1
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Liu J, Prahl LS, Huang AZ, Hughes AJ. Measurement of adhesion and traction of cells at high yield reveals an energetic ratchet operating during nephron condensation. Proc Natl Acad Sci U S A 2024; 121:e2404586121. [PMID: 39292750 DOI: 10.1073/pnas.2404586121] [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: 03/05/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
Developmental biology-inspired strategies for tissue-building have extraordinary promise for regenerative medicine, spurring interest in the relationship between cell biophysical properties and morphological transitions. However, mapping gene or protein expression data to cell biophysical properties to physical morphogenesis remains challenging with current techniques. Here, we present multiplexed adhesion and traction of cells at high yield (MATCHY). MATCHY advances the multiplexing and throughput capabilities of existing traction force and cell-cell adhesion assays using microfabrication and a semiautomated computation scheme with machine learning-driven cell segmentation. Both biophysical assays are coupled with serial downstream immunofluorescence to extract cell type/signaling state information. MATCHY is especially suited to complex primary tissue-, organoid-, or biopsy-derived cell mixtures since it does not rely on a priori knowledge of cell surface markers, cell sorting, or use of lineage-specific reporter animals. We first validate MATCHY on canine kidney epithelial cells engineered for rearranged during transfection (RET) tyrosine kinase expression and quantify a relationship between downstream signaling and cell traction. We then use MATCHY to create a biophysical atlas of mouse embryonic kidney primary cells and identify distinct biophysical states along the nephron differentiation trajectory. Our data complement expression-level knowledge of adhesion molecule changes that accompany nephron differentiation with quantitative biophysical information. These data reveal an "energetic ratchet" that accounts for spatial trends in nephron progenitor cell condensation as they differentiate into early nephron structures, which we validate through agent-based computational simulation. MATCHY offers semiautomated cell biophysical characterization at >10,000-cell throughput, an advance benefiting fundamental studies and new synthetic tissue strategies for regenerative medicine.
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Affiliation(s)
- Jiageng Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
| | - Louis S Prahl
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA 19104
| | - Aria Zheyuan Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
- Center for Precision Engineering for Health, University of Pennsylvania, Philadelphia, PA 19104
- Materials Research Science and Engineering Center, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104
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2
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Kang S, Chen EC, Cifuentes H, Co JY, Cole G, Graham J, Hsia R, Kiyota T, Klein JA, Kroll KT, Nieves Lopez LM, Norona LM, Peiris H, Potla R, Romero-Lopez M, Roth JG, Tseng M, Fullerton AM, Homan KA. Complex in vitromodels positioned for impact to drug testing in pharma: a review. Biofabrication 2024; 16:042006. [PMID: 39189069 DOI: 10.1088/1758-5090/ad6933] [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: 12/22/2023] [Accepted: 07/30/2024] [Indexed: 08/28/2024]
Abstract
Recent years have seen the creation and popularization of various complexin vitromodels (CIVMs), such as organoids and organs-on-chip, as a technology with the potential to reduce animal usage in pharma while also enhancing our ability to create safe and efficacious drugs for patients. Public awareness of CIVMs has increased, in part, due to the recent passage of the FDA Modernization Act 2.0. This visibility is expected to spur deeper investment in and adoption of such models. Thus, end-users and model developers alike require a framework to both understand the readiness of current models to enter the drug development process, and to assess upcoming models for the same. This review presents such a framework for model selection based on comparative -omics data (which we term model-omics), and metrics for qualification of specific test assays that a model may support that we term context-of-use (COU) assays. We surveyed existing healthy tissue models and assays for ten drug development-critical organs of the body, and provide evaluations of readiness and suggestions for improving model-omics and COU assays for each. In whole, this review comes from a pharma perspective, and seeks to provide an evaluation of where CIVMs are poised for maximum impact in the drug development process, and a roadmap for realizing that potential.
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Affiliation(s)
- Serah Kang
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Eugene C Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Helen Cifuentes
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Julia Y Co
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Gabrielle Cole
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Jessica Graham
- Product Quality & Occupational Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of Americaica
| | - Rebecca Hsia
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Tomomi Kiyota
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Jessica A Klein
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Katharina T Kroll
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Lenitza M Nieves Lopez
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Leah M Norona
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Heshan Peiris
- Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Ratnakar Potla
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Monica Romero-Lopez
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Julien G Roth
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Min Tseng
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Aaron M Fullerton
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Kimberly A Homan
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
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3
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Lancaster MA. Pluripotent stem cell-derived organoids: A brief history of curiosity-led discoveries. Bioessays 2024:e2400105. [PMID: 39101295 DOI: 10.1002/bies.202400105] [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: 04/29/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024]
Abstract
Organoids are quickly becoming an accepted model for understanding human biology and disease. Pluripotent stem cells (PSC) provide a starting point for many organs and enable modeling of the embryonic development and maturation of such organs. The foundation of PSC-derived organoids can be found in elegant developmental studies demonstrating the remarkable ability of immature cells to undergo histogenesis even when taken out of the embryo context. PSC-organoids are an evolution of earlier methods such as embryoid bodies, taken to a new level with finer control and in some cases going beyond tissue histogenesis to organ-like morphogenesis. But many of the discoveries that led to organoids were not necessarily planned, but rather the result of inquisitive minds with freedom to explore. Protecting such curiosity-led research through flexible funding will be important going forward if we are to see further ground-breaking discoveries.
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Wang G, Wu H, Zhai X, Zhang L, Zhang C, Cheng C, Xu X, Gao E, Xiong X, Zhang J, Liu Z. Kidney Organoid Modeling of WT1 Mutations Reveals Key Regulatory Paths Underlying Podocyte Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308556. [PMID: 38810140 PMCID: PMC11304319 DOI: 10.1002/advs.202308556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/16/2024] [Indexed: 05/31/2024]
Abstract
Wilms tumor-1(WT1) is a crucial transcription factor that regulates podocyte development. However, the epigenomic mechanism underlying the function of WT1 during podocyte development has yet to be fully elucidated. Here, single-cell chromatin accessibility and gene expression maps of foetal kidneys and kidney organoids are generated. Functional implications of WT1-targeted genes, which are crucial for the development of podocytes and the maintenance of their structure, including BMPER/PAX2/MAGI2 that regulates WNT signaling pathway, MYH9 that maintains actin filament organization and NPHS1 that modulates cell junction assembly are identified. To further illustrate the functional importance of WT1-mediated transcriptional regulation during podocyte development, cultured and implanted patient-derived kidney organoids derived from the Induced Pluripotent Stem Cell (iPSCs) of a patient with a heterozygous missense mutation in WT1 are generated. Results from single-cell RNA sequencing (scRNA-seq) and functional assays confirm that the WT1 mutation leads to delays in podocyte development and causes damage to cell structures, due to its failure to activate the targeting genes MAGI2, MYH9, and NPHS1. Notably, correcting the mutation in the patient iPSCs using CRISPR-Cas9 gene editing rescues the podocyte phenotype. Collectively, this work elucidates the WT1-related epigenomic landscape with respect to human podocyte development and identifies the disease-causing role of a WT1 mutation.
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Affiliation(s)
- Gang Wang
- National Clinical Research Center of Kidney DiseasesJinling HospitalNanjing University School of MedicineNanjingJiangsu210002China
| | - Hangdi Wu
- Department of Basic Medical SciencesZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Xiuwen Zhai
- National Clinical Research Center of Kidney DiseasesJinling HospitalNanjing University School of MedicineNanjingJiangsu210002China
| | - Li Zhang
- Department of Basic Medical SciencesZhejiang University School of MedicineHangzhouZhejiang310058China
- Liangzhu LaboratoryZhejiang UniversityHangzhou311121China
- Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical Sciences & The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Changming Zhang
- National Clinical Research Center of Kidney DiseasesJinling HospitalNanjing University School of MedicineNanjingJiangsu210002China
| | - Chen Cheng
- Department of Basic Medical SciencesZhejiang University School of MedicineHangzhouZhejiang310058China
- Liangzhu LaboratoryZhejiang UniversityHangzhou311121China
- Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical Sciences & The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Xiaodong Xu
- National Clinical Research Center of Kidney DiseasesJinling HospitalNanjing University School of MedicineNanjingJiangsu210002China
| | - Erzhi Gao
- National Clinical Research Center of Kidney DiseasesJinling HospitalNanjing University School of MedicineNanjingJiangsu210002China
| | - Xushen Xiong
- Department of Basic Medical SciencesZhejiang University School of MedicineHangzhouZhejiang310058China
- Liangzhu LaboratoryZhejiang UniversityHangzhou311121China
- State Key Laboratory of Transvascular Implantation DevicesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou311121China
| | - Jin Zhang
- Department of Basic Medical SciencesZhejiang University School of MedicineHangzhouZhejiang310058China
- Liangzhu LaboratoryZhejiang UniversityHangzhou311121China
- Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical Sciences & The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- Hematology InstituteZhejiang UniversityHangzhouZhejiang310058China
| | - Zhihong Liu
- National Clinical Research Center of Kidney DiseasesJinling HospitalNanjing University School of MedicineNanjingJiangsu210002China
- Liangzhu LaboratoryZhejiang UniversityHangzhou311121China
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5
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Yang H, Niu S, Guo M, Xue Y. Applications of 3D organoids in toxicological studies: a comprehensive analysis based on bibliometrics and advances in toxicological mechanisms. Arch Toxicol 2024; 98:2309-2330. [PMID: 38806717 DOI: 10.1007/s00204-024-03777-4] [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: 01/22/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024]
Abstract
A mechanism exploration is an important part of toxicological studies. However, traditional cell and animal models can no longer meet the current needs for in-depth studies of toxicological mechanisms. The three-dimensional (3D) organoid derived from human embryonic stem cells (hESC) or induced pluripotent stem cells (hiPSC) is an ideal experimental model for the study of toxicological effects and mechanisms, which further recapitulates the human tissue microenvironment and provides a reliable method for studying complex cell-cell interactions. This article provides a comprehensive overview of the state of the 3D organoid technology in toxicological studies, including a bibliometric analysis of the existing literature and an exploration of the latest advances in toxicological mechanisms. The use of 3D organoids in toxicology research is growing rapidly, with applications in disease modeling, organ-on-chips, and drug toxicity screening being emphasized, but academic communications among countries/regions, institutions, and research scholars need to be further strengthened. Attempts to study the toxicological mechanisms of exogenous chemicals such as heavy metals, nanoparticles, drugs and organic pollutants are also increasing. It can be expected that 3D organoids can be better applied to the safety evaluation of exogenous chemicals by establishing a standardized methodology.
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Affiliation(s)
- Haitao Yang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Shuyan Niu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Menghao Guo
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Yuying Xue
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
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6
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Porter CM, Qian GC, Grindel SH, Hughes AJ. Highly parallel production of designer organoids by mosaic patterning of progenitors. Cell Syst 2024; 15:649-661.e9. [PMID: 38981488 PMCID: PMC11257788 DOI: 10.1016/j.cels.2024.06.004] [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: 11/14/2023] [Revised: 04/09/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
Organoids derived from human stem cells are a promising approach for disease modeling, regenerative medicine, and fundamental research. However, organoid variability and limited control over morphological outcomes remain as challenges. One open question is the extent to which engineering control over culture conditions can guide organoids to specific compositions. Here, we extend a DNA "velcro" cell patterning approach, precisely controlling the number and ratio of human induced pluripotent stem cell-derived progenitors contributing to nephron progenitor (NP) organoids and mosaic NP/ureteric bud (UB) tip cell organoids within arrays of microwells. We demonstrate long-term control over organoid size and morphology, decoupled from geometric constraints. We then show emergent trends in organoid tissue proportions that depend on initial progenitor cell composition. These include higher nephron and stromal cell representation in mosaic NP/UB organoids vs. NP-only organoids and a "goldilocks" initial cell ratio in mosaic organoids that optimizes the formation of proximal tubule structures.
