The Organoid Platform: Promises and Challenges as Tools in the Fight against COVID-19

Abstract

Many pathogenic viruses that affect man display species specificity, limiting the use of animal models. Studying viral biology and identifying potential treatments therefore benefits from the development of in vitro cell systems that closely mimic human physiology. In the current COVID-19 pandemic, rapid scientific insights are of the utmost importance to limit its impact on public health and society. Organoids are emerging as versatile tools to progress the understanding of SARS-CoV-2 biology and to aid in the quest for novel treatments. Many pathogenic viruses that affect man display species specificity, limiting the use of animal models. Studying viral biology and identifying potential treatments therefore benefits from the development of in vitro cell systems that closely mimic human physiology. In the current COVID-19 pandemic, rapid scientific insights are of the utmost importance to limit its impact on public health and society. Organoids are emerging as versatile tools to progress the understanding of SARS-CoV-2 biology and to aid in the quest for novel treatments. The global outbreak of the novel coronavirus SARS-CoV-2 strains healthcare systems around the world and has already caused over a million deaths. COVID-19 is the third appearance of a lethal coronavirus, after the emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome virus (MERS-CoV) in 2012. It appears likely that more novel viruses will emerge to infect humans on a global scale. To develop effective treatments for current and future infectious diseases, it is key to establish in vitro models that closely resemble the physiology of the viral host and that are likely to allow—and model—infection by any type of virus. Much of the insight on coronavirus biology has been gathered using “classical” 2D cell lines, such as the Vero E6 cell line, derived from the kidney of the African green monkey (Matsuyama et al., 2020Matsuyama S. Nao N. Shirato K. Kawase M. Saito S. Takayama I. Nagata N. Sekizuka T. Katoh H. Kato F. et al.Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells.Proc. Natl. Acad. Sci. U S A. 2020; 117: 7001-7003https://doi.org/10.1073/pnas.2002589117Crossref PubMed Scopus (952) Google Scholar). These cell lines are often easily infectable by viruses and—if so—can be used to propagate the virus for downstream experiments. However, cell lines are typically malignantly transformed and consist of a homogeneous population of poorly differentiated cells, which hampers culturing of “picky” viruses. As a case in point, Norovirus has remained unculturable on such cell lines as it requires a differentiated intestinal cell type as its target (Alvarado et al., 2018Alvarado G. Ettayebi K. Atmar R.L. Bombardi R.G. Kose N. Estes M.K. Crowe J.E. Human monoclonal antibodies that neutralize pandemic GII.4 noroviruses.Gastroenterology. 2018; 155: 1898-1907https://doi.org/10.1053/j.gastro.2018.08.039Abstract Full Text Full Text PDF PubMed Scopus (52) Google Scholar; Ettayebi et al., 2016Ettayebi K. Sue E. Crawford K.M. Broughman J.R. Umesh Karandikar Tenge Victoria R. Frederick H. Neill S.E.B. Zeng Xi-Lei Qu Lin Kou Baijun Antone R. Opekun D.B. et al.Replication of human noroviruses in stem cell-derived human enteroids.Science. 2016; 353: 1387-1394Crossref PubMed Scopus (980) Google Scholar). Also, the biology of infection and specific pathological effects seen in a patient's tissue may not be reproduced on these transformed cell lines. As an example, the pathogenic effects of Zika virus on the fetal human brain cannot be modeled using cell lines (Qian et al., 2017Qian X. Nguyen H.N. Jacob F. Song H. Ming G.L. Using brain organoids to understand Zika virus-induced microcephaly.Development (Cambridge). 