1
|
Cambra HM, Tallapragada NP, Mannam P, Breault DT, Klein AM. Triple-Decker Sandwich Cultures of Intestinal Organoids for Long-Term Live Imaging, Uniform Perturbation, and Statistical Sampling. Curr Protoc 2022; 2:e330. [PMID: 35030297 PMCID: PMC9006308 DOI: 10.1002/cpz1.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Three-dimensional organoid cultures enable the study of stem cell and tissue biology ex vivo, providing improved access to cells for perturbation and live imaging. Typically, organoids are grown in hydrogel domes that are simple to prepare but that lead to non-uniform tissue growth and viability. We recently developed a simple alternative culture method to embed intestinal organoids in multilayered hydrogels, called "triple-decker sandwiches," that align organoids in a common z-plane with uniform access to medium. This culture configuration improves the growth and survival of organoids over a wide working area and facilitates long-term confocal imaging and molecular perturbation. Here, we present protocols for preparing organoids in triple-decker sandwich cultures and using them for live imaging, immunostaining, and single-cell RNA sequencing. We have tested our methods on mouse and human intestinal organoids and expect them to be useful for other highly proliferative three-dimensional cell cultures. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Pre-coating plates with PolyHEMA to prepare them for triple-decker sandwich culture Support Protocol 1: Preparing PolyHEMA solution to coat glass-bottom dishes Basic Protocol 2: Embedding intestinal organoids in triple-decker sandwiches Alternate Protocol 1: Seeding single cells or organoids at low density in triple-decker sandwiches Support Protocol 2: Embedding intestinal organoids in hydrogel domes Support Protocol 3: Production of Wnt3a-conditioned medium Support Protocol 4: Production of Rspo1-conditioned medium Basic Protocol 3: Live imaging of mouse intestinal organoids in triple-decker sandwich cultures Alternate Protocol 2: Live imaging of vital dye-treated mouse intestinal organoids in triple-decker sandwich cultures Basic Protocol 4: Immunofluorescence imaging of mouse organoids liberated from triple-decker sandwich cultures Alternate Protocol 3: Liberating and fixing mouse intestinal organoids from dome cultures Support Protocol 5: Measuring cell proliferation by EdU staining of mouse intestinal organoids Basic Protocol 5: Single-cell RNA sequencing and analysis of mouse intestinal organoids.
Collapse
Affiliation(s)
- Hailey M. Cambra
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Naren P. Tallapragada
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Prabhath Mannam
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David T. Breault
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA,Harvard Stem Cell Institute, Harvard University, Boston, MA 02139, USA
| | - Allon M. Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA,Lead contact,Correspondence:
| |
Collapse
|
2
|
Lawlor KT, Zappia L, Lefevre J, Park JS, Hamilton NA, Oshlack A, Little MH, Combes AN. Nephron progenitor commitment is a stochastic process influenced by cell migration. eLife 2019; 8:41156. [PMID: 30676318 PMCID: PMC6363379 DOI: 10.7554/elife.41156] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Progenitor self-renewal and differentiation is often regulated by spatially restricted cues within a tissue microenvironment. Here, we examine how progenitor cell migration impacts regionally induced commitment within the nephrogenic niche in mice. We identify a subset of cells that express Wnt4, an early marker of nephron commitment, but migrate back into the progenitor population where they accumulate over time. Single cell RNA-seq and computational modelling of returning cells reveals that nephron progenitors can traverse the transcriptional hierarchy between self-renewal and commitment in either direction. This plasticity may enable robust regulation of nephrogenesis as niches remodel and grow during organogenesis.