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Affiliation(s)
- Catherine M Porter
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Precision Engineering for Health (CPE4H), University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Grace C Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samuel H Grindel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Precision Engineering for Health (CPE4H), University of Pennsylvania, Philadelphia, PA 19104, USA; Materials Research Science and Engineering Center (MRSEC), University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Precision Engineering for Health (CPE4H), University of Pennsylvania, Philadelphia, PA 19104, USA; Materials Research Science and Engineering Center (MRSEC), University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Musah S, Bhattacharya R, Himmelfarb J. Kidney Disease Modeling with Organoids and Organs-on-Chips. Annu Rev Biomed Eng 2024; 26:383-414. [PMID: 38424088 DOI: 10.1146/annurev-bioeng-072623-044010] [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] [Indexed: 03/02/2024]
Abstract
Kidney disease is a global health crisis affecting more than 850 million people worldwide. In the United States, annual Medicare expenditures for kidney disease and organ failure exceed $81 billion. Efforts to develop targeted therapeutics are limited by a poor understanding of the molecular mechanisms underlying human kidney disease onset and progression. Additionally, 90% of drug candidates fail in human clinical trials, often due to toxicity and efficacy not accurately predicted in animal models. The advent of ex vivo kidney models, such as those engineered from induced pluripotent stem (iPS) cells and organ-on-a-chip (organ-chip) systems, has garnered considerable interest owing to their ability to more accurately model tissue development and patient-specific responses and drug toxicity. This review describes recent advances in developing kidney organoids and organ-chips by harnessing iPS cell biology to model human-specific kidney functions and disease states. We also discuss challenges that must be overcome to realize the potential of organoids and organ-chips as dynamic and functional conduits of the human kidney. Achieving these technological advances could revolutionize personalized medicine applications and therapeutic discovery for kidney disease.
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Affiliation(s)
- Samira Musah
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, USA;
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, North Carolina, USA
- Developmental and Stem Cell Biology Program and Department of Cell Biology, Duke University, Durham, North Carolina, USA
| | - Rohan Bhattacharya
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, USA;
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, North Carolina, USA
| | - Jonathan Himmelfarb
- Department of Medicine, Kidney Research Institute, and Division of Nephrology, University of Washington School of Medicine, Seattle, Washington, USA;
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Cheng C, Wang G, Zhu Y, Wu H, Zhang L, Liu Z, Huang Y, Zhang J. Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids. Nat Commun 2024; 15:3946. [PMID: 38729950 PMCID: PMC11087505 DOI: 10.1038/s41467-024-48282-5] [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: 07/28/2022] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Disease modeling with isogenic Induced Pluripotent Stem Cell (iPSC)-differentiated organoids serves as a powerful technique for studying disease mechanisms. Multiplexed coculture is crucial to mitigate batch effects when studying the genetic effects of disease-causing variants in differentiated iPSCs or organoids, and demultiplexing at the single-cell level can be conveniently achieved by assessing natural genetic barcodes. Here, to enable cost-efficient time-series experimental designs via multiplexed bulk and single-cell RNA-seq of hybrids, we introduce a computational method in our Vireo Suite, Vireo-bulk, to effectively deconvolve pooled bulk RNA-seq data by genotype reference, and thereby quantify donor abundance over the course of differentiation and identify differentially expressed genes among donors. Furthermore, with multiplexed scRNA-seq and bulk RNA-seq, we demonstrate the usefulness and necessity of a pooled design to reveal donor iPSC line heterogeneity during macrophage cell differentiation and to model rare WT1 mutation-driven kidney disease with chimeric organoids. Our work provides an experimental and analytic pipeline for dissecting disease mechanisms with chimeric organoids.
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Affiliation(s)
- Chen Cheng
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow for Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Gang Wang
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow for Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Hangdi Wu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow for Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Zhihong Liu
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yuanhua Huang
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow for Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China.
- Center of Gene/Cell Engineering and Genome Medicine of Zhejiang Province, Hangzhou, China.
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9
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Oishi H, Tabibzadeh N, Morizane R. Advancing preclinical drug evaluation through automated 3D imaging for high-throughput screening with kidney organoids. Biofabrication 2024; 16:10.1088/1758-5090/ad38df. [PMID: 38547531 PMCID: PMC11304660 DOI: 10.1088/1758-5090/ad38df] [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: 11/14/2023] [Accepted: 03/28/2024] [Indexed: 04/09/2024]
Abstract
High-throughput drug screening is crucial for advancing healthcare through drug discovery. However, a significant limitation arises from availablein vitromodels using conventional 2D cell culture, which lack the proper phenotypes and architectures observed in three-dimensional (3D) tissues. Recent advancements in stem cell biology have facilitated the generation of organoids-3D tissue constructs that mimic human organsin vitro. Kidney organoids, derived from human pluripotent stem cells, represent a significant breakthrough in disease representation. They encompass major kidney cell types organized within distinct nephron segments, surrounded by stroma and endothelial cells. This tissue allows for the assessment of structural alterations such as nephron loss, a characteristic of chronic kidney disease. Despite these advantages, the complexity of 3D structures has hindered the use of organoids for large-scale drug screening, and the drug screening pipelines utilizing these complexin vitromodels remain to be established for high-throughput screening. In this study, we address the technical limitations of kidney organoids through fully automated 3D imaging, aided by a machine-learning approach for automatic profiling of nephron segment-specific epithelial morphometry. Kidney organoids were exposed to the nephrotoxic agent cisplatin to model severe acute kidney injury. An U.S. Food and Drug Administration (FDA)-approved drug library was tested for therapeutic and nephrotoxicity screening. The fully automated pipeline of 3D image acquisition and analysis identified nephrotoxic or therapeutic drugs during cisplatin chemotherapy. The nephrotoxic potential of these drugs aligned with previousin vivoand human reports. Additionally, Imatinib, a tyrosine kinase inhibitor used in hematological malignancies, was identified as a potential preventive therapy for cisplatin-induced kidney injury. Our proof-of-concept report demonstrates that the automated screening process, using 3D morphometric assays with kidney organoids, enables high-throughput screening for nephrotoxicity and therapeutic assessment in 3D tissue constructs.
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Affiliation(s)
- Haruka Oishi
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
| | - Nahid Tabibzadeh
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Ryuji Morizane
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, United States of America
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10
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Ng-Blichfeldt JP, Stewart BJ, Clatworthy MR, Williams JM, Röper K. Identification of a core transcriptional program driving the human renal mesenchymal-to-epithelial transition. Dev Cell 2024; 59:595-612.e8. [PMID: 38340720 PMCID: PMC7616043 DOI: 10.1016/j.devcel.2024.01.011] [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: 05/15/2023] [Revised: 11/28/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
During kidney development, nephron epithelia arise de novo from fate-committed mesenchymal progenitors through a mesenchymal-to-epithelial transition (MET). Downstream of fate specification, transcriptional mechanisms that drive establishment of epithelial morphology are poorly understood. We used human iPSC-derived renal organoids, which recapitulate nephrogenesis, to investigate mechanisms controlling renal MET. Multi-ome profiling via snRNA-seq and ATAC-seq of organoids identified dynamic changes in gene expression and chromatin accessibility driven by activators and repressors throughout MET. CRISPR interference identified that paired box 8 (PAX8) is essential for initiation of MET in human renal organoids, contrary to in vivo mouse studies, likely by activating a cell-adhesion program. While Wnt/β-catenin signaling specifies nephron fate, we find that it must be attenuated to allow hepatocyte nuclear factor 1-beta (HNF1B) and TEA-domain (TEAD) transcription factors to drive completion of MET. These results identify the interplay between fate commitment and morphogenesis in the developing human kidney, with implications for understanding both developmental kidney diseases and aberrant epithelial plasticity following adult renal tubular injury.
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Affiliation(s)
- John-Poul Ng-Blichfeldt
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Julie M Williams
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Katja Röper
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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11
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Long HY, Qian ZP, Lan Q, Xu YJ, Da JJ, Yu FX, Zha Y. Human pluripotent stem cell-derived kidney organoids: Current progress and challenges. World J Stem Cells 2024; 16:114-125. [PMID: 38455108 PMCID: PMC10915962 DOI: 10.4252/wjsc.v16.i2.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 02/26/2024] Open
Abstract
Human pluripotent stem cell (hPSC)-derived kidney organoids share similarities with the fetal kidney. However, the current hPSC-derived kidney organoids have some limitations, including the inability to perform nephrogenesis and lack of a corticomedullary definition, uniform vascular system, and coordinated exit pathway for urinary filtrate. Therefore, further studies are required to produce hPSC-derived kidney organoids that accurately mimic human kidneys to facilitate research on kidney development, regeneration, disease modeling, and drug screening. In this review, we discussed recent advances in the generation of hPSC-derived kidney organoids, how these organoids contribute to the understanding of human kidney development and research in disease modeling. Additionally, the limitations, future research focus, and applications of hPSC-derived kidney organoids were highlighted.
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Affiliation(s)
- Hong-Yan Long
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Zu-Ping Qian
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Qin Lan
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Yong-Jie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Jing-Jing Da
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Fu-Xun Yu
- Key Laboratory of Diagnosis and Treatment of Pulmonary Immune Diseases, National Health Commission, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Yan Zha
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China.
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12
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Liu J, Prahl LS, Huang A, Hughes AJ. Measurement of adhesion and traction of cells at high yield (MATCHY) reveals an energetic ratchet driving nephron condensation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579368. [PMID: 38370771 PMCID: PMC10871361 DOI: 10.1101/2024.02.07.579368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Engineering of embryonic strategies for tissue-building has extraordinary promise for regenerative medicine. This has led to a resurgence in interest in the relationship between cell biophysical properties and morphological transitions. However, mapping gene or protein expression data to cell biophysical properties to physical morphogenesis remains challenging with current techniques. Here we present MATCHY (multiplexed adhesion and traction of cells at high yield). MATCHY advances the multiplexing and throughput capabilities of existing traction force and cell-cell adhesion assays using microfabrication and an automated computation scheme with machine learning-driven cell segmentation. Both biophysical assays are coupled with serial downstream immunofluorescence to extract cell type/signaling state information. MATCHY is especially suited to complex primary tissue-, organoid-, or biopsy-derived cell mixtures since it does not rely on a priori knowledge of cell surface markers, cell sorting, or use of lineage-specific reporter animals. We first validate MATCHY on canine kidney epithelial cells engineered for RET tyrosine kinase expression and quantify a relationship between downstream signaling and cell traction. We go on to create a biophysical atlas of primary cells dissociated from the mouse embryonic kidney and use MATCHY to identify distinct biophysical states along the nephron differentiation trajectory. Our data complement expression-level knowledge of adhesion molecule changes that accompany nephron differentiation with quantitative biophysical information. These data reveal an 'energetic ratchet' that explains spatial nephron progenitor cell condensation from the niche as they differentiate, which we validate through agent-based computational simulation. MATCHY offers automated cell biophysical characterization at >104-cell throughput, a highly enabling advance for fundamental studies and new synthetic tissue design strategies for regenerative medicine.
