1
|
Wilson AP, Moshal KS, Franca AP, Ramani S, Gallucci R, Chaaban H, Burge KY. Analyzing efficiency of a lentiviral shRNA knockdown system in human enteroids using western blot and flow cytometry. STAR Protoc 2024; 5:103082. [PMID: 38781076 PMCID: PMC11145376 DOI: 10.1016/j.xpro.2024.103082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/11/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Enteroids are in vitro models to study gastrointestinal pathologies and test personalized therapeutics; however, the inherent complexity of enteroids often renders standard gene editing approaches ineffective. Here, we introduce a refined lentiviral transfection protocol, ensuring sufficient lentiviral engagement with enteroids while considering spatiotemporal growth variability throughout the extracellular matrix. Additionally, we highlight a selection process for transduced cells, introduce a protocol to accurately measure transduction efficiency, and explore methodologies to gauge effects of gene knockdown on biological processes.
Collapse
Affiliation(s)
- Adam P Wilson
- Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Karni S Moshal
- Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Addison P Franca
- Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sasirekha Ramani
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Randle Gallucci
- Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Hala Chaaban
- Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Kathryn Y Burge
- Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| |
Collapse
|
2
|
Laudadio I, Carissimi C, Scafa N, Bastianelli A, Fulci V, Renzini A, Russo G, Oliva S, Vitali R, Palone F, Cucchiara S, Stronati L. Characterization of patient-derived intestinal organoids for modelling fibrosis in Inflammatory Bowel Disease. Inflamm Res 2024:10.1007/s00011-024-01901-9. [PMID: 38842554 DOI: 10.1007/s00011-024-01901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND AND AIMS Intestinal fibrosis is a common complication of Inflammatory Bowel Disease (IBD), namely Crohn's disease (CD) and ulcerative colitis (UC), but the precise mechanism by which it occurs is incompletely understood hampering the development of effective therapeutic strategies. Here, we aimed at inducing and characterizing an inflammation-mediated fibrosis in patient-derived organoids (PDOs) issued from crypts isolated from colonic mucosal biopsies of IBD pediatric patients and age matched-control subjects (CTRLs). METHODS Inflammatory-driven fibrosis was induced by exposing CTRL-, CD- and UC-PDOs to the pro-inflammatory cytokine TNF-α for one day, followed by a co-treatment with TNF-α and TGF-β1 for three days. Fibrotic response was proven by analyzing inflammatory and fibrotic markers by RT-qPCR and immunofluorescence. Transcriptomic changes were assessed by RNA-sequencing. RESULTS Co-treatment with TNF-α and TGF-β1 caused in CTRL- and IBD-PDOs morphological changes towards a mesenchymal-like phenotype and up-regulation of inflammatory, mesenchymal, and fibrotic markers. Transcriptomic profiling highlighted that in all intestinal PDOs, regardless of the disease, the co-exposure to TNF-α and TGF-β1 regulated EMT genes and specifically increased genes involved in positive regulation of cell migration. Finally, we demonstrated that CD-PDOs display a specific response to fibrosis compared to both CTRL- and UC-PDOs, mainly characterized by upregulation of nuclear factors controlling transcription. CONCLUSIONS This study demonstrates that intestinal PDOs may develop an inflammatory-derived fibrosis thus representing a promising tool to study fibrogenesis in IBD. Fibrotic PDOs show increased expression of EMT genes. In particular, fibrotic CD-PDOs display a specific gene expression signature compared to UC and CTRL-PDOs.
Collapse
Affiliation(s)
- Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Noemi Scafa
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alex Bastianelli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alessandra Renzini
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Via. A. Scarpa, 16, 00161, Rome, Italy
| | - Giusy Russo
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Salvatore Oliva
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Roberta Vitali
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Francesca Palone
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Salvatore Cucchiara
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
| |
Collapse
|
3
|
Marin ND, Becker-Hapak M, Song WM, Alayo QA, Marsala L, Sonnek N, Berrien-Elliott MM, Foster M, Foltz JA, Tran J, Wong P, Cubitt CC, Pence P, Hwang K, Zhou AY, Jacobs MT, Schappe T, Russler-Germain DA, Fields RC, Ciorba MA, Fehniger TA. Memory-like differentiation enhances NK cell responses against colorectal cancer. Oncoimmunology 2024; 13:2348254. [PMID: 38737793 PMCID: PMC11086027 DOI: 10.1080/2162402x.2024.2348254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/23/2024] [Indexed: 05/14/2024] Open
Abstract
Metastatic (m) colorectal cancer (CRC) is an incurable disease with a poor prognosis and thus remains an unmet clinical need. Immune checkpoint blockade (ICB)-based immunotherapy is effective for mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) mCRC patients, but it does not benefit the majority of mCRC patients. NK cells are innate lymphoid cells with potent effector responses against a variety of tumor cells but are frequently dysfunctional in cancer patients. Memory-like (ML) NK cells differentiated after IL-12/IL-15/IL-18 activation overcome many challenges to effective NK cell anti-tumor responses, exhibiting enhanced recognition, function, and in vivo persistence. We hypothesized that ML differentiation enhances the NK cell responses to CRC. Compared to conventional (c) NK cells, ML NK cells displayed increased IFN-γ production against both CRC cell lines and primary patient-derived CRC spheroids. ML NK cells also exhibited improved killing of CRC target cells in vitro in short-term and sustained cytotoxicity assays, as well as in vivo in NSG mice. Mechanistically, enhanced ML NK cell responses were dependent on the activating receptor NKG2D as its blockade significantly decreased ML NK cell functions. Compared to cNK cells, ML NK cells exhibited greater antibody-dependent cytotoxicity when targeted against CRC by cetuximab. ML NK cells from healthy donors and mCRC patients exhibited increased anti-CRC responses. Collectively, our findings demonstrate that ML NK cells exhibit enhanced responses against CRC targets, warranting further investigation in clinical trials for mCRC patients, including those who have failed ICB.
Collapse
Affiliation(s)
- Nancy D. Marin
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Michelle Becker-Hapak
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Wilbur M. Song
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Quazim A. Alayo
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lynne Marsala
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Naomi Sonnek
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Melissa M. Berrien-Elliott
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mark Foster
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer A. Foltz
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer Tran
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pamela Wong
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Celia C. Cubitt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Pence
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kimberly Hwang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alice Y. Zhou
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Miriam T. Jacobs
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy Schappe
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - David A. Russler-Germain
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan C. Fields
- Section of Surgical Oncology, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew A. Ciorba
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Todd A. Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
4
|
Wang B, Iglesias-Ledon L, Bishop M, Chadha A, Rudolph SE, Longo BN, Cairns DM, Chen Y, Kaplan DL. Impact of Micro- and Nano-Plastics on Human Intestinal Organoid-Derived Epithelium. Curr Protoc 2024; 4:e1027. [PMID: 38588063 DOI: 10.1002/cpz1.1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The development of patient-derived intestinal organoids represents an invaluable model for simulating the native human intestinal epithelium. These stem cell-rich cultures outperform commonly used cell lines like Caco-2 and HT29-MTX in reflecting the cellular diversity of the native intestinal epithelium after differentiation. In our recent study examining the effects of polystyrene (PS), microplastics (MPs), and nanoplastics (NPs), widespread pollutants in our environment and food chain, on the human intestinal epithelium, these organoids have been instrumental in elucidating the absorption mechanisms and potential biological impacts of plastic particles. Building on previously established protocols in human intestinal organoid culture, we herein detail a streamlined protocol for the cultivation, differentiation, and generation of organoid-derived monolayers. This protocol is tailored to generate monolayers incorporating microfold cells (M cells), key for intestinal particle uptake but often absent in current in vitro models. We provide validated protocols for the characterization of MPs/NPs via scanning electron microscopy (SEM) for detailed imaging and their introduction to intestinal epithelial monolayer cells via confocal immunostaining. Additionally, protocols to test the impacts of MP/NP exposure on the functions of the intestinal barrier using transendothelial electrical resistance (TEER) measurements and assessing inflammatory responses using cytokine profiling are detailed. Overall, our protocols enable the generation of human intestinal organoid monolayers, complete with the option of including or excluding M cells, offering crucial techniques for observing particle uptake and identifying inflammatory responses in intestinal epithelial cells to advance our knowledge of the potential effects of plastic pollution on human gut health. These approaches are also amendable to the study of other gut-related chemical and biological exposures and physiological responses due to the robust nature of the systems. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Human intestinal organoid culture and generation of monolayers with and without M cells Support Protocol 1: Culture of L-WRN and production of WRN-conditioned medium Support Protocol 2: Neuronal cell culture and integration into intestinal epithelium Support Protocol 3: Immune cell culture and integration into intestinal epithelium Basic Protocol 2: Scanning electron microscopy: sample preparation and imaging Basic Protocol 3: Immunostaining and confocal imaging of MP/NP uptake in organoid-derived monolayers Basic Protocol 4: Assessment of intestinal barrier function via TEER measurements Basic Protocol 5: Cytokine profiling using ELISA post-MP/NP exposure.
Collapse
Affiliation(s)
- Brooke Wang
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | | | - Matthew Bishop
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Anushka Chadha
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Sara E Rudolph
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Brooke N Longo
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Dana M Cairns
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| |
Collapse
|
5
|
Salerno-Goncalves R, Chen H, Bafford AC, Izquierdo M, Hormazábal JC, Lagos R, Tettelin H, D'Mello A, Booth JS, Fasano A, Levine MM, Sztein MB. Early host immune responses in a human organoid-derived gallbladder monolayer to Salmonella Typhi strains from patients with acute and chronic infections: a comparative analysis. Front Immunol 2024; 15:1334762. [PMID: 38533492 PMCID: PMC10963533 DOI: 10.3389/fimmu.2024.1334762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi), a human-restricted pathogen, invades the host through the gut to cause typhoid fever. Recent calculations of the typhoid fever burden estimated that more than 10 million new typhoid fever cases occur in low and middle-income countries, resulting in 65,400-187,700 deaths yearly. Interestingly, if not antibiotic-treated, upon the resolution of acute disease, 1%-5% of patients become asymptomatic chronic carriers. Chronically infected hosts are not only critical reservoirs of infection that transmit the disease to naive individuals but are also predisposed to developing gallbladder carcinoma. Nevertheless, the molecular mechanisms involved in the early interactions between gallbladder epithelial cells and S. Typhi remain largely unknown. Based on our previous studies showing that closely related S. Typhi strains elicit distinct innate immune responses, we hypothesized that host molecular pathways activated by S. Typhi strains derived from acutely and chronically infected patients would differ. To test this hypothesis, we used a novel human organoid-derived polarized gallbladder monolayer model, and S. Typhi strains derived from acutely and chronically infected patients. We found that S. Typhi strains derived from acutely and chronically infected patients differentially regulate host mitogen-activated protein kinase (MAPK) and S6 transcription factors. These variations might be attributed to differential cytokine signaling, predominantly via TNF-α and IL-6 production and appear to be influenced by the duration the isolate was subjected to selective pressures in the gallbladder. These findings represent a significant leap in understanding the complexities behind chronic S. Typhi infections in the gallbladder and may uncover potential intervention targets.
