Advances in Oncology

Organoid models continue to evolve, growing in popularity among researchers who seek methods to accelerate the pace of drug screening to identify more precise treatment options for patients. Scientists at Columbia University Irving Medical Center and Weill Cornell Medicine are pursuing organoid research that encompasses methods to improve their congruence to human cells, testing in an increasing number of tumor types, and developing a comprehensive atlas of all organoids now available that will help researchers nationwide to expedite their applications to real-time clinical care.

Organoids created from the bladder cancers of patients mimic the characteristics of each patient’s tumor and may be used in the future to identify the best treatment for each patient. (Courtesy of Dr. Michael Shen)

Tumoroids: Patient Surrogates for Testing Treatments

Dr. Olivier Elemento

Olivier Elemento, PhD, is Director of the Englander Institute for Precision Medicine, Associate Director of the Institute for Computational Medicine, and Director of the Laboratory of Cancer Systems Biology at Weill Cornell Medicine. Dr. Elemento and his team are currently exploring how far they can push the concept of organoids as a clinical tool. “The motivation behind our work is being able to test a variety of different medicines on tumors coming from the patient – tumor organoids, or tumoroids as we call them – before actually treating the patient,” says Dr. Elemento. “Our philosophy is to think about this model as a way to test therapies in a patient surrogate.”

A number of hurdles confront the researchers in creating the patient-derived organoids, notes Dr. Elemento, including a race against the clock. “These are cells coming from the patient and you have to grow enough of them so that you can test multiple drugs, allowing for a number of fails. The task is to develop a list of drugs to test that are compatible with the number of cells that you have. If you wait longer to grow more cells, the patient’s disease is likely to have progressed and become harder to treat. Part of the challenge behind the organoid becoming a clinical tool is how do we grow the cells to do testing quickly so that we can achieve a timeline that is compatible with the patient’s disease course.”

According to Dr. Elemento, the time from creating the organoid to treating the patient is typically one to three months. “As an example, a patient with newly diagnosed advanced lung cancer is going to have surgery to remove the tumor. The tumor may come back, but it won’t come back for three, four, or even six months. That gives you a window of time in which you can grow the organoid, do the drug screening, and then when and if the tumor comes back you have the information available to be able to treat the patient in a timely way.”

“Part of the challenge behind the organoid becoming a clinical tool is how do we grow the cells to do testing quickly so that we can achieve a timeline that is compatible with the patient’s disease course.”

— Dr. Olivier Elemento

While organoid models are certainly assuming a prominent role in cancer research, there are still obstacles that investigators face when using this model. “In in vitro cancer cultures, including 3D organoids, there are very few if any immune cells,” explains Dr. Elemento. “Whatever immune cells there are, they don’t survive very long. Trying to keep the immune cells alive long enough to add them back into the tumor culture is a major area of our research now. This would enable us to create more effective organoids that would expand the types of therapies we can test.”

In addition to exploring other ways to optimize immune competent organoids, Dr. Elemento and his team are working with scientists at Weill Cornell to create vascularized organoids. “Every tumor has blood vessels providing nutrients to that tumor,” he says. “Organoids do not have this vasculature, so we are trying to produce functional blood vessels as a way to bring nutrients or immune cells into a tumor. We want these cultures to eventually be near perfect copies of a patient’s tumor in such a way that we know for sure that any therapy that works in those tumor cells is also likely to work in the patient.”

Applying Evolutionary Biology to Bladder Cancer

Dr. Michael M. Shen

With success in developing organoid culture approaches in prostate cancer, Michael M. Shen, PhD, Co-Leader, Tumor Biology and Microenvironment at the Herbert Irving Comprehensive Cancer Center, and his research team have for the past five years generated patient-derived bladder organoids, applying methods and concepts from stem cell and developmental biology to a translational problem. “Initially, we were generating organoids from transurethral resections, typically for non-muscle invasive bladder cancer,” says Dr. Shen. “This was important because previously there haven’t been many cell lines derived from non-muscle invasive bladder cancer. It turns out that these grow quite well as organoids, so we have provided, for the first time, a good model system for studying this type of cancer.”

As Dr. Shen explains, the organoid culture approach has considerable advantages over conventional, two-dimensional cell lines in that not only do they recapitulate the mutational profile of the primary tumors, but they also retain the heterogeneity of the original tumors. “Because they are quite heterogeneous, I think that these organoids provide a good model system for studying tumor evolution and the types of events that might take place during a treatment response, for example,” notes Dr. Shen. “While organoids are often used to see if they can predict drug response, I believe that organoids are also valuable as models for studying important questions in cancer biology.”

Dr. Shen points to the considerable evidence in the literature that organoids have predictive value for drug response based on retrospective trials. “What has not yet been done is to test the ability of organoids to predict responses to therapy prospectively, something that we’re interested in doing in the case of bladder cancer,” says Dr. Shen. “What I am particularly excited about is the ability to pursue studies of questions that have been largely inaccessible because we haven’t had a good way to model tumor heterogeneity.”

