Organoid
An organoid is a miniaturized and simplified version of an organ produced in vitro in three dimensions that shows realistic micro-anatomy. They are derived from one or a few cells from a tissue, embryonic stem cells or induced pluripotent stem cells, which can self-organize in three-dimensional culture owing to their self-renewal and differentiation capacities. The technique for growing organoids has rapidly improved since the early 2010s, and it was named by "The Scientist" as one of the biggest scientific advancements of 2013. Organoids are used by scientists to study disease and treatments in a laboratory . History. Attempts to create organs "in vitro" started with one of the first dissociation-reaggregation experiments where Henry Van Peters Wilson demonstrated that mechanically dissociated sponge cells can reaggregate and self-organize to generate a whole organism. In the subsequent decades, multiple labs were able to generate different types of organs "in vitro" through the dissociation and reaggregation of organ tissues obtained from amphibians and embryonic chicks. The phenomena of mechanically dissociated cells aggregating and reorganizing to reform the tissue they were obtained from subsequently led to the development of the differential adhesion hypothesis by Malcolm Steinberg. With the advent  of the field of stem cell biology, the potential of stem cells to form organs "in vitro" was realized early on with the observation that when stem cells form teratomas or embryoid bodies, the differentiated cells can organize into different structures resembling those found in multiple tissue types. The advent of the field of organoids, started with a shift from culturing and differentiating stem cells in 2D media, to 3D media to allow for the development of the complex 3-dimensional structures of organs. Since 1987, researchers have devised different methods for 3-D culturing, and were able to utilize  different types of stem cells to generate organoids resembling a multitude of organs. In 2006, Yaakov Nahmias and David Odde showed the self-assembly of vascular liver organoid maintained for over 50 days "in vitro". In 2008, Yoshiki Sasai and his team at RIKEN institute demonstrated that stem cells can be coaxed into balls of neural cells that self-organize into distinctive layers. In 2009 the Laboratory of Hans Clevers at Hubrecht Institute and University Medical Center Utrecht, Netherlands, showed that single LGR5-expressing intestinal stem cells self-organize to crypt-villus structures "in vitro" without necessity of a mesenchymal  niche. In 2010, Mathieu Unbekandt & Jamie A. Davies demonstrated the production of renal organoids from murine fetus-derived renogenic stem cells. Subsequent reports showed significant physiological function of these organoids "in vitro" and "in vivo". In 2013, Madeline Lancaster at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences established a protocol for culturing cerebral organoids derived from stem cells that mimic the developing human brain's cellular organization. In 2014, Artem Shkumatov et al. at the University of Illinois at Urbana-Champaign demonstrated that cardiovascular organoids can be formed from ES cells through modulation of the substrate  stiffness, to which they adhere. Physiological stiffness promoted three-dimensionality of EBs and cardiomyogenic differentiation. Takebe et al. demonstrate a generalized method for organ bud formation from diverse tissues by combining pluripotent stem cell-derived tissue-specific progenitors or relevant tissue samples with endothelial cells and mesenchymal stem cells. They suggested that the less mature tissues, or organ buds, generated through the self-organized condensation principle might be the most efficient approach toward the reconstitution of mature organ functions after transplantation, rather than condensates generated from cells of a more advanced stage. Properties. Lancaster and Knoblich define an organoid as  a collection of organ-specific cell types that develops from stem cells or organ progenitors, self-organizes through cell sorting and spatially restricted lineage commitment in a manner similar to "in vivo", and exhibits the following properties: Process. Organoid formation generally requires culturing the stem cells or progenitor cells in a 3D medium. The 3D medium can be made using an extracellular matrix hydrogel such as Matrigel or Cultrex BME, which is a laminin-rich extracellular matrix that is secreted by the Engelbreth-Holm-Swarm tumor line. Organoid bodies can then be made through embedding stem cells in the 3D  medium. When pluripotent stem cells are used for the creation of the organoid, the cells are usually, but not all the time, allowed to form embryoid bodies. Those embryoid bodies are then pharmacologically treated with patterning factors to drive the formation of the desired