI: 10.1172/jci.insight.154302] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
Vertical sleeve gastrectomy (VSG) results in an increase in the number of hormone-secreting enteroendocrine cells (EECs) in the intestinal epithelium; however, the mechanism remains unclear. Notably, the beneficial effects of VSG are lost in a mouse model lacking the nuclear bile acid receptor farnesoid X receptor (FXR). FXR is a nuclear transcription factor that has been shown to regulate intestinal stem cell (ISC) function in cancer models. Therefore, we hypothesized that the VSG-induced increase in EECs is due to changes in intestinal differentiation driven by an increase in bile acid signaling through FXR. To test this, we performed VSG in mice that express EGFP in ISC/progenitor cells and performed RNA-Seq on GFP-positive cells sorted from the intestinal epithelia. We also assessed changes in EEC number (marked by glucagon-like peptide-1, GLP-1) in mouse intestinal organoids following treatment with bile acids, an FXR agonist, and an FXR antagonist. RNA-Seq of ISCs revealed that bile acid receptors are expressed in ISCs and that VSG explicitly alters expression of several genes that regulate EEC differentiation. Mouse intestinal organoids treated with bile acids and 2 different FXR agonists increased GLP-1-positive cell numbers, and administration of an FXR antagonist blocked these effects. Taken together, these data indicate that VSG drives ISC fate toward EEC differentiation through bile acid signaling.
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Affiliation(s)
- Ki-Suk Kim
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bailey Ce Peck
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Yu-Han Hung
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | | | - Landon Wood
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Priya H Dedhia
- Department of Surgery, The Ohio State University Comprehensive Cancer Center and The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Randy J Seeley
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Darleen A Sandoval
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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33
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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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34
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Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M. SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.125.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys, and gut. Angiotensin-converting enzyme 2 (ACE2), the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid, and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-κB as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines but did not affect NF-κB–regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-κB signaling could potentially have clinical application for severe COVID-19.
This research was financed by the National Heart, Lung, and Blood Institute of the NIH (grant 5K22HL125593 to M. Kazemian; R01HL119215 to J.R.S.); National Institute of General Medical Sciences of the NIH (grant R35GM138283 to M. Kazemian); and Deutsche Forschungsgemeinschaft (fellowship FR3851/2-1 to T. Freiwald) and supported, in part, by the Intramural Research Program of the NIH; the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) (project number ZIA/DK075149 to B.A.); the National Heart, Lung, and Blood Institute (NHLBI) (project number ZIA/Hl006223 to C.K.); and the National Institute of Allergy and Infectious Diseases (NIAID) (project number ZIA/AI001175 to M.S.L.). T. Frum is supported by T32DE007057. Funding for part of the work was provided by the University of Michigan Biological Scholars Program (to C.E.W.), LifeARC Charity (to S.K.), and CRUK KHP Centre (to S.K.).
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Affiliation(s)
- Bingyu Yan
- 1Department of Biochemistry, Purdue University
| | - Tilo Freiwald
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
- 3Complement and Inflammation Research Section, NHLBI, NIH
- 4Department of Nephrology, University Hospital Frankfurt, Goethe-University, Germany
| | - Daniel Chauss
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
| | - Luopin Wang
- 5Department of Computer Science, Purdue University
| | - Erin West
- 3Complement and Inflammation Research Section, NHLBI, NIH
| | - Carmen Mirabelli
- 6Department of Microbiology and Immunology, University of Michigan
| | | | | | | | | | | | | | | | - Tristan Frum
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
| | - Jason R. Spence
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
- 10Department of Cell and Developmental Biology, University of Michigan
| | - Jonathan Z. Sexton
- 7Department of Medicinal Chemistry, University of Michigan
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
| | - Konstantinos D. Alysandratos
- 11Center for Regenerative Medicine of Boston University and Boston Medical Center
- 12Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Darrell N. Kotton
- 11Center for Regenerative Medicine of Boston University and Boston Medical Center
- 12Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | | | - Jack Bibby
- 3Complement and Inflammation Research Section, NHLBI, NIH
| | - Nathalie Niyonzima
- 14Center of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Norway
| | | | - Shahram Kordasti
- 16CRUK KHP Centre, Comprehensive Cancer Centre, King’s College London, United Kingdom
- 17Haematology Department, Guy’s Hospital, United Kingdom
| | - Didier Portilla
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
- 18Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia
| | | | - Arian Laurence
- 19Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Michail S. Lionakis
- 20Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH
| | - Claudia Kemper
- 3Complement and Inflammation Research Section, NHLBI, NIH
- 21Institute for Systemic Inflammation Research, University of Lübeck, Germany
| | - Behdad Afzali
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
| | - Majid Kazemian
- 1Department of Biochemistry, Purdue University
- 5Department of Computer Science, Purdue University
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35