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Affiliation(s)
- Jiageng Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Louis S. Prahl
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Aria Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Alex J. Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
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13
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Li M, Guo X, Cheng L, Zhang H, Zhou M, Zhang M, Yin Z, Guo T, Zhao L, Liu H, Liang X, Li R. Porcine Kidney Organoids Derived from Naïve-like Embryonic Stem Cells. Int J Mol Sci 2024; 25:682. [PMID: 38203853 PMCID: PMC10779635 DOI: 10.3390/ijms25010682] [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: 11/16/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
The scarcity of donor kidneys greatly impacts the survival of patients with end-stage renal failure. Pigs are increasingly becoming potential organ donors but are limited by immunological rejection. Based on the human kidney organoid already established with the CHIR99021 and FGF9 induction strategy, we generated porcine kidney organoids from porcine naïve-like ESCs (nESCs). The derived porcine organoids had a tubule-like constructure and matrix components. The porcine organoids expressed renal markers including AQP1 (proximal tubule), WT1 and PODO (podocyte), and CD31 (vascular endothelial cells). These results imply that the organoids had developed the majority of the renal cell types and structures, including glomeruli and proximal tubules. The porcine organoids were also identified to have a dextran absorptive function. Importantly, porcine organoids have a certain abundance of vascular endothelial cells, which are the basis for investigating immune rejection. The derived porcine organoids might serve as materials for immunosuppressor screening for xenotransplantation.
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Affiliation(s)
- Meishuang Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xiyun Guo
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Linxin Cheng
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hong Zhang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Meng Zhou
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Manling Zhang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhibao Yin
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Tianxu Guo
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Lihua Zhao
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Han Liu
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xiubin Liang
- Department of Pathophysiology, Nanjing Medical University, Nanjing 211166, China;
| | - Rongfeng Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (M.L.); (X.G.); (L.C.); (H.Z.); (M.Z.); (M.Z.); (Z.Y.); (T.G.); (L.Z.); (H.L.)
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
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14
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Wang L, Hu D, Xu J, Hu J, Wang Y. Complex in vitro Model: A Transformative Model in Drug Development and Precision Medicine. Clin Transl Sci 2023; 17:e13695. [PMID: 38062923 PMCID: PMC10828975 DOI: 10.1111/cts.13695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/25/2023] [Accepted: 11/18/2023] [Indexed: 02/02/2024] Open
Abstract
In vitro and in vivo models play integral roles in preclinical drug research, evaluation, and precision medicine. In vitro models primarily involve research platforms based on cultured cells, typically in the form of two-dimensional (2D) cell models. However, notable disparities exist between 2D cultured cells and in vivo cells across various aspects, rendering the former inadequate for replicating the physiologically relevant functions of human or animal organs and tissues. Consequently, these models failed to accurately reflect real-life scenarios post-drug administration. Complex in vitro models (CIVMs) refer to in vitro models that integrate a multicellular environment and a three-dimensional (3D) structure using bio-polymer or tissue-derived matrices. These models seek to reconstruct the organ- or tissue-specific characteristics of the extracellular microenvironment. The utilization of CIVMs allows for enhanced physiological correlation of cultured cells, thereby better mimicking in vivo conditions without ethical concerns associated with animal experimentation. Consequently, CIVMs have gained prominence in disease research and drug development. This review aimed to comprehensively examine and analyze the various types, manufacturing techniques, and applications of CIVM in the domains of drug discovery, drug development, and precision medicine. The objective of this study was to provide a comprehensive understanding of the progress made in CIVMs and their potential future use in these fields.
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Affiliation(s)
- Luming Wang
- Department of Thoracic SurgeryThe First Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Clinical Evaluation Technology for Medical Device of Zhejiang ProvinceHangzhouChina
| | - Danping Hu
- Hangzhou Chexmed Technology Co., Ltd.HangzhouChina
| | - Jinming Xu
- Department of Thoracic SurgeryThe First Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Clinical Evaluation Technology for Medical Device of Zhejiang ProvinceHangzhouChina
| | - Jian Hu
- Department of Thoracic SurgeryThe First Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Clinical Evaluation Technology for Medical Device of Zhejiang ProvinceHangzhouChina
| | - Yifei Wang
- Hangzhou Chexmed Technology Co., Ltd.HangzhouChina
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15
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Co JY, Klein JA, Kang S, Homan KA. Toward Inclusivity in Preclinical Drug Development: A Proposition to Start with Intestinal Organoids. Adv Biol (Weinh) 2023; 7:e2200333. [PMID: 36932900 DOI: 10.1002/adbi.202200333] [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: 12/20/2022] [Revised: 02/08/2023] [Indexed: 03/19/2023]
Abstract
Representation of humans from diverse backgrounds in the drug development process is key to advancing health equity, and while clinical trial design has recently made strides toward greater inclusivity, preclinical drug development has struggled to make those same gains. One barrier to inclusion is the current lack of robust and established in vitro model systems that simultaneously capture the complexity of human tissues while representing patient diversity. Here, the use of primary human intestinal organoids as a mechanism to advance inclusive preclinical research is proposed. This in vitro model system not only recapitulates tissue functions and disease states, but also retains the genetic identity and epigenetic signatures of the donors from which they are derived. Thus, intestinal organoids are an ideal in vitro prototype for capturing human diversity. In this perspective, the authors call for an industry-wide effort to leverage intestinal organoids as a starting point to actively and intentionally incorporate diversity into preclinical drug programs.
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Affiliation(s)
- Julia Y Co
- Complex in vitro Systems, Safety Assessment, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jessica A Klein
- Complex in vitro Systems, Safety Assessment, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Serah Kang
- Complex in vitro Systems, Safety Assessment, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kimberly A Homan
- Complex in vitro Systems, Safety Assessment, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
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16
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Roberto de Barros N, Wang C, Maity S, Peirsman A, Nasiri R, Herland A, Ermis M, Kawakita S, Gregatti Carvalho B, Hosseinzadeh Kouchehbaghi N, Donizetti Herculano R, Tirpáková Z, Mohammad Hossein Dabiri S, Lucas Tanaka J, Falcone N, Choroomi A, Chen R, Huang S, Zisblatt E, Huang Y, Rashad A, Khorsandi D, Gangrade A, Voskanian L, Zhu Y, Li B, Akbari M, Lee J, Remzi Dokmeci M, Kim HJ, Khademhosseini A. Engineered organoids for biomedical applications. Adv Drug Deliv Rev 2023; 203:115142. [PMID: 37967768 PMCID: PMC10842104 DOI: 10.1016/j.addr.2023.115142] [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: 04/18/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
As miniaturized and simplified stem cell-derived 3D organ-like structures, organoids are rapidly emerging as powerful tools for biomedical applications. With their potential for personalized therapeutic interventions and high-throughput drug screening, organoids have gained significant attention recently. In this review, we discuss the latest developments in engineering organoids and using materials engineering, biochemical modifications, and advanced manufacturing technologies to improve organoid culture and replicate vital anatomical structures and functions of human tissues. We then explore the diverse biomedical applications of organoids, including drug development and disease modeling, and highlight the tools and analytical techniques used to investigate organoids and their microenvironments. We also examine the latest clinical trials and patents related to organoids that show promise for future clinical translation. Finally, we discuss the challenges and future perspectives of using organoids to advance biomedical research and potentially transform personalized medicine.
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Affiliation(s)
| | - Canran Wang
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Surjendu Maity
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Arne Peirsman
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Plastic and Reconstructive Surgery, Ghent University Hospital, Ghent, Belgium
| | - Rohollah Nasiri
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Anna Herland
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Menekse Ermis
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Satoru Kawakita
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Bruna Gregatti Carvalho
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Department of Material and Bioprocess Engineering, School of Chemical Engineering, University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
| | - Negar Hosseinzadeh Kouchehbaghi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Department of Textile Engineering, Amirkabir University of Technology (Tehran Polytechnic), Hafez Avenue, 1591634311 Tehran, Iran
| | - Rondinelli Donizetti Herculano
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA; São Paulo State University (UNESP), Bioengineering and Biomaterials Group, School of Pharmaceutical Sciences, Araraquara, SP, Brazil
| | - Zuzana Tirpáková
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia
| | - Seyed Mohammad Hossein Dabiri
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Jean Lucas Tanaka
- Butantan Institute, Viral Biotechnology Laboratory, São Paulo, SP Brazil; University of São Paulo (USP), São Paulo, SP Brazil
| | - Natashya Falcone
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Auveen Choroomi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - RunRun Chen
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA
| | - Shuyi Huang
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA
| | - Elisheva Zisblatt
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Yixuan Huang
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Ahmad Rashad
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Danial Khorsandi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Ankit Gangrade
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Leon Voskanian
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Bingbing Li
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA
| | - Mohsen Akbari
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Junmin Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, Republic of Korea
| | | | - Han-Jun Kim
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; College of Pharmacy, Korea University, Sejong 30019, Republic of Korea.
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA.
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17
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Vanslambrouck JM, Tan KS, Mah S, Little MH. Generation of proximal tubule-enhanced kidney organoids from human pluripotent stem cells. Nat Protoc 2023; 18:3229-3252. [PMID: 37770563 DOI: 10.1038/s41596-023-00880-1] [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: 01/16/2023] [Accepted: 06/26/2023] [Indexed: 09/30/2023]
Abstract
Kidney organoids derived from human pluripotent stem cells (hPSCs) are now being used as models of renal disease and nephrotoxicity screening. However, the proximal tubules (PTs), which are responsible for most kidney reabsorption functions, remain immature in kidney organoids with limited expression of critical transporters essential for nephron functionality. Here, we describe a protocol for improved specification of nephron progenitors from hPSCs that results in kidney organoids with elongated proximalized nephrons displaying improved PT maturity compared with those generated using standard kidney organoid protocols. We also describe a methodology for assessing the functionality of the PTs within the organoids and visualizing maturation markers via immunofluorescence. Using these assays, PT-enhanced organoids display increased expression of a range of critical transporters, translating to improved functionality measured by substrate uptake and transport. This protocol consists of an extended (13 d) monolayer differentiation phase, during which time hPSCs are exposed to nephron progenitor maintenance media (CDBLY2), better emulating human metanephric progenitor specification in vivo. Following nephron progenitor specification, the cells are aggregated and cultured as a three-dimensional micromass on an air-liquid interface to facilitate further differentiation and segmentation into proximalized nephrons. Experience in culturing hPSCs is required to conduct this protocol and expertise in kidney organoid generation is advantageous.
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Affiliation(s)
- Jessica M Vanslambrouck
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ker Sin Tan
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sophia Mah
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Melissa H Little
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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18
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Porter CM, Qian GC, Grindel SH, Hughes AJ. Highly-parallel production of designer organoids by mosaic patterning of progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564017. [PMID: 37961546 PMCID: PMC10634829 DOI: 10.1101/2023.10.25.564017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Human organoids are a promising approach for disease modeling and regenerative medicine. However, organoid variability and limited control over morphological outcomes remain significant challenges. Here we extend a DNA 'velcro' cell patterning approach, precisely controlling the number and ratio of human stem cell-derived progenitors contributing to nephron and mosaic nephron/ureteric bud organoids within arrays of microwells. We demonstrate long-term control over organoid size and morphology, decoupled from geometric constraints.
