Genomic characterization and development of therapies for pediatric sarcoma

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

The goal of this project is to enable precision oncology for patients with deadly subtypes of rhabdomyosarcoma (RMS), which is the most common soft tissue sarcoma of childhood. The prognosis for those with RMS remains poor in particular, for children with intermediate- or high-risk RMS where patients today are still treated with the intense chemotherapy/radiation/surgery regimen devised in the 1970s. My work has helped define high-risk molecular subtypes of RMS and translate these findings as prognostic tools into the current risk stratification used on national trials performed by the Children's Oncology Group. This project tackles two of the worst molecular subtypes of RMS where the current therapies dramatically fail. In Aim 1, we are pursuing mechanistic work and preclinical testing of a drug combination for the treatment of MYOD1L122R mutant RMS (MM-RMS). We and others have described RMS tumors harboring a point mutation in the MYOD1 gene as an ultra-high-risk population with very limited responses to current therapy. We also described the co-existence of activating PIK3CA mutations in at least 50% of MM-RMS. This provides a potential targeted therapy for these patients. Recent experimental data from the lab has demonstrated that activation of PIK3CA upregulates the expression of mutant MYOD1, providing a mechanistic insight into why these mutations are selected for in MM-RMS. Excitingly, we have collaborated with the National Center for Advancing Translational Sciences (NCATS) to perform the first high-throughput drug screening of MM-RMS tumor lines that has led us to hypothesize that a combination strategy of a PIK3CA inhibitor with a topoisomerase 1 inhibitor would provide significant responses in xenograft models and patients. Our data suggest that PI3K inhibition disrupts the functions of MYOD1L122R in RMS and we hypothesize that PI3K signaling results in chromatin accessibility changes that are permissive to MYOD1L122R. In addition, we are exploring how the phosphorylation of MYOD1 effects the ability of the transcription factor to bind DNA. Intersection of these proteomic efforts with the epigenetic studies utilizes the laboratories expertise in bioinformatic analysis. In addition, we are exploring combination strategies that might be useful in increasing the potency of single agent PIK3 inhibitors. Drug screening efforts have nominated topoisomerase 1 as a potential synergizing partner and preclinical studies are underway to understand the mechanism of this observation. Finally, we are envisioning a clinical trial for patients with MM-RMS using a small molecule inhibitor of PI3K. We are planning for this trial to be open in 2026. Detailed correlative studies are planned to be conducted using the collected patient samples. In Aim 2, we are pursuing a second high risk molecular subtype of RMS driven by the fusion oncogene PAX3-FOXO1 (P3F). These tumors have long been known to be at high risk for relapse after therapy, yet standard therapy for these patients has not changed over several decades. In collaborative work with the U54 funded FusOnc Cancer Moonshot team targeting P3F, I contributed to the discovery that the cyclin kinase, CDK8, interacts with P3F, and the transcriptional machinery utilized by P3F, making it a unique vulnerability in these tumors. Unlike other cyclin dependent kinases, CDK8 and its regulatory subunit, cyclin C, are components of the Mediator transcriptional regulatory complex that is involved in both transcriptional activation and repression by phosphorylation of the carboxy-terminal domain of the largest subunit of RNA polymerase. Using the high-throughput drug screening combination platform of NCATS, my group has defined a highly synergistic drug combination between CDK8 inhibitors and antifolates. We have detailed the mechanism associated with the observed synergy and demonstrated that CDK8 is involved in the upregulation of genes required for the cell to tolerate the metabolic stress induced by antifolates. We have tested this combination in preclinical models in anticipation of clinical translation. Finally in Aim 3, we build on our expertise in cfDNA profiling of RMS patients on clinical trials and the observation that the chromatin structure enforced by P3F can be detected and dynamically measured in the peripheral blood of patients on treatment. We have optimized this assay and method in preclinical model systems. The method uses methylation based whole genome sequencing and we are studying if this tool could be used to enable real time understanding of the gene programs that a P3F tumor cell uses to survive treatment. Ultimately, we plan to employ the tool for analysis of samples collected on current Children's Oncology Group (COG) clinical trials.