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Jo K, Teague S, Chen B, Khan HA, Freeburne E, Li H, Li B, Ran R, Spence JR, Heemskerk I. Efficient differentiation of human primordial germ cells through geometric control reveals a key role for Nodal signaling. eLife 2022; 11:72811. [PMID: 35394424 PMCID: PMC9106331 DOI: 10.7554/elife.72811] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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] [Received: 08/05/2021] [Accepted: 04/07/2022] [Indexed: 11/30/2022] Open
Abstract
Human primordial germ cells (hPGCs) form around the time of implantation and are the precursors of eggs and sperm. Many aspects of hPGC specification remain poorly understood because of the inaccessibility of the early postimplantation human embryo for study. Here, we show that micropatterned human pluripotent stem cells (hPSCs) treated with BMP4 give rise to hPGC-like cells (hPGCLC) and use these as a quantitatively reproducible and simple in vitro model to interrogate this important developmental event. We characterize micropatterned hPSCs up to 96 hr and show that hPGCLC populations are stable and continue to mature. By perturbing signaling during hPGCLC differentiation, we identify a previously unappreciated role for Nodal signaling and find that the relative timing and duration of BMP and Nodal signaling are critical parameters controlling the number of hPGCLCs. We formulate a mathematical model for a network of cross-repressive fates driven by Nodal and BMP signaling, which predicts the measured fate patterns after signaling perturbations. Finally, we show that hPSC colony size dictates the efficiency of hPGCLC specification, which led us to dramatically improve the efficiency of hPGCLC differentiation. In humans and other animals, eggs and sperm are unique cells that pass on genetic material to the next generation. They originate from a small group of cells called primordial germ cells that form early in life in the developing embryo. Several different signal molecules including ones known as BMP4, Wnt, and Nodal, instruct certain cells in the embryo to become primordial germ cells. The process by which primordial germ cells are made in humans is very different to how primordial germ cells are made in mice and other so-called model animals that are commonly used in research. This has made it more challenging to uncover the details of the process in humans. Fortunately, new methods have recently been created that mimic aspects of how human embryos develop using human stem cells in a laboratory dish, providing an opportunity to gain a deeper understanding of how human germ cells form. Jo et al. used a technique called micropatterning to control the shape and size of groups of human stem cells growing in a laboratory dish. Treating these cells with a signal known as BMP4 gave rise to cells that resembled primordial germ cells. The team then used this system as a model to study how primordial germ cells form in humans. The experiments found that reducing Wnt signals in stem cells stopped primordial germ cells from forming in response to BMP4, confirming that Wnt signals made by the cells in response to BMP4 are essential. However, this block was overcome by providing the stem cells with another signal called Nodal. This suggests that the role of Wnt signaling in primordial germ cell formation is in part indirect by switching on Nodal in stem cells. Defects in eggs and sperm may lead to infertility, therefore, the findings of Jo et al. have the potential to help researchers develop new fertility treatments that use eggs or sperm grown in a laboratory from the patients’ own stem cells. Such research would benefit from first developing a better understanding of how to make primordial germ cells.
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Affiliation(s)
- Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Seth Teague
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, United States
| | - Bohan Chen
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Hina Aftab Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Hunter Li
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Bolin Li
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Ran Ran
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Idse Heemskerk
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
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Kadur Lakshminarasimha Murthy P, Sontake V, Tata A, Kobayashi Y, Macadlo L, Okuda K, Conchola AS, Nakano S, Gregory S, Miller LA, Spence JR, Engelhardt JF, Boucher RC, Rock JR, Randell SH, Tata PR. Human distal lung maps and lineage hierarchies reveal a bipotent progenitor. Nature 2022; 604:111-119. [PMID: 35355018 PMCID: PMC9169066 DOI: 10.1038/s41586-022-04541-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/09/2022] [Indexed: 12/22/2022]
Abstract
Mapping the spatial distribution and molecular identity of constituent cells is essential for understanding tissue dynamics in health and disease. We lack a comprehensive map of human distal airways, including the terminal and respiratory bronchioles (TRBs), which are implicated in respiratory diseases1-4. Here, using spatial transcriptomics and single-cell profiling of microdissected distal airways, we identify molecularly distinct TRB cell types that have not-to our knowledge-been previously characterized. These include airway-associated LGR5+ fibroblasts and TRB-specific alveolar type-0 (AT0) cells and TRB secretory cells (TRB-SCs). Connectome maps and organoid-based co-cultures reveal that LGR5+ fibroblasts form a signalling hub in the airway niche. AT0 cells and TRB-SCs are conserved in primates and emerge dynamically during human lung development. Using a non-human primate model of lung injury, together with human organoids and tissue specimens, we show that alveolar type-2 cells in regenerating lungs transiently acquire an AT0 state from which they can differentiate into either alveolar type-1 cells or TRB-SCs. This differentiation programme is distinct from that identified in the mouse lung5-7. Our study also reveals mechanisms that drive the differentiation of the bipotent AT0 cell state into normal or pathological states. In sum, our findings revise human lung cell maps and lineage trajectories, and implicate an epithelial transitional state in primate lung regeneration and disease.