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Affiliation(s)
- Catherine M. Porter
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace C. Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Samuel H. Grindel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Alex J. Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
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19
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Juste-Lanas Y, Hervas-Raluy S, García-Aznar JM, González-Loyola A. Fluid flow to mimic organ function in 3D in vitro models. APL Bioeng 2023; 7:031501. [PMID: 37547671 PMCID: PMC10404142 DOI: 10.1063/5.0146000] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/20/2023] [Indexed: 08/08/2023] Open
Abstract
Many different strategies can be found in the literature to model organ physiology, tissue functionality, and disease in vitro; however, most of these models lack the physiological fluid dynamics present in vivo. Here, we highlight the importance of fluid flow for tissue homeostasis, specifically in vessels, other lumen structures, and interstitium, to point out the need of perfusion in current 3D in vitro models. Importantly, the advantages and limitations of the different current experimental fluid-flow setups are discussed. Finally, we shed light on current challenges and future focus of fluid flow models applied to the newest bioengineering state-of-the-art platforms, such as organoids and organ-on-a-chip, as the most sophisticated and physiological preclinical platforms.
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Affiliation(s)
| | - Silvia Hervas-Raluy
- Department of Mechanical Engineering, Engineering Research Institute of Aragón (I3A), University of Zaragoza, Zaragoza, Spain
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20
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Lassé M, El Saghir J, Berthier CC, Eddy S, Fischer M, Laufer SD, Kylies D, Hutzfeldt A, Bonin LL, Dumoulin B, Menon R, Vega-Warner V, Eichinger F, Alakwaa F, Fermin D, Billing AM, Minakawa A, McCown PJ, Rose MP, Godfrey B, Meister E, Wiech T, Noriega M, Chrysopoulou M, Brandts P, Ju W, Reinhard L, Hoxha E, Grahammer F, Lindenmeyer MT, Huber TB, Schlüter H, Thiel S, Mariani LH, Puelles VG, Braun F, Kretzler M, Demir F, Harder JL, Rinschen MM. An integrated organoid omics map extends modeling potential of kidney disease. Nat Commun 2023; 14:4903. [PMID: 37580326 PMCID: PMC10425428 DOI: 10.1038/s41467-023-39740-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/27/2023] [Indexed: 08/16/2023] Open
Abstract
Kidney organoids are a promising model to study kidney disease, but their use is constrained by limited knowledge of their functional protein expression profile. Here, we define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increase deposition of extracellular matrix but decrease expression of glomerular proteins. Single cell transcriptome integration reveals that most proteome changes localize to podocytes, tubular and stromal cells. TNFα treatment of organoids results in 322 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 322 proteins is significantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFα-associated protein (C3 and VCAM1) expression is increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing with human data, we provide crucial evidence for the functional relevance of the kidney organoid model to human kidney disease.
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Affiliation(s)
- Moritz Lassé
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jamal El Saghir
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Celine C Berthier
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Matthew Fischer
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Sandra D Laufer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Kylies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arvid Hutzfeldt
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Bernhard Dumoulin
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Felix Eichinger
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Fadhl Alakwaa
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Damian Fermin
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Anja M Billing
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Akihiro Minakawa
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Phillip J McCown
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Michael P Rose
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Bradley Godfrey
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Elisabeth Meister
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Wiech
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Mercedes Noriega
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Paul Brandts
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wenjun Ju
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Linda Reinhard
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elion Hoxha
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja T Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fatih Demir
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA.
| | - Markus M Rinschen
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Aarhus Institute of Advanced Studies (AIAS), Aarhus, Denmark.
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21
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Kim R. Advanced Organotypic In Vitro Model Systems for Host-Microbial Coculture. BIOCHIP JOURNAL 2023; 17:1-27. [PMID: 37363268 PMCID: PMC10201494 DOI: 10.1007/s13206-023-00103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 06/28/2023]
Abstract
In vitro model systems have been advanced to recapitulate important physiological features of the target organ in vivo more closely than the conventional cell line cultures on a petri dish. The advanced organotypic model systems can be used as a complementary or alternative tool for various testing and screening. Numerous data from germ-free animal studies and genome sequencings of clinical samples indicate that human microbiota is an essential part of the human body, but current in vitro model systems rarely include them, which can be one of the reasons for the discrepancy in the tissue phenotypes and outcome of therapeutic intervention between in vivo and in vitro tissues. A coculture model system with appropriate microbes and host cells may have great potential to bridge the gap between the in vitro model and the in vivo counterpart. However, successfully integrating two species in one system introduces new variables to consider and poses new challenges to overcome. This review aims to provide perspectives on the important factors that should be considered for developing organotypic bacterial coculture models. Recent advances in various organotypic bacterial coculture models are highlighted. Finally, challenges and opportunities in developing organotypic microbial coculture models are also discussed.
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Affiliation(s)
- Raehyun Kim
- Department of Biological and Chemical Engineering, Hongik University, Sejong, Republic of Korea
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22
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Dilz J, Auge I, Groeneveld K, Reuter S, Mrowka R. A proof-of-concept assay for quantitative and optical assessment of drug-induced toxicity in renal organoids. Sci Rep 2023; 13:6167. [PMID: 37061575 PMCID: PMC10105743 DOI: 10.1038/s41598-023-33110-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/07/2023] [Indexed: 04/17/2023] Open
Abstract
Kidneys are complex organs, and reproducing their function and physiology in a laboratory setting remains difficult. During drug development, potential compounds may exhibit unexpected nephrotoxic effects, which imposes a significant financial burden on pharmaceutical companies. As a result, there is an ongoing need for more accurate model systems. The use of renal organoids to simulate responses to nephrotoxic insults has the potential to bridge the gap between preclinical drug efficacy studies in cell cultures and animal models, and the stages of clinical trials in humans. Here we established an accessible fluorescent whole-mount approach for nuclear and membrane staining to first provide an overview of the organoid histology. Furthermore, we investigated the potential of renal organoids to model responses to drug toxicity. For this purpose, organoids were treated with the chemotherapeutic agent doxorubicin for 48 h. When cell viability was assessed biochemically, the organoids demonstrated a significant, dose-dependent decline in response to the treatment. Confocal microscopy revealed visible tubular disintegration and a loss of cellular boundaries at high drug concentrations. This observation was further reinforced by a dose-dependent decrease of the nuclear area in the analyzed images. In contrast to other approaches, in this study, we provide a straightforward experimental framework for drug toxicity assessment in renal organoids that may be used in early research stages to assist screen for potential adverse effects of compounds.
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Affiliation(s)
- Jasmin Dilz
- Department of Internal Medicine III, Experimental Nephrology, Jena University Hospital, Nonnenplan 4, 07745, Jena, Germany.
| | - Isabel Auge
- Department of Internal Medicine III, Experimental Nephrology, Jena University Hospital, Nonnenplan 4, 07745, Jena, Germany
| | - Kathrin Groeneveld
- Department of Internal Medicine III, Experimental Nephrology, Jena University Hospital, Nonnenplan 4, 07745, Jena, Germany
| | - Stefanie Reuter
- ThIMEDOP, Jena University Hospital, Nonnenplan 4, 07745, Jena, Germany
| | - Ralf Mrowka
- Department of Internal Medicine III, Experimental Nephrology, Jena University Hospital, Nonnenplan 4, 07745, Jena, Germany.
- ThIMEDOP, Jena University Hospital, Nonnenplan 4, 07745, Jena, Germany.
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23
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Treacy NJ, Clerkin S, Davis JL, Kennedy C, Miller AF, Saiani A, Wychowaniec JK, Brougham DF, Crean J. Growth and differentiation of human induced pluripotent stem cell (hiPSC)-derived kidney organoids using fully synthetic peptide hydrogels. Bioact Mater 2023; 21:142-156. [PMID: 36093324 PMCID: PMC9420433 DOI: 10.1016/j.bioactmat.2022.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived kidney organoids have prospective applications ranging from basic disease modelling to personalised medicine. However, there remains a necessity to refine the biophysical and biochemical parameters that govern kidney organoid formation. Differentiation within fully-controllable and physiologically relevant 3D growth environments will be critical to improving organoid reproducibility and maturation. Here, we matured hiPSC-derived kidney organoids within fully synthetic self-assembling peptide hydrogels (SAPHs) of variable stiffness (storage modulus, G'). The resulting organoids contained complex structures comparable to those differentiated within the animal-derived matrix, Matrigel. Single-cell RNA sequencing (scRNA-seq) was then used to compare organoids matured within SAPHs to those grown within Matrigel or at the air-liquid interface. A total of 13,179 cells were analysed, revealing 14 distinct clusters. Organoid compositional analysis revealed a larger proportion of nephron cell types within Transwell-derived organoids, while SAPH-derived organoids were enriched for stromal-associated cell populations. Notably, differentiation within a higher G' SAPH generated podocytes with more mature gene expression profiles. Additionally, maturation within a 3D microenvironment significantly reduced the derivation of off-target cell types, which are a known limitation of current kidney organoid protocols. This work demonstrates the utility of synthetic peptide-based hydrogels with a defined stiffness, as a minimally complex microenvironment for the selected differentiation of kidney organoids.
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Affiliation(s)
- Niall J Treacy
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Shane Clerkin
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Jessica L Davis
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Ciarán Kennedy
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
| | - Aline F Miller
- Department of Materials & Manchester Institute of Biotechnology (MIB), School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Alberto Saiani
- Department of Materials & Manchester Institute of Biotechnology (MIB), School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Jacek K Wychowaniec
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dermot F Brougham
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - John Crean
- Diabetes Complications Research Centre, University College Dublin (UCD) Conway Institute of Biomolecular and Biomedical Research and Belfield, Dublin 4, Ireland.,UCD School of Biomolecular and Biomedical Science, Belfield, Dublin 4, Ireland
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24
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The "3Ds" of Growing Kidney Organoids: Advances in Nephron Development, Disease Modeling, and Drug Screening. Cells 2023; 12:cells12040549. [PMID: 36831216 PMCID: PMC9954122 DOI: 10.3390/cells12040549] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
A kidney organoid is a three-dimensional (3D) cellular aggregate grown from stem cells in vitro that undergoes self-organization, recapitulating aspects of normal renal development to produce nephron structures that resemble the native kidney organ. These miniature kidney-like structures can also be derived from primary patient cells and thus provide simplified context to observe how mutations in kidney-disease-associated genes affect organogenesis and physiological function. In the past several years, advances in kidney organoid technologies have achieved the formation of renal organoids with enhanced numbers of specialized cell types, less heterogeneity, and more architectural complexity. Microfluidic bioreactor culture devices, single-cell transcriptomics, and bioinformatic analyses have accelerated the development of more sophisticated renal organoids and tailored them to become increasingly amenable to high-throughput experimentation. However, many significant challenges remain in realizing the use of kidney organoids for renal replacement therapies. This review presents an overview of the renal organoid field and selected highlights of recent cutting-edge kidney organoid research with a focus on embryonic development, modeling renal disease, and personalized drug screening.
