ORGANOIDS
We and others have defined methods to grow a variety of normal tissues in a dish as 3–dimensional “organoids” or mini–organs. These organoids are clusters of cells that recapitulate the architecture and multilineage differentiation of organs in the body.
One of many methods that we use involves an “air–liquid interface” where organoids are grown in a gel and exposed directly to air instead of being submerged underneath nutrient medium (Nature Medicine 2009; Nature Medicine 2014; Cell 2018).
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This allows numerous tissues such as intestine, stomach and pancreas to be grown as organoids with both epithelium and supporting mesenchymal stroma, recapitulating the normal structure of organs.
Growing Normal Tissues as Organoids
Intestine
Stomach
Pancreas
Growing normal tissues in a dish certainly has applications such as regenerative medicine and organ transplantation. However, we have also used organoids to model cancer. Indeed, we have converted normal colon, stomach and pancreas organoids into their respective malignancies in the dish by adding combinations of 2–4 cancerous mutations. These cancerous mutations induce the organoids to convert into a tumor–like appearance, to grow and invade aggressively, and even to form tumors when transplanted into mice, all characteristics of human cancers.
Transforming normal organoids into cancer
Being able to convert normal tissues/organoids into cancer in a dish represents a powerful system for discovering and proving the function of new cancer-causing mutations. Tumor cells often have hundreds if not thousands of mutations and other/epigenetic alterations, but only a minority are critical “drivers” that cause cancer, versus the vast majority of irrelevant “passenger” mutations. With collaborators we utilize computational and systems biology principles to interrogate large tumor DNA sequencing datasets to identify candidate cancer driver genes. We then exploit the power of organoids for cancer gene discovery, systematically inserting mutations found in cancer cells (from projects such as TCGA) to test if such mutations successfully convert the organoids to a cancerous phenotype (Cancer Discovery 2021, Nature 2023). Accelerating the functional validation of cancer–causing mutation will allow therapies and diagnostics to be developed against these genes.
We also create organoid cultures from tumor biopsies. This allows a patient's tumor cells to be grown in an incubator. In this way we are attempting to understand why tumors are sensitive or resistant to certain treatments. Some examples of tumor organoid cultures are shown below:
Traditional organoids typically only contain epithelial cells. We are interested in making organoids with higher cellular complexity that preserve epithelium together with the vast diversity of immune cells that are present in normal tissues as well as diseases such as cancer. For instance, we can create air-liquid interface organoids from human tumor biopsies that contain cancer cells and their endogenous infiltrating immune cells as a cohesive unit that does not require reconstitution.
An exciting application of our cancer organoids that contain tumor-infiltrating immune populations is the ability to model immunotherapies such as immune-checkpoint inhibitors. Indeed, our tumor-immune organoids actively respond to anti-PD-1 treatment (Cell 2018). This provides a human experimental system to understand how immunotherapy works, to test novel immunotherapies, and to potentially even predict to which immunotherapies a patient might best respond (Nature Reviews Cancer 2024).
Organoids that contain immune cells can also be used to model autoimmune diseases. For example, we have created organoids from intestinal biopsies of celiac disease patients to create "celiac disease in a dish." We can add gluten to these organoids, which activates resident T and B cells to destroy the intestinal epithelium, mimicking human celiac disease. This has potential to understand how celiac disease occurs, to test new celiac disease therapies, and to potentially aid in celiac disease diagnosis (Nature 2024). Further, other autoimmune diseases could be modeled in this manner.
We also use organoids to model different types of viral and bacterial infections. In recent studies we have infected our recently developed human lung alveolar and bronchiolar cultures with SARS-CoV-2, using a method to turn organoids “inside-out”, in collaboration with Catherine Blish and Manuel Amieva.
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