organoid identity. Organoids have also been created using adult stem cells extracted from the target organ, and cultured in 3D media. Types. A multitude of organ structures have been recapitulated using organoids. This section aims to outline the state of the field as of now through providing an abridged list of the organoids that have been  successfully created, along with a brief outline based on the most recent literature for each organoid, and examples of how it has been utilized in research. Cerebral organoid. A cerebral organoid describes artificially grown, "in vitro", miniature organs resembling the brain. Cerebral organoids are created by culturing human pluripotent stem cells in a three-dimensional structure using rotational bioreactor and develop over a course of months. The procedure has potential applications in the study of brain development, physiology and function. Cerebral organoids may experience "simple sensations" in response to external stimulation and neuroscientists Andrea Lavazza, Elan Ohayon and Hideya Sakaguchi  are among those expressing concern that such organs could develop sentience. They propose that further evolution of the technique needs to be subject to a rigorous oversight procedure. Gut organoid. Gut organoids refer to organoids that recapitulate structures of the gastrointestinal tract. The gastrointestinal tract arises from the endoderm, which during development forms a tube that can be divided in three distinct regions, which give rise to, along with other organs, the following sections of the gastrointestinal tract: Organoids have been created for the following structures of the gastrointestinal tract: Intestinal organoid. Intestinal organoids have thus far been among the  gut organoids to be generated directly from pluripotent stem cells. One way human pluripotent stem cells can be driven to form intestinal organoids is through first the application of activin A to drive the cells into a mesoendodermal identity, followed by the pharmacological upregulation of Wnt3a and Fgf4 signaling pathways as they have been demonstrated to promote posterior gut fate. Intestinal organoids have also been generated from intestinal stem cells, extracted from adult tissue and cultured in 3D media. These adult stem cell-derived organoids are often referred to as enteroids or colonoids, depending on their segment of origin, and  have been established from both the human and murine intestine. Intestinal organoids consist of a single layer of polarized intestinal epithelial cells surrounding a central lumen. As such, recapitulate the crypt-villus structure of the intestine, by recapitulating its function, physiology and organization, and maintaining all the cell types found normally in the structure including intestinal stem cells. Thus, intestinal organoids are a valuable model to study intestinal nutrient transport, drug absorption, incretin hormone secretion, and infection by various enteropathogens. Intestinal organoids recapitulate the crypt-Villus structure to high degree of fidelity that they have been successfully transplanted to mouse  intestines, and are hence highly regarded as a valuable model for research. One of the fields of research that intestinal organoids have been utilized is that of stem cell niche. Intestinal organoids were used to study the nature of the intestinal stem cell niche, and research done with them demonstrated the positive role IL-22 has in maintaining in intestinal stem cells, along with demonstrating the roles of other cell types like neurons and fibroblasts in maintenance of intestinal stem cells. In the field of infection biology, different intestinal organoid-based model systems have been explored. On one hand, organoids can  be infected in bulk by simply mixing them with the enteropathogen of interest. However, to model infection via a more natural route starting from the intestinal lumen, microinjection of the pathogen is required. In addition, the polarity of intestinal organoids can be inverted, and they can even be dissociated into single cells and cultured as 2D monolayers in order to make both the apical and basolateral sides of the epithelium more easily accessible. Intestinal organoids have also demonstrated therapeutic potential. In order to more accurately recapitulate the intestine in vivo, co-cultures of intestinal organoids and immune cells have been  developed. Furthermore, organ-on-a-chip models combine intestinal organoids with other cell types such as endothelial or immune cells as well as peristaltic flow. Stomach or gastric organoid. Gastric organoids recapitulate at least partly the physiology of the stomach. Gastric organoids have been generated directly from pluripotent stem cells through the temporal manipulation of the FGF, WNT, BMP, retinoic acid and EGF signalling pathways in three-dimensional culture conditions. Gastric