En route to better treatment of rhabdomyosarcoma: signaling pathways, tumor organoid models and single-cell RNA-sequencing

Abstract

Rhabdomyosarcomas (RMS) are the most common tumors of the soft tissues (sarcomas) in children and adolescents. RMS grow aggressively and show a propensity to spread in the body (metastasize). Treatment is harsh and consists of chemotherapy and local therapy which can be radiotherapy and/or surgical removal. Depending on the localization in the body, children with localized disease can be cured in 50-70% of cases, often at the cost of severe long-term effects. Children with metastases, however, face poor survival with 40% survival at best. Thus, new therapies are needed for patients with RMS. The development of such new therapies has been hampered by several factors of which a number are addressed in this thesis. First, we explore the relationship between aberrant so-called Hedgehog signaling pathway activity and programmed cell death (PCD) in RMS cell lines. We propose mechanisms by which RMS cells evade PCD induction and thereby acquire a growth advantage. Furthermore, we study how to overcome this mechanism by using combination treatments. Cell lines are in vitro models derived from primary tumor material which have been altered to allow for indefinite growth. However, due to these alterations, cell lines reflect patient tumors to a lesser degree, thereby limiting their applicability. Thus, we sought to generate novel preclinical models of RMS which more closely resemble patient tumors. To this end, we established so-called tumor organoid models of RMS. Extensive characterization experiments indicate that RMS tumor organoid models indeed reflect patient tumors to a high degree. We could establish such models from most RMS subtypes, thereby expanding the arsenal of preclinical RMS models. A key characteristic of tumors is their cellular heterogeneity, i.e., the variation between tumor cells within one or between tumors. Furthermore, it is important to understand what other cell types are present in a tumor as their presence and activation state (such as it is the case for immune cells) can be crucial for the survival of tumor cells. To address these two aspects, we performed single-cell RNA-sequencing of primary RMS tumors. With this novel technique, the gene expression of individual cells within a tumor sample can be measured. Using this information, we show that the relative contribution of tumor cells within a tumor exhibiting certain so-called transcriptional meta-programs is predictive for the survival of a patient. Furthermore, we propose a direct cell-cell interaction between tumor and immune cells by which the tumor cells inactivate the immune cells, thereby facilitating their own survival. In conclusion, this thesis provides novel insights into the biology of RMS and proposes avenues for development of new treatment options.