2017; 144: 952-957https://doi.org/10.1242/dev.140707Crossref PubMed Scopus (171) Google Scholar; Watanabe et al., 2017Watanabe M. Buth J.E. Vishlaghi N. Taxidis J. Khakh B. Coppola G. Pearson C.A. Gong D. Dai X. Damoiseaux R. et al.Self-organized cerebral organoids with human-specific features predict effective drugs to combat Zika virus infection.Cell Rep. 2017; 21: 517-532https://doi.org/10.1016/j.celrep.2017.09.047.Self-organizedAbstract Full Text Full Text PDF PubMed Scopus (256) Google Scholar). Moreover, treatment efficacy may not be directly extrapolated to the clinic, as illustrated by the recent controversy around the use of the anti-malaria drug hydroxychloroquine. This drug was quickly adapted worldwide as a promising treatment against SARS-CoV-2 as it was shown to be effective in Vero cells (Wang et al., 2020aWang M. Cao R. Zhang L. Yang X. Liu J. Xu M. Shi Z. Hu Z. Zhong W. Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro.Cell Res. 2020; 30: 269-271https://doi.org/10.1038/s41422-020-0282-0Crossref PubMed Scopus (5032) Google Scholar). However, besides countless side effects, hydroxychloroquine has now been proven to be ineffective in humans (Hernandez et al., 2020Hernandez A.V. Roman Y.M. Pasupuleti V. Barboza J.J. White C.M. Hydroxychloroquine or chloroquine for treatment or prophylaxis of COVID-19: a living systematic review.Ann. Intern. Med. 2020; 173: 287-296https://doi.org/10.7326/M20-2496Crossref PubMed Scopus (158) Google Scholar). In the search for the most optimal in vitro model, organoids are now emerging. Organoids are 3D structures grown from stem cells and consist of organ-specific cell types that self-organize through cell sorting and spatially restricted lineage commitment (Clevers, 2016Clevers H. Modeling development and disease with organoids.Cell. 2016; 165: 1586-1597https://doi.org/10.1016/j.cell.2016.05.082Abstract Full Text Full Text PDF PubMed Scopus (1857) Google Scholar; Lancaster and Knoblich, 2014Lancaster M.A. Knoblich J.A. Organogenesisin a dish: modeling development and disease using organoid technologies.Science. 2014; 345https://doi.org/10.1126/science.1247125Crossref Scopus (1855) Google Scholar). They can be established from either induced pluripotent stem cells (iPSCs) or multipotent adult tissue stem cells (ASCs). Under optimal culture conditions, stem cell differentiation generates a complete arsenal of cell types as present in the tissue of interest. Organoid models are genetically stable and can be expanded over long periods of time. Organoid derivation from iPSCs or ASCs differs greatly. iPSC-derived organoids are formed by first creating a 3D aggregate of iPSCs, a so-called embryoid body, after which organ and cell-type specialization is initiated by closely mimicking the developmental signals. This process can take multiple weeks, a time during which gastrulation and organogenesis are mimicked in a dish. Apart from the epithelial cell types produced, suboptimal specification of iPSCs can also lead to the production of non-epithelial lineages, such as fibroblasts and muscle. ASC-derived organoids are established by directly dissociating the tissue of interest, containing the intrinsic ASCs and propagating these cells over extended periods of time under tissue-specific growth factor conditions (van der Vaart and Clevers, 2020van der Vaart J. Clevers H. Airway organoids as models of human disease.J. Intern. Med. 2020; : 1-10https://doi.org/10.1111/joim.13075Crossref Scopus (48) Google Scholar). ASC-derived organoids are now readily established from most murine and human epithelial tissues (Driehuis et al., 2020Driehuis E. Kretzschmar K. Clevers H. Establishment of patient-derived cancer organoids for drug-screening applications.Nat. Protoc. 