Organoids: application overview
With only a few millimeters across, clusters of cultured cells that self-organize into three-dimensional structures can look like tiny droplets. But these tissues, called organoids, allow scientists to study biological processes related to health and diseases and find new potential treatment strategies.
Organoids can mimic anatomical and functional features of a wide variety of human tissues, and for some types of tissues they can be more effective than other models, for example, cell lines or animal models. Three-dimensional organization allows you to cover most of the complex characteristics of organs and cellular relationships that can be of great importance for the living tissues of the patient. And organoids created from patients' cells make it possible to create individualized models of the disease.
Researchers from the Broad Institute of the Massachusetts Institute of Technology and Harvard University have developed a technique for growing various types of organoids. Over the past few years, these methods have improved so much that they have allowed researchers to obtain organoids in a reliable and reproducible way. This has made them an effective research tool that offers many advantages.
Organoids are much more convenient for laboratory tests than whole organs or animal models. They can be modified using genetic engineering or treated with chemicals to investigate the work of certain genes, proteins or signaling pathways. They are also well suited for high-resolution imaging and single-cell genomics, revealing the potential for scientific discoveries.
Below are three examples of research works in which various types of organoids were produced and used to search for new targets for therapy and to identify the mechanisms of the disease.
Brain organoids for studying the formation of the nervous system
In order to understand the development and functions of the human brain, especially the cerebral cortex, which controls the complex process of behavior, studies on rodents and cell lines cannot be used.
Paola Arlotta and her group from Harvard University and the Massachusetts Institute of Technology decided to use human brain organoids for this purpose. These organoids lack blood vessels and recognizable structures or layers of the brain, but at the ultrastructural level, the tissue looks almost indistinguishable from the tissue of the real brain with most of the main cell types, connections between neurons and even active circuits.
Moreover, if brain organoids are grown from cells with gene variants that have been associated with complex mental disorders or disorders of neural development, such as schizophrenia or autism, they can reproduce the effects of these genetic changes and be a more informative model than others.
Arlotta and her group have devoted many years to improving the protocols for creating organoids and developing methods for growing tissues for longer periods (from several months to several years) in order to better represent the later stages of brain maturation. In a 2019 paper published in the journal Nature, researchers proved that they can generate long-growing organoids that contain a full range of cortical cell types, even if they are produced from different stem cells and cultured under different conditions. The main success of the work is that organoids could reproduce cortical cells, creating the same set of cells in each organoid each time.
Brain organoid after 180 days of cultivation. It contains glial cells (purple) and astrocytes (green and red).
Reliable methods of creating brain organoids allowed Arlotta's group to use them to study the biological mechanisms of disorders of the nervous system, including autism. Autism is most often associated with a complex genetic background in which different gene variants are likely to contribute to the development of the disorder. But in rare cases, the development of autism-related traits may be associated with one or more specific mutations. Arlotta's group creates organoids carrying such mutations associated with autism, and then compares them with organoids grown from the same cell lines, but without mutations.
This type of work is important for understanding how genetic changes affect the functioning of brain circuits over time. Researchers can also compare brain organoids containing the same mutation with a different genetic background, which will allow us to assess its impact on the manifestation of the disorder. Someday, perhaps, brain organoids derived from cells of people with autism will be able to clarify the breadth and diversity of underlying genetic features.
Thus, organoids are not intended to replace mice and other model systems. But on some issues, they help to study what was previously inaccessible: the ability to observe the development of the disease in human tissues.
Kidney organoids: a platform for creating medicines
Kidneys are inferior in complexity of structure except for the human brain. Anna Greki's group from Brigham Women's Hospital and Harvard Medical School demonstrated that kidney organoids can serve as reproducible high-quality representations of human kidneys. In a paper published last year in the journal Nature Communications, they analyzed more than 450,000 individual cells from 49 organoids obtained using widely used methods from four people of different ages and genders. The group showed that organoids are closely comparable both to each other and to human kidneys.
The kidney organoid derived from human induced pluripotent stem cells contains many cell types, including podocytes (red), proximal tubule cells (green) and distal tubule cells (blue).