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Affiliation(s)
| | - Vishwaraj Sontake
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Lauren Macadlo
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ansley S Conchola
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simon Gregory
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Lisa A Miller
- California National Primate Research Center, Davis, CA, USA
- Department of Anatomy, Physiology and Cell biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John F Engelhardt
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason R Rock
- Department of Immunology Discovery, Genentech, South San Francisco, CA, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA.
- Division of Pulmonary Critical Care, Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
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Steiner CA, Berinstein JA, Louissaint J, Higgins PDR, Spence JR, Shannon C, Lu C, Stidham RW, Fletcher JG, Bruining DH, Feagan BG, Jairath V, Baker ME, Bettenworth D, Rieder F. Biomarkers for the Prediction and Diagnosis of Fibrostenosing Crohn's Disease: A Systematic Review. Clin Gastroenterol Hepatol 2022; 20:817-846.e10. [PMID: 34089850 PMCID: PMC8636551 DOI: 10.1016/j.cgh.2021.05.054] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Intestinal strictures are a common complication of Crohn's disease (CD). Biomarkers of intestinal strictures would assist in their prediction, diagnosis, and monitoring. Herein we provide a comprehensive systematic review of studies assessing biomarkers that may predict or diagnose CD-associated strictures. METHODS We performed a systematic review of PubMed, EMBASE, ISI Web of Science, Cochrane Library, and Scopus to identify citations pertaining to biomarkers of intestinal fibrosis through July 6, 2020, that used a reference standard of full-thickness histopathology or cross-sectional imaging or endoscopy. Studies were categorized based on the type of biomarker they evaluated (serum, genetic, histopathologic, or fecal). RESULTS Thirty-five distinct biomarkers from 3 major groups were identified: serum (20 markers), genetic (9 markers), and histopathology (6 markers). Promising markers include cartilage oligomeric matrix protein, hepatocyte growth factor activator, and lower levels of microRNA-19-3p (area under the curves were 0.805, 0.738, and 0.67, respectively), and multiple anti-flagellin antibodies (A4-Fla2 [odds ratio, 3.41], anti Fla-X [odds ratio, 2.95], and anti-CBir1 [multiple]). Substantial heterogeneity was observed and none of the markers had undergone formal validation. Specific limitations to acceptance of these markers included failure to use a standardized definition of stricturing disease, lack of specificity, and insufficient relevance to the pathogenesis of intestinal strictures or incomplete knowledge regarding their operating properties. CONCLUSIONS There is a lack of well-defined studies on biomarkers of intestinal stricture. Development of reliable and accurate biomarkers of stricture is a research priority. Biomarkers can support the clinical management of CD patients and aid in the stratification and monitoring of patients during clinical trials of future antifibrotic drug candidates.
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Affiliation(s)
- Calen A Steiner
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
| | - Jeffrey A Berinstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jeremy Louissaint
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Peter D R Higgins
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Carol Shannon
- Taubman Health Sciences Library, University of Michigan, Ann Arbor, Michigan
| | - Cathy Lu
- Division of Gastroenterology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ryan W Stidham
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | | | - David H Bruining
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brian G Feagan
- Alimentiv Inc, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada; Department of Biostatistics and Epidemiology, Western University, London, Ontario, Canada
| | - Vipul Jairath
- Alimentiv Inc, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada; Department of Biostatistics and Epidemiology, Western University, London, Ontario, Canada
| | - Mark E Baker
- Section of Abdominal Imaging, Imaging Institute, Digestive Diseases and Surgery Institute and Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Dominik Bettenworth
- Department of Medicine B, Gastroenterology and Hepatology, University of Münster, Münster, Germany
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio; Department of Gastroenterology, Hepatology, and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, Ohio
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38
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Harford TJ, Rezaee F, Dye BR, Fan J, Spence JR, Piedimonte G. RSV-induced changes in a 3-dimensional organoid model of human fetal lungs. PLoS One 2022; 17:e0265094. [PMID: 35263387 PMCID: PMC8906588 DOI: 10.1371/journal.pone.0265094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
We have shown that respiratory syncytial virus (RSV) can spread hematogenously from infected airways of a pregnant woman to the developing fetal lungs in utero. This study sought to measure RSV replication, cytopathic effects, and protein expression in human lung organoids (HLOs) reproducing architecture and transcriptional profiles of human fetal lungs during the 1st trimester of gestation. HLOs derived from human pluripotent stem cells were microinjected after 50 or 100 days in culture with medium or recombinant RSV-A2 expressing the red fluorescent protein gene (rrRSV). Infection was monitored by fluorescent microscopy and PCR. Immunohistochemistry and proteomic analysis were performed. RSV infected HLOs in a dose- and time-dependent manner. RSV-infected HLOs increased expression of CC10 (Club cells), but had sparse FOXJ1 (ciliated cells). Disruption of F-actin cytoskeleton was consistent with proteomic data showing a significant increase in Rho GTPases proteins. RSV upregulated the transient receptor potential vanilloid 1 (TRPV1) channel and, while β2 adrenergic receptor (β2AR) expression was decreased overall, its phosphorylated form increased. Our data suggest that prenatal RSV infection produces profound changes in fetal lungs' architecture and expression profiles and maybe an essential precursor of chronic airway dysfunction. expression profiles, and possibly be an important precursor of chronic airway dysfunction.
