FOXO1 Fusion Research Articles

Whole Lung Irradiation in Rhabdomyosarcoma With Lung Metastases: A Report From the Soft Tissue Sarcoma Committee of the Children's Oncology Group.

Patients with rhabdomyosarcoma with metastatic disease have a poor prognosis despite therapy intensification. The aim of this study was to investigate the efficacy of whole lung irradiation (WLI) in patients with rhabdomyosarcoma and lung metastases. Patients with rhabdomyosarcoma with lung metastases enrolled on four Children's Oncology Group protocols (D9802, D9803, ARST08P1, ARST0431) were retrospectively reviewed. Event-free survival (EFS) and overall survival (OS) were compared between patients who received and did not receive WLI. In 143 patients with rhabdomyosarcoma with lung metastases, 65 patients (45.5%) received WLI and 78 patients (54.5%) did not receive WLI despite protocol requirements. The 5-year EFS was 38.3% (95% CI, 24.8 to 51.8) in patients who received WLI and 25.2% (95% CI, 13.8 to 36.6) in patients who did not receive WLI (P = .0496). The 5-year OS was 45.5% (95% CI, 31.8 to 59.3) in patients who received WLI and 32.4% (95% CI, 20.4 to 44.4) in patients who did not receive WLI (P = .08). In exploratory subgroup analyses, the benefit of WLI on EFS and OS was significant in patients 10 years and older. Other clinical factors associated with EFS on univariable analysis included age, histology FOXO1 fusion status, number of metastatic sites, location of metastatic sites, and Oberlin Score. WLI is associated with improved EFS in patients with rhabdomyosarcoma with lung metastases. These results highlight the potential importance of WLI and need for more stringent protocol compliance for administering WLI.

Improving Individualized Rhabdomyosarcoma Prognosis Predictions Using Somatic Molecular Biomarkers.

Molecular markers, such as FOXO1 fusion genes and TP53 and MYOD1 mutations, increasingly influence risk-stratified treatment selection for pediatric rhabdomyosarcoma (RMS). This study aims to integrate molecular and clinical data to produce individualized prognosis predictions that can further improve treatment selection. Clinical variables and somatic mutation data for 20 genes from 641 RMS patients in the United Kingdom and the United States were used to develop three Cox proportional hazard models for predicting event-free survival (EFS). The 'Baseline Clinical' (BC) model included treatment location, age, fusion status, and risk group. The 'Gene Enhanced 2' (GE2) model added TP53 and MYOD1 mutations to the BC predictors. The 'Gene Enhanced 6' (GE6) model further included NF1, MET, CDKN2A, and MYCN mutations, selected through LASSO regression. Model performance was assessed using likelihood ratio (LR) tests and optimism-adjusted, bootstrapped validation and calibration metrics. The GE6 model demonstrated superior predictive performance, offering 39% more predictive information than the BC model (LR p<0.001) and 15% more than the GE2 model (LR p<0.001). The GE6 model achieved the highest discrimination with a C-index of 0.7087, a Nagalkerke R2 of 0.205, and appropriate calibration. Mutations in TP53, MYOD1, CDKN2A, MET, and MYCN were associated with higher hazards, while NF1 mutation correlated with lower hazard. Individual prognosis predictions varied between models in ways that may suggest different treatments for the same patient. For example, the 5-year EFS for a 10-year-old patient with high-risk, fusion-negative, NF1-positive disease was 50.0% (95% confidence interval: 39-64%) from BC but 76% (64-90%) from GE6. Incorporating molecular markers into RMS prognosis models improves prognosis predictions. Individualized prognosis predictions may suggest alternative treatment regimens compared to traditional risk-classification schemas. Improved clinical variables and external validation are required prior to implementing these models into clinical practice.

Transcriptome profiling of pediatric extracranial solid tumors and lymphomas enables rapid low-cost diagnostic classification

Approximately 80% of pediatric tumors occur in low- and middle-income countries (LMIC), where diagnostic tools essential for treatment decisions are often unavailable or incomplete. Development of cost-effective molecular diagnostics will help bridge the cancer diagnostic gap and ultimately improve pediatric cancer outcomes in LMIC settings. We investigated the feasibility of using nanopore whole transcriptome sequencing on formalin-fixed paraffin embedded (FFPE)-derived RNA and a composite machine learning model for pediatric solid tumor diagnosis. Transcriptome cDNA sequencing was performed on a heterogenous set of 221 FFPE and 32 fresh frozen pediatric solid tumor and lymphoma specimens on Oxford Nanopore Technologies’ sequencing platforms. A composite machine learning model was then used to classify transcriptional profiles into clinically actionable tumor types and subtypes. In total, 95.6% and 89.7% of pediatric solid tumors and lymphoma specimens were correctly classified, respectively. 71.5% of pediatric solid tumors had prediction probabilities > 0.8 and were classified with 100% accuracy. Similarly, for lymphomas, 72.4% of samples that had prediction probabilities > 0.6 were classified with 97.6% accuracy. Additionally, FOXO1 fusion status was predicted accurately for 97.4% of rhabdomyosarcomas and MYCN amplification was predicted with 88% accuracy in neuroblastoma. Whole transcriptome sequencing from FFPE-derived pediatric solid tumor and lymphoma samples has the potential to provide clinical classification of both tissue lineage and core genomic classification. Further expansion, refinement, and validation of this approach is necessary to explore whether this technology could be part of the solution of addressing the diagnostic limitations in LMIC.