Collapse
Affiliation(s)
- Rosângela Salerno-Goncalves
- Center for Vaccine Development and Global Health and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Haiyan Chen
- Center for Vaccine Development and Global Health and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Andrea C Bafford
- Division of General and Oncologic Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mariana Izquierdo
- Center for Vaccine Development and Global Health and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Juan Carlos Hormazábal
- Seccion Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Rosanna Lagos
- Seccion Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Hervé Tettelin
- Department of Microbiology and Immunology and Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, United States
| | - Adonis D'Mello
- Department of Microbiology and Immunology and Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jayaum S Booth
- Center for Vaccine Development and Global Health and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Boston, MA, United States
| | - Myron M Levine
- Center for Vaccine Development and Global Health and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Marcelo B Sztein
- Center for Vaccine Development and Global Health and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
- Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
| |
Collapse
|
6
|
Flood P, Hanrahan N, Nally K, Melgar S. Human intestinal organoids: Modeling gastrointestinal physiology and immunopathology - current applications and limitations. Eur J Immunol 2024; 54:e2250248. [PMID: 37957831 DOI: 10.1002/eji.202250248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023]
Abstract
Human intestinal organoids are an ideal model system for studying gastrointestinal physiology and immunopathology. Altered physiology and mucosal immune response are hallmarks of numerous intestinal functional and inflammatory diseases, including inflammatory bowel disease (IBD), coeliac disease, irritable bowel syndrome (IBS), and obesity. These conditions impact the normal epithelial functions of the intestine, such as absorption, barrier function, secretion, and host-microbiome communication. They are accompanied by characteristic intestinal symptoms and have significant societal, economic, and healthcare burdens. To develop new treatment options, cutting-edge research is required to investigate their etiology and pathology. Human intestinal organoids derived from patient tissue recapitulate the key physiological and immunopathological aspects of these conditions, providing a promising platform for elucidating disease mechanisms. This review will summarize recent reports on patient-derived human small intestinal and colonic organoids and highlight how these models have been used to study intestinal epithelial functions in the context of inflammation, altered physiology, and immune response. Furthermore, it will elaborate on the various organoid systems in use and the techniques/assays currently available to study epithelial functions. Finally, it will conclude by discussing the limitations and future perspectives of organoid technology.
Collapse
Affiliation(s)
- Peter Flood
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Naomi Hanrahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, School of Medicine, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
7
|
Malique A, Sun S, Chandwe K, Amadi B, Haritunians T, Jain U, Muegge BD, Frein J, Sasaki Y, Foster A, Storer CE, Mengesha E, Kern J, McGovern DPB, Head RD, Kelly P, Liu TC. NAD + precursors and bile acid sequestration treat preclinical refractory environmental enteric dysfunction. Sci Transl Med 2024; 16:eabq4145. [PMID: 38170788 DOI: 10.1126/scitranslmed.abq4145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Environmental enteric dysfunction (EED) is a diffuse small bowel disorder associated with poor growth, inadequate responses to oral vaccines, and nutrient malabsorption in millions of children worldwide. We identify loss of the small intestinal Paneth and goblet cells that are critical for innate immunity, reduced villous height, increased bile acids, and dysregulated nicotinamide adenine dinucleotide (NAD+) synthesis signaling as potential mechanisms underlying EED and which also correlated with diminished length-for-age z score. Isocaloric low-protein diet (LPD) consumption in mice recapitulated EED histopathology and transcriptomic changes in a microbiota-independent manner, as well as increases in serum and fecal bile acids. Children with refractory EED harbor single-nucleotide polymorphisms in key enzymes involved in NAD+ synthesis. In mice, deletion of Nampt, the gene encoding the rate-limiting enzyme in the NAD+ salvage pathway, from intestinal epithelium also reduced Paneth cell function, a deficiency that was further aggravated by LPD. Separate supplementation with NAD+ precursors or bile acid sequestrant partially restored LPD-associated Paneth cell defects and, when combined, fully restored all histopathology defects in LPD-fed mice. Therapeutic regimens that increase protein and NAD+ contents while reducing excessive bile acids may benefit children with refractory EED.
Collapse
Affiliation(s)
- Atika Malique
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shengxiang Sun
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kanta Chandwe
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
| | - Beatrice Amadi
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jennifer Frein
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amanda Foster
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Justin Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
- Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| |
Collapse
|
8
|
Greigert V, Saraav I, Son J, Zhu Y, Dayao D, Antia A, Tzipori S, Witola WH, Stappenbeck TS, Ding S, Sibley LD. Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. Gut Microbes 2024; 16:2297897. [PMID: 38189373 PMCID: PMC10793699 DOI: 10.1080/19490976.2023.2297897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024] Open
Abstract
Cryptosporidiosis is a major cause of severe diarrheal disease in infants from resource poor settings. The majority of infections are caused by the human-specific pathogen C. hominis and absence of in vitro growth platforms has limited our understanding of host-pathogen interactions and development of effective treatments. To address this problem, we developed a stem cell-derived culture system for C. hominis using human enterocytes differentiated under air-liquid interface (ALI) conditions. Human ALI cultures supported robust growth and complete development of C. hominis in vitro including all life cycle stages. Cryptosporidium infection induced a strong interferon response from enterocytes, possibly driven, in part, by an endogenous dsRNA virus in the parasite. Prior infection with Cryptosporidium induced type III IFN secretion and consequently blunted infection with Rotavirus, including live attenuated vaccine strains. The development of hALI provides a platform for further studies on human-specific pathogens, including clinically important coinfections that may alter vaccine efficacy.
Collapse
Affiliation(s)
- Valentin Greigert
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Iti Saraav
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yinxing Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Denise Dayao
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - William H. Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Thaddeus S. Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
9
|
Davoudi Z, Atherly T, Borcherding DC, Jergens AE, Wannemuehler M, Barrett TA, Wang Q. Study Transportation of Drugs within Newly Established Murine Colon Organoid Systems. Adv Biol (Weinh) 2023; 7:e2300103. [PMID: 37607116 PMCID: PMC10840714 DOI: 10.1002/adbi.202300103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/18/2023] [Indexed: 08/24/2023]
Abstract
The development of 3D organoids of the small intestine is a tremendous breakthrough in drug development and biological research. However, the development of colonic organoids (i.e., colonoids) is particularly challenging due to a lack of simple, cost-effective protocols for colonoid cultivation. Here, intestinal homogenates are described as a supplement to the culture medium for maintaining and replicating colonic stem cells. Colonoids generated by this cultivation protocol demonstrate substantial proliferation and differentiation (3 months). There is a similarity between cultured colonoids and primary colon tissue regarding structure and functionality. To evaluate the functionality of colonoids, permeability testing is performed with suspensions of 4 and 40 kDa fluorescein isothiocyanate-dextran (FITC-DEX). It is observed that neither can permeate the healthy epithelial barrier. The P-glycoprotein receptor, a vital drug efflux pump mitigating potential drug toxicity, is functionally manipulated, as evidenced by its inhibition function by verapamil and monitoring uptake of Rhodamin 123. In addition, Forskolin treatment which affects chloride transport results in organoid swelling; this confirms the functional expression of the CFTR transporter in the colonoids. This protocol to generate colonoids is promising for high-throughput drug screening, toxicity testing, and oral drug development.
Collapse
Affiliation(s)
- Zahra Davoudi
- Department of Chemical and Biological Engineering, Iowa State University
| | - Todd Atherly
- Department of Veterinary Clinical Sciences, Iowa State University
| | | | | | | | - Terrence A. Barrett
- Department of Internal Medicine, Division of Gastroenterology, University of Kentucky
| | - Qun Wang
- Department of Chemical and Biological Engineering, Iowa State University
| |
Collapse
|
10
|
Mahdally SM, Izquierdo M, Viscardi RM, Magder LS, Crowley HM, Bafford AC, Drachenberg CB, Farfan MJ, Fasano A, Sztein MB, Salerno-Goncalves R. Secretory-IgA binding to intestinal microbiota attenuates inflammatory reactions as the intestinal barrier of preterm infants matures. Clin Exp Immunol 2023; 213:339-356. [PMID: 37070830 PMCID: PMC10570995 DOI: 10.1093/cei/uxad042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/09/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
Previous work has shown that Secretory-IgA (SIgA) binding to the intestinal microbiota is variable and may regulate host inflammatory bowel responses. Nevertheless, the impact of the SIgA functional binding to the microbiota remains largely unknown in preterm infants whose immature epithelial barriers make them particularly susceptible to inflammation. Here, we investigated SIgA binding to intestinal microbiota isolated from stools of preterm infants <33 weeks gestation with various levels of intestinal permeability. We found that SIgA binding to intestinal microbiota attenuates inflammatory reactions in preterm infants. We also observed a significant correlation between SIgA affinity to the microbiota and the infant's intestinal barrier maturation. Still, SIgA affinity was not associated with developing host defenses, such as the production of mucus and inflammatory calprotectin protein, but it depended on the microbiota shifts as the intestinal barrier matures. In conclusion, we reported an association between the SIgA functional binding to the microbiota and the maturity of the preterm infant's intestinal barrier, indicating that the pattern of SIgA coating is altered as the intestinal barrier matures.
Collapse
Affiliation(s)
- Sarah M Mahdally
- Division of Neonatology, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mariana Izquierdo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rose M Viscardi
- Division of Neonatology, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Laurence S Magder
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Helena M Crowley
- Division of Pediatric Surgery and Urology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea C Bafford
- Division of General and Oncologic Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cinthia B Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mauricio J Farfan
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Marcelo B Sztein
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rosangela Salerno-Goncalves
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
11
|
Felici M, Tugnoli B, Ghiselli F, Baldo D, Ratti C, Piva A, Grilli E. Investigating the effects of essential oils and pure botanical compounds against Eimeria tenella in vitro. Poult Sci 2023; 102:102898. [PMID: 37573847 PMCID: PMC10448326 DOI: 10.1016/j.psj.2023.102898] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/18/2023] [Accepted: 06/24/2023] [Indexed: 08/15/2023] Open
Abstract
Essential oils (EO) and natural bioactive compounds are well-known antibacterial and anti-inflammatory factors; however, little is known about their anticoccidial activity and mode of action. EO deriving from basil (BEO), garlic (GAR), oregano (OEO), thyme (TEO), and their main bioactive compounds were investigated for their anticoccidial proprieties and compared to salinomycin (SAL) and amprolium (AMP) in vitro. The invasion of Eimeria tenella sporozoites was studied on 2 cell models: Madin-Darby Bovine Kidney (MDBK) cells and primary chicken epithelial cells (cIEC). Invasion efficiency was evaluated at 2 and 24 h postinfection (hpi) with counts of extracellular sporozoites and by detection of intracellular E. tenella DNA by PCR. Results show that at both timepoints, the EO were most effective in preventing the invasion of E. tenella with an average reduction of invasion at 24 hpi by 36% in cIEC and 55% in MDBK. The study also examined cytokine gene expression in cIEC at 24 hpi and found that AMP, BEO, OEO, TEO, carvacrol (CAR), and thymol (THY) significantly reduced interleukin (IL)8 expression, with CAR also reducing expression of IL1β and IL6 compared to the infected control. In addition, this work investigated the morphology of E. tenella sporozoites treated with anticoccidial drugs and EO using a scanning electron microscope. All the treatments induced morphological anomalies, characterized by a reduction of area, perimeter and length of sporozoites. SAL had a significant impact on altering sporozoite shape only at 24 h, whereas CAR and THY significantly compromised the morphology already at 2 hpi, compared to the untreated control. OEO and GAR showed the most significant alterations among all the treatments. The findings of this study highlight the potential of EO as an alternative to traditional anticoccidial drugs in controlling E. tenella invasion and in modulating primary immune response.