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Affiliation(s)
- Terri J. Harford
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Fariba Rezaee
- Center for Pediatric Pulmonary Medicine, Cleveland Clinic Children’s, Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Briana R. Dye
- Departments of Internal Medicine and Cell & Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jia Fan
- Department of Biochemistry and Molecular Biology, Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Jason R. Spence
- Departments of Internal Medicine and Cell & Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Giovanni Piedimonte
- Department of Biochemistry and Molecular Biology, Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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39
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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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40
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Ginga NJ, Slyman R, Kim GA, Parigoris E, Huang S, Yadagiri VK, Young VB, Spence JR, Takayama S. Perfusion System for Modification of Luminal Contents of Human Intestinal Organoids and Realtime Imaging Analysis of Microbial Populations. Micromachines (Basel) 2022; 13:131. [PMID: 35056297 PMCID: PMC8779378 DOI: 10.3390/mi13010131] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023]
Abstract
Intestinal organoids are 3D cell structures that replicate some aspects of organ function and are organized with a polarized epithelium facing a central lumen. To enable more applications, new technologies are needed to access the luminal cavity and apical cell surface of organoids. We developed a perfusion system utilizing a double-barrel glass capillary with a pressure-based pump to access and modify the luminal contents of a human intestinal organoid for extended periods of time while applying cyclic cellular strain. Cyclic injection and withdrawal of fluorescent FITC-Dextran coupled with real-time measurement of fluorescence intensity showed discrete changes of intensity correlating with perfusion cycles. The perfusion system was also used to modify the lumen of organoids injected with GFP-expressing E. coli. Due to the low concentration and fluorescence of the E. coli, a novel imaging analysis method utilizing bacteria enumeration and image flattening was developed to monitor E. coli within the organoid. Collectively, this work shows that a double-barrel perfusion system provides constant luminal access and allows regulation of luminal contents and luminal mixing.
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Affiliation(s)
- Nicholas J. Ginga
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Raleigh Slyman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ge-Ah Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sha Huang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (J.R.S.)
| | - Veda K. Yadagiri
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (V.K.Y.); (V.B.Y.)
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (V.K.Y.); (V.B.Y.)
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (J.R.S.)
- 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
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Jaiswal S, Joshi B, Chen J, Wang F, Dame MK, Spence JR, Newsome GM, Katz EL, Shah YM, Ramakrishnan SK, Li G, Lee M, Appelman HD, Kuick R, Wang TD. Membrane Bound Peroxiredoxin-1 Serves as a Biomarker for In Vivo Detection of Sessile Serrated Adenomas. Antioxid Redox Signal 2022; 36:39-56. [PMID: 34409853 PMCID: PMC8792500 DOI: 10.1089/ars.2020.8244] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aim: Sessile serrated adenomas (SSAs) are premalignant lesions driven by the BRAFV600E mutation to give rise to colorectal cancers (CRCs). They are often missed during white light colonoscopy because of their subtle appearance. Previously, a fluorescently labeled 7mer peptide KCCFPAQ was shown to detect SSAs in vivo. We aim to identify the target of this peptide. Results: Peroxiredoxin-1 (Prdx1) was identified as the binding partner of the peptide ligand. In vitro binding assays and immunofluorescence staining of human colon specimens ex vivo supported this result. Prdx1 was overexpressed on the membrane of cells with the BRAFV600E mutation, and this effect was dependent on oxidative stress. RKO cells harboring the BRAFV600E mutation and human SSA specimens showed higher oxidative stress as well as elevated levels of Prdx1 on the cell membrane. Innovation and Conclusion: These results suggest that Prdx1 is overexpressed on the cell surface in the presence of oxidative stress and can serve as an imaging biomarker for in vivo detection of SSAs. Antioxid. Redox Signal. 36, 39-56.