2020; : 1-30https://doi.org/10.1038/s41596-020-0379-4Crossref Scopus (297) Google Scholar). Tissue-specific cell types can subsequently be enriched by modulating individual signaling pathways, such as Notch or BMP (Beumer and Clevers, 2020Beumer J. Clevers H. Cell fate specification and differentiation in the adult mammalian intestine.Nat. Rev. Mol. Cell Biol. 2020; https://doi.org/10.1038/s41580-020-0278-0Crossref PubMed Scopus (263) Google Scholar). The ability to generate a variety of human tissues in the form of organoids has become important in the study of COVID-19 when it was realized that patients present with systemic symptoms beyond the respiratory infection. The vast majority of airborne viruses, including respiratory and enteroviruses, enter the human body through infection of epithelial cells. Multiple studies have used ASC-derived organoids from the intestinal lining, oral mucosa, or airway as infection models for their respective viruses. Human oral mucosal organoids recapitulate the stratified architecture of the oral mucosa and have been shown to be receptive to infection by herpes simplex virus type 1 and human papilloma virus (Driehuis et al., 2019Driehuis E. Kolders S. Spelier S. Lõhmussaar K. Willems S.M. Devriese L.A. de Bree R. de Ruiter E.J. Korving J. Begthel H. et al.Oral mucosal organoids as a potential platform for personalized cancer therapy.Cancer Discov. 2019; 9: 852-871https://doi.org/10.1158/2159-8290.CD-18-1522Crossref PubMed Scopus (218) Google Scholar). Human intestinal organoids have become the first in vitro model system to study viral entry and replication of noroviruses (Ettayebi et al., 2016Ettayebi K. Sue E. Crawford K.M. Broughman J.R. Umesh Karandikar Tenge Victoria R. Frederick H. Neill S.E.B. Zeng Xi-Lei Qu Lin Kou Baijun Antone R. Opekun D.B. et al.Replication of human noroviruses in stem cell-derived human enteroids.Science. 2016; 353: 1387-1394Crossref PubMed Scopus (980) Google Scholar; Haga et al., 2020Haga K. Ettayebi K. Tenge V.R. Karandikar U.C. Lewis M.A. Lin S.C. Neill F.H. Ayyar B.V. Zeng X.L. Larson G. et al.Genetic manipulation of human intestinal enteroids demonstrates the necessity of a functional fucosyltransferase 2 gene for secretor-dependent human norovirus infection.MBio. 2020; 11: 1-10https://doi.org/10.1128/mBio.00251-20Crossref Scopus (55) Google Scholar). Norovirus infectivity and replication efficiency differ greatly between individuals. Intestinal organoids from individuals indeed recapitulated the diverging norovirus replication efficiency in vitro (Estes et al., 2019Estes M.K. Ettayebi K. Tenge V.R. Murakami K. Karandikar U. Lin S.C. Ayyar B.V. Cortes-Penfield N.W. Haga K. Neill F.H. et al.Human norovirus cultivation in nontransformed stem cell-derived human intestinal enteroid cultures: success and challenges.Viruses. 2019; 11: 9-11https://doi.org/10.3390/v11070638Crossref Scopus (75) Google Scholar). The pulmonary organoid epithelium is susceptible to a wide range of viruses. Sachs et al., 2019Sachs N. Papaspyropoulos A. Zomer-van Ommen D.D. Heo I. Böttinger L. Klay D. Weeber F. Huelsz-Prince G. Iakobachvili N. Amatngalim G.D. et al.Long-term expanding human airway organoids for disease modeling.EMBO J. 2019; 38: e100300https://doi.org/10.15252/embj.2018100300Crossref PubMed Scopus (553) Google Scholar used the 3D structure of organoids to identify increased cellular motility after infection with respiratory syncytial virus (RSV). This phenomenon was identified in vivo but could not be recapitulated and studied in traditional 2D cell lines or primary cells in air-liquid interface (ALI) cultures. Subsequent analysis of this increased cellular motility showed that overexpression of the RSV non-structural protein NS2 led to increased motility and fusion with This study an of cellular motility for viral in the airway epithelium et al., 2019Sachs N. Papaspyropoulos A. Zomer-van Ommen D.D. Heo I. Böttinger L. Klay D. Weeber F. Huelsz-Prince G. Iakobachvili N. Amatngalim G.D. et al.Long-term expanding human airway organoids for disease modeling.EMBO J. 2019; 38: e100300https://doi.org/10.15252/embj.2018100300Crossref PubMed Scopus (553) Google Scholar). Airway organoids have also emerged as tools for viruses that display et al., J. Sachs N. H. D. X. L. et human airway organoids to infectivity of emerging Natl. Acad. Sci. U S A. 2018; PubMed Scopus Google Scholar showed that human airway organoids are readily with human infectious virus showed replication caused a pandemic in from humans readily in airway organoids the virus from showed replication Organoids could be used to study potential et al., J. Sachs N. H. D. X. L. et human airway organoids to infectivity of emerging Natl. Acad. Sci. U S A. 2018; PubMed Scopus Google Scholar). the Zika virus cerebral organoids derived from iPSCs used to that this virus in (Qian et al., 2017Qian X. Nguyen H.N. Jacob F. Song H. Ming G.L. Using brain organoids to understand Zika virus-induced microcephaly.Development (Cambridge). 