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Closing in on cancer heterogeneity with organoids – Nature Methods

Unquestionably, says Tak Mak, a cancer researcher at Princess Margaret Cancer Centre in Toronto, organoids are superior to work in cancer cell lines. But an important current shortfall with organoids is the absence of an immune system, he says. Some experimenters try to reintroduce lymphocytes into organoids, which in his view does not adequately address the ways immune cells function in the physiological or pathophysiological setting. This is true of both lymphocytes and myeloid cells, such as macrophages and others. These cells’ half-lives, says Mak, especially those of macrophages, are short. To reflect the physiological modus, fresh monocyte infiltration and differentiation are needed. Nerves and blood vessels, which are important in healthy organs, “are missing in organoids,” he says. But sensory, parasympathetic and sympathetic nerves play important roles. Blood vessels bring key factors and nutrients into organs.

Organoids certainly complement cancer research done with mouse models, says Mak. Mice can be readily generated. One can access tissues and immune cells in these animals and match the peptide–major histocompatibility complexes and antigen-specific T cells in the mice. But mice and humans differ in many pathophysiology aspects. In mice, telomeres — the DNA sequences at the outermost chromosome tips — are three times as long as in humans. Mice and people have different myeloid cells. For example, PirA and PirB, the mouse immunoglobulin-like signaling receptors on myeloid cells, have five to six human equivalents, including human immunoglobulin-like receptors LILRA and LILRB.

Currently, labs making organoids lack an efficient way to synthetically generate functioning immune cells from stem cells, says Takebe. Coculture with immune cells retrieved from patient’s blood is a way to capture an individual’s immune profile. But even this, he says, is not obvious to do, and it’s, he says, “kind of a dream experiment.” The fetal liver environment is a niche for hematopoietic cell and blood cell development processes. One could add such a niche component to a liver organoid to try to orchestrate development and differentiate the lineages. He and his team are developing fetal liver ecosystems in organoid culture to generate systems with model immune systems.

Takebe thinks highly of approaches such as those in the Lütolf lab to build engineered perfusable systems. Another approach he and his group apply is to implant the organoids into animals such as immunocompromised mice to leverage the animals’ circulatory and endocrine systems. This extends the lifespan of organoids and lets the scientists characterize a gradually maturing organoid in vivo. The scientists are adding complexities to the liver organoids, such as by adding cell types at the right time in organ development and at the right spatial coordinates. The plan is to translate learned principles to coax immature progenitor cells into a complex tissue.

Bao uses patient-derived organoids to study therapies and mechanisms of drug resistance. She and her team explore how well p38 mitogen-activated protein kinase (MAPK) inhibitors combine with immune checkpoint inhibitors. The idea came from a clinical trial in which patients on this regime for whom conventional therapies hadn’t worked had cancers go into remission. Both patient-derived organoids and mouse models will help to understand differing responses.

In a perfect world, she says, one would have an organoid “avatar” of every patient’s tumor so that one could treat that system and then monitor treatment in patients. She also wants to coculture tumor organoids with immune cells from the tumor microenvironment.

In her work on pediatric cancer, Rios focuses on immune mechanisms and the harsh reality that, in children, cancer is the number one killer from disease. Treatment options for pediatric cancers lag behind those of adult cancers, especially for solid and brain tumors, she says. Unlike adult cancer, childhood cancer stems from embryonic tissues, “but we’re still using treatments designed for adults,” she says. Pediatric cancers are, compared to breast cancer, relatively rare and receive less funding. She and her team hope to uncover what makes pediatric cancers different by using BEHAV3D9, which she and her team and colleagues at other universities developed. This imaging-based platform is for assessing engineered T cells used in immunotherapy, which harnesses the ability of T cells to locate and physically destroy cancer cells. BEHAV3D reveals behavioral differences between T cells engineered with different types of T cell receptors. Transcriptomic profiling and analysis of imaging-based readouts indicate which are “super-engager killer T cells.”

Engineered T cells have shown some encouraging results in patients with diffuse midline glioma. Alas, the cancer relapses after a few months. The scientists are using BEHAV3D on patient-derived tumor organoids to compare how well several engineered T cells targeting this brain tumor perform. They want to identify the engineered T cell product with the most super-engagers. Once they find the cancer organoid, “they stick to it and don’t let go until the organoid is killed,” she says. These super-engagers could indicate an immunotherapy approach to these currently incurable pediatric brain tumors. The platform is a way to thoroughly characterize an engineered T cell product’s cell composition, function, strengths and pitfalls.

BEHAV3D, she says, can capture how complexity and composition of individual tumors shape how T cells respond. It can show when treatment stops working — when T cells seemingly get lazy and slow down or even ignore tumor organoids rather than attack them. BEHAV3D has a module for comparing different responses to T cells between tumors from different patients, and it can be used to assess variations within the same tumor. With organoids one can simulate these differences and variations.

Thus the way organoids show biological differences mimics the complexity of individual tumors. Variations can influence T cell therapy effectiveness in terms of timing; perhaps not all organoids are killed simultaneously. Some organoids may be more susceptible to engineered T cells than others. “We are currently studying how this relates to the observed heterogeneity of response observed in patients for such therapy,” she says. Future plans, she says, are about broadening the platform’s capabilities to include other immunotherapies, such as bispecific antibodies.

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