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Affiliation(s)
- Sangeeta Jaiswal
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Bishnu Joshi
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jing Chen
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fa Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael K Dame
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gina M Newsome
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Erica L Katz
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yatrik M Shah
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sadeesh K Ramakrishnan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gaoming Li
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Miki Lee
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Henry D Appelman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rork Kuick
- Department of Biostatistics, and University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas D Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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42
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Abuaita BH, Lawrence ALE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Wobus CE, Spence JR, Young VB, O’Riordan MX. Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids. PLoS Pathog 2021; 17:e1009987. [PMID: 34669717 PMCID: PMC8570492 DOI: 10.1371/journal.ppat.1009987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/05/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
Salmonella enterica represents over 2500 serovars associated with a wide-ranging spectrum of disease; from self-limiting gastroenteritis to invasive infections caused by non-typhoidal serovars (NTS) and typhoidal serovars, respectively. Host factors strongly influence infection outcome as malnourished or immunocompromised individuals can develop invasive infections from NTS, however, comparative analyses of serovar-specific host responses have been constrained by reliance on limited model systems. Here we used human intestinal organoids (HIOs), a three-dimensional “gut-like” in vitro system derived from human embryonic stem cells, to elucidate similarities and differences in host responses to NTS and typhoidal serovars. HIOs discriminated between the two most prevalent NTS, Salmonella enterica serovar Typhimurium (STM) and Salmonella enterica serovar Enteritidis (SE), and typhoidal serovar Salmonella enterica serovar Typhi (ST) in epithelial cell invasion, replication and transcriptional responses. Pro-inflammatory signaling and cytokine output was reduced in ST-infected HIOs compared to NTS infections, consistent with early stages of NTS and typhoidal diseases. While we predicted that ST would induce a distinct transcriptional profile from the NTS strains, more nuanced expression profiles emerged. Notably, pathways involved in cell cycle, metabolism and mitochondrial functions were downregulated in STM-infected HIOs and upregulated in SE-infected HIOs. These results correlated with suppression of cellular proliferation and induction of host cell death in STM-infected HIOs and in contrast, elevated levels of reactive oxygen species production in SE-infected HIOs. Collectively, these results suggest that the HIO model is well suited to reveal host transcriptional programming specific to infection by individual Salmonella serovars, and that individual NTS may provoke unique host epithelial responses during intestinal stages of infection. Salmonella enterica is the major causative agent of bacterial infections associated with contaminated food and water. Salmonella enterica consists of over 2500 serovars of which Typhimurium (STM), Enteritidis (SE) and Typhi (ST) are the three major serovars with medical relevance to humans. These serovars elicit distinctive immune responses and cause different diseases in humans, including self-limiting diarrhea, gastroenteritis and typhoid fever. Differences in the human host response to these serovars are likely to be a major contributing factor to distinct disease outcomes but are not well characterized, possibly due to the limitations of human-derived physiological infection models. Distinct from immortalized epithelial cell culture models, human intestinal organoids (HIOs) are three-dimensional structures derived from embryonic stem cells that differentiate into intestinal mesenchymal and epithelial cells, mirroring key organizational aspects of the intestine. In this study, we used HIOs to monitor transcriptional changes during early stages of STM, SE and ST infection. Our comparative analysis showed that HIO inflammatory responses are the dominant response in all infections, but ST infection induces the weakest upregulation of inflammatory mediators relative to the other serovars. In addition, we identified several cellular processes, including cell cycle and mitochondrial functions, that were inversely regulated between STM and SE infection despite these serovars causing similar localized intestinal infection in humans. Our findings reinforce HIOs as an emerging model system to study Salmonella serovar infection and define global host transcriptional response profiles as a foundation for understanding human infection outcomes.