Collapse
Affiliation(s)
- Kynan T Lawlor
- Murdoch Children's Research Institute, Parkville, Australia
| | - Luke Zappia
- Murdoch Children's Research Institute, Parkville, Australia.,School of Biosciences, University of Melbourne, Melbourne, Australia
| | - James Lefevre
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Joo-Seop Park
- Division of Pediatric Urology and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Nicholas A Hamilton
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Alicia Oshlack
- Murdoch Children's Research Institute, Parkville, Australia.,School of Biosciences, University of Melbourne, Melbourne, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia
| | - Alexander N Combes
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia
| |
Collapse
|
3
|
Daniel E, Cleaver O. Vascularizing organogenesis: Lessons from developmental biology and implications for regenerative medicine. Curr Top Dev Biol 2019; 132:177-220. [PMID: 30797509 DOI: 10.1016/bs.ctdb.2018.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Organogenesis requires tightly coordinated and patterned growth of numerous cell types to form a fully mature and vascularized organ. Endothelial cells (ECs) that line blood vessels develop alongside the growing organ, but only recently has their role in directing epithelial and stromal growth been appreciated. Endothelial, epithelial, and stromal cells in embryonic organs actively communicate with one another throughout development to ensure that the organ forms appropriately. What signals tell blood vessel progenitors where to go? How are tissues influenced by the vasculature that pervades it? In this chapter, we review the ways in which crosstalk between ECs and epithelial or stromal cells during development leads to a fully patterned pancreas, lung, or kidney. ECs in all of these organs are necessary for proper epithelial and stromal growth, but how they direct this process is organ- and time-specific, highlighting the concept of dynamic EC heterogeneity. We end with a discussion on how understanding cell-cell crosstalk during development can be applied therapeutically through the generation of transplantable miniature organ-like tissues called "organoids." We will discuss the current state of organoid technology and highlight the major challenges in forming a properly patterned vascular network that will be critical in transforming them into a viable therapeutic option.
Collapse
Affiliation(s)
- Edward Daniel
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Ondine Cleaver
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| |
Collapse
|
4
|
Abstract
Kidney organogenesis has been a widely used classical model system to study inductive tissue interactions that guide differentiation of many organs. The basis for this is in the pioneering work done during the early 1950s when the conditions of how to support ex vivo growth and differentiation of developing kidneys were revealed. Importantly, culturing developing kidneys remains as an essential instrument to advance our understanding of molecular and cellular regulation of morphogenesis even today. Despite the fact that embryonic kidneys have been cultured for decades, it is not a trivial method and requires specific anatomical and developmental biology knowledge. This chapter outlines the general steps in organ culture and details the requirements for successful kidney explant differentiation.
Collapse
|
5
|
Short KM, Combes AN, Lisnyak V, Lefevre JG, Jones LK, Little MH, Hamilton NA, Smyth IM. Branching morphogenesis in the developing kidney is not impacted by nephron formation or integration. eLife 2018; 7:38992. [PMID: 30063208 PMCID: PMC6115188 DOI: 10.7554/elife.38992] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
Branching morphogenesis of the ureteric bud is integral to kidney development; establishing the collecting ducts of the adult organ and driving organ expansion via peripheral interactions with nephron progenitor cells. A recent study suggested that termination of tip branching within the developing kidney involved stochastic exhaustion in response to nephron formation, with such a termination event representing a unifying developmental process evident in many organs. To examine this possibility, we have profiled the impact of nephron formation and maturation on elaboration of the ureteric bud during mouse kidney development. We find a distinct absence of random branch termination events within the kidney or evidence that nephrogenesis impacts the branching program or cell proliferation in either tip or progenitor cell niches. Instead, organogenesis proceeds in a manner indifferent to the development of these structures. Hence, stochastic cessation of branching is not a unifying developmental feature in all branching organs. During development and before birth, many organs develop from branched tubes. Whether forming the airways of the lungs, the collecting ducts of the kidneys or the milk ducts of the breast, there are many similarities between these structures. Given their shared tree-like structures, one possibility is that these tissues all form through the same general process. A key challenge is understanding why branched networks develop and pattern in such a way as to assume their functional roles in the adult organ. A unifying theory, which proposes that certain tips stop growing in a random manner, has been proposed to solve this problem. In this theory, the branched mammary gland structures stop growing when the tips of the structure impinge on neighbouring branches. In the kidney, this cessation has been proposed to occur when nephrons – the structures that filter urine from blood – form near the end of the collecting ducts. By growing kidneys in the laboratory and studying developing kidneys in mice, Short et al. investigated whether nephrons do affect collecting duct growth and branch development. The results of these experiments instead suggest that nephron formation has no effect on duct growth or branching. The nephrons also do not appear to affect how quickly the duct cells grow and divide. Moreover, there is no evidence that the cell proliferation in individual branch tips ceases randomly by any other mechanism. Overall, the experiments Short et al. performed suggest that a unifying theory of branching in developing organs may not hold true, at least not in the way that has been envisioned previously.