2017; 144: 952-957https://doi.org/10.1242/dev.140707Crossref PubMed Scopus (171) Google Scholar; Watanabe et al., 2017Watanabe M. Buth J.E. Vishlaghi N. Taxidis J. Khakh B. Coppola G. Pearson C.A. Gong D. Dai X. Damoiseaux R. et al.Self-organized cerebral organoids with human-specific features predict effective drugs to combat Zika virus infection.Cell Rep. 2017; 21: 517-532https://doi.org/10.1016/j.celrep.2017.09.047.Self-organizedAbstract Full Text Full Text PDF PubMed Scopus (256) Google Scholar). This the the fetal human brain was the virus was to the Many human viruses from and have to example, multiple species are of viruses that to including the and and ASC-derived intestinal organoids have been derived from including and This has the of strains of directly from et al., G. R. S. of and organoids and their potential use to coronavirus 2020; 9: Scopus Google Scholar; et al., J. Liu X. X. D. A. Zhang H. et of and human intestinal organoids by Med. 2020; PubMed Scopus Google Scholar). These organoids can be to study viruses with The ASC-derived organoid system is also to such as and could viruses of the animal et al., In this may be for example, have become the primary of in et al., S. M. D. M. B. K. the of in J. 2020; PubMed Scopus Google Scholar). Moreover, organoids could also the impact of of the and such as and SARS-CoV-2 first emerged in in the of in and has led to more 1 million to this of the is for symptoms in the the virus has been studied using culturing airway as as airway organoids et al., J. Vaart J. K. J. et human 2020; PubMed Scopus Google Scholar; et al., A. J. de S.M. M. J. A. et and SARS-CoV-2 infection in human organoid 2020; PubMed Google Scholar). of adult organoids by of the virus to the SARS-CoV-2 infection was in cells, which the that these cells the primary target of the virus. these could be from the the organoids by et al., A. J. de S.M. M. J. A. et and SARS-CoV-2 infection in human organoid 2020; PubMed Google Scholar to be to generate an could be by these to SARS-CoV-2 cells but not cells. The development of a culture system for cells the of an model for SARS-CoV-2 replication et al., A. J. de S.M. M. J. A. et and SARS-CoV-2 infection in human organoid 2020; PubMed Google Scholar). Apart from the respiratory symptoms have been identified in a of patients et al., A. K. N. S. B. N. et of Med. 2020; PubMed Scopus Google Scholar). To of human intestinal organoids by SARS-CoV-2 in study used 2D from organoids to the the use of the 3D architecture and the organoids in after their studies that of the intestinal by SARS-CoV-2 et al., J. Vaart J. K. J. et human 2020; PubMed Scopus Google Scholar; et al., R. Zeng Liu Z. X. et and SARS-CoV-2 infection of human intestinal 2020; Scopus Google Scholar; et al., J. Liu X. X. D. A. Zhang H. et of and human intestinal organoids by Med. 2020; PubMed Scopus Google Scholar). These studies that the is a potential of SARS-CoV-2 symptoms in to the cellular of these intestinal insights in host could be readily of organoids the of the epithelium over with multiple and et al., J. Vaart J. K. J. et human 2020; PubMed Scopus Google Scholar). multiple iPSC-derived organoids have been to SARS-CoV-2 replication and study its in tissues organoids are et al., A. L. E. A. A. H. A. et of 3D human brain J. 2020; : Scopus Google Scholar showed that SARS-CoV-2 iPSC-derived cerebral organoids 2 replication could be in cell was seen in with of the protein et al., V. H. A. M. A. E. F. et of SARS-CoV-2 in human tissues using human 2020; Full