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Affiliation(s)
- Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Anna-Lisa E. Lawrence
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan P. Berger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Veda K. Yadagiri
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brooke Bons
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Courtney Fields
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Vincent B. Young
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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43
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Ray P, Nancarrow DJ, Ferrer-Torres D, Wang Z, San Martinho M, Hinton T, Wu JH, Wu A, Turgeon DK, Hammer MA, Dame MK, Lawrence TS, O'Brien PJ, Spence JR, Beer DG, Ray D. UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma. Cell Mol Gastroenterol Hepatol 2021; 13:129-149. [PMID: 34416429 PMCID: PMC8593620 DOI: 10.1016/j.jcmgh.2021.08.003] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/10/2022]
Abstract
BACKGROUND & AIMS TP53 mutations underlie Barrett's esophagus (BE) progression to dysplasia and cancer. During BE progression, the ubiquitin ligase (E3) RNF128/GRAIL switches expression from isoform 2 (Iso2) to Iso1, stabilizing mutant p53. However, the ubiquitin-conjugating enzyme (E2) that partners with Iso1 to stabilize mutant p53 is unknown. METHODS Single-cell RNA sequencing of paired normal esophagus and BE tissues identified candidate E2s, further investigated in expression data from BE to esophageal adenocarcinoma (EAC) progression samples. Biochemical and cellular studies helped clarify the role of RNF128-E2 on mutant p53 stability. RESULTS The UBE2D family member 2D3 (UBCH5C) is the most abundant E2 in normal esophagus. However, during BE to EAC progression, loss of UBE2D3 copy number and reduced expression of RNF128 Iso2 were noted, 2 known p53 degraders. In contrast, expression of UBE2D1 (UBCH5A) and RNF128 Iso1 in dysplastic BE and EAC forms an inactive E2-E3 complex, stabilizing mutant p53. To destabilize mutant p53, we targeted RNF128 Iso1 either by mutating asparagine (N48, 59, and 101) residues to block glycosylation to facilitate β-TrCP1-mediated degradation or by mutating proline (P54 and 105) residues to restore p53 polyubiquitinating ability. In addition, either loss of UBCH5A catalytic activity, or disruption of the Iso1-UBCH5A interaction promoted Iso1 loss. Consequently, overexpression of either catalytically dead or Iso1-binding-deficient UBCH5A mutants destabilized Iso1 to degrade mutant p53, thus compromising the clonogenic survival of mutant p53-dependent BE cells. CONCLUSIONS Loss of RNF128 Iso2-UBCH5C and persistence of the Iso1-UBCH5A complex favors mutant p53 stability to promote BE cell survival. Therefore, targeting of Iso1-UBCH5A may provide a novel therapeutic strategy to prevent BE progression.
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Affiliation(s)
- Paramita Ray
- Department of Radiation Oncology, Ann Arbor, Michigan
| | | | | | | | | | - Tonaye Hinton
- Department of Radiation Oncology, Ann Arbor, Michigan
| | - Joshua H Wu
- Department of Internal Medicine, Ann Arbor, Michigan
| | - Angeline Wu
- Department of Internal Medicine, Ann Arbor, Michigan
| | | | - Max A Hammer
- Department of Internal Medicine, Ann Arbor, Michigan
| | | | | | | | - Jason R Spence
- Department of Internal Medicine, Ann Arbor, Michigan; Department of Cell and Developmental Biology, Ann Arbor, Michigan; Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - David G Beer
- Department of Radiation Oncology, Ann Arbor, Michigan; Department of Surgery, Ann Arbor, Michigan
| | - Dipankar Ray
- Department of Radiation Oncology, Ann Arbor, Michigan.
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44
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Chen KG, Park K, Spence JR. Studying SARS-CoV-2 infectivity and therapeutic responses with complex organoids. Nat Cell Biol 2021; 23:822-833. [PMID: 34341531 PMCID: PMC8355201 DOI: 10.1038/s41556-021-00721-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 06/22/2021] [Indexed: 12/15/2022]
Abstract
Clinical management of patients with severe complications of COVID-19 has been hindered by a lack of effective drugs and a failure to capture the extensive heterogeneity of the disease with conventional methods. Here we review the emerging roles of complex organoids in the study of SARS-CoV-2 infection, modelling of COVID-19 disease pathology and in drug, antibody and vaccine development. We discuss opportunities for COVID-19 research and remaining challenges in the application of organoids.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Kyeyoon Park
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jason R Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
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45
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Johnson LA, Rodansky ES, Tran A, Collins SG, Eaton KA, Malamet B, Steiner CA, Huang S, Spence JR, Higgins PDR. Effect of ABT-263 on Intestinal Fibrosis in Human Myofibroblasts, Human Intestinal Organoids, and the Mouse Salmonella typhimurium Model. Inflamm Bowel Dis 2021; 28:161-175. [PMID: 34302470 PMCID: PMC9017142 DOI: 10.1093/ibd/izab166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Intestinal fibrosis and subsequent intestinal obstruction are common complications of Crohn's disease (CD). Current therapeutics combat inflammation, but no pharmacological therapy exists for fibrostenotic disease. Pathological persistence of activated intestinal myofibroblasts is a key driver of fibrosis in CD. In other organ systems, BH-3 mimetic drugs that affect Bcl-2 apoptotic pathways induce apoptosis in activated myofibroblasts and reduce fibrogenic gene expression, thereby reducing fibrosis. METHODS We evaluated the proapoptotic and antifibrotic efficacy of several classes of BH-3 mimetics in 2 in vitro fibrogenesis models. The candidate molecule, ABT-263, was advanced to a 3-dimensional human intestinal organoid (HIO) model. Finally, the therapeutic efficacy of ABT-263 was evaluated in the mouse Salmonella typhimurium intestinal fibrosis model. RESULTS The BH-3 mimetics induced apoptosis, repressed fibrotic protein expression, and reduced fibrogenic gene expression in normal human intestinal myofibroblasts. The BH-3 mimetics that target Bcl-2 and Bcl-xl demonstrated the greatest efficacy in vitro. The ABT-199 and ABT-263 induced apoptosis and ameliorated fibrogenesis in the in vitro myofibroblast models. In the HIO model, ABT-263 inhibited fibrogenesis and induced apoptosis. In the mouse S. typhimurium model, dose-dependent reduction in macroscopic pathology, histological inflammation, inflammatory and fibrotic gene expression, and extracellular matrix protein expression indicated ABT-263 may reduce intestinal fibrosis. CONCLUSIONS In vitro, the antifibrotic efficacy of BH-3 mimetics identifies the Bcl-2 pathway as a druggable target and BH-3 mimetics as putative therapeutics. Reduction of inflammation and fibrosis in the mouse intestinal fibrosis model by ABT-263 indicates BH-3 mimetics as potential, novel antifibrotic therapeutics for Crohn's disease.