organoids have also been generated using LGR5 expressing stomach adult stem cells. Gastric organoids have been used as model for the study of cancer along with human disease and  development. For example one study investigated the underlying genetic alterations behind a patient's metastatic tumor population, and identified that unlike the patient's primary tumor, the metastasis had both alleles of the TGFBR2 gene mutated. To further assess the role of TGFBR2 in the metastasis, the investigators created organoids where TGFBR2 expression is knocked down, through which they were able to demonstrate that reduced TGFBR2 activity leads to invasion and metastasis of cancerous tumors both "in vitro" and "in vivo". Lingual organoid. Lingual organoids are organoids that recapitulate, at least partly, aspects of the tongue physiology. Epithelial lingual organoids  have been generated using BMI1 expressing epithelial stem cells in three-dimensional culture conditions through the manipulation of EGF, WNT, and TGF-β. This organoid culture, however, lacks taste receptors, as these cells do not arise from Bmi1 expressing epithelial stem cells. Lingual taste bud organoids containing taste cells, however, have been created using the LGR5+ or CD44+ stem/progenitor cells of circumvallate (CV) papilla tissue. These taste bud organoids have been successfully created both directly from isolated Lgr5- or LGR6-expressing taste stem/progenitor cells. and indirectly, through the isolation, digestion, and subsequent culturing of CV tissue  containing Lgr5+ or CD44+ stem/progenitor cells. Basic research. Organoids enable to study how cells interact together in an organ, their interaction with their environment, how diseases affect them and the effect of drugs. "In vitro" culture makes this system easy to manipulate and facilitates their monitoring. While organs are difficult to culture because their size limits the penetration of nutrients, the small size of organoids limits this problem. On the other hand, they don't exhibit all organ features and interactions with other organs are not recapitulated "in vitro". While research on stem cells and regulation of  stemness was the first field of application of intestinal organoids, they are now also used to study e.g. uptake of nutrients, drug transport and secretion of incretin hormones. This is of great relevance in the context of malabsorption diseases as well as metabolic diseases such as obesity, insulin resistance, and diabetes. Models of disease. Organoids provide an opportunity to create cellular models of human disease, which can be studied in the laboratory to better understand the causes of disease and identify possible treatments. In one example, the genome editing system called CRISPR was applied to human pluripotent stem cells to  introduce targeted mutations in genes relevant to two different kidney diseases, polycystic kidney disease and focal segmental glomerulosclerosis. These CRISPR-modified pluripotent stem cells were subsequently grown into human kidney organoids, which exhibited disease-specific phenotypes. Kidney organoids from stem cells with polycystic kidney disease mutations formed large, translucent cyst structures from kidney tubules. When cultured in the absence of adherent cues (in suspension), these cysts reached sizes of 1 cm in diameter over several months. Kidney organoids with mutations in a gene linked to focal segmental glomerulosclerosis developed junctional defects between podocytes, the filtering cells affected in that disease . Importantly, these disease phenotypes were absent in control organoids of identical genetic background, but lacking the CRISPR mutations. Comparison of these organoid phenotypes to diseased tissues from mice and humans suggested similarities to defects in early development. As first developed by Takahashi and Yamanaka in 2007, induced pluripotent stem cells (iPSC) can also be reprogrammed from patient skin fibroblasts. These stem cells carry the exact genetic background of the patient including any genetic mutations which might contribute to the development of human disease. Differentiation of these cells into kidney organoids has been performed from patients with Lowe Syndrome due to  ORCL1 mutations. This report compared kidney organoids differentiated from patient iPSC to unrelated control iPSC and demonstrated an inability of patient kidney cells to mobilise transcription factor SIX2 from the golgi complex. Because "SIX2" is a well characterised marker of nephron progenitor cells in the cap mesenchyme, the authors concluded that renal disease frequently seen in Lowe Syndrome (global failure of proximal tubule reabsorption or renal Fanconi syndrome) could be related to alteration in nephron patterning arising from nephron progenitor cells lacking this important "SIX2" gene expression. Other studies have used CRISPR gene editing