Collapse
Affiliation(s)
- Kieran M Short
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Alexander N Combes
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Anatomy and Neuroscience, School of Biomedical Sciences, University of Melbourne, Parkville, Australia
| | - Valerie Lisnyak
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - James G Lefevre
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Lynelle K Jones
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Anatomy and Neuroscience, School of Biomedical Sciences, University of Melbourne, Parkville, Australia.,Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Nicholas A Hamilton
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| |
Collapse
|
6
|
Held M, Santeramo I, Wilm B, Murray P, Lévy R. Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy. PLoS One 2018; 13:e0199918. [PMID: 30048451 PMCID: PMC6062017 DOI: 10.1371/journal.pone.0199918] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/16/2018] [Indexed: 12/28/2022] Open
Abstract
Screening cells for their differentiation potential requires a combination of tissue culture models and imaging methods that allow for long-term tracking of the location and function of cells. Embryonic kidney re-aggregation in vitro assays have been established which allow for the monitoring of organotypic cell behaviour in re-aggregated and chimeric renal organoids. However, evaluation of cell integration is hampered by the high photonic load of standard fluorescence microscopy which poses challenges for imaging three-dimensional systems in real-time over a time course. Therefore, we employed light sheet microscopy, a technique that vastly reduces photobleaching and phototoxic effects. We have also developed a new method for culturing the re-aggregates which involves immersed culture, generating organoids which more closely reflect development in vivo. To facilitate imaging from various angles, we embedded the organoids in a freely rotatable hydrogel cylinder. Endpoint fixing and staining were performed to provide additional biomolecular information. We succeeded in imaging labelled cells within re-aggregated kidney organoids over 15 hours and tracking their fate while simultaneously monitoring the development of organotypic morphological structures. Our results show that Wt1-expressing embryonic kidney cells obtained from transgenic mice could integrate into re-aggregated chimeric kidney organoids and contribute to developing nephrons. Furthermore, the nascent proximal tubules that formed in the re-aggregated tissues using the new culture method displayed secretory function, as evidenced by their ability to secrete an organic anion mimic into the tubular lumen.
Collapse
Affiliation(s)
- Marie Held
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ilaria Santeramo
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Bettina Wilm
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Patricia Murray
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Raphaël Lévy
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
7
|
Munro DAD, Davies JA. Vascularizing the Kidney in the Embryo and Organoid: Questioning Assumptions about Renal Vasculogenesis. J Am Soc Nephrol 2018; 29:1593-1595. [PMID: 29748327 DOI: 10.1681/asn.2018020179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- David A D Munro
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jamie A Davies
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
8
|
Krause M, Rak-Raszewska A, Naillat F, Saarela U, Schmidt C, Ronkainen VP, Bart G, Ylä-Herttuala S, Vainio SJ. Exosomes as secondary inductive signals involved in kidney organogenesis. J Extracell Vesicles 2018; 7:1422675. [PMID: 29410779 PMCID: PMC5795705 DOI: 10.1080/20013078.2017.1422675] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 12/22/2017] [Indexed: 12/16/2022] Open
Abstract
The subfraction of extracellular vesicles, called exosomes, transfers biological molecular information not only between cells but also between tissues and organs as nanolevel signals. Owing to their unique properties such that they contain several RNA species and proteins implicated in kidney development, exosomes are putative candidates to serve as developmental programming units in embryonic induction and tissue interactions. We used the mammalian metanephric kidney and its nephron-forming mesenchyme containing the nephron progenitor/stem cells as a model to investigate if secreted exosomes could serve as a novel type of inductive signal in a process defined as embryonic induction that controls organogenesis. As judged by several characteristic criteria, exosomes were enriched and purified from a cell line derived from embryonic kidney ureteric bud (UB) and from primary embryonic kidney UB cells, respectively. The cargo of the UB-derived exosomes was analysed by qPCR and proteomics. Several miRNA species that play a role in Wnt pathways and enrichment of proteins involved in pathways regulating the organization of the extracellular matrix as well as tissue homeostasis were identified. When labelled with fluorescent dyes, the uptake of the exosomes by metanephric mesenchyme (MM) cells and the transfer of their cargo to the cells can be observed. Closer inspection revealed that besides entering the cytoplasm, the exosomes were competent to also reach the nucleus. Furthermore, fluorescently labelled exosomal RNA enters into the cytoplasm of the MM cells. Exposure of the embryonic kidney-derived exosomes to the whole MM in an ex vivo organ culture setting did not lead to an induction of nephrogenesis but had an impact on the overall organization of the tissue. We conclude that the exosomes provide a novel signalling system with an apparent role in secondary embryonic induction regulating organogenesis.