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Affiliation(s)
- Laura A Johnson
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA
| | - Eva S Rodansky
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA
| | - Anhdao Tran
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA
| | - Stephen G Collins
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of
Michigan, Ann Arbor, MI, USA
| | - Benjamin Malamet
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA
| | - Calen A Steiner
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of
Michigan, Ann Arbor, MI, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of
Michigan, Ann Arbor, MI, USA
| | - Peter D R Higgins
- Division of Gastroenterology, Department of Internal Medicine,
University of Michigan, Ann Arbor, MI,
USA,Address correspondence to: Peter Higgins, MD, PhD, MS, Department
of Internal Medicine, University of Michigan, SPC 5682, 1150 West Medical Center
Drive, Ann Arbor, MI 48109, USA ()
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46
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Schwartz AJ, Goyert JW, Solanki S, Kerk SA, Chen B, Castillo C, Hsu PP, Do BT, Singhal R, Dame MK, Lee HJ, Spence JR, Lakhal-Littleton S, Vander Heiden MG, Lyssiotis CA, Xue X, Shah YM. Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells. Nat Metab 2021; 3:969-982. [PMID: 34155415 PMCID: PMC8316354 DOI: 10.1038/s42255-021-00406-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) requires massive iron stores, but the complete mechanisms by which CRC modulates local iron handling are poorly understood. Here, we demonstrate that hepcidin is activated ectopically in CRC. Mice deficient in hepcidin specifically in the colon tumour epithelium, compared with wild-type littermates, exhibit significantly diminished tumour number, burden and size in a sporadic model of CRC, whereas accumulation of intracellular iron by deletion of the iron exporter ferroportin exacerbates these tumour parameters. Metabolomic analysis of three-dimensional patient-derived CRC tumour enteroids indicates a prioritization of iron in CRC for the production of nucleotides, which is recapitulated in our hepcidin/ferroportin mouse CRC models. Mechanistically, our data suggest that iron chelation decreases mitochondrial function, thereby altering nucleotide synthesis, whereas exogenous supplementation of nucleosides or aspartate partially rescues tumour growth in patient-derived enteroids and CRC cell lines in the presence of an iron chelator. Collectively, these data suggest that ectopic hepcidin in the tumour epithelium establishes an axis to sequester iron in order to maintain the nucleotide pool and sustain proliferation in colorectal tumours.
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Affiliation(s)
- Andrew J Schwartz
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua W Goyert
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Sumeet Solanki
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Samuel A Kerk
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Brandon Chen
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Cristina Castillo
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Peggy P Hsu
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
| | - Brian T Do
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rashi Singhal
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Michael K Dame
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
| | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
| | | | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Xue
- Department of Biochemistry and Molecular Biology, University of New Mexico, Albuquerque, NM, USA.
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA.