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25
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Tubuloid culture enables long-term expansion of functional human kidney tubule epithelium from iPSC-derived organoids. Proc Natl Acad Sci U S A 2023; 120:e2216836120. [PMID: 36724260 PMCID: PMC9963523 DOI: 10.1073/pnas.2216836120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Kidney organoids generated from induced pluripotent stem cells (iPSC) have proven valuable for studies of kidney development, disease, and therapeutic screening. However, specific applications have been hampered by limited expansion capacity, immaturity, off-target cells, and inability to access the apical side. Here, we apply recently developed tubuloid protocols to purify and propagate kidney epithelium from d7+18 (post nephrogenesis) iPSC-derived organoids. The resulting 'iPSC organoid-derived (iPSCod)' tubuloids can be exponentially expanded for at least 2.5 mo, while retaining expression of important tubular transporters and segment-specific markers. This approach allows for selective propagation of the mature tubular epithelium, as immature cells, stroma, and undesirable off-target cells rapidly disappeared. iPSCod tubuloids provide easy apical access, which enabled functional evaluation and demonstration of essential secretion and electrolyte reabsorption processes. In conclusion, iPSCod tubuloids provide a different, complementary human kidney model that unlocks opportunities for functional characterization, disease modeling, and regenerative nephrology.
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26
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Roundhill EA, Pantziarka P, Liddle DE, Shaw LA, Albadrani G, Burchill SA. Exploiting the Stemness and Chemoresistance Transcriptome of Ewing Sarcoma to Identify Candidate Therapeutic Targets and Drug-Repurposing Candidates. Cancers (Basel) 2023; 15:cancers15030769. [PMID: 36765727 PMCID: PMC9913297 DOI: 10.3390/cancers15030769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Outcomes for most patients with Ewing sarcoma (ES) have remained unchanged for the last 30 years, emphasising the need for more effective and tolerable treatments. We have hypothesised that using small-molecule inhibitors to kill the self-renewing chemotherapy-resistant cells (Ewing sarcoma cancer stem-like cells; ES-CSCs) responsible for progression and relapse could improve outcomes and minimise treatment-induced morbidities. For the first time, we demonstrate that ABCG1, a potential oncogene in some cancers, is highly expressed in ES-CSCs independently of CD133. Using functional models, transcriptomics and a bespoke in silico drug-repurposing pipeline, we have prioritised a group of tractable small-molecule inhibitors for further preclinical studies. Consistent with the cellular origin of ES, 21 candidate molecular targets of pluripotency, stemness and chemoresistance were identified. Small-molecule inhibitors to 13 of the 21 molecular targets (62%) were identified. POU5F1/OCT4 was the most promising new therapeutic target in Ewing sarcoma, interacting with 10 of the 21 prioritised molecular targets and meriting further study. The majority of small-molecule inhibitors (72%) target one of two drug efflux proteins, p-glycoprotein (n = 168) or MRP1 (n = 13). In summary, we have identified a novel cell surface marker of ES-CSCs and cancer/non-cancer drugs to targets expressed by these cells that are worthy of further preclinical evaluation. If effective in preclinical models, these drugs and drug combinations might be repurposed for clinical evaluation in patients with ES.
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Affiliation(s)
- Elizabeth Ann Roundhill
- Children’s Cancer Research Group, Leeds Institute of Medical Research, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
- Correspondence: (E.A.R.); (S.A.B.)
| | - Pan Pantziarka
- Anticancer Fund, Brusselsesteenweg 11, 1860 Meise, Belgium
| | - Danielle E. Liddle
- Children’s Cancer Research Group, Leeds Institute of Medical Research, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Lucy A. Shaw
- Children’s Cancer Research Group, Leeds Institute of Medical Research, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Ghadeer Albadrani
- Children’s Cancer Research Group, Leeds Institute of Medical Research, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Susan Ann Burchill
- Children’s Cancer Research Group, Leeds Institute of Medical Research, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
- Correspondence: (E.A.R.); (S.A.B.)
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27
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Sander V, Przepiorski A, Hukriede NA, Davidson AJ. Large-Scale Production of Kidney Organoids from Human Pluripotent Stem Cells. Methods Mol Biol 2023; 2664:69-83. [PMID: 37423983 DOI: 10.1007/978-1-0716-3179-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Kidney organoids differentiated from human pluripotent stem cells (hPSC) have advanced the study of kidney diseases by providing an in vitro system that outperforms traditional monolayer cell culture and complements animal models. This chapter describes a simple two-stage protocol that generates kidney organoids in suspension culture in less than 2 weeks. In the first stage, hPSC colonies are differentiated into nephrogenic mesoderm. In the second stage of the protocol, renal cell lineages develop and self-organize into kidney organoids that contain fetal-like nephrons with proximal and distal tubule segmentation. A single assay generates up to 1000 organoids, thereby providing a rapid and cost-efficient method for the bulk production of human kidney tissue. Applications include the study of fetal kidney development, genetic disease modelling, nephrotoxicity screening, and drug development.
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Affiliation(s)
- Veronika Sander
- Department of Molecular Medicine & Pathology, University of Auckland, Auckland, New Zealand.
| | - Aneta Przepiorski
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alan J Davidson
- Department of Molecular Medicine & Pathology, University of Auckland, Auckland, New Zealand
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28
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Ramadan R, Wouters VM, van Neerven SM, de Groot NE, Garcia TM, Muncan V, Franklin OD, Battle M, Carlson KS, Leach J, Sansom OJ, Boulard O, Chamaillard M, Vermeulen L, Medema JP, Huels DJ. The extracellular matrix controls stem cell specification and crypt morphology in the developing and adult mouse gut. Biol Open 2022; 11:bio059544. [PMID: 36350252 PMCID: PMC9713296 DOI: 10.1242/bio.059544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/22/2022] [Indexed: 11/01/2023] Open
Abstract
The rapid renewal of the epithelial gut lining is fuelled by stem cells that reside at the base of intestinal crypts. The signal transduction pathways and morphogens that regulate intestinal stem cell self-renewal and differentiation have been extensively characterised. In contrast, although extracellular matrix (ECM) components form an integral part of the intestinal stem cell niche, their direct influence on the cellular composition is less well understood. We set out to systematically compare the effect of two ECM classes, the interstitial matrix and the basement membrane, on the intestinal epithelium. We found that both collagen I and laminin-containing cultures allow growth of small intestinal epithelial cells with all cell types present in both cultures, albeit at different ratios. The collagen cultures contained a subset of cells enriched in fetal-like markers. In contrast, laminin increased Lgr5+ stem cells and Paneth cells, and induced crypt-like morphology changes. The transition from a collagen culture to a laminin culture resembled gut development in vivo. The dramatic ECM remodelling was accompanied by a local expression of the laminin receptor ITGA6 in the crypt-forming epithelium. Importantly, deletion of laminin in the adult mouse resulted in a marked reduction of adult intestinal stem cells. Overall, our data support the hypothesis that the formation of intestinal crypts is induced by an increased laminin concentration in the ECM.
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Affiliation(s)
- Rana Ramadan
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Valérie M. Wouters
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sanne M. van Neerven
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nina E. de Groot
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tania Martins Garcia
- Department of Gastroenterology and Hepatology, Tytgat Institute for Intestinal and Liver Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam UMC University of Amsterdam, 1015 BK Amsterdam, The Netherlands
| | - Vanessa Muncan
- Department of Gastroenterology and Hepatology, Tytgat Institute for Intestinal and Liver Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam UMC University of Amsterdam, 1015 BK Amsterdam, The Netherlands
| | - Olivia D. Franklin
- The Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Michelle Battle
- The Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Karen Sue Carlson
- The Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
- The Blood Research Institute of Wisconsin, part of Versiti, and the Medical College of Wisconsin, Department of Internal Medicine, Milwaukee, WI 53226, USA
| | - Joshua Leach
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Olivier Boulard
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 8204 – Centre d'Infection et d'Immunité de Lille (CIIL), Université de Lille, 59019 Lille, France
| | - Mathias Chamaillard
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 8204 – Centre d'Infection et d'Immunité de Lille (CIIL), Université de Lille, 59019 Lille, France
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - David J. Huels
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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29
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Cable J, Lutolf MP, Fu J, Park SE, Apostolou A, Chen S, Song CJ, Spence JR, Liberali P, Lancaster M, Meier AB, Pek NMQ, Wells JM, Capeling MM, Uzquiano A, Musah S, Huch M, Gouti M, Hombrink P, Quadrato G, Urenda JP. Organoids as tools for fundamental discovery and translation-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1518:196-208. [PMID: 36177906 PMCID: PMC11293861 DOI: 10.1111/nyas.14874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complex three-dimensional in vitro organ-like models, or organoids, offer a unique biological tool with distinct advantages over two-dimensional cell culture systems, which can be too simplistic, and animal models, which can be too complex and may fail to recapitulate human physiology and pathology. Significant progress has been made in driving stem cells to differentiate into different organoid types, though several challenges remain. For example, many organoid models suffer from high heterogeneity, and it can be difficult to fully incorporate the complexity of in vivo tissue and organ development to faithfully reproduce human biology. Successfully addressing such limitations would increase the viability of organoids as models for drug development and preclinical testing. On April 3-6, 2022, experts in organoid development and biology convened at the Keystone Symposium "Organoids as Tools for Fundamental Discovery and Translation" to discuss recent advances and insights from this relatively new model system into human development and disease.
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Affiliation(s)
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Lausanne, Switzerland
- Institute of Chemical Sciences and Engineering, School of Basic Science (SB), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Roche Institute for Translational Bioengineering (ITB), Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sunghee Estelle Park
- Department of Bioengineering and NSF Science and Technology Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Athanasia Apostolou
- Emulate Inc, Boston, Massachusetts, USA
- Department of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York City, New York, USA
| | - Cheng Jack Song
- Keck Medicine of University of Southern California, Los Angeles, California, USA
| | - Jason R Spence
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI) and University of Basel, Basel, Switzerland
| | | | - Anna B Meier
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Nicole Min Qian Pek
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - James M Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Developmental Biology and Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samira Musah
- Developmental and Stem Cell Biology Program and Division of Nephrology, Department of Medicine and Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Center for Biomolecular and Tissue Engineering, Durham, North Carolina, USA
- Department of Biomedical Engineering, Pratt School of Engineering, Durham, North Carolina, USA
- Duke Regeneration Center, Duke University, Durham, North Carolina, USA
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mina Gouti
- Stem Cell Modelling of Development & Disease Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pleun Hombrink
- University Medical Center Utrecht and HUB Organoids, Utrecht, Netherlands
| | - Giorgia Quadrato
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
| | - Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
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Dorison A, Forbes TA, Little MH. What can we learn from kidney organoids? Kidney Int 2022; 102:1013-1029. [PMID: 35970244 DOI: 10.1016/j.kint.2022.06.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022]
Abstract
The ability to generate 3-dimensional models of the developing human kidney via the directed differentiation of pluripotent stem cells-termed kidney organoids-has been hailed as a major advance in experimental nephrology. Although these provide an opportunity to interrogate human development, model-specific kidney diseases facilitate drug screening and even deliver bioengineered tissue; most of these prophetic end points remain to be realized. Indeed, at present we are still finding out what we can learn and what we cannot learn from this approach. In this review, we will summarize the approaches available to generate models of the human kidney from stem cells, the existing successful applications of kidney organoids, their limitations, and remaining challenges.