When considering how tumors become resistant to a drug, heterogeneity is important for two possible reasons, notes Dr. Shen. “One is that a tumor acquires a new mutation or epigenetic modification that allows the tumor cells to become resistant to the drug. The other possibility is that the tumor is heterogeneous and a rare subclone emerges that was already resistant and takes over the tumor. This is evolutionary biology that we’re studying. The competition between clones is occurring all the time due to varying selective pressures that happen within the tumor microenvironment. Of course, drug treatment imposes a very severe selection pressure and so typically only a small handful of cells is going to be resistant. The question is what is the nature of those cells? If we understood this problem, we would have more insights into how potentially to develop more effective treatment regimens.”

“What I am particularly excited about is the ability to pursue studies of questions that have been largely inaccessible because we haven’t had a good way to model tumor heterogeneity.”

— Dr. Michael M. Shen

Another area of focus for Dr. Shen is cell plasticity in bladder cancer as there is now some evidence that plasticity can be involved in the transition from non-muscle-invasive to muscle-invasive bladder cancer, a transition by which tumor cells that formerly had a liminal phenotype convert to having more of a basal phenotype. “This transition can be considered to be a type of cellular plasticity,” says Dr. Shen. “Tumor plasticity is a topic of great interest because it is often involved with drug resistance, but in this case, it’s associated with tumor progression. We now have the ability potentially to model this phenomenon in culture and examine the molecular mechanisms that are responsible for this plasticity.”

Dr. Shen and his colleagues are also very interested in developing approaches to model these types of interactions to reconstitute stromal and immune components in the context of organoid culture. “In conventional organoid culture, typically, stromal or immune components are not present,” explains Dr. Shen. “So, for example, you are not able to study the effect of the vasculature or various T-cell subsets. In the area of bladder cancer, this is particularly relevant in that immunotherapy is effective for a proportion of bladder cancer patients. We would like to be able to have model systems to understand the basis of patient response to immunotherapy.”

Creating a Single Source of Organoid Intelligence

Dr. Anil K. Rustgi

Anil K. Rustgi, MD, Director of the Herbert Irving Comprehensive Cancer Center at NewYork-Presbyterian/Columbia University Irving Medical Center, acknowledges that research in organoids is labor intensive and scaling up is difficult. “We want to be cautious as we try to take this work from a research setting into a clinical arena,” he says. “It has to be CLIA certified, and many of these studies are done in the setting of research labs, which don’t have the infrastructure for CLIA certification.”

A major physician-scientist in the field of gastrointestinal cancers, Dr. Rustgi pursues research on molecular genetics and factors in the tumor microenvironment that lead to the development, progression, and metastasis of esophageal, pancreas, and colon cancer. Dr. Rustgi and his research team have provided innovative scientific contributions to the development of 3D organoids for these cancers with the goal of expanding the applications of precision oncology.

“By manipulating the cells in 3D organoids, we were able to recreate the original tissue microenvironment,” says Dr. Rustgi. “As the name implies, with organoids, you are trying to mimic the original epithelial tissue architecture of the organ. We obtain these tissues in surgery or through biopsy from procedures such as endoscopy, colonoscopy, or interventional bronchoscopy. We then dissociate the tissue into single cells, which divide, and after about a week, the surface or the epithelium looks like the original tissue. We have found a nearly one-to-one ratio of response when we treat the organoids with the same drugs administered to the patient, and amazingly, if there’s no response in the patient, we’re not seeing a response in the organoids, so-called personalized medicine. This is still under research and not ready for prime time in the clinical setting, when our hope is that we can generate a report for the physician that might help in decision making about treatment.”

“We have found a nearly one-to-one ratio of response when we treat the organoids with the same drugs administered to the patient, and amazingly, if there's no response in the patient, we're not seeing a response in the organoids.”

— Dr. Anil K. Rustgi

Dr. Rustgi and his team have been the architects of esophageal cancer organoids for both squamous cell carcinoma and adenocarcinoma and have developed protocols and applications that have been highly published. He notes that the risk factors are different for each, but they have developed techniques either from surgery or from biopsies to develop organoids for both. In the June 2020 issue of Current Protocols in Stem Biology, Dr. Rustgi, his Columbia colleagues, and researchers from multiple sites worldwide, describe protocols to initiate, grow, passage, and characterize patient-derived organoids of esophageal cancers. 

With the number of patient-derived 3D organoids rapidly increasing for numerous cancers, Dr. Rustgi is pursuing the development of a centralized facility that generates organoids from different tissue types. “While the protocols of each lab might vary slightly, the goal is to centralize the information, making the process more efficient for all the labs,” he says. “This model could achieve scale in terms of protocols and staffing. In addition, a comprehensive atlas of organoids by tumor type, including data on therapeutic response, would be much more suitable to providing information back to the clinic.”

Dr. Rustgi cites The Cancer Genome Atlas (TCGA), a project of the National Cancer Institute that catalogues genetic mutations responsible for cancer. “That information is in the public domain. We use it all the time,” notes Dr. Rustgi. “My personal hope is that we can accomplish a similar atlas, sharing information not only within Columbia, Weill Cornell, and NewYork-Presbyterian, but also across the country.”