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47
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Shen YC, Shami AN, Moritz L, Larose H, Manske GL, Ma Q, Zheng X, Sukhwani M, Czerwinski M, Sultan C, Chen H, Gurczynski SJ, Spence JR, Orwig KE, Tallquist M, Li JZ, Hammoud SS. TCF21 + mesenchymal cells contribute to testis somatic cell development, homeostasis, and regeneration in mice. Nat Commun 2021; 12:3876. [PMID: 34162856 PMCID: PMC8222243 DOI: 10.1038/s41467-021-24130-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 05/19/2020] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Testicular development and function rely on interactions between somatic cells and the germline, but similar to other organs, regenerative capacity declines in aging and disease. Whether the adult testis maintains a reserve progenitor population remains uncertain. Here, we characterize a recently identified mouse testis interstitial population expressing the transcription factor Tcf21. We found that TCF21lin cells are bipotential somatic progenitors present in fetal testis and ovary, maintain adult testis homeostasis during aging, and act as potential reserve somatic progenitors following injury. In vitro, TCF21lin cells are multipotent mesenchymal progenitors which form multiple somatic lineages including Leydig and myoid cells. Additionally, TCF21+ cells resemble resident fibroblast populations reported in other organs having roles in tissue homeostasis, fibrosis, and regeneration. Our findings reveal that the testis, like other organs, maintains multipotent mesenchymal progenitors that can be potentially leveraged in development of future therapies for hypoandrogenism and/or infertility.
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Affiliation(s)
- Yu-Chi Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Lindsay Moritz
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Hailey Larose
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel L Manske
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Meena Sukhwani
- Department of Obstetrics, Gynecology and Reproductive Sciences, Integrative Systems Biology Graduate Program, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael Czerwinski
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Sultan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Haolin Chen
- Biochemistry and Molecular Biology, Bloomberg School of Public Health, John Hopkins, USA
| | | | - Jason R Spence
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology and Reproductive Sciences, Integrative Systems Biology Graduate Program, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michelle Tallquist
- University of Hawaii, Center for Cardiovascular Research, Honolulu, HI, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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48
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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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49
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Chang DF, Gilliam EA, Nucho LMA, Garcia J, Shevchenko Y, Zuber SM, Squillaro AI, Maselli KM, Huang S, Spence JR, Grikscheit TC. NH 2-terminal deletion of specific phosphorylation sites on PHOX2B disrupts the formation of enteric neurons in vivo. Am J Physiol Gastrointest Liver Physiol 2021; 320:G1054-G1066. [PMID: 33881351 DOI: 10.1152/ajpgi.00073.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mutations in the paired-like homeobox 2 b (PHOX2B) gene are associated with congenital central hypoventilation syndrome (CCHS), which is a rare condition in which both autonomic dysregulation with hypoventilation and an enteric neuropathy may occur. The majority of patients with CCHS have a polyalanine repeat mutation (PARM) in PHOX2B, but a minority of patients have nonpolyalanine repeat mutations (NPARMs), some of which have been localized to exon 1. A PHOX2B-Y14X nonsense mutation previously generated in a human pluripotent stem cell (hPSC) line results in an NH2-terminus truncated product missing the first 17 or 20 amino acids, possibly due to translational reinitiation at an alternate ATG start site. This NH2-terminal truncation in the PHOX2B protein results in the loss of two key phosphorylation residues. Though the deletion does not affect the potential for PHOX2BY14X/Y14X mutant hPSC to differentiate into enteric neural crest cells (ENCCs) in culture, it impedes in vivo development of neurons in an in vivo model of human aganglionic small intestine.NEW & NOTEWORTHY A mutation that affects only 17-20 NH2-terminal amino acids in the paired-like homeobox 2 b (PHOX2B) gene hinders the subsequent in vivo establishment of intestinal neuronal cells, but not the in vitro differentiation of these cells.
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Affiliation(s)
- David F Chang
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Elizabeth A Gilliam
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Laura-Marie A Nucho
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Jazmin Garcia
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Yevheniya Shevchenko
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Samuel M Zuber
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Anthony I Squillaro
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Kathryn M Maselli
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Sha Huang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jason R Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan.,Program of Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Tracy C Grikscheit
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California.,Division of Pediatric Surgery, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California.,Keck Medical School, University of Southern California, Los Angeles, California
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50
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Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M. SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. Sci Immunol 2021; 6:6/58/eabg0833. [PMID: 33827897 PMCID: PMC8139422 DOI: 10.1126/sciimmunol.abg0833] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/31/2021] [Indexed: 12/26/2022]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys and gut. Angiotensin converting enzyme (ACE) 2, the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-B as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines, but did not affect NF-B-regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-B-signaling could potentially have clinical application for severe COVID-19.
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Affiliation(s)
- Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Tilo Freiwald
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.,Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA.,Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt, Germany
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Erin West
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Charles J Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 1702118, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 1702118, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Jack Bibby
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nathalie Niyonzima
- Center of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Matthew R Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shahram Kordasti
- CRUK-KHP Centre, Comprehensive Cancer Centre, King's College London, London, UK.,Haematology Department, Guy's Hospital, London, UK
| | - Didier Portilla
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.,Division of Nephrology and the Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, VA, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Arian Laurence
- Nuffield Department of Medicine, University of Oxford, UK
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Claudia Kemper
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA. .,Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Department of Computer Science, Purdue University, West Lafayette, IN, USA
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