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Affiliation(s)
- Aude Dorison
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia; Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas A Forbes
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia; Department of Nephrology, Royal Children's Hospital, Parkville, Melbourne, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia; Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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31
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Mansour F, Hinze C, Telugu NS, Kresoja J, Shaheed IB, Mosimann C, Diecke S, Schmidt-Ott KM. The centrosomal protein 83 (CEP83) regulates human pluripotent stem cell differentiation toward the kidney lineage. eLife 2022; 11:e80165. [PMID: 36222666 PMCID: PMC9629839 DOI: 10.7554/elife.80165] [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: 05/11/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
During embryonic development, the mesoderm undergoes patterning into diverse lineages including axial, paraxial, and lateral plate mesoderm (LPM). Within the LPM, the so-called intermediate mesoderm (IM) forms kidney and urogenital tract progenitor cells, while the remaining LPM forms cardiovascular, hematopoietic, mesothelial, and additional progenitor cells. The signals that regulate these early lineage decisions are incompletely understood. Here, we found that the centrosomal protein 83 (CEP83), a centriolar component necessary for primary cilia formation and mutated in pediatric kidney disease, influences the differentiation of human-induced pluripotent stem cells (hiPSCs) toward IM. We induced inactivating deletions of CEP83 in hiPSCs and applied a 7-day in vitro protocol of IM kidney progenitor differentiation, based on timed application of WNT and FGF agonists. We characterized induced mesodermal cell populations using single-cell and bulk transcriptomics and tested their ability to form kidney structures in subsequent organoid culture. While hiPSCs with homozygous CEP83 inactivation were normal regarding morphology and transcriptome, their induced differentiation into IM progenitor cells was perturbed. Mesodermal cells induced after 7 days of monolayer culture of CEP83-deficient hiPCS exhibited absent or elongated primary cilia, displayed decreased expression of critical IM genes (PAX8, EYA1, HOXB7), and an aberrant induction of LPM markers (e.g. FOXF1, FOXF2, FENDRR, HAND1, HAND2). Upon subsequent organoid culture, wildtype cells differentiated to form kidney tubules and glomerular-like structures, whereas CEP83-deficient cells failed to generate kidney cell types, instead upregulating cardiomyocyte, vascular, and more general LPM progenitor markers. Our data suggest that CEP83 regulates the balance of IM and LPM formation from human pluripotent stem cells, identifying a potential link between centriolar or ciliary function and mesodermal lineage induction.
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Affiliation(s)
- Fatma Mansour
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin BerlinBerlinGermany
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Department of Pathology, Faculty of Veterinary Medicine, Cairo UniversityCairoEgypt
| | - Christian Hinze
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin BerlinBerlinGermany
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Berlin Institute of HealthBerlinGermany
- Department of Nephrology and Hypertension, Hannover Medical SchoolHannoverGermany
| | - Narasimha Swamy Telugu
- Berlin Institute of HealthBerlinGermany
- Technology Platform Pluripotent Stem Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Jelena Kresoja
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical CampusAuroraUnited States
| | - Iman B Shaheed
- Department of Pathology, Faculty of Veterinary Medicine, Cairo UniversityCairoEgypt
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical CampusAuroraUnited States
| | - Sebastian Diecke
- Berlin Institute of HealthBerlinGermany
- Technology Platform Pluripotent Stem Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Kai M Schmidt-Ott
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin BerlinBerlinGermany
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Department of Nephrology and Hypertension, Hannover Medical SchoolHannoverGermany
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Pitstick AL, Poling HM, Sundaram N, Lewis PL, Kechele DO, Sanchez JG, Scott MA, Broda TR, Helmrath MA, Wells JM, Mayhew CN. Aggregation of cryopreserved mid-hindgut endoderm for more reliable and reproducible hPSC-derived small intestinal organoid generation. Stem Cell Reports 2022; 17:1889-1902. [PMID: 35905739 PMCID: PMC9391520 DOI: 10.1016/j.stemcr.2022.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023] Open
Abstract
A major technical limitation hindering the widespread adoption of human pluripotent stem cell (hPSC)-derived gastrointestinal (GI) organoid technologies is the need for de novo hPSC differentiation and dependence on spontaneous morphogenesis to produce detached spheroids. Here, we report a method for simple, reproducible, and scalable production of small intestinal organoids (HIOs) based on the aggregation of cryopreservable hPSC-derived mid-hindgut endoderm (MHE) monolayers. MHE aggregation eliminates variability in spontaneous spheroid production and generates HIOs that are comparable to those arising spontaneously. With a minor modification to the protocol, MHE can be cryopreserved, thawed, and aggregated, facilitating HIO production without de novo hPSC differentiation. Finally, aggregation can also be used to generate antral stomach organoids and colonic organoids. This improved method removes significant barriers to the implementation and successful use of hPSC-derived GI organoid technologies and provides a framework for improved dissemination and increased scalability of GI organoid production.
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Affiliation(s)
- Amy L Pitstick
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Holly M Poling
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Phillip L Lewis
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Daniel O Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - J Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Melissa A Scott
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Taylor R Broda
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Michael A Helmrath
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Division of Endocrinology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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Gehling K, Parekh S, Schneider F, Kirchner M, Kondylis V, Nikopoulou C, Tessarz P. RNA-sequencing of single cholangiocyte-derived organoids reveals high organoid-to organoid variability. Life Sci Alliance 2022; 5:e202101340. [PMID: 35914813 PMCID: PMC9348635 DOI: 10.26508/lsa.202101340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/13/2022] Open
Abstract
Over the last decades, organoids have been established from most of the tissue-resident stem and iPS cells. They hold great promise for our understanding of mammalian organ development, but also for the study of disease or even personalised medicine. In recent years, several reports hinted at intraculture organoid variability, but a systematic analysis of such heterogeneity has not been performed before. Here, we used RNA-seq of individual intrahepatic cholangiocyte organoids to address this question. We find that batch-to-batch variation is very low, whereas passage number has a profound impact on gene expression profiles. On the other hand, there is organoid-to-organoid variability within a culture. Using differential gene expression, we did not identify specific pathways that drive this variability, pointing towards possible effects of the microenvironment within the culture condition. Taken together, our study provides a framework for organoid researchers to properly consider experimental design.
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Affiliation(s)
- Kristin Gehling
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
| | - Swati Parekh
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Farina Schneider
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Marcel Kirchner
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Vangelis Kondylis
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Chrysa Nikopoulou
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group "Chromatin and Ageing," Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
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Bejoy J, Farry JM, Peek JL, Cabatu MC, Williams FM, Welch RC, Qian ES, Woodard LE. Podocytes derived from human induced pluripotent stem cells: characterization, comparison, and modeling of diabetic kidney disease. Stem Cell Res Ther 2022; 13:355. [PMID: 35883199 PMCID: PMC9327311 DOI: 10.1186/s13287-022-03040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/06/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In diabetic kidney disease, high glucose damages specialized cells called podocytes that filter blood in the glomerulus. In vitro culture of podocytes is crucial for modeling of diabetic nephropathy and genetic podocytopathies and to complement animal studies. Recently, several methods have been published to derive podocytes from human-induced pluripotent stem cells (iPSCs) by directed differentiation. However, these methods have major variations in media composition and have not been compared. METHODS We characterized our accelerated protocol by guiding the cells through differentiation with four different medias into MIXL1+ primitive streak cells with Activin A and CHIR for Wnt activation, intermediate mesoderm PAX8+ cells via increasing the CHIR concentration, nephron progenitors with FGF9 and Heparin for stabilization, and finally into differentiated podocytes with Activin A, BMP-7, VEGF, reduced CHIR, and retinoic acid. The podocyte morphology was characterized by scanning and transmission electron microscopy and by flow cytometry analysis for podocyte markers. To confirm cellular identity and niche localization, we performed cell recombination assays combining iPSC-podocytes with dissociated mouse embryonic kidney cells. Finally, to test iPSC-derived podocytes for the modeling of diabetic kidney disease, human podocytes were exposed to high glucose. RESULTS Podocyte markers were expressed at similar or higher levels for our accelerated protocol as compared to previously published protocols that require longer periods of tissue culture. We confirmed that the human podocytes derived from induced pluripotent stem cells in twelve days integrated into murine glomerular structures formed following seven days of culture of cellular recombinations. We found that the high glucose-treated human podocytes displayed actin rearrangement, increased cytotoxicity, and decreased viability. CONCLUSIONS We found that our accelerated 12-day method for the differentiation of podocytes from human-induced pluripotent stem cells yields podocytes with comparable marker expression to longer podocytes. We also demonstrated that podocytes created with this protocol have typical morphology by electron microscopy. The podocytes have utility for diabetes modeling as evidenced by lower viability and increased cytotoxicity when treated with high glucose. We found that multiple, diverse methods may be utilized to create iPSC-podocytes, but closely mimicking developmental cues shortened the time frame required for differentiation.
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Affiliation(s)
- Julie Bejoy
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Justin M Farry
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jennifer L Peek
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Mariana C Cabatu
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Felisha M Williams
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Richard C Welch
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Eddie S Qian
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Lauren E Woodard
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, 37212, USA.
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Tran T, Song CJ, Nguyen T, Cheng SY, McMahon JA, Yang R, Guo Q, Der B, Lindström NO, Lin DCH, McMahon AP. A scalable organoid model of human autosomal dominant polycystic kidney disease for disease mechanism and drug discovery. Cell Stem Cell 2022; 29:1083-1101.e7. [PMID: 35803227 PMCID: PMC11088748 DOI: 10.1016/j.stem.2022.06.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/28/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Human pluripotent stem-cell-derived organoids are models for human development and disease. We report a modified human kidney organoid system that generates thousands of similar organoids, each consisting of 1-2 nephron-like structures. Single-cell transcriptomic profiling and immunofluorescence validation highlighted patterned nephron-like structures utilizing similar pathways, with distinct morphogenesis, to human nephrogenesis. To examine this platform for therapeutic screening, the polycystic kidney disease genes PKD1 and PKD2 were inactivated by gene editing. PKD1 and PKD2 mutant models exhibited efficient and reproducible cyst formation. Cystic outgrowths could be propagated for months to centimeter-sized cysts. To shed new light on cystogenesis, 247 protein kinase inhibitors (PKIs) were screened in a live imaging assay identifying compounds blocking cyst formation but not overall organoid growth. Scaling and further development of the organoid platform will enable a broader capability for kidney disease modeling and high-throughput drug screens.