Collapse
Affiliation(s)
| | | | | | - David Baldo
- DISTAL, University of Bologna, Bologna, Italy
| | | | - Andrea Piva
- DIMEVET, University of Bologna, Bologna, Italy; Vetagro S.p.A., Reggio Emilia, Italy
| | - Ester Grilli
- DIMEVET, University of Bologna, Bologna, Italy; Vetagro Inc., Chicago, IL 60603, USA.
| |
Collapse
|
12
|
Sockell A, Wong W, Longwell S, Vu T, Karlsson K, Mokhtari D, Schaepe J, Lo YH, Cornelius V, Kuo C, Van Valen D, Curtis C, Fordyce PM. A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids. Cell Syst 2023; 14:764-776.e6. [PMID: 37734323 DOI: 10.1016/j.cels.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Organoids are powerful experimental models for studying the ontogeny and progression of various diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, bulk-cultured organoids physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or differences in the microenvironment. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can further be retrieved from their microwells for molecular profiling. Coupled with a deep learning image-processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- Alexandra Sockell
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Wing Wong
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Scott Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Thy Vu
- Department of Biochemistry, UT Austin, Austin, TX 78712, USA
| | - Kasper Karlsson
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yuan-Hung Lo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Vincent Cornelius
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Calvin Kuo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina Curtis
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
13
|
Greigert V, Saraav I, Son J, Dayao D, Antia A, Tzipori S, Witola WH, Stappenbeck TS, Ding S, Sibley LD. Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555581. [PMID: 37693422 PMCID: PMC10491271 DOI: 10.1101/2023.08.30.555581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cryptosporidiosis is a major cause of severe diarrheal disease in infants from resource poor settings. The majority of infections are caused by the human-specific pathogen C. hominis and absence of in vitro growth platforms has limited our understanding of host-pathogen interactions and development of effective treatments. To address this problem, we developed a stem cell-derived culture system for C. hominis using human enterocytes differentiated under air-liquid interface (ALI) conditions. Human ALI cultures supported robust growth and complete development of C. hominis in vitro including all life cycle stages. C. hominis infection induced a strong interferon response from enterocytes, likely driven by an endogenous dsRNA virus in the parasite. Prior infection with Cryptosporidium induced type III IFN secretion and consequently blunted infection with Rotavirus, including live attenuated vaccine strains. The development of hALI provides a platform for further studies on human-specific pathogens, including clinically important coinfections that may alter vaccine efficacy.
Collapse
Affiliation(s)
- Valentin Greigert
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Iti Saraav
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Denise Dayao
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, 01536, USA
| | - Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, 01536, USA
| | - William H. Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Thaddeus S. Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| |
Collapse
|
14
|
Walz S, Pollehne P, Vollmer P, Aicher WK, Stenzl A, Harland N, Amend B. Effects of Scaffolds on Urine- and Urothelial Carcinoma Tissue-Derived Organoids from Bladder Cancer Patients. Cells 2023; 12:2108. [PMID: 37626918 PMCID: PMC10453567 DOI: 10.3390/cells12162108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Organoids are three-dimensional constructs generated by placing cells in scaffolds to facilitate the growth of cultures with cell-cell and cell-matrix interactions close to the in vivo situation. Organoids may contain different types of cells, including cancer cells, progenitor cells, or differentiated cells. As distinct culture conditions have significant effects on cell metabolism, we explored the expansion of cells and expression of marker genes in bladder cancer cells expanded in two different common scaffolds. The cells were seeded in basement membrane extract (BME; s.c., Matrigel®) or in a cellulose-derived hydrogel (GrowDex®, GD) and cultured. The size of organoids and expression of marker genes were studied. We discovered that BME facilitated the growth of significantly larger organoids of cancer cell line RT112 (p < 0.05), cells from a solid tumor (p < 0.001), and a voiding urine sample (p < 0.001). Expression of proliferation marker Ki76, transcription factor TP63, cytokeratin CK20, and cell surface marker CD24 clearly differed in these different tumor cells upon expansion in BME when compared to cells in GD. We conclude that the choice of scaffold utilized for the generation of organoids has an impact not only on cell growth and organoid size but also on protein expression. The disadvantages of batch-to-batch-variations of BME must be balanced with the phenotypic bias observed with GD scaffolds when standardizing organoid cultures for clinical diagnoses.
Collapse
Affiliation(s)
- Simon Walz
- Department of Urology, University of Tuebingen Hospital, 72076 Tübingen, Germany
| | - Paul Pollehne
- Center for Medical Research, University of Tuebingen, 72074 Tübingen, Germany
| | - Philipp Vollmer
- Center for Medical Research, University of Tuebingen, 72074 Tübingen, Germany
| | - Wilhelm K. Aicher
- Center for Medical Research, University of Tuebingen, 72074 Tübingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University of Tuebingen Hospital, 72076 Tübingen, Germany
| | - Niklas Harland
- Department of Urology, University of Tuebingen Hospital, 72076 Tübingen, Germany
| | - Bastian Amend
- Department of Urology, University of Tuebingen Hospital, 72076 Tübingen, Germany
| |
Collapse
|
15
|
Frazer LC, Yamaguchi Y, Jania CM, Lanik WE, Gong Q, Singh DK, Mackay S, Akopyants NS, Good M. Microfluidic Model of Necrotizing Enterocolitis Incorporating Human Neonatal Intestinal Enteroids and a Dysbiotic Microbiome. J Vis Exp 2023:10.3791/65605. [PMID: 37590536 PMCID: PMC11003451 DOI: 10.3791/65605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Abstract
Necrotizing enterocolitis (NEC) is a severe and potentially fatal intestinal disease that has been difficult to study due to its complex pathogenesis, which remains incompletely understood. The pathophysiology of NEC includes disruption of intestinal tight junctions, increased gut barrier permeability, epithelial cell death, microbial dysbiosis, and dysregulated inflammation. Traditional tools to study NEC include animal models, cell lines, and human or mouse intestinal organoids. While studies using those model systems have improved the field's understanding of disease pathophysiology, their ability to recapitulate the complexity of human NEC is limited. An improved in vitro model of NEC using microfluidic technology, named NEC-on-a-chip, has now been developed. The NEC-on-a-chip model consists of a microfluidic device seeded with intestinal enteroids derived from a preterm neonate, co-cultured with human endothelial cells and the microbiome from an infant with severe NEC. This model is a valuable tool for mechanistic studies into the pathophysiology of NEC and a new resource for drug discovery testing for neonatal intestinal diseases. In this manuscript, a detailed description of the NEC-on-a-chip model will be provided.
Collapse
Affiliation(s)
- Lauren C Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill
| | - Yukihiro Yamaguchi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill
| | - Corey M Jania
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill
| | | | - Qingqing Gong
- Department of Surgery, Washington University School of Medicine
| | - Dhirendra K Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill
| | - Stephen Mackay
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill
| | - Natalia S Akopyants
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill;
| |
Collapse
|
16
|
Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Schriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD. Microbiota-produced indole metabolites disrupt mitochondrial function and inhibit Cryptosporidium parvum growth. Cell Rep 2023; 42:112680. [PMID: 37384526 PMCID: PMC10530208 DOI: 10.1016/j.celrep.2023.112680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. To explore microbial influences on susceptibility, we screened 85 microbiota-associated metabolites for their effects on Cryptosporidium parvum growth in vitro. We identify eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B6 precursor, and indoles. Growth restriction of C. parvum by indoles does not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impairs host mitochondrial function and reduces total cellular ATP, as well as directly reducing the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole-producing bacteria, delays life cycle progression of the parasite in vitro and reduces the severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites impair mitochondrial function and contribute to colonization resistance to Cryptosporidium infection.
Collapse
Affiliation(s)
- Lisa J Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence A Schriefer
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Heyde Makimaa
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth A Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
17
|
Overcast GR, Meibers HE, Eshleman EM, Saha I, Waggoner L, Patel KN, Jain VG, Haslam DB, Alenghat T, VanDussen KL, Pasare C. IEC-intrinsic IL-1R signaling holds dual roles in regulating intestinal homeostasis and inflammation. J Exp Med 2023; 220:e20212523. [PMID: 36976181 PMCID: PMC10067527 DOI: 10.1084/jem.20212523] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 12/20/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023] Open
Abstract
Intestinal epithelial cells (IECs) constitute a critical first line of defense against microbes. While IECs are known to respond to various microbial signals, the precise upstream cues regulating diverse IEC responses are not clear. Here, we discover a dual role for IEC-intrinsic interleukin-1 receptor (IL-1R) signaling in regulating intestinal homeostasis and inflammation. Absence of IL-1R in epithelial cells abrogates a homeostatic antimicrobial program including production of antimicrobial peptides (AMPs). Mice deficient for IEC-intrinsic IL-1R are unable to clear Citrobacter rodentium (C. rodentium) but are protected from DSS-induced colitis. Mechanistically, IL-1R signaling enhances IL-22R-induced signal transducer and activator of transcription 3 (STAT3) phosphorylation in IECs leading to elevated production of AMPs. IL-1R signaling in IECs also directly induces expression of chemokines as well as genes involved in the production of reactive oxygen species. Our findings establish a protective role for IEC-intrinsic IL-1R signaling in combating infections but a detrimental role during colitis induced by epithelial damage.
Collapse
Affiliation(s)
- Garrett R. Overcast
- Immunology Graduate Program, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Hannah E. Meibers
- Immunology Graduate Program, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Emily M. Eshleman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Irene Saha
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lisa Waggoner
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Krupaben N. Patel
- Divisions of Gastroenterology, Hepatology, and Nutrition and of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Viral G. Jain
- Division of Neonatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David B. Haslam
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Theresa Alenghat
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Kelli L. VanDussen
- Divisions of Gastroenterology, Hepatology, and Nutrition and of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Chandrashekhar Pasare
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| |
Collapse
|
18
|
Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Shriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD. Microbiota produced indole metabolites disrupt host cell mitochondrial energy production and inhibit Cryptosporidium parvum growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542157. [PMID: 37292732 PMCID: PMC10245909 DOI: 10.1101/2023.05.25.542157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. Susceptibility rapidly declines with age, associated with changes in the microbiota. To explore microbial influences on susceptibility, we screened 85 microbiota- associated metabolites enriched in the adult gut for their effects on C. parvum growth in vitro. We identified eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B 6 precursor, and indoles. Growth restriction of C. parvum by indoles did not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impaired host mitochondrial function and reduced total cellular ATP, as well as directly reduced the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole producing bacteria, delayed life cycle progression of the parasite in vitro and reduced severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites contribute to colonization resistance to Cryptosporidium infection.
