Autologous immune-organoids: A new approach to study cancer development and identify efficient treatments in children and adolescents with cancer

Pediatric cancers, including brain cancers, neuroblastomas, sarcomas and kidney tumors, present significant challenges due to their complexity and the limited efficacy of current treatments. Despite advances in personalized medicine and targeted therapies, survival rates have stagnated for many of these diseases. Immunotherapies, although promising, have shown limited success due to the difficulty in recreating the unique and complex pediatric tumor microenvironment (TME) in preclinical models. Furthermore, the cellular and molecular interactions within the TME are poorly understood, especially when it comes to tissue-resident immune cells such as macrophages, which play crucial roles in cancer progression and immune regulation.

To address these gaps, we are developing advanced models that better reflect the complexity of pediatric cancer, particularly by integrating immune cells into tumor microenvironment studies. Three-dimensional (3D) organoid/tumoroids cultures represent an exciting new avenue for in vitro modeling. However, a major challenge is recapitulating the immune components of the TME, such as macrophages and other immune cells. To solve this, we have developed a protocol to generate patient-derived macrophages, or iMacs, from induced pluripotent stem cells (iPSCs). These iMacs resemble tissue-resident macrophages and can differentiate into microglia-like cells in the case of brain tumors, or into macrophages within other tissues like the lungs.

When co-cultured with iPSC-derived tumor cells, these iMacs contribute to tumor progression by influencing tumor growth, immune suppression, and resistance to treatment. We aim to use these advanced models to investigate the role of immune cells in pediatric cancer progression, focusing on their interactions with cancer cells in a more representative TME. Specifically, we will employ multiomic analyses, including single-cell RNA sequencing, epigenomic profiling, and high-dimensional flow cytometry, to identify the molecular pathways and immune markers that regulate tumor growth and metastasis.

Our ultimate goal is to translate these findings into new therapeutic strategies that target immune cells within the TME. Using CRISPR/Cas9-based genome editing, we will identify and validate critical genes involved in immune suppression and tumor progression. We will also develop personalized immune-organoid models, which will allow us to test patient-specific therapies and determine the most effective immunotherapies for individual patients. These "patient avatar" models, which combine tumor cells with patient-derived immune cells, will be used to test various immunotherapies and identify the most promising treatments for each child.

This research is being conducted as part of the “Immune Organoids” institutional protocol at Gustave Roussy (PIs: Dr Florent Ginhoux, Dr Claudia Pasqualini), where we are collaborating with pediatric oncologists, immunologists, bioinformaticians, and imaging experts to better understand the complex interactions between tumor and immune cells. Through this innovative approach, we aim to identify new therapeutic targets and develop effective immunotherapies that could improve outcomes for pediatric cancer patients. By combining advanced technologies and a collaborative approach, we hope to make significant strides in the fight against pediatric cancers, ultimately providing more personalized and effective treatments for children with cancer.