In addition, the group of Greeks demonstrates the potential of organoids as models of diseases for the discovery of new drugs. During the so-called "mini–in vitro efficacy study", scientists created organoids from cells donated by three patients with tubulointerstitial nephritis, a genetic kidney disease associated with mutation of the mucin 1 protein gene, and compared them with others obtained from healthy siblings of patients. As described in a 2019 article published in the journal Cell, researchers found an improperly assembled mutant protein mucin 1 stuck in the tubules of patients' organoids, as well as in their patients' organs.
With this knowledge, the group tested potential drug compounds and found one that eliminates the mutant protein in organoids, and subsequent studies in the kidneys of mice that synthesize the same abnormal protein. They identified the target for treatment – the TMED9 molecule – and showed in organoids with nephrite that it is activated wherever the mutant protein accumulates.
Thus, the researchers were able to use organoids as a system that allowed them to get an idea of the possible mechanisms and even the treatment of genetic kidney disease. They continue to work in this direction and analyze the role of the patient's genetic background. Organoids provide an opportunity to explore the "context" – the genetic background of individual patients to show how it affects the variability of human disease manifestations.
The TMED9 study has shown the importance of organoids for studying mechanisms and clinically relevant issues, but the real proof of this will be the approval of the first drug developed on the basis of organoids.
Tumor organoids are the future in cancer research
Cancer cell lines have long been a workhorse in cancer research for decades, but tumor organoids that are grown from patients' tumor cells are easier and faster to create. Jesse Boehm and his team from the National Cancer Institute (NCI) Human Cancer Models Initiative plan to create 1,000 cultures of tumor organoids obtained from patients and add them to the NCI tumor model library.
At the moment, Boehm's group has created hundreds of tumor organoids, many of which are rare forms of cancer. Each organoid model is annotated with its main molecular characteristics, including the DNA sequences of the germ line and primary tumor, and, importantly, the patient's clinical data: demographic data, stage of the disease, drug resistance, reactions to previous treatment, and much more.
These tumor organoids were created from a biopsy of the brain of a patient with breast cancer metastases.
With more and more cancer models to analyze, researchers are using the organoid library to search for genetic vulnerabilities in more cancers. The ultimate goal is to find targeted treatments aimed at these weaknesses in more patients. According to Boehm, only 25% of cancer patients today receive treatment selected according to the genetic composition of their tumors. It is no secret that the genetic background of a patient can have a strong influence on the course of the disease or the best treatment.
Bem is the scientific director of the Cancer Dependency Map initiative, DepMap, which systematizes the genetic mutations necessary for tumor growth. The literal translation of "Cancer dependency map" is clearly not suitable here, except to expand it into a "Map of cancer-related genes".
Since the survival of tumor cells largely depends on these mutations, they are also targets that anti-cancer drugs can use to destroy atypical cells.
Tumor organoids will expand DepMap's capabilities by offering models of a wider range of tumors. For example, the relative ease of production means that researchers can obtain organoids from the same patient at different points in time or at different stages of tumor development. This will allow scientists to learn more about how tumors change over time and, for example, about the development of drug resistance.
In order to integrate tumor organoids into DepMap, Bem and several employees of the Broad Institute are developing high-performance approaches for screening tumor organoids for genetic vulnerability. They use CRISPR technology to systematically knock out every gene in an organoid, and then test the organoid for potential drug targets. To date, they have managed to optimize about 12 screenings, and now they are solving the problem of scaling the process.
Boehm predicts that tumor organoids will outpace cancer cell lines in mainstream cancer research within a few years, not because they are better, but because they are easier to obtain. Tumor organoids will play an important role in precision medicine, when it will be possible to sequence the tumor genome to a cancer patient and, based on this molecular profile, prescribe a treatment that is likely to be effective.
Article by S.Velasco et al. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex published in the journal Nature; A.Subramanian et al. Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation – in the journal Nature Communications; M.Dvela-Levitt et al. Small molecule targets TMED9 and promotes lysosomal degradation to reverse proteinopathy – in the journal Cell.
Aminat Adzhieva, portal "Eternal Youth" http://vechnayamolodost.ru based on the materials of the Broad Institute: Organoids emerge as powerful tools for disease modeling and drug discovery.