Collapse
Affiliation(s)
- Lisa J. Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Lawrence A. Shriefer
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Heyde Makimaa
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Elizabeth A. Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kelli L. VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| |
Collapse
|
19
|
Tindle C, Katkar GD, Fonseca AG, Taheri S, Lee J, Maity P, Sayed IM, Ibeawuchi SR, Vidales E, Pranadinata RF, Fuller M, Stec DL, Anandachar MS, Perry K, Le HN, Ear J, Boland BS, Sandborn WJ, Sahoo D, Das S, Ghosh P. A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532245. [PMID: 36993763 PMCID: PMC10054961 DOI: 10.1101/2023.03.11.532245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Crohn's disease (CD) is a complex, clinically heterogeneous disease of multifactorial origin; there is no perfect pre-clinical model, little insight into the basis for such heterogeneity, and still no cure. To address these unmet needs, we sought to explore the translational potential of adult stem cell-derived organoids that not only retain their tissue identity, but also their genetic and epigenetic disease-driving traits. We prospectively created a biobank of CD patient-derived organoid cultures (PDOs) using biopsied tissues from colons of 34 consecutive subjects representing all clinical subtypes (Montreal Classification B1-B3 and perianal disease). PDOs were generated also from healthy subjects. Comparative gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and revealed that despite the clinical heterogeneity there are two major molecular subtypes: immune-deficient infectious-CD [IDICD] and stress and senescence-induced fibrostenotic-CD [S2FCD]. The transcriptome, genome and phenome show a surprising degree of internal consistency within each molecular subtype. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. These insights enabled drug screens that reversed subtype-specific phenotypes, e.g., impaired microbial clearance in IDICD was reversed using agonists for nuclear receptors, and senescence in S2FCD was rectified using senotherapeutics, but not vice versa . Phenotyped-genotyped CD-PDOs may fill the gap between basic biology and patient trials by enabling pre-clinical Phase '0' human trials for personalized therapeutics. GRAPHIC ABSTRACT In Brief This work creates a prospectively biobanked phenotyped-genotyped Crohn's disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTS Prospectively biobanked CD-organoids recapitulate the disease epithelium in patientsThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypesOne subtype shows impaired microbial clearance, another increased cellular senescencePhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics.
Collapse
|
20
|
Chen Z, Leung TCN, Lui YL, Ngai SM, Chung HY. Combination of untargeted and targeted proteomics for secretome analysis of L-WRN cells. Anal Bioanal Chem 2023; 415:1465-1476. [PMID: 36656349 DOI: 10.1007/s00216-023-04534-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/25/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023]
Abstract
Organoid culture is a promising biomedical technology that requires specialized growth factors. Recently, a recombinant L-WRN cell line has been extensively used to generate conditioned medium (L-CM) for organoid culture. Nevertheless, methods for evaluating the stability of the L-WRN cells have been limited. In this study, a novel proteomics-based approach was developed to analyze the secretome of the cells. Serum-free L-CM was lyophilized, precipitated by trichloroacetic acid, and desalted prior to analysis by liquid chromatography-tandem mass spectrometry. Data-dependent acquisition (DDA) was conducted for the untargeted secretome profiling of the cells, and parallel reaction monitoring (PRM) was applied for the targeted quantification of the Wnt3A, R-spondin3, and noggin proteins (WRNs). This study also compared the performance of two types of PRM methods, namely MS1-independent PRM and MS1-dependent PRM, that can be executed on an Orbitrap instrument. The results showed that the growth of mouse intestinal organoids was closely related to the use of L-CM. The composition of L-CM could be markedly affected by the medium collection scheme. A total of 1725, 2302, and 2681 proteins were identified from the L-CM collected on day 5, day 9, and day 13, respectively. The MS1-independent PRM outperformed the MS1-dependent PRM and effectively quantified the WRNs with high repeatability and specificity. In conclusion, by integrating untargeted and targeted proteomics, this study develops a mass spectrometry-based method for the secretome analysis and quality control of the L-WRN cells. The methodology and findings of the present work will benefit future studies on organoids and secretomes.
Collapse
Affiliation(s)
- Zixing Chen
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Thomas Chun Ning Leung
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Ying Lam Lui
- Cell and Molecular Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hau Yin Chung
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
| |
Collapse
|
21
|
Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D. A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection. Gut Microbes 2023; 15:2186109. [PMID: 36939013 PMCID: PMC10038062 DOI: 10.1080/19490976.2023.2186109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Infection research largely relies on classical cell culture or mouse models. Despite having delivered invaluable insights into host-pathogen interactions, both have limitations in translating mechanistic principles to human pathologies. Alternatives can be derived from modern Tissue Engineering approaches, allowing the reconstruction of functional tissue models in vitro. Here, we combined a biological extracellular matrix with primary tissue-derived enteroids to establish an in vitro model of the human small intestinal epithelium exhibiting in vivo-like characteristics. Using the foodborne pathogen Salmonella enterica serovar Typhimurium, we demonstrated the applicability of our model to enteric infection research in the human context. Infection assays coupled to spatio-temporal readouts recapitulated the established key steps of epithelial infection by this pathogen in our model. Besides, we detected the upregulation of olfactomedin 4 in infected cells, a hitherto unrecognized aspect of the host response to Salmonella infection. Together, this primary human small intestinal tissue model fills the gap between simplistic cell culture and animal models of infection, and shall prove valuable in uncovering human-specific features of host-pathogen interplay.
Collapse
Affiliation(s)
- Thomas Däullary
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Faculty of Biology, Biocenter, Chair of Microbiology, Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany
| | - Fabian Imdahl
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Oliver Dietrich
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Laura Hepp
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
| | - Tobias Krammer
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Christina Fey
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
| | - Winfried Neuhaus
- Austrian Institute of Technology (AIT), Vienna, Austria
- Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University (DPU), Krems, Austria
| | - Marco Metzger
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
- Fraunhofer Institute for Silicate Research, Project Center for Stem Cell Process Engineering, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Daniela Zdzieblo
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
- Fraunhofer Institute for Silicate Research, Project Center for Stem Cell Process Engineering, Würzburg, Germany
| |
Collapse
|
22
|
Gopalakrishnan S, Bakke I, Hansen MD, Skovdahl HK, Granlund AVB, Sandvik AK, Bruland T. Comprehensive protocols for culturing and molecular biological analysis of IBD patient-derived colon epithelial organoids. Front Immunol 2023; 14:1097383. [PMID: 36911731 PMCID: PMC9995983 DOI: 10.3389/fimmu.2023.1097383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/02/2023] [Indexed: 02/25/2023] Open
Abstract
There are many unanswered questions regarding responses to proinflammatory signals in intestinal epithelial cells (IECs). For example, chemokines secreted by IECs upon external stimuli play multifunctional roles in both homeostasis and during inflammation. Several chemokines are upregulated during active inflammatory bowel disease (IBD), which is associated with an increased influx of immune cells into the gut mucosa. Therefore, studies on how chemokines are regulated in the intestinal epithelium may identify putative treatment targets in IBD. More recently, patient-derived ex vivo models such as intestinal organoids have facilitated molecular analysis of epithelial alterations in IBD patients own cells. Here, we describe refined experimental protocols and methods for the generation and maintenance of IBD patient-derived colonic organoids (colonoids) culture. We also give detailed description of medium, and supplements needed for colonoid establishment, growth, and differentiation, including production of Wnt-3A and Rspondin1 enriched media. Further, we present protocols for RNA and protein isolation from human colonoids, and subsequent gene expression analysis and Western blotting for e.g., signal transduction studies. We also describe how to process colonoids for chemokine protein expression analysis such as immunostaining, confocal imaging, and detection of secreted chemokines by e.g., enzyme-linked immunosorbent assay (ELISA). As proof of principle, we give examples of how the chemoattractant CCL20 can be regulated and expressed in colonoids derived from IBD-patients and healthy controls upon ligands-driven inflammation.
Collapse
Affiliation(s)
- Shreya Gopalakrishnan
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Bakke
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Marianne Doré Hansen
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Helene Kolstad Skovdahl
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Centre of Molecular Inflammation Research (CEMIR), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle van Beelen Granlund
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Centre of Molecular Inflammation Research (CEMIR), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway.,Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Arne K Sandvik
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Centre of Molecular Inflammation Research (CEMIR), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Torunn Bruland
- Department of Clinical and Molecular Medicine (IKOM), Faculty of Medicine and Health Sciences, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.,Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway.,Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| |
Collapse
|
23
|
Differential Response to the Course of Cryptosporidium parvum Infection and Its Impact on Epithelial Integrity in Differentiated versus Undifferentiated Human Intestinal Enteroids. Infect Immun 2022; 90:e0039722. [PMID: 36286526 PMCID: PMC9671013 DOI: 10.1128/iai.00397-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cryptosporidium is a leading cause of diarrhea and death in young children and untreated AIDS patients and causes waterborne outbreaks. Pathogenic mechanisms underlying diarrhea and intestinal dysfunction are poorly understood. We previously developed stem-cell derived human intestinal enteroid (HIE) models for Cryptosporidium parvum which we used in this study to investigate the course of infection and its effect on intestinal epithelial integrity. By immunofluorescence and confocal microscopy, there was robust infection of undifferentiated and differentiated HIEs in two and three-dimensional (2D, 3D) models. Infection of differentiated HIEs in the 2D model was greater than that of undifferentiated HIEs but lasted only for 3 days, whereas infection persisted for 21 days and resulted in completion of the life cycle in undifferentiated HIEs. Infection of undifferentiated HIE monolayers suggest that C. parvum infects LGR5+ stem cells. Transepithelial electrical resistance measurement of HIEs in the 2D model revealed that infection resulted in decreased epithelial integrity which persisted in differentiated HIEs but recovered in undifferentiated HIEs. Compromised epithelial integrity was reflected in disorganization of the tight and adherens junctions as visualized using the markers ZO-1 and E-cadherin, respectively. Quantitation using the image analysis tools Tight Junction Organizational Rate and Intercellular Junction Organization Quantification, measurement of monolayer height, and RNA transcripts of both proteins by quantitative reverse transcription PCR confirmed that disruption persisted in differentiated HIEs but recovered in undifferentiated HIEs. These models, which more accurately recapitulate human infection, will be useful tools to dissect pathogenic mechanisms underlying diarrhea and intestinal dysfunction in cryptosporidiosis.
Collapse
|
24
|
Strine MS, Alfajaro MM, Graziano VR, Song J, Hsieh LL, Hill R, Guo J, VanDussen KL, Orchard RC, Baldridge MT, Lee S, Wilen CB. Tuft-cell-intrinsic and -extrinsic mediators of norovirus tropism regulate viral immunity. Cell Rep 2022; 41:111593. [PMID: 36351394 PMCID: PMC9662704 DOI: 10.1016/j.celrep.2022.111593] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/19/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
Murine norovirus (MNoV) is a model for human norovirus and for interrogating mechanisms of viral tropism and persistence. We previously demonstrated that the persistent strain MNoVCR6 infects tuft cells, which are dispensable for the non-persistent strain MNoVCW3. We now show that diverse MNoV strains require tuft cells for chronic enteric infection. We also demonstrate that interferon-λ (IFN-λ) acts directly on tuft cells to cure chronic MNoVCR6 infection and that type I and III IFNs signal together via STAT1 in tuft cells to restrict MNoVCW3 tropism. We then develop an enteroid model and find that MNoVCR6 and MNoVCW3 similarly infect tuft cells with equal IFN susceptibility, suggesting that IFN derived from non-epithelial cells signals on tuft cells in trans to restrict MNoVCW3 tropism. Thus, tuft cell tropism enables MNoV persistence and is determined by tuft cell-intrinsic factors (viral receptor expression) and -extrinsic factors (immunomodulatory signaling by non-epithelial cells).
Collapse
Affiliation(s)
- Madison S Strine
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Vincent R Graziano
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jaewon Song
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Leon L Hsieh
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ryan Hill
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jun Guo
- Department of Surgery, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kelli L VanDussen
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| | - Robert C Orchard
- Department of Immunology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sanghyun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
25
|
Csukovich G, Pratscher B, Burgener IA. The World of Organoids: Gastrointestinal Disease Modelling in the Age of 3R and One Health with Specific Relevance to Dogs and Cats. Animals (Basel) 2022; 12:ani12182461. [PMID: 36139322 PMCID: PMC9495014 DOI: 10.3390/ani12182461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
One Health describes the importance of considering humans, animals, and the environment in health research. One Health and the 3R concept, i.e., the replacement, reduction, and refinement of animal experimentation, shape today’s research more and more. The development of organoids from many different organs and animals led to the development of highly sophisticated model systems trying to replace animal experiments. Organoids may be used for disease modelling in various ways elucidating the manifold host–pathogen interactions. This review provides an overview of disease modelling approaches using organoids of different kinds with a special focus on animal organoids and gastrointestinal diseases. We also provide an outlook on how the research field of organoids might develop in the coming years and what opportunities organoids hold for in-depth disease modelling and therapeutic interventions.