Collapse
Affiliation(s)
- Mirja Krause
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- The Ritchie Centre, Hudson Institute of Medical Research Core, Clayton, Australia
| | - Aleksandra Rak-Raszewska
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Florence Naillat
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ulla Saarela
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Christina Schmidt
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Veli-Pekka Ronkainen
- Biocenter Oulu, Tissue Imaging Center, Light Microscopy Facility, Faculty of Biochemistry and Molecular Medicine, Developmental Biology Lab, University of Oulu, Oulu, Finland
| | - Geneviève Bart
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Seppo Ylä-Herttuala
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo J. Vainio
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| |
Collapse
|
9
|
Abstract
Summary: This Editorial provides an overview of the entire contents of the Special Issue, highlighting some of the important findings and major themes therein.
Collapse
Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Melbourne 3052, Australia
| |
Collapse
|
10
|
Desgrange A, Heliot C, Skovorodkin I, Akram SU, Heikkilä J, Ronkainen VP, Miinalainen I, Vainio SJ, Cereghini S. HNF1B controls epithelial organization and cell polarity during ureteric bud branching and collecting duct morphogenesis. Development 2017; 144:4704-4719. [PMID: 29158444 DOI: 10.1242/dev.154336] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022]
Abstract
Kidney development depends crucially on proper ureteric bud branching giving rise to the entire collecting duct system. The transcription factor HNF1B is required for the early steps of ureteric bud branching, yet the molecular and cellular events regulated by HNF1B are poorly understood. We report that specific removal of Hnf1b from the ureteric bud leads to defective cell-cell contacts and apicobasal polarity during the early branching events. High-resolution ex vivo imaging combined with a membranous fluorescent reporter strategy show decreased mutant cell rearrangements during mitosis-associated cell dispersal and severe epithelial disorganization. Molecular analysis reveals downregulation of Gdnf-Ret pathway components and suggests that HNF1B acts both upstream and downstream of Ret signaling by directly regulating Gfra1 and Etv5 Subsequently, Hnf1b deletion leads to massively mispatterned ureteric tree network, defective collecting duct differentiation and disrupted tissue architecture, which leads to cystogenesis. Consistently, mRNA-seq analysis shows that the most impacted genes encode intrinsic cell-membrane components with transporter activity. Our study uncovers a fundamental and recurring role of HNF1B in epithelial organization during early ureteric bud branching and in further patterning and differentiation of the collecting duct system in mouse.
Collapse
Affiliation(s)
- Audrey Desgrange
- Sorbonne Universités, UPMC Université Paris 06, IBPS - UMR7622, F-75005 Paris, France .,CNRS, UMR7622, Institut de Biologie Paris-Seine (IBPS) - Developmental Biology Laboratory, F-75005 Paris, France
| | - Claire Heliot
- Sorbonne Universités, UPMC Université Paris 06, IBPS - UMR7622, F-75005 Paris, France.,CNRS, UMR7622, Institut de Biologie Paris-Seine (IBPS) - Developmental Biology Laboratory, F-75005 Paris, France
| | - Ilya Skovorodkin
- Faculty of Biochemistry and Molecular Medicine, Biocenter, University of Oulu; Laboratory of Developmental Biology, Biocenter Oulu and InfoTech, Department of Medical Biochemistry and Molecular Medicine, Oulu Center for Cell Matrix Research, 90220 Oulu, Finland
| | - Saad U Akram
- Center for Machine Vision Research and Signal Analysis (CMVS), University of Oulu, FIN-90014, Oulu, Finland
| | - Janne Heikkilä
- Center for Machine Vision Research and Signal Analysis (CMVS), University of Oulu, FIN-90014, Oulu, Finland
| | | | | | - Seppo J Vainio
- Faculty of Biochemistry and Molecular Medicine, Biocenter, University of Oulu; Laboratory of Developmental Biology, Biocenter Oulu and InfoTech, Department of Medical Biochemistry and Molecular Medicine, Oulu Center for Cell Matrix Research, 90220 Oulu, Finland
| | - Silvia Cereghini
- Sorbonne Universités, UPMC Université Paris 06, IBPS - UMR7622, F-75005 Paris, France .,CNRS, UMR7622, Institut de Biologie Paris-Seine (IBPS) - Developmental Biology Laboratory, F-75005 Paris, France
| |
Collapse
|