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Affiliation(s)
- Tracy Tran
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Cheng Jack Song
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Amgen Research, Cardiometabolic Disorders, 1120 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Trang Nguyen
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Shun-Yang Cheng
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Rui Yang
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Balint Der
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel C-H Lin
- Amgen Research, Cardiometabolic Disorders, 1120 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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36
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Parihar A, Pandita V, Khan R. 3D printed human organoids: High throughput system for drug screening and testing in current COVID-19 pandemic. Biotechnol Bioeng 2022; 119:2669-2688. [PMID: 35765706 DOI: 10.1002/bit.28166] [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: 11/05/2021] [Revised: 04/27/2022] [Accepted: 06/24/2022] [Indexed: 11/07/2022]
Abstract
In the current pandemic, scenario the world is facing a huge shortage of effective drugs and other prophylactic medicine to treat patients which created havoc in several countries with poor resources. With limited demand and supply of effective drugs, researchers rushed to repurpose the existing approved drugs for the treatment of COVID-19. The process of drug screening and testing is very costly and requires several steps for validation and treatment efficacy evaluation ranging from in-vitro to in-vivo setups. After these steps, a clinical trial is mandatory for the evaluation of treatment efficacy and side effects in humans. These processes enhance the overall cost and sometimes the lead molecule show adverse effects in humans and the trial ends up in the final stages. Recently with the advent of 3D organoid culture which mimics the human tissue exactly the process of drug screening and testing can be done in a faster and cost-effective manner. Further 3D organoids prepared from stems cells taken from individuals can be beneficial for personalized drug therapy which could save millions of lives. This review discussed approaches and techniques for the synthesis of 3D-printed human organoids for drug screening. The key findings of the usage of organoids for personalized medicine for the treatment of COVID-19 have been discussed. In the end, the key challenges for the wide applicability of human organoids for drug screening with prospects of future orientation have been included. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026, MP, India
| | - Vasundhara Pandita
- Department of Biosciences, Barkatullah University, Habib Ganj, Bhopal, Madhya Pradesh, 462026, India
| | - Raju Khan
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026, MP, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification. Nat Methods 2022; 19:881-892. [PMID: 35697835 DOI: 10.1038/s41592-022-01508-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/02/2022] [Indexed: 01/31/2023]
Abstract
Current imaging approaches limit the ability to perform multi-scale characterization of three-dimensional (3D) organotypic cultures (organoids) in large numbers. Here, we present an automated multi-scale 3D imaging platform synergizing high-density organoid cultures with rapid and live 3D single-objective light-sheet imaging. It is composed of disposable microfabricated organoid culture chips, termed JeWells, with embedded optical components and a laser beam-steering unit coupled to a commercial inverted microscope. It permits streamlining organoid culture and high-content 3D imaging on a single user-friendly instrument with minimal manipulations and a throughput of 300 organoids per hour. We demonstrate that the large number of 3D stacks that can be collected via our platform allows training deep learning-based algorithms to quantify morphogenetic organizations of organoids at multi-scales, ranging from the subcellular scale to the whole organoid level. We validated the versatility and robustness of our approach on intestine, hepatic, neuroectoderm organoids and oncospheres.
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38
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Quality criteria for in vitro human pluripotent stem cell-derived models of tissue-based cells. Reprod Toxicol 2022; 112:36-50. [PMID: 35697279 DOI: 10.1016/j.reprotox.2022.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/21/2022]
Abstract
The advent of the technology to isolate or generate human pluripotent stem cells provided the potential to develop a wide range of human models that could enhance understanding of mechanisms underlying human development and disease. These systems are now beginning to mature and provide the basis for the development of in vitro assays suitable to understand the biological processes involved in the multi-organ systems of the human body, and will improve strategies for diagnosis, prevention, therapies and precision medicine. Induced pluripotent stem cell lines are prone to phenotypic and genotypic changes and donor/clone dependent variability, which means that it is important to identify the most appropriate characterization markers and quality control measures when sourcing new cell lines and assessing differentiated cell and tissue culture preparations for experimental work. This paper considers those core quality control measures for human pluripotent stem cell lines and evaluates the state of play in the development of key functional markers for their differentiated cell derivatives to promote assurance of reproducibility of scientific data derived from pluripotent stem cell-based systems.
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Vanslambrouck JM, Wilson SB, Tan KS, Groenewegen E, Rudraraju R, Neil J, Lawlor KT, Mah S, Scurr M, Howden SE, Subbarao K, Little MH. Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.10.14.464320. [PMID: 35665006 PMCID: PMC9164445 DOI: 10.1101/2021.10.14.464320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
While pluripotent stem cell-derived kidney organoids are now being used to model renal disease, the proximal nephron remains immature with limited evidence for key functional solute channels. This may reflect early mispatterning of the nephrogenic mesenchyme and/or insufficient maturation. Here we show that enhanced specification to metanephric nephron progenitors results in elongated and radially aligned proximalised nephrons with distinct S1 - S3 proximal tubule cell types. Such PT-enhanced organoids possess improved albumin and organic cation uptake, appropriate KIM-1 upregulation in response to cisplatin, and improved expression of SARS-CoV-2 entry factors resulting in increased viral replication. The striking proximo-distal orientation of nephrons resulted from localized WNT antagonism originating from the organoid stromal core. PT-enhanced organoids represent an improved model to study inherited and acquired proximal tubular disease as well as drug and viral responses.
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Affiliation(s)
- Jessica M. Vanslambrouck
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Sean B. Wilson
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Ker Sin Tan
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
| | - Ella Groenewegen
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
| | - Rajeev Rudraraju
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia
| | - Jessica Neil
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia
| | - Kynan T. Lawlor
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Sophia Mah
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
| | - Michelle Scurr
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
| | - Sara E. Howden
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia
| | - Melissa H. Little
- Murdoch Children’s Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, VIC, Australia
- Author for correspondence: M.H.L.: +61 3 9936 6206;
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Nunez-Nescolarde AB, Nikolic-Paterson DJ, Combes AN. Human Kidney Organoids and Tubuloids as Models of Complex Kidney Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:738-749. [PMID: 35181335 DOI: 10.1016/j.ajpath.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
Abstract
Kidney organoids derived from pluripotent stem cells and epithelial organoids derived from adult tissue (tubuloids) have been used to study various kidney disorders with a strong genetic component, such as polycystic kidney disease, Wilms tumor, and congenital nephrotic syndrome. However, complex disorders without clear genetic associations, such as acute kidney injury and many forms of chronic kidney disease, are only just beginning to be investigated using these in vitro approaches. Although organoids are a reductionist model, they contain clinically relevant cell populations that may help to elucidate human-specific pathogenic mechanisms. Thus, organoids may complement animal disease models to accelerate the translation of laboratory proof-of-concept research into clinical practice. This review discusses whether kidney organoids and tubuloids are suitable models for the study of complex human kidney disease and highlights their advantages and limitations compared with monolayer cell culture and animal models.
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Affiliation(s)
- Ana B Nunez-Nescolarde
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - David J Nikolic-Paterson
- Department of Nephrology, Monash Health and Monash University Centre for Inflammatory Diseases, Monash Medical Centre, Clayton, Victoria, Australia.
| | - Alexander N Combes
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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Nystrom SE, Li G, Datta S, Soldano K, Silas D, Weins A, Hall G, Thomas DB, Olabisi OA. JAK inhibitor blocks COVID-19-cytokine-induced JAK-STAT-APOL1 signaling in glomerular cells and podocytopathy in human kidney organoids. JCI Insight 2022; 7:157432. [PMID: 35472001 PMCID: PMC9220952 DOI: 10.1172/jci.insight.157432] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/20/2022] [Indexed: 11/17/2022] Open
Abstract
COVID-19 infection causes collapse of glomerular capillaries and loss of podocytes, culminating in a severe kidney disease called COVID-19–associated nephropathy (COVAN). The underlying mechanism of COVAN is unknown. We hypothesized that cytokines induced by COVID-19 trigger expression of pathogenic APOL1 via JAK/STAT signaling, resulting in podocyte loss and COVAN phenotype. Here, based on 9 biopsy-proven COVAN cases, we demonstrated for the first time, to the best of our knowledge, that APOL1 protein was abundantly expressed in podocytes and glomerular endothelial cells (GECs) of COVAN kidneys but not in controls. Moreover, a majority of patients with COVAN carried 2 APOL1 risk alleles. We show that recombinant cytokines induced by SARS-CoV-2 acted synergistically to drive APOL1 expression through the JAK/STAT pathway in primary human podocytes, GECs, and kidney micro-organoids derived from a carrier of 2 APOL1 risk alleles, but expression was blocked by a JAK1/2 inhibitor, baricitinib. We demonstrate that cytokine-induced JAK/STAT/APOL1 signaling reduced the viability of kidney organoid podocytes but was rescued by baricitinib. Together, our results support the conclusion that COVID-19–induced cytokines are sufficient to drive COVAN-associated podocytopathy via JAK/STAT/APOL1 signaling and that JAK inhibitors could block this pathogenic process. These findings suggest JAK inhibitors may have therapeutic benefits for managing cytokine-induced, APOL1-mediated podocytopathy.
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Affiliation(s)
- Sarah E Nystrom
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
| | - Guojie Li
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
| | - Somenath Datta
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
| | - Karen Soldano
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
| | - Daniel Silas
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
| | - Astrid Weins
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Gentzon Hall
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
| | - David B Thomas
- Department of Pathology, Nephrocor, Memphis, United States of America
| | - Opeyemi A Olabisi
- Division of Nephrology, Duke University School of Medicine, Durham, United States of America
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42
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Fine-tuning of epithelial taste bud organoid to promote functional recapitulation of taste reactivity. Cell Mol Life Sci 2022; 79:211. [PMID: 35344108 PMCID: PMC8958342 DOI: 10.1007/s00018-022-04242-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/23/2022] [Accepted: 03/09/2022] [Indexed: 11/03/2022]
Abstract
Taste stem/progenitor cells from posterior mouse tongues have been used to generate taste bud organoids. However, the inaccessible location of taste receptor cells is observed in conventional organoids. In this study, we established a suspension-culture method to fine-tune taste bud organoids by apicobasal polarity alteration to form the accessible localization of taste receptor cells. Compared to conventional Matrigel-embedded organoids, suspension-cultured organoids showed comparable differentiation and renewal rates to those of taste buds in vivo and exhibited functional taste receptor cells and cycling progenitor cells. Accessible taste receptor cells enabled the direct application of calcium imaging to evaluate the taste response. Moreover, suspension-cultured organoids can be genetically altered. Suspension-cultured taste bud organoids harmoniously integrated with the recipient lingual epithelium, maintaining the taste receptor cells and gustatory innervation capacity. We propose that suspension-cultured organoids may provide an efficient model for taste research, including taste bud development, regeneration, and transplantation.
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Liu M, Cardilla A, Ngeow J, Gong X, Xia Y. Studying Kidney Diseases Using Organoid Models. Front Cell Dev Biol 2022; 10:845401. [PMID: 35309912 PMCID: PMC8927804 DOI: 10.3389/fcell.2022.845401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
The prevalence of chronic kidney disease (CKD) is rapidly increasing over the last few decades, owing to the global increase in diabetes, and cardiovascular diseases. Dialysis greatly compromises the life quality of patients, while demand for transplantable kidney cannot be met, underscoring the need to develop novel therapeutic approaches to stop or reverse CKD progression. Our understanding of kidney disease is primarily derived from studies using animal models and cell culture. While cross-species differences made it challenging to fully translate findings from animal models into clinical practice, primary patient cells quickly lose the original phenotypes during in vitro culture. Over the last decade, remarkable achievements have been made for generating 3-dimensional (3D) miniature organs (organoids) by exposing stem cells to culture conditions that mimic the signaling cues required for the development of a particular organ or tissue. 3D kidney organoids have been successfully generated from different types of source cells, including human pluripotent stem cells (hPSCs), adult/fetal renal tissues, and kidney cancer biopsy. Alongside gene editing tools, hPSC-derived kidney organoids are being harnessed to model genetic kidney diseases. In comparison, adult kidney-derived tubuloids and kidney cancer-derived tumoroids are still in their infancy. Herein, we first summarize the currently available kidney organoid models. Next, we discuss recent advances in kidney disease modelling using organoid models. Finally, we consider the major challenges that have hindered the application of kidney organoids in disease modelling and drug evaluation and propose prospective solutions.