Collapse
|
26
|
Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CFD, Liss AS, Ting DT, Jacks T, Regev A. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nat Genet 2022; 54:1178-1191. [PMID: 35902743 DOI: 10.1038/s41588-022-01134-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.
Collapse
Affiliation(s)
- William L Hwang
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karthik A Jagadeesh
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jimmy A Guo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Hannah I Hoffman
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT MD/PhD and Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Payman Yadollahpour
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Rahul Mohan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | | | | | | | - George Eng
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Shiau
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William A Freed-Pastor
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina Kem
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clifton Rodrigues
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Debora Ciprani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge Roldan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vjola Jorgji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zackery Ely
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | - Jay S Loeffler
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David P Ryan
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin D Weekes
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rakesh K Jain
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer Y Wo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
| |
Collapse
|
27
|
Jaeger AM, Stopfer LE, Ahn R, Sanders EA, Sandel DA, Freed-Pastor WA, Rideout WM, Naranjo S, Fessenden T, Nguyen KB, Winter PS, Kohn RE, Westcott PMK, Schenkel JM, Shanahan SL, Shalek AK, Spranger S, White FM, Jacks T. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature 2022; 607:149-155. [PMID: 35705813 PMCID: PMC9945857 DOI: 10.1038/s41586-022-04839-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex class I (MHC-I) molecules1-5. Current approaches to profiling of MHC-I-associated peptides, collectively known as the immunopeptidome, are limited to in vitro investigation or bulk tumour lysates, which limits our understanding of cancer-specific patterns of antigen presentation in vivo6. To overcome these limitations, we engineered an inducible affinity tag into the mouse MHC-I gene (H2-K1) and targeted this allele to the KrasLSL-G12D/+Trp53fl/fl mouse model (KP/KbStrep)7. This approach enabled us to precisely isolate MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma and from lung adenocarcinoma (LUAD) in vivo. In addition, we profiled the LUAD immunopeptidome from the alveolar type 2 cell of origin up to late-stage disease. Differential peptide presentation in LUAD was not predictable by mRNA expression or translation efficiency and is probably driven by post-translational mechanisms. Vaccination with peptides presented by LUAD in vivo induced CD8+ T cell responses in naive mice and tumour-bearing mice. Many peptides specific to LUAD, including immunogenic peptides, exhibited minimal expression of the cognate mRNA, which prompts the reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance8. Beyond cancer, the KbStrep allele is compatible with other Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease and autoimmunity.
Collapse
Affiliation(s)
- Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Lauren E Stopfer
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryuhjin Ahn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emma A Sanders
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Demi A Sandel
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Tim Fessenden
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Kim B Nguyen
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter S Winter
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan E Kohn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jason M Schenkel
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Alex K Shalek
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Stefani Spranger
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Forest M White
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
28
|
DiProspero TJ, Brown LG, Fachko TD, Lockett MR. HepaRG cells adopt zonal-like drug-metabolizing phenotypes under physiologically relevant oxygen tensions and Wnt/β-catenin signaling. Drug Metab Dispos 2022; 50:DMD-AR-2022-000870. [PMID: 35701181 PMCID: PMC9341261 DOI: 10.1124/dmd.122.000870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 11/22/2022] Open
Abstract
The cellular microenvironment plays an important role in liver zonation, the spatial distribution of metabolic tasks amongst hepatocytes lining the sinusoid. Standard tissue culture practices provide an excess of oxygen and a lack of signaling molecules typically found in the liver. We hypothesized that incorporating physiologically relevant environments would promote post-differentiation patterning of hepatocytes and result in zonal-like characteristics. To test this hypothesis, we evaluated the transcriptional regulation and activity of drug-metabolizing enzymes in HepaRG cells exposed to three different oxygen tensions, in the presence or absence of Wnt/β-catenin signaling. The drug-metabolizing activity of cells exposed to representative periportal (11% O2) or perivenous (5% O2) oxygen tensions were significantly less than cells exposed to ambient oxygen. A comparison of cytochrome P450 (CYP) 1A2, 2D6, and 3A4 activity at PP and PV oxygen tensions showed significant increases at the lower oxygen tension. The activation of the Wnt/β-catenin pathway only modestly impacted CYP activity at PV oxygen tension, despite a significant increase in CYP expression under this condition. Our results suggest oxygen tension is the major contributor to zonal patterning in HepaRG cells, with the Wnt/β-catenin signaling pathway playing a lesser albeit important role. Our datasets also highlight the importance of including activity-based assays, as transcript data alone does not provide an accurate picture of metabolic competence. Significance Statement This work investigates the post-differentiation patterning of HepaRG cells cultured at physiologically relevant oxygen tensions, in the presence and absence of Wnt/β-catenin signaling. HepaRG cells exposed to periportal (11% O2) or perivenous (5% O2) oxygen tensions display zonation-like patterning of both cytochrome P450 (CYP) and glucuronosyltransferase (UGT) enzymes. These datasets also suggest that oxygen is a primary regulator of post-differentiation patterning, with Wnt/β-catenin having a lesser effect on activity but a significant effect on transcriptional regulation of these enzymes.
Collapse
Affiliation(s)
| | - Lauren G Brown
- Chemistry, Univeristy of North Carolina at Chapel Hill, United States
| | - Trevor D Fachko
- Chemistry, University of North Carolina at Chapel Hill, United States
| | - Matthew R Lockett
- Chemistry, University of North Carolina at Chapel Hill, United States
| |
Collapse
|
29
|
Weiß F, Holthaus D, Kraft M, Klotz C, Schneemann M, Schulzke JD, Krug SM. Human duodenal organoid-derived monolayers serve as a suitable barrier model for duodenal tissue. Ann N Y Acad Sci 2022; 1515:155-167. [PMID: 35666953 DOI: 10.1111/nyas.14804] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Usually, duodenal barriers are investigated using intestinal cell lines like Caco-2, which in contrast to native tissue are limited in cell-type representation. Organoids can consist of all intestinal cell types and are supposed to better reflect the in vivo situation. Growing three-dimensionally, with the apical side facing the lumen, application of typical physiological techniques to analyze the barrier is difficult. Organoid-derived monolayers (ODMs) were developed to overcome this. After optimizing culturing conditions, ODMs were characterized and compared to Caco-2 and duodenal tissue. Tight junction composition and appearance were analyzed, and electrophysiological barrier properties, like paracellular and transcellular barrier function and macromolecule permeability, were evaluated. Furthermore, transcriptomic data were analyzed. ODMs had tight junction protein expression and paracellular barrier properties much more resembling the originating tissue than Caco-2. Transcellular barrier was similar between ODMs and native tissue but was increased in Caco-2. Transcriptomic data showed that Caco-2 expressed fewer solute carriers than ODMs and native tissue. In conclusion, while Caco-2 cells differ mostly in transcellular properties, ODMs reflect trans- and paracellular properties of the originating tissue. If cultured under optimized conditions, ODMs possess reproducible functionality, and the variety of different cell types makes them a suitable model for human tissue-specific investigations.
Collapse
Affiliation(s)
- Franziska Weiß
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - David Holthaus
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Martin Kraft
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Martina Schneemann
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Jörg D Schulzke
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Susanne M Krug
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| |
Collapse
|
30
|
Rapid establishment of murine gastrointestinal organoids using mechanical isolation method. Biochem Biophys Res Commun 2022; 608:30-38. [DOI: 10.1016/j.bbrc.2022.03.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/22/2022]
|
31
|
Abstract
Human colonic organoids derived from biopsy or autopsy tissues are a vital tool to study mucosal homeostasis, model colonic diseases, and develop therapeutics. Rapid and reliable generation of knockout organoid lines from multiple donors enables analysis of specific gene functions. Here, we report protocols to produce colonic organoid knockout lines within 1 to 2 weeks using lentiviral delivery of CRISPR-Cas9, achieving knockout efficiency of 90% or greater. These lines are suitable for multi-lineage differentiation and downstream analysis. For complete details on the use and execution of this protocol, please refer to Gu et al. (2022). Optimized 3D culture of primary human colonic organoids Protocol for efficient gene knockout with CRISPR-Cas9 Enables multilineage mucosal differentiation
Collapse
|
32
|
Humayun M, Ayuso JM, Park KY, Martorelli Di Genova B, Skala MC, Kerr SC, Knoll LJ, Beebe DJ. Innate immune cell response to host-parasite interaction in a human intestinal tissue microphysiological system. SCIENCE ADVANCES 2022; 8:eabm8012. [PMID: 35544643 PMCID: PMC9075809 DOI: 10.1126/sciadv.abm8012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/23/2022] [Indexed: 05/03/2023]
Abstract
Protozoan parasites that infect humans are widespread and lead to varied clinical manifestations, including life-threatening illnesses in immunocompromised individuals. Animal models have provided insight into innate immunity against parasitic infections; however, species-specific differences and complexity of innate immune responses make translation to humans challenging. Thus, there is a need for in vitro systems that can elucidate mechanisms of immune control and parasite dissemination. We have developed a human microphysiological system of intestinal tissue to evaluate parasite-immune-specific interactions during infection, which integrates primary intestinal epithelial cells and immune cells to investigate the role of innate immune cells during epithelial infection by the protozoan parasite, Toxoplasma gondii, which affects billions of people worldwide. Our data indicate that epithelial infection by parasites stimulates a broad range of effector functions in neutrophils and natural killer cell-mediated cytokine production that play immunomodulatory roles, demonstrating the potential of our system for advancing the study of human-parasite interactions.
Collapse
Affiliation(s)
- Mouhita Humayun
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose M. Ayuso
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA
| | - Keon Young Park
- Department of Surgery, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Melissa C. Skala
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Sheena C. Kerr
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Laura J. Knoll
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - David J. Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
33
|
Lin SC, Haga K, Zeng XL, Estes MK. Generation of CRISPR-Cas9-mediated genetic knockout human intestinal tissue-derived enteroid lines by lentivirus transduction and single-cell cloning. Nat Protoc 2022; 17:1004-1027. [PMID: 35197604 PMCID: PMC9059808 DOI: 10.1038/s41596-021-00669-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022]
Abstract
Human intestinal tissue-derived enteroids (HIEs; also called organoids) are a powerful ex vivo model for gastrointestinal research. Genetic modification of these nontransformed cultures allows new insights into gene function and biological processes involved in intestinal diseases as well as gastrointestinal and donor segment-specific function. Here we provide a detailed technical pipeline and protocol for using the CRISPR-Cas9 genome editing system to knock out a gene of interest specifically in HIEs by lentiviral transduction and single-cell cloning. This protocol differs from a previously published alternative using electroporation of human colonoids to deliver piggyback transposons or CRISPR-Cas9 constructs, as this protocol uses a modified, fused LentiCRISPRv2-small-guiding RNA to express Cas9 and small-guiding RNA in a lentivirus. The protocol also includes the steps of gene delivery and subsequent single-cell cloning of the knockout cells as well as verification of clones and sequence identification of the mutation sites to establish knockout clones. An overview flowchart, step-by-step guidelines and troubleshooting suggestions are provided to aid the researcher in obtaining the genetic knockout HIE line within 2-3 months. In this protocol, we further describe how to use HIEs as an ex vivo model to assess host restriction factors for viral replication (using human norovirus replication as an example) by knocking out host attachment factors or innate immunity genes. Other applications are discussed to broaden the utility of this system, for example, to generate knockin or conditional knockout HIE lines to investigate the function of essential genes in many biological processes including other types of organoids.