to correct the patient's mutation  in the patient iPSC cells to create an isogenic control, which can be performed simultaneously with iPSC reprogramming. Comparison of a patient iPSC derived organoid against an isogenic control is the current gold standard in the field as it permits isolation of the mutation of interest as the only variable within the experimental model. In one such report, kidney organoids derived from iPSC of a patient with Mainzer-Saldino Syndrome due to compound heterozygous mutations in "IFT140" were compared to an isogenic control organoid in which an "IFT140" variant giving rise to a non-viable mRNA transcript was corrected by  CRISPR. Patient kidney organoids demonstrated abnormal ciliary morphology consistent with existing animal models which was rescued to wild type morphology in the gene corrected organoids. Comparative transcriptional profiling of epithelial cells purified from patient and control organoids highlighted pathways involved in cell polarity, cell-cell junctions and dynein motor assembly, some of which had been implicated for other genotypes within the phenotypic family of renal ciliopathies. Another report utilising an isogenic control demonstrated abnormal nephrin localisation in the glomeruli of kidney organoids generated from a patient with congenital nephrotic syndrome. Personalised medicine. Intestinal organoids grown from rectal biopsies using culture  protocols established by the Clevers group have been used to model cystic fibrosis, and led to the first application of organoids for personalised treatment. Cystic fibrosis is an inherited disease that is caused by gene mutations of the cystic fibrosis transmembrane conductance regulator gene that encodes an epithelial ion channel necessary for healthy epithelial surface fluids. Studies by the laboratory of Jeffrey Beekman (Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands) described in 2013 that stimulation of colorectal organoids with cAMP-raising agonists such as forskolin or cholera toxin induced rapid swelling of organoids in a fully CFTR  dependent manner. Whereas organoids from non-cystic fibrosis subjects swell in response to forskolin as a consequence of fluid transport into the organoids' lumens, this is severely reduced or absent in organoids derived from people with cystic fibrosis. Swelling could be restored by therapeutics that repair the CFTR protein (CFTR modulators), indicating that individual responses to CFTR modulating therapy could be quantitated in a preclinical laboratory setting. Schwank et al. also demonstrated that the intestinal cystic fibrosis organoid phenotype could be repaired by CRISPR-Cas9 gene editing in 2013. Follow-up studies by Dekkers et al. in 2016 revealed that  quantitative differences in forskolin-induced swelling between intestinal organoids derived from people with cystic fibrosis associate with known diagnostic and prognostic markers such as CFTR gene mutations or in vivo biomarkers of CFTR function. In addition, the authors demonstrated that CFTR modulator responses in intestinal organoids with specific CFTR mutations correlated with published clinical trial data of these treatments. This led to preclinical studies where organoids from patients with extremely rare CFTR mutations for who no treatment was registered were found to respond strongly to a clinically available CFTR modulator. The suggested clinical benefit of treatment for these subjects based  on the preclinical organoid test was subsequently confirmed upon clinical introduction of treatment by members of the clinical CF center under supervision of Kors van der Ent (Department of Paediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands). These studies show for the first time that organoids can be used for the individual tailoring of therapy or personalised medicine. As a model for developmental biology. Organoids offer researchers an exceptional model to study developmental biology. Since the identification of pluripotent stem cells, there have been great advancements in directing pluripotent stem cells fate "in vitro" using 2D  cultures. These advancements in PSC fate direction, coupled with the advancements in 3D culturing techniques allowed for the creation of organoids that recapitulate the properties of various specific subregions of a multitude of organs. The use of these organoids has thus greatly contributed to expanding our understanding of the processes of organogenesis, and the field of developmental biology. In central nervous system development, for example, organoids have contributed to our understanding of the physical forces that underlie retinal cup formation. More recent work has extended cortical organoid growth periods extensively and at nearly a year under specific differentiation conditions, the  organoids persist and have some features of human fetal development stages.