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Affiliation(s)
- Meng Liu
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Angelysia Cardilla
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Cancer Genetics Service, National Cancer Centre Singapore, Singapore, Singapore
| | - Ximing Gong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- *Correspondence: Ximing Gong, ; Yun Xia,
| | - Yun Xia
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- *Correspondence: Ximing Gong, ; Yun Xia,
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44
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Bejoy J, Qian ES, Woodard LE. Tissue Culture Models of AKI: From Tubule Cells to Human Kidney Organoids. J Am Soc Nephrol 2022; 33:487-501. [PMID: 35031569 PMCID: PMC8975068 DOI: 10.1681/asn.2021050693] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
AKI affects approximately 13.3 million people around the world each year, causing CKD and/or mortality. The mammalian kidney cannot generate new nephrons after postnatal renal damage and regenerative therapies for AKI are not available. Human kidney tissue culture systems can complement animal models of AKI and/or address some of their limitations. Donor-derived somatic cells, such as renal tubule epithelial cells or cell lines (RPTEC/hTERT, ciPTEC, HK-2, Nki-2, and CIHP-1), have been used for decades to permit drug toxicity screening and studies into potential AKI mechanisms. However, tubule cell lines do not fully recapitulate tubular epithelial cell properties in situ when grown under classic tissue culture conditions. Improving tissue culture models of AKI would increase our understanding of the mechanisms, leading to new therapeutics. Human pluripotent stem cells (hPSCs) can be differentiated into kidney organoids and various renal cell types. Injury to human kidney organoids results in renal cell-type crosstalk and upregulation of kidney injury biomarkers that are difficult to induce in primary tubule cell cultures. However, current protocols produce kidney organoids that are not mature and contain off-target cell types. Promising bioengineering techniques, such as bioprinting and "kidney-on-a-chip" methods, as applied to kidney nephrotoxicity modeling advantages and limitations are discussed. This review explores the mechanisms and detection of AKI in tissue culture, with an emphasis on bioengineered approaches such as human kidney organoid models.
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Affiliation(s)
- Julie Bejoy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eddie S. Qian
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lauren E. Woodard
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
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45
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Heo JH, Kang D, Seo SJ, Jin Y. Engineering the Extracellular Matrix for Organoid Culture. Int J Stem Cells 2022; 15:60-69. [PMID: 35220292 PMCID: PMC8889330 DOI: 10.15283/ijsc21190] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Organoids show great potential in clinical translational research owing to their intriguing properties to represent a near physiological model for native tissues. However, the dependency of organoid generation on the use of poorly defined matrices has hampered their clinical application. Current organoid culture systems mostly reply on biochemical signals provided by medium compositions and cell-cell interactions to control growth. Recent studies have highlighted the importance of the extracellular matrix (ECM) composition, cell-ECM interactions, and mechanical signals for organoid expansion and differentiation. Thus, several hydrogel systems prepared using natural or synthetic-based materials have been designed to recreate the stem cell niche in vitro, providing biochemical, biophysical, and mechanical signals. In this review, we discuss how recapitulating multiple aspects of the tissue-specific environment through designing and applying matrices could contribute to accelerating the translation of organoid technology from the laboratory to therapeutic and pharmaceutical applications.
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Affiliation(s)
- Jeong Hyun Heo
- Department of Physiology, Yonsei University College of Medicine, Seoul, Korea
| | - Dongyun Kang
- Department of Physiology, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Ju Seo
- Department of Physiology, Yonsei University College of Medicine, Seoul, Korea
| | - Yoonhee Jin
- Department of Physiology, Yonsei University College of Medicine, Seoul, Korea
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46
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Wilson SB, Howden SE, Vanslambrouck JM, Dorison A, Alquicira-Hernandez J, Powell JE, Little MH. DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets. Genome Med 2022. [PMID: 35189942 DOI: 10.1101/2021.01.20.427346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND While single-cell transcriptional profiling has greatly increased our capacity to interrogate biology, accurate cell classification within and between datasets is a key challenge. This is particularly so in pluripotent stem cell-derived organoids which represent a model of a developmental system. Here, clustering algorithms and selected marker genes can fail to accurately classify cellular identity while variation in analyses makes it difficult to meaningfully compare datasets. Kidney organoids provide a valuable resource to understand kidney development and disease. However, direct comparison of relative cellular composition between protocols has proved challenging. Hence, an unbiased approach for classifying cell identity is required. METHODS The R package, scPred, was trained on multiple single cell RNA-seq datasets of human fetal kidney. A hierarchical model classified cellular subtypes into nephron, stroma and ureteric epithelial elements. This model, provided in the R package DevKidCC ( github.com/KidneyRegeneration/DevKidCC ), was then used to predict relative cell identity within published kidney organoid datasets generated using distinct cell lines and differentiation protocols, interrogating the impact of such variations. The package contains custom functions for the display of differential gene expression within cellular subtypes. RESULTS DevKidCC was used to directly compare between distinct kidney organoid protocols, identifying differences in relative proportions of cell types at all hierarchical levels of the model and highlighting variations in stromal and unassigned cell types, nephron progenitor prevalence and relative maturation of individual epithelial segments. Of note, DevKidCC was able to distinguish distal nephron from ureteric epithelium, cell types with overlapping profiles that have previously confounded analyses. When applied to a variation in protocol via the addition of retinoic acid, DevKidCC identified a consequential depletion of nephron progenitors. CONCLUSIONS The application of DevKidCC to kidney organoids reproducibly classifies component cellular identity within distinct single-cell datasets. The application of the tool is summarised in an interactive Shiny application, as are examples of the utility of in-built functions for data presentation. This tool will enable the consistent and rapid comparison of kidney organoid protocols, driving improvements in patterning to kidney endpoints and validating new approaches.
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Affiliation(s)
- Sean B Wilson
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia
| | - Sara E Howden
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia
| | | | - Aude Dorison
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
| | - Jose Alquicira-Hernandez
- Garvan-Weizmann Centre for Cellular Genomics, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia.
- Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia.
- Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Parkville, Australia.
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Copenhagen, Denmark.
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47
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Wilson SB, Howden SE, Vanslambrouck JM, Dorison A, Alquicira-Hernandez J, Powell JE, Little MH. DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets. Genome Med 2022; 14:19. [PMID: 35189942 PMCID: PMC8862535 DOI: 10.1186/s13073-022-01023-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
Background While single-cell transcriptional profiling has greatly increased our capacity to interrogate biology, accurate cell classification within and between datasets is a key challenge. This is particularly so in pluripotent stem cell-derived organoids which represent a model of a developmental system. Here, clustering algorithms and selected marker genes can fail to accurately classify cellular identity while variation in analyses makes it difficult to meaningfully compare datasets. Kidney organoids provide a valuable resource to understand kidney development and disease. However, direct comparison of relative cellular composition between protocols has proved challenging. Hence, an unbiased approach for classifying cell identity is required. Methods The R package, scPred, was trained on multiple single cell RNA-seq datasets of human fetal kidney. A hierarchical model classified cellular subtypes into nephron, stroma and ureteric epithelial elements. This model, provided in the R package DevKidCC (github.com/KidneyRegeneration/DevKidCC), was then used to predict relative cell identity within published kidney organoid datasets generated using distinct cell lines and differentiation protocols, interrogating the impact of such variations. The package contains custom functions for the display of differential gene expression within cellular subtypes. Results DevKidCC was used to directly compare between distinct kidney organoid protocols, identifying differences in relative proportions of cell types at all hierarchical levels of the model and highlighting variations in stromal and unassigned cell types, nephron progenitor prevalence and relative maturation of individual epithelial segments. Of note, DevKidCC was able to distinguish distal nephron from ureteric epithelium, cell types with overlapping profiles that have previously confounded analyses. When applied to a variation in protocol via the addition of retinoic acid, DevKidCC identified a consequential depletion of nephron progenitors. Conclusions The application of DevKidCC to kidney organoids reproducibly classifies component cellular identity within distinct single-cell datasets. The application of the tool is summarised in an interactive Shiny application, as are examples of the utility of in-built functions for data presentation. This tool will enable the consistent and rapid comparison of kidney organoid protocols, driving improvements in patterning to kidney endpoints and validating new approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01023-z.
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Affiliation(s)
- Sean B Wilson
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia
| | - Sara E Howden
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia
| | | | - Aude Dorison
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
| | - Jose Alquicira-Hernandez
- Garvan-Weizmann Centre for Cellular Genomics, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia. .,Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia. .,Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Parkville, Australia. .,Novo Nordisk Foundation Centre for Stem Cell Medicine, Copenhagen, Denmark.
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48
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Experimental models of acute kidney injury for translational research. Nat Rev Nephrol 2022; 18:277-293. [PMID: 35173348 DOI: 10.1038/s41581-022-00539-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/20/2022]
Abstract
Preclinical models of human disease provide powerful tools for therapeutic discovery but have limitations. This problem is especially apparent in the field of acute kidney injury (AKI), in which clinical trial failures have been attributed to inaccurate modelling performed largely in rodents. Multidisciplinary efforts such as the Kidney Precision Medicine Project are now starting to identify molecular subtypes of human AKI. In addition, over the past decade, there have been developments in human pluripotent stem cell-derived kidney organoids as well as zebrafish, rodent and large animal models of AKI. These organoid and AKI models are being deployed at different stages of preclinical therapeutic development. However, the traditionally siloed, preclinical investigator-driven approaches that have been used to evaluate AKI therapeutics to date rarely account for the limitations of the model systems used and have given rise to false expectations of clinical efficacy in patients with different AKI pathophysiologies. To address this problem, there is a need to develop more flexible and integrated approaches, involving teams of investigators with expertise in a range of different model systems, working closely with clinical investigators, to develop robust preclinical evidence to support more focused interventions in patients with AKI.
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49
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Capeling MM, Huang S, Childs CJ, Wu JH, Tsai YH, Wu A, Garg N, Holloway EM, Sundaram N, Bouffi C, Helmrath M, Spence JR. Suspension culture promotes serosal mesothelial development in human intestinal organoids. Cell Rep 2022; 38:110379. [PMID: 35172130 PMCID: PMC9002973 DOI: 10.1016/j.celrep.2022.110379] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 09/08/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Pluripotent-stem-cell-derived human intestinal organoids (HIOs) model some aspects of intestinal development and disease, but current culture methods do not fully recapitulate the diverse cell types and complex organization of the human intestine and are reliant on 3D extracellular matrix or hydrogel systems, which limit experimental control and translational potential for regenerative medicine. We describe suspension culture as a simple, low-maintenance method for culturing HIOs and for promoting in vitro differentiation of an organized serosal mesothelial layer that is similar to primary human intestinal serosal mesothelium based on single-cell RNA sequencing and histological analysis. Functionally, HIO serosal mesothelium has the capacity to differentiate into smooth-muscle-like cells and exhibits fibrinolytic activity. An inhibitor screen identifies Hedgehog and WNT signaling as regulators of human serosal mesothelial differentiation. Collectively, suspension HIOs represent a three-dimensional model to study the human serosal mesothelium.
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Affiliation(s)
- Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Neil Garg
- School of Kinesiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Carine Bouffi
- Division of Pediatric General and Thoracic Surgery Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Michael Helmrath
- Division of Pediatric General and Thoracic Surgery Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Jason R Spence
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Abstract
The kidney is a highly complex organ in the human body. Although creating an in vitro model of the human kidney is challenging, tremendous advances have been made in recent years. Kidney organoids are in vitro kidney models that are generated from stem cells in three-dimensional (3D) cultures. They exhibit remarkable degree of similarities with the native tissue in terms of cell type, morphology, and function. The establishment of 3D kidney organoids facilitates a mechanistic study of cell communications, and these organoids can be used for drug screening, disease modeling, and regenerative medicine applications. This review discusses the cellular complexity during in vitro kidney generation. We intend to highlight recent progress in kidney organoids and the applications of these relatively new technologies.
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