Collapse
Affiliation(s)
- Shih-Ching Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kei Haga
- Department of Infection Control and Immunology, Kitasato University, Tokyo, Japan
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
34
|
Peng ZT, Liu H. Puerarin attenuates LPS-induced inflammatory injury in gastric epithelial cells by repressing NLRP3 inflammasome-mediated apoptosis. Toxicol In Vitro 2022; 81:105350. [PMID: 35331853 DOI: 10.1016/j.tiv.2022.105350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
The NLRP3 inflammasome plays a crucial role in microbially induced gastric epithelial injury, but the underlying mechanisms remain unclear. Here, we aimed to assess the impacts of puerarin on LPS-induced inflammatory damage and the involvement of the AMPK/SIRT1/NLRP3 signaling pathways in this process in GES-1 cells. Cell viability and cytotoxicity were determined using CCK-8 and lactate dehydrogenase assay kits. Apoptosis was measured using annexin staining followed by flow cytometry. Cytokine levels were detected by ELISA, and protein expression was analyzed using western blotting. Protein overexpression was achieved by transfection with relevant pcDNA3.1 vectors, and protein knockdown was achieved by transfection with relevant siRNAs. Puerarin ameliorated LPS-induced cytotoxicity and apoptosis, while repressing LPS-stimulated NLRP3 inflammasome-mediated pyroptosis in GES-1 cells, as evidenced by significantly decreased expression of NLRP3, ASC, cleaved caspase-1, IL-1β and IL-18. NLRP3 knockdown efficiently repressed LPS-induced inflammatory injury in GES-1 cells. Puerarin activated the AMPK/SIRT1 pathway in LPS-treated GES-1 cells, and knockdown of both AMPK and SIRT1 reversed the protective effects of puerarin against LPS-induced inflammatory damage. AMPK overexpression strengthened, while AMPK knockdown weakened, the ability of puerarin to inhibit NLRP3-mediated inflammatory injury in LPS-treated GES-1 cells. Our findings suggest that puerarin may ameliorate LPS-induced inflammatory injury in GES-1 cells by activating the AMPK/SIRT1 signaling pathway and thereby repressing NLRP3 inflammasome-mediated apoptosis.
Collapse
Affiliation(s)
- Zi-Tan Peng
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Hubei, People's Republic of China; Hubei Key Laboratory of Kidney Disease Pathogenesis and InterventionHubei, Huangshi, Hubei, People's Republic of China
| | - Hui Liu
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Hubei, People's Republic of China; Hubei Key Laboratory of Kidney Disease Pathogenesis and InterventionHubei, Huangshi, Hubei, People's Republic of China.
| |
Collapse
|
35
|
Warschkau D, Delgado-Betancourt E, Holthaus D, Müller A, Kliem G, Krug SM, Schulzke JD, Aebischer T, Klotz C, Seeber F. From 3D to 2D: Harmonization of Protocols for Two-dimensional Cultures on Cell Culture Inserts of Intestinal Organoids from Various Species. Bio Protoc 2022; 12:e4295. [PMID: 35127985 PMCID: PMC8799680 DOI: 10.21769/bioprotoc.4295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 09/25/2023] Open
Abstract
In the expanding field of intestinal organoid research, various protocols for three- and two-dimensional organoid-derived cell cultures exist. Two-dimensional organoid-derived monolayers are used to overcome some limitations of three-dimensional organoid cultures. They are increasingly used also in infection research, to study physiological processes and tissue barrier functions, where easy experimental access of pathogens to the luminal and/or basolateral cell surface is required. This has resulted in an increasing number of publications reporting different protocols and media compositions for organoid manipulation, precluding direct comparisons of research outcomes in some cases. With this in mind, here we describe a protocol aimed at the harmonization of seeding conditions for three-dimensional intestinal organoids of four commonly used research species onto cell culture inserts, to create organoid-derived monolayers that form electrophysiologically tight epithelial barriers. We give an in-depth description of media compositions and culture conditions for creating these monolayers, enabling also the less experienced researchers to obtain reproducible results within a short period of time, and which should simplify the comparison of future studies between labs, but also encourage others to consider these systems as alternative cell culture models in their research. Graphic abstract: Schematic workflow of organoid-derived monolayer generation from intestinal spheroid cultures. ECM, extracellular matrix; ODM, organoid-derived monolayer.
Collapse
Affiliation(s)
- David Warschkau
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | | | - David Holthaus
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Antonia Müller
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Gudrun Kliem
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Susanne M. Krug
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Joerg-Dieter Schulzke
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Toni Aebischer
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Christian Klotz
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Frank Seeber
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| |
Collapse
|
36
|
Häfliger J, Morsy Y, Scharl M, Wawrzyniak M. From Patient Material to New Discoveries: a Methodological Review and Guide for Intestinal Stem Cell Researchers. Stem Cell Rev Rep 2022; 18:1309-1321. [PMID: 35038103 DOI: 10.1007/s12015-021-10307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Intestinal stem cells (ISC) are characterized by their ability to continuously self-renew and differentiate into various functionally distinct intestinal epithelial cell types. Impaired stem cell proliferation and differentiation can cause severe dysfunction of the gastrointestinal tract and lead to the development of several clinical disorders. Animal mouse models provide a valuable platform to study ISC function, disease mechanisms, and the intestinal epithelium's regenerative capacity upon tissue damage. However, advanced in vitro systems that are more relevant to human physiology are needed to understand better the diverse disease-triggering factors and the heterogeneity in clinical manifestations. Intestinal biopsies from patients might serve as potent starting material for such "gut-in-a-dish" approaches. While many promising tools for intestinal tissue processing, in vitro expansion, and downstream analysis have been developed in recent years, a comprehensive guide with recommendations to successfully launch or improve intestinal stem cell culture is missing. In this review, we present a selection of currently established methods, highlight recent publications and discuss the potential and limitations of those methodological approaches to facilitate and support the future design of novel and more personalized therapeutic options.
Collapse
Affiliation(s)
- Janine Häfliger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Sternwartstrasse 14, 8091, Zurich, Switzerland
| | - Yasser Morsy
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Sternwartstrasse 14, 8091, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Sternwartstrasse 14, 8091, Zurich, Switzerland
| | - Marcin Wawrzyniak
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Sternwartstrasse 14, 8091, Zurich, Switzerland.
| |
Collapse
|
37
|
Gu W, Wang H, Huang X, Kraiczy J, Singh PNP, Ng C, Dagdeviren S, Houghton S, Pellon-Cardenas O, Lan Y, Nie Y, Zhang J, Banerjee KK, Onufer EJ, Warner BW, Spence J, Scherl E, Rafii S, Lee RT, Verzi MP, Redmond D, Longman R, Helin K, Shivdasani RA, Zhou Q. SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling. Cell Stem Cell 2022; 29:101-115.e10. [PMID: 34582804 PMCID: PMC8741647 DOI: 10.1016/j.stem.2021.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 01/09/2023]
Abstract
Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.
Collapse
Affiliation(s)
- Wei Gu
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Hua Wang
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA
| | - Xiaofeng Huang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Judith Kraiczy
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Pratik N. P. Singh
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Charles Ng
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Sezin Dagdeviren
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Sean Houghton
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ying Lan
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Yaohui Nie
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jiaoyue Zhang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Emily J. Onufer
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Jason Spence
- Department of Internal Medicine, University of Michigan, 1500 E Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Shahin Rafii
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Richard T. Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - David Redmond
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200 Denmark,The Novo Nordisk Foundation for Stem Cell Biology (Danstem), University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ramesh A. Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Qiao Zhou
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA,Lead Contact ()
| |
Collapse
|
38
|
Cambra HM, Tallapragada NP, Mannam P, Breault DT, Klein AM. Triple-Decker Sandwich Cultures of Intestinal Organoids for Long-Term Live Imaging, Uniform Perturbation, and Statistical Sampling. Curr Protoc 2022; 2:e330. [PMID: 35030297 PMCID: PMC9006308 DOI: 10.1002/cpz1.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Three-dimensional organoid cultures enable the study of stem cell and tissue biology ex vivo, providing improved access to cells for perturbation and live imaging. Typically, organoids are grown in hydrogel domes that are simple to prepare but that lead to non-uniform tissue growth and viability. We recently developed a simple alternative culture method to embed intestinal organoids in multilayered hydrogels, called "triple-decker sandwiches," that align organoids in a common z-plane with uniform access to medium. This culture configuration improves the growth and survival of organoids over a wide working area and facilitates long-term confocal imaging and molecular perturbation. Here, we present protocols for preparing organoids in triple-decker sandwich cultures and using them for live imaging, immunostaining, and single-cell RNA sequencing. We have tested our methods on mouse and human intestinal organoids and expect them to be useful for other highly proliferative three-dimensional cell cultures. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Pre-coating plates with PolyHEMA to prepare them for triple-decker sandwich culture Support Protocol 1: Preparing PolyHEMA solution to coat glass-bottom dishes Basic Protocol 2: Embedding intestinal organoids in triple-decker sandwiches Alternate Protocol 1: Seeding single cells or organoids at low density in triple-decker sandwiches Support Protocol 2: Embedding intestinal organoids in hydrogel domes Support Protocol 3: Production of Wnt3a-conditioned medium Support Protocol 4: Production of Rspo1-conditioned medium Basic Protocol 3: Live imaging of mouse intestinal organoids in triple-decker sandwich cultures Alternate Protocol 2: Live imaging of vital dye-treated mouse intestinal organoids in triple-decker sandwich cultures Basic Protocol 4: Immunofluorescence imaging of mouse organoids liberated from triple-decker sandwich cultures Alternate Protocol 3: Liberating and fixing mouse intestinal organoids from dome cultures Support Protocol 5: Measuring cell proliferation by EdU staining of mouse intestinal organoids Basic Protocol 5: Single-cell RNA sequencing and analysis of mouse intestinal organoids.