Text Full Text PDF PubMed Scopus Google Scholar used and kidney organoids derived from iPSCs and that these cells SARS-CoV-2 They used these to human as an of infection of the of and iPSC-derived organoids a platform to study tissue-specific SARS-CoV-2 infection in and models. Much has been the SARS-CoV-2 host cells using from in vitro cell culture systems to it is as the virus is in the of the the the protein of which the virus the cells in an et al., M. H. S. N. T. S. G. A. et cell entry on and and is by a proven 2020; Full Text Full Text PDF PubMed Scopus Google Scholar). However, besides these host such as and are from have been to a in the infection to the cell entry of SARS-CoV-2 a of et al., M. D.B. The of host in coronavirus of animal and systematic of human J. 2020; Full Text Full Text PDF PubMed Scopus Google Scholar). of this could be by is by cell lines with the use of target by a the a in This in of and The lead to of of the protein of et al., Yang L. K.M. J. M. J.E. J.E. human PubMed Scopus Google Scholar). was effectively in organoids by et al., R. Zeng Liu Z. X. et and SARS-CoV-2 infection of human intestinal 2020; Scopus Google Scholar to of and in enteroids using a of led to a of SARS-CoV-2 not in a can be in a to identify host in an a of in a a cell containing individual of in the can be have become an emerging for identifying in a of and have recently been in recent studies have this in Vero cells and cells and identified host the and to a in viral infection (Wang et al., R. J. M. K. J. J. K. et identify human host for SARS-CoV-2 and 2020; : Scopus Google Scholar; et al., J. M. R. M. W. Zhang V. J. et host that SARS-CoV-2 2020; Scopus Google Scholar). study to the of a drug that is now to SARS-CoV-2 patients et al., E. M. Lin L. G. M. et of through and 2020; PubMed Scopus Google Scholar). These insights gathered from cell lines, in more such as studies the first in the in organoids to SARS-CoV-2 biology et al., T. K. T. E. S. J. et in vitro and in vivo in human 2020; Full Text Full Text PDF PubMed Scopus Google Scholar; et al., T. N. F. S. S. S. S. M. G. L. et in human intestinal organoids of 2020; Full Text Full Text PDF PubMed Scopus Google Scholar). Organoids are an emerging for drug efficacy and drug that are to drug organoids for example, predict the success of in cancer patients et al., Weeber F. C.M. S. E. L. L. de J. et organoids can predict to in cancer Med. 2019; 11: Scopus Google Scholar). intestinal organoids from patients from the disease can be to effective drugs et al., de I. de K.M. de et functional using primary intestinal Med. PubMed Scopus Google Scholar). Organoids are their in the efficacy of treatments. Intestinal organoids with noroviruses to antibodies to identify that viral (Alvarado et al., 2018Alvarado G. Ettayebi K. Atmar R.L. Bombardi R.G. Kose N. Estes M.K. Crowe J.E. Human monoclonal antibodies that neutralize pandemic GII.4 noroviruses.Gastroenterology. 2018; 155: 1898-1907https://doi.org/10.1053/j.gastro.2018.08.039Abstract Full Text Full Text PDF PubMed Scopus (52) Google Scholar). organoids have a platform to identify drugs of Zika virus-induced cell in (Qian et al., 2017Qian X. Nguyen H.N. Jacob F. Song H. Ming G.L. Using brain organoids to understand Zika virus-induced microcephaly.Development (Cambridge). 2017; 144: 952-957https://doi.org/10.1242/dev.140707Crossref PubMed Scopus (171) Google Scholar; Watanabe et al., 2017Watanabe M. Buth J.E. Vishlaghi N. Taxidis J. Khakh B. Coppola G. Pearson C.A. Gong D. Dai X. Damoiseaux R. et al.Self-organized cerebral organoids with human-specific features predict effective drugs to combat Zika virus infection.Cell Rep. 2017; 21: 517-532https://doi.org/10.1016/j.celrep.2017.09.047.Self-organizedAbstract Full Text Full Text PDF PubMed Scopus (256) Google Scholar). In the multiple studies have organoids to predict success of SARS-CoV-2 treatments. viral cells may as of these was identified SARS-CoV-2 infection in organoids and COVID-19 patients and is to be effective in of multiple viruses. This from of organoids with greatly SARS-CoV-2 through the of cellular and fusion of the viral with cells (Wang et al., 2020aWang M. Cao R. Zhang L. Yang X. Liu J. Xu M. Shi Z. Hu Z. Zhong W. Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro.Cell Res. 2020; 30: 269-271https://doi.org/10.1038/s41422-020-0282-0Crossref PubMed Scopus (5032) Google et al., R. J. M. K. J. J. K. et identify human host for SARS-CoV-2 and 2020; : Scopus Google Scholar). of as is effectively by the in with the organoid et al., S. J. L. H. S. J. et is a SARS-CoV-2 Res. 2020; : PubMed Scopus Google Scholar). not have these and appears to be a for studies iPSC-derived intestinal organoids and adult human organoids to multiple drugs in including the the and the et al., J. R. J.A. L. D. T. S. et but not SARS-CoV-2 replication in human pluripotent stem cell-derived intestinal 2020; PubMed Google Scholar; et al., T. Saito A. D. D. S. T. T. T. Takayama K. of human organoids for SARS-CoV-2 2020; Google Scholar). The studies a on coronavirus biology or viral greatly from drug to the of drug on organoids are on or that cellular However, not of epithelial cells and may of drug specific for drug using pathogenic viruses, such as the which could the use of recent study used containing SARS-CoV-2 protein to a drug in iPSC-derived organoids in a was used as a of viral entry and replication et al., et of COVID-19 using Scholar). This multiple including the and the to be effective in viral study using human iPSC-derived organoids a and more drugs et al., X. Yang L. B. Zhang T. J. Xu D. X. S. et of SARS-CoV-2 Using Human Google Scholar). Many of these with in effective viral in epithelial These studies the first of organoids can aid in the quest for novel COVID-19 by drug in a these in organoids on that mimic of viral entry but of downstream using strains effective of viral which was recently by a SARS-CoV-2 et al., K. T. Kato T. et a infection in the respiratory 2020; Full Text Full Text PDF PubMed Scopus Google Scholar). However, the of these viral with the viral to the epithelial cells could be genetically to the of viral such as organoids could be tools to study viral entry and of any pandemic virus that are to such of viral also from cells. The could be used for of epithelial to the virus. have shown recently that of intestinal organoids can be genetically to of (Beumer et al., 2020Beumer J. J. J. A. R. A. D. B. et and of human 2020; Full Text Full Text PDF PubMed Scopus Google Scholar). COVID-19 drug in organoids could also on modulating the or of host important for the viral replication Multiple are to be for viral including and the and have been but display effects that could The that organoids closely resemble their tissue these models in an to the of key host could be as a of protein or Organoids are in SARS-CoV-2 including its cellular In to cell lines, human organoids can readily be with SARS-CoV-2 of key host such as To the of epithelial organoids could be with cell ASC-derived organoids consist of epithelial cells, systems can lineages, such as fibroblasts or muscle. systems cells, such as and cells, cells, and that in mucosal of these important in viral including as in et al., N. S. J. M. R. L. A. et of COVID-19: current of the 2020; Full Text Full Text PDF PubMed Scopus Google Organoids from and cell cancer have been with cells from study of organoid cells to cells, which subsequently et al., C.M. Weeber F. M. de J. M. der S. S. et of cells by of and organoids.Cell. 2018; Full Text Full Text PDF PubMed Scopus Google Scholar). could be to predict that development and of the organoid viral including and genetically drug using viral strains from These the for COVID-19 organoids can be used to viral between individuals. In this have the current and future potential of organoids in of this culturing could COVID-19 and future viral and the first of the was in and the to for on modeling coronavirus with is an on to organoid is and

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