Collapse
Affiliation(s)
- Hailey M. Cambra
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Naren P. Tallapragada
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Prabhath Mannam
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David T. Breault
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA,Harvard Stem Cell Institute, Harvard University, Boston, MA 02139, USA
| | - Allon M. Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA,Lead contact,Correspondence:
| |
Collapse
|
39
|
Zhao D, Farnell MB, Kogut MH, Genovese KJ, Chapkin RS, Davidson LA, Berghman LR, Farnell YZ. From crypts to enteroids: establishment and characterization of avian intestinal organoids. Poult Sci 2021; 101:101642. [PMID: 35016046 PMCID: PMC8749297 DOI: 10.1016/j.psj.2021.101642] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/29/2021] [Accepted: 11/17/2021] [Indexed: 12/30/2022] Open
Abstract
Intestinal organoids (IO), known as “mini-guts”, derived from intestinal crypts, are self-organizing three-dimensional (3D) multicellular ex vivo models that recapitulate intestine epithelial structure and function and have been widely used for studying intestinal physiology, pathophysiology, molecular mechanisms of host-pathogen interactions, and intestinal disease in mammals. However, studies on avian IO are limited and the development of long-term cultures of IO model for poultry research is lacking. Therefore, the objectives of this study were to generate crypt-derived organoids from chicken intestines and to optimize conditions for cell growth and enrichments, passages, and cryopreservation. Crypts were collected from the small intestines of birds at embryonic d-19 and ceca from layer and broiler chickens with ages ranging from d 1 to 20 wk, embedded in a basement membrane matrix, and cultured with organoid growth media (OGM) prepared in house. The crypt-derived organoids were successfully grown and propagated to form 3D spheres like structures that were cultured for up to 3 wk. Organoids were formed on d one, budding appeared on d 3, and robust budding was observed on d 7 and beyond. For cryopreservation, dissociated organoids were resuspended in a freezing medium. The characteristics of IO upon extended passages and freeze-thaw cycles were analyzed using reverse transcription (RT)-PCR, immunoblotting, and live cell imaging. Immunoblotting and RT-PCR using E-cadherin (the marker for epithelial cells), leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5, the marker for stem cells), chromogranin A (the marker for enteroendocrine cells), lysozyme (the marker for Paneth cells), and mucin (the biomarker for goblet cells) confirmed that IO were composed of heterogeneous cell populations, including epithelial cells, stem cells, enteroendocrine cells, Paneth cells, and goblet cells. Furthermore, OGM supplemented with both valproic acid and CHIR99021, a glycogen synthase kinase 3β inhibitor and a histone deacetylase inhibitor, increased the size of the avian IO (P < 0.001). To the best of our knowledge, this is the first comprehensive report for establishing long-term, organoid culture models from small intestines and ceca of layer and broiler chickens. This model will facilitate elucidation of the mechanisms impacting host-pathogen interactions, eventually leading to the discovery of pathogen intervention strategies in poultry.
Collapse
Affiliation(s)
- Dan Zhao
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843
| | - Morgan B Farnell
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843
| | - Michael H Kogut
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, TX 77845
| | - Kenneth J Genovese
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, TX 77845
| | - Robert S Chapkin
- Program in Integrative Nutrition & Complex Diseases, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843
| | - Laurie A Davidson
- Program in Integrative Nutrition & Complex Diseases, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843
| | - Luc R Berghman
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843; Department of Veterinary Pathobiology, Texas A&M University, TX 77843
| | - Yuhua Z Farnell
- Department of Poultry Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843.
| |
Collapse
|
40
|
Freed-Pastor WA, Lambert LJ, Ely ZA, Pattada NB, Bhutkar A, Eng G, Mercer KL, Garcia AP, Lin L, Rideout WM, Hwang WL, Schenkel JM, Jaeger AM, Bronson RT, Westcott PMK, Hether TD, Divakar P, Reeves JW, Deshpande V, Delorey T, Phillips D, Yilmaz OH, Regev A, Jacks T. The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer. Cancer Cell 2021; 39:1342-1360.e14. [PMID: 34358448 PMCID: PMC8511341 DOI: 10.1016/j.ccell.2021.07.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 02/08/2023]
Abstract
The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune-based strategies to combat this disease have been largely unsuccessful to date. We corroborate prior reports that a substantial portion of PDAC harbors predicted high-affinity MHC class I-restricted neoepitopes and extend these findings to advanced/metastatic disease. Using multiple preclinical models of neoantigen-expressing PDAC, we demonstrate that intratumoral neoantigen-specific CD8+ T cells adopt multiple states of dysfunction, resembling those in tumor-infiltrating lymphocytes of PDAC patients. Mechanistically, genetic and/or pharmacologic modulation of the CD155/TIGIT axis was sufficient to promote immune evasion in autochthonous neoantigen-expressing PDAC. Finally, we demonstrate that the CD155/TIGIT axis is critical in maintaining immune evasion in PDAC and uncover a combination immunotherapy (TIGIT/PD-1 co-blockade plus CD40 agonism) that elicits profound anti-tumor responses in preclinical models, now poised for clinical evaluation.
Collapse
Affiliation(s)
- William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laurens J Lambert
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zackery A Ely
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nimisha B Pattada
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - George Eng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kim L Mercer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ana P Garcia
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lin Lin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William L Hwang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason M Schenkel
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roderick T Bronson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Omer H Yilmaz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aviv Regev
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
41
|
Perrone F, Zilbauer M. Biobanking of human gut organoids for translational research. Exp Mol Med 2021; 53:1451-1458. [PMID: 34663935 PMCID: PMC8569164 DOI: 10.1038/s12276-021-00606-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/10/2021] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
The development of human organoid culture models has led to unprecedented opportunities to generate self-organizing, three-dimensional miniature organs that closely mimic in vivo conditions. The ability to expand, culture, and bank such organoids now provide researchers with the opportunity to generate next-generation living biobanks, which will substantially contribute to translational research in a wide range of areas, including drug discovery and testing, regenerative medicine as well as the development of a personalized treatment approach. However, compared to traditional tissue repositories, the generation of a living organoid biobank requires a much higher level of coordination, additional resources, and scientific expertise. In this short review, we discuss the opportunities and challenges associated with the generation of a living organoid biobank. Focusing on human intestinal organoids, we highlight some of the key aspects that need to be considered and provide an outlook for future development in this exciting field.
Collapse
Affiliation(s)
- Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, UK.
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
42
|
Intestinal Organoids in Colitis Research: Focusing on Variability and Cryopreservation. Stem Cells Int 2021; 2021:9041423. [PMID: 34580592 PMCID: PMC8464427 DOI: 10.1155/2021/9041423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/23/2021] [Accepted: 08/14/2021] [Indexed: 11/18/2022] Open
Abstract
In recent years, stem cell-derived organoids have become a cell culture standard that is widely used for studying various scientific issues that were previously investigated through animal experiments and using common tumor cell lines. After their initial hype, concerns regarding their standardization have been raised. Here, we aim to provide some insights into our experience in standardizing murine colonic epithelial organoids, which we use as a replacement method for research on inflammatory bowel disease. Considering good scientific practice, we examined various factors that might challenge the design and outcome of experiments using these organoids. First, to analyze the impact of antibiotics/antimycotics, we performed kinetic experiments using ZellShield® and measured the gene expression levels of the tight junction markers Ocln, Zo-1, and Cldn4, the proliferation marker Ki67, and the proinflammatory cytokine Tnfα. Because we found no differences between cultivations with and without ZellShield®, we then performed infection experiments using the probiotic Escherichia coli Nissle 1917 as an already established model setup to analyze the impact of technical, interexperimental, and biologic replicates. We demonstrate that interexperimental differences pose the greatest challenge for reproducibility and explain our strategies for addressing these differences. Additionally, we conducted infection experiments using freshly isolated and cryopreserved/thawed organoids and found that cryopreservation influenced the experimental outcome during early passages. Formerly cryopreserved colonoids exhibited a premature appearance and a higher proinflammatory response to bacterial stimulation. Therefore, we recommend analyzing the growth characteristics and reliability of cryopreserved organoids before to their use in experiments together with conducting several independent experiments under standardized conditions. Taken together, our findings demonstrate that organoid culture, if standardized, constitutes a good tool for reducing the need for animal experiments and might further improve our understanding of, for example, the role of epithelial cells in inflammatory bowel disease development.
Collapse
|
43
|
Nickerson KP, Llanos-Chea A, Ingano L, Serena G, Miranda-Ribera A, Perlman M, Lima R, Sztein MB, Fasano A, Senger S, Faherty CS. A Versatile Human Intestinal Organoid-Derived Epithelial Monolayer Model for the Study of Enteric Pathogens. Microbiol Spectr 2021; 9:e0000321. [PMID: 34106568 PMCID: PMC8552518 DOI: 10.1128/spectrum.00003-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
Gastrointestinal infections cause significant morbidity and mortality worldwide. The complexity of human biology and limited insights into host-specific infection mechanisms are key barriers to current therapeutic development. Here, we demonstrate that two-dimensional epithelial monolayers derived from human intestinal organoids, combined with in vivo-like bacterial culturing conditions, provide significant advancements for the study of enteropathogens. Monolayers from the terminal ileum, cecum, and ascending colon recapitulated the composition of the gastrointestinal epithelium, in which several techniques were used to detect the presence of enterocytes, mucus-producing goblet cells, and other cell types following differentiation. Importantly, the addition of receptor activator of nuclear factor kappa-B ligand (RANKL) increased the presence of M cells, critical antigen-sampling cells often exploited by enteric pathogens. For infections, bacteria were grown under in vivo-like conditions known to induce virulence. Overall, interesting patterns of tissue tropism and clinical manifestations were observed. Shigella flexneri adhered efficiently to the cecum and colon; however, invasion in the colon was best following RANKL treatment. Both Salmonella enterica serovars Typhi and Typhimurium displayed different infection patterns, with S. Typhimurium causing more destruction of the terminal ileum and S. Typhi infecting the cecum more efficiently than the ileum, particularly with regard to adherence. Finally, various pathovars of Escherichia coli validated the model by confirming only adherence was observed with these strains. This work demonstrates that the combination of human-derived tissue with targeted bacterial growth conditions enables powerful analyses of human-specific infections that could lead to important insights into pathogenesis and accelerate future vaccine development. IMPORTANCE While traditional laboratory techniques and animal models have provided valuable knowledge in discerning virulence mechanisms of enteric pathogens, the complexity of the human gastrointestinal tract has hindered our understanding of physiologically relevant, human-specific interactions; and thus, has significantly delayed successful vaccine development. The human intestinal organoid-derived epithelial monolayer (HIODEM) model closely recapitulates the diverse cell populations of the intestine, allowing for the study of human-specific infections. Differentiation conditions permit the expansion of various cell populations, including M cells that are vital to immune recognition and the establishment of infection by some bacteria. We provide details of reproducible culture methods and infection conditions for the analyses of Shigella, Salmonella, and pathogenic Escherichia coli in which tissue tropism and pathogen-specific infection patterns were detected. This system will be vital for future studies that explore infection conditions, health status, or epigenetic differences and will serve as a novel screening platform for therapeutic development.
Collapse
Affiliation(s)
- Kourtney P. Nickerson
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Alejandro Llanos-Chea
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Laura Ingano
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gloria Serena
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Alba Miranda-Ribera
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Meryl Perlman
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosiane Lima
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcelo B. Sztein
- Center for Vaccine Development and Global Health, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stefania Senger
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christina S. Faherty
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
44
|
Bittenglova K, Habart D, Saudek F, Koblas T. The Potential of Pancreatic Organoids for Diabetes Research and Therapy. Islets 2021; 13:85-105. [PMID: 34523383 PMCID: PMC8528407 DOI: 10.1080/19382014.2021.1941555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/04/2021] [Indexed: 10/20/2022] Open
Abstract
The success of clinical transplantation of pancreas or isolated pancreatic islets supports the concept of cell-based cure for diabetes. One limitation is the shortage of cadaver human pancreata. The demand-supply gap could potentially be bridged by harnessing the self-renewal capacity of stem cells. Pluripotent stem cells and adult pancreatic stem cells have been explored as possible cell sources. Recently, a system for long-term culture of proposed adult pancreatic stem cells in a form of organoids was developed. Generated organoids partially mimic the architecture and cell-type composition of pancreatic tissue. Here, we review the attempts over the past decade, to utilize the organoid cell culture principles in order to identify, expand, and differentiate the adult pancreatic stem cells from different compartments of mouse and human pancreata. The development of the culture conditions, effects of specific growth factors and small molecules is discussed. The potential utility of the adult pancreatic stem cells is considered in the context of other cell sources.
Collapse
Affiliation(s)
- Katerina Bittenglova
- Department of Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Habart
- Department of Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Frantisek Saudek
- Department of Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Tomas Koblas
- Department of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| |
Collapse
|
45
|
Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar GD, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S. Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. eLife 2021; 10:e66417. [PMID: 34463615 PMCID: PMC8463074 DOI: 10.7554/elife.66417] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. Methods We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Results Infected ALO monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Conclusions Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines. Funding This work was supported by the National Institutes for Health (NIH) grants 1R01DK107585-01A1, 3R01DK107585-05S1 (to SD); R01-AI141630, CA100768 and CA160911 (to PG) and R01-AI 155696 (to PG, DS and SD); R00-CA151673 and R01-GM138385 (to DS), R01- HL32225 (to PT), UCOP-R00RG2642 (to SD and PG), UCOP-R01RG3780 (to P.G. and D.S) and a pilot award from the Sanford Stem Cell Clinical Center at UC San Diego Health (P.G, S.D, D.S). GDK was supported through The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. L.C.A's salary was supported in part by the VA San Diego Healthcare System. This manuscript includes data generated at the UC San Diego Institute of Genomic Medicine (IGC) using an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (#S10 OD026929).
Collapse
Affiliation(s)
- Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
- HUMANOID CoRE, University of California San Diego, San Diego, United States
| | - MacKenzie Fuller
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
- HUMANOID CoRE, University of California San Diego, San Diego, United States
| | - Ayden Fonseca
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
- HUMANOID CoRE, University of California San Diego, San Diego, United States
| | - Sahar Taheri
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, San Diego, United States
| | - Stella-Rita Ibeawuchi
- Department of Pathology, University of California San Diego, San Diego, United States
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Gajanan Dattatray Katkar
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
| | - Amanraj Claire
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
- HUMANOID CoRE, University of California San Diego, San Diego, United States
| | - Vanessa Castillo
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
| | - Moises Hernandez
- Division of Cardiothoracic Surgery, University of California San Diego, San Diego, United States
| | - Hana Russo
- Department of Pathology, University of California San Diego, San Diego, United States
| | - Jason Duran
- Division of Cardiology, Department of Internal Medicine, UC San Diego Medical Center, San Diego, United States
| | - Laura E Crotty Alexander
- Pulmonary Critical Care Section, Veterans Affairs (VA) San Diego Healthcare System, La Jolla, United States
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Ann Tipps
- Department of Pathology, University of California San Diego, San Diego, United States
| | - Grace Lin
- Department of Pathology, University of California San Diego, San Diego, United States
| | | | - Ranajoy Chattopadhyay
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
- HUMANOID CoRE, University of California San Diego, San Diego, United States
- Cell Applications Inc., La Jolla, CA, United States
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, San Diego, United States
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, United States
- HUMANOID CoRE, University of California San Diego, San Diego, United States
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Soumita Das
- HUMANOID CoRE, University of California San Diego, San Diego, United States
- Department of Pathology, University of California San Diego, San Diego, United States
| |
Collapse
|
46
|
Zhang J, Hernandez-Gordillo V, Trapecar M, Wright C, Taketani M, Schneider K, Chen WLK, Stas E, Breault DT, Carrier RL, Voigt CA, Griffith LG. Coculture of primary human colon monolayer with human gut bacteria. Nat Protoc 2021; 16:3874-3900. [PMID: 34183870 PMCID: PMC9109719 DOI: 10.1038/s41596-021-00562-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
The presence of microbes in the colon impacts host physiology. Therefore, microbes are being evaluated as potential treatments for colorectal diseases. Humanized model systems that enable robust culture of primary human intestinal cells with bacteria facilitate evaluation of potential treatments. Here, we describe a protocol that can be used to coculture a primary human colon monolayer with aerotolerant bacteria. Primary human colon cells maintained as organoids are dispersed into single-cell suspensions and then seeded on collagen-coated Transwell inserts, where they attach and proliferate to form confluent monolayers within days of seeding. The confluent monolayers are differentiated for an additional 4 d and then cocultured with bacteria. As an example application, we describe how to coculture differentiated colon cells for 8 h with four strains of Bacteroides thetaiotaomicron, each engineered to detect different colonic microenvironments via genetically embedded logic circuits incorporating deoxycholic acid and anhydrotetracycline sensors. Characterization of this coculture system reveals that barrier function remains intact in the presence of engineered B. thetaiotaomicron. The bacteria stay close to the mucus layer and respond in a microenvironment-specific manner to the inducers (deoxycholic acid and anhydrotetracycline) of the genetic circuits. This protocol thus provides a useful mucosal barrier system to assess the effects of bacterial cells that respond to the colonic microenvironment, and may also be useful in other contexts to model human intestinal barrier properties and microbiota-host interactions.
Collapse
Affiliation(s)
- Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Martin Trapecar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles Wright
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mao Taketani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kirsten Schneider
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wen Li Kelly Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric Stas
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rebecca L Carrier
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
47
|
Ojo BA, VanDussen KL, Rosen MJ. The Promise of Patient-Derived Colon Organoids to Model Ulcerative Colitis. Inflamm Bowel Dis 2021; 28:299-308. [PMID: 34251431 PMCID: PMC8804507 DOI: 10.1093/ibd/izab161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Indexed: 12/11/2022]
Abstract
Physiologic, molecular, and genetic findings all point to impaired intestinal epithelial function as a key element in the multifactorial pathogenesis of ulcerative colitis (UC). The lack of epithelial-directed therapies is a conspicuous weakness of our UC therapeutic armamentarium. However, a critical barrier to new drug discovery is the lack of preclinical human models of UC. Patient tissue-derived colon epithelial organoids (colonoids) are primary epithelial stem cell-derived in vitro structures capable of self-organization and self-renewal that hold great promise as a human preclinical model for UC drug development. Several single and multi-tissue systems for colonoid culture have been developed, including 3-dimensional colonoids grown in a gelatinous extracellular matrix, 2-dimensional polarized monolayers, and colonoids on a chip that model luminal and blood flow and nutrient delivery. A small number of pioneering studies suggest that colonoids derived from UC patients retain some disease-related transcriptional and epigenetic changes, but they also raise questions regarding the persistence of inflammatory transcriptional programs in culture over time. Additional research is needed to fully characterize the extent to which and under what conditions colonoids accurately model disease-associated epithelial molecular and functional aberrations. With further advancement and standardization of colonoid culture methodology, colonoids will likely become an important tool for realizing precision medicine in UC.
Collapse
Affiliation(s)
- Babajide A Ojo
- Divisions of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States
| | - Kelli L VanDussen
- Divisions of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States,Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Michael J Rosen
- Divisions of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States,Address correspondence to: Michael J. Rosen, MD, MSCI, Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 2010, Cincinnati, Ohio, 45229, United States. E-mail:
| |
Collapse
|
48
|
Mihi B, Gong Q, Nolan LS, Gale SE, Goree M, Hu E, Lanik WE, Rimer JM, Liu V, Parks OB, Lewis AN, Agrawal P, Laury ML, Kumar P, Huang E, Bidani SS, Luke CJ, Kolls JK, Good M. Interleukin-22 signaling attenuates necrotizing enterocolitis by promoting epithelial cell regeneration. Cell Rep Med 2021; 2:100320. [PMID: 34195684 PMCID: PMC8233697 DOI: 10.1016/j.xcrm.2021.100320] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 03/17/2021] [Accepted: 05/20/2021] [Indexed: 12/27/2022]
Abstract
Necrotizing enterocolitis (NEC) is a deadly intestinal inflammatory disorder that primarily affects premature infants and lacks adequate therapeutics. Interleukin (IL)-22 plays a critical role in gut barrier maintenance, promoting epithelial regeneration, and controlling intestinal inflammation in adult animal models. However, the importance of IL-22 signaling in neonates during NEC remains unknown. We investigated the role of IL-22 in the neonatal intestine under homeostatic and inflammatory conditions by using a mouse model of NEC. Our data reveal that Il22 expression in neonatal murine intestine is negligible until weaning, and both human and murine neonates lack IL-22 production during NEC. Mice deficient in IL-22 or lacking the IL-22 receptor in the intestine display a similar susceptibility to NEC, consistent with the lack of endogenous IL-22 during development. Strikingly, treatment with recombinant IL-22 during NEC substantially reduces inflammation and enhances epithelial regeneration. These findings may provide a new therapeutic strategy to attenuate NEC.
Collapse
MESH Headings
- Animals
- Animals, Newborn
- Chemokine CXCL1/genetics
- Chemokine CXCL1/immunology
- Chemokine CXCL2/genetics
- Chemokine CXCL2/immunology
- Disease Models, Animal
- Enterocolitis, Necrotizing/drug therapy
- Enterocolitis, Necrotizing/immunology
- Enterocolitis, Necrotizing/microbiology
- Enterocolitis, Necrotizing/pathology
- Gastrointestinal Microbiome/immunology
- Gene Expression Regulation, Developmental
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/immunology
- Infant, Newborn, Diseases/microbiology
- Infant, Newborn, Diseases/pathology
- Infant, Premature
- Interleukin-1beta/genetics
- Interleukin-1beta/immunology
- Interleukins/genetics
- Interleukins/immunology
- Intestinal Mucosa/immunology
- Intestinal Mucosa/metabolism
- Intestinal Mucosa/microbiology
- Mice
- Mice, Knockout
- Protein Isoforms/genetics
- Protein Isoforms/immunology
- Receptors, Interleukin/genetics
- Receptors, Interleukin/immunology
- Recombinant Proteins/pharmacology
- Regeneration/genetics
- Regeneration/immunology
- Signal Transduction
- Weaning
- Interleukin-22
Collapse
Affiliation(s)
- Belgacem Mihi
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Qingqing Gong
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lila S. Nolan
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sarah E. Gale
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martin Goree
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elise Hu
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wyatt E. Lanik
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jamie M. Rimer
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victoria Liu
- Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Olivia B. Parks
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Angela N. Lewis
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pranjal Agrawal
- Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Marie L. Laury
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pawan Kumar
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth Huang
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shay S. Bidani
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cliff J. Luke
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jay K. Kolls
- Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA, USA
| | - Misty Good
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
49
|
Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar G, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S. Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.17.344002. [PMID: 33106807 PMCID: PMC7587781 DOI: 10.1101/2020.10.17.344002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19 which can be immediately utilized to investigate COVID-19 pathogenesis, and vet new therapies and vaccines.
Collapse
|
50
|
Jin RU, Brown JW, Li QK, Bayguinov PO, Wang JS, Mills JC. Tropism of Severe Acute Respiratory Syndrome Coronavirus 2 for Barrett's Esophagus May Increase Susceptibility to Developing Coronavirus Disease 2019. Gastroenterology 2021; 160:2165-2168.e4. [PMID: 33484686 PMCID: PMC7816599 DOI: 10.1053/j.gastro.2021.01.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/05/2021] [Accepted: 01/10/2021] [Indexed: 01/10/2023]
Affiliation(s)
- Ramon U Jin
- Division of Oncology, Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, Missouri
| | - Jeffrey W Brown
- Division of Gastroenterology, Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, Missouri.
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St Louis, Missouri
| | - Jean S Wang
- Division of Gastroenterology, Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, Missouri
| | - Jason C Mills
- Division of Gastroenterology, Department of Medicine, Washington University in St Louis, School of Medicine, St Louis, Missouri; Department of Pathology and Immunology, Washington University in St Louis, School of Medicine, St Louis, Missouri; Department of Developmental Biology, Washington University in St Louis, School of Medicine, St Louis, Missouri.
| |
Collapse
|