Entinostat as a combinatorial therapeutic for rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common childhood soft tissue sarcoma. For the alveolar subtype (ARMS), the presence of the PAX3::FOXO1 fusion gene and/or metastases are strong predictors of poor outcome. Metastatic PAX3::FOXO1+ ARMS often responds to chemotherapies initially, only to subsequently relapse and become resistant with most patients failing to survive beyond 8 years post-diagnosis. No curative intent phase II or phase III clinical trial has been available for patients in the past 10 years (ARST0921). Thus, metastatic ARMS represents a significantly unmet clinical need. Chemotherapy resistance in ARMS has previously been attributed to PAX3::FOXO1-mediated cell cycle checkpoint adaptation, which is mediated by an HDAC3-SMARCA4-miR-27a-PAX3::FOXO1 circuit that can be disrupted by HDAC3 inhibition. In this study, we investigated the therapeutic efficacy of combining the epigenetic regulator entinostat, a Class I Histone Deacetylase (HDAC1-3) inhibitor, with RMS-specific chemotherapies in patient derived xenograft (PDX) models of RMS. We identified single agent, additive or synergistic relationships between relapse-specific chemotherapies and clinically relevant drug exposures of entinostat in three PAX3::FOXO1+ ARMS mouse models. This preclinical data provides further rationale for clinical investigation of entinostat, already known to be well tolerated in a pediatric phase I clinical trial (ADVL1513).

Novel PAX3::MAML3 Fusion Identified in Alveolar Rhabdomyosarcoma, Using DNA Methylation Profiling to Expand the Genetic Spectrum of “Fusion-Positive” Cases

Alveolar rhabdomyosarcoma (ARMS) with FOXO1 gene rearrangements is an aggressive pediatric rhabdomyosarcoma subtype that is prognostically distinct from embryonal rhabdomyosarcoma and fusion-negative ARMS. Here, we report 2 cases of ARMS with PAX3::MAML3 fusions. The tumors arose in an infant and an adolescent as stage IV metastatic disease (by Children’s Oncology Group staging system). Histologically, both cases were small round blue cell tumors arranged in vague nests and solid sheets that were diffusely positive for desmin and myogenin. By methylation profiling and unsupervised clustering analysis, the tumors clustered with ARMS with classic FOXO1 rearrangements and ARMS with variant PAX3::NCOA1/INO80D fusions, but not with biphenotypic sinonasal sarcoma (BSNS) with PAX3::MAML3/NCOA2/FOXO1/YAP1 fusions nor with other small round blue cell tumors, including embryonal rhabdomyosarcoma. The differentially methylated genes between ARMS and BSNS were highly enriched in genes involved in myogenesis, and 21% of these genes overlap with target genes of the PAX3::FOXO1 fusion transcription factor. On follow-up after initiation of vincristine/actinomycin/cyclophosphamide chemotherapy, the tumors showed partial and complete clinical responses, consistent with typical upfront chemotherapy responsiveness of ARMS with the classic FOXO1 rearrangement. We conclude that PAX3::MAML3 is a novel variant fusion of ARMS, which displays a methylation signature distinct from BSNS despite sharing similar PAX3 fusions. These findings highlight the utility of methylation profiling in classifying ARMS with noncanonical fusions.

Children and young adults with newly diagnosed rhabdomyosarcoma metastatic to bone treated on Children's Oncology Group studies.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Despite bone metastases being present in 5% of patients at diagnosis, there are limited studies examining these outcomes. We sought to define the prognostic factors, clinical courses, and outcomes of children treated on Children's Oncology Group (COG) clinical trials with RMS metastatic to bone at diagnosis. We performed a retrospective analysis of patients diagnosed with bone metastatic RMS enrolled on COG RMS clinical trials (D9802, D9803, ARST0431, or ARST08P1) between 1997 and 2013. RMS metastatic to bone was identified in 154 patients at a median age of 14.9years at diagnosis. Fifty-eight percent of patients were male, 90% had metastases at additional sites, 74% had alveolar histology, and extremity was the most common primary site (31%). Eighty-six percent of patients (n=133) received radiation therapy. The 3- and 5-year event-free survival (EFS) was 15.4% and 14.5%, respectively. The 3- and 5-year overall survival (OS) was 30.4% and 18.0%, respectively. We identified alveolar histology, FOXO1 fusion presence, unfavorable primary location, higher Oberlin score, and lack of radiation as poor prognostic characteristics for both EFS and OS in univariate analysis. Lack of radiation was not significant when excluding patients with events prior to 20weeks. This study is the largest analysis of patients with bone metastatic RMS, and defines the poor overall outcomes and negative prognostic factors for these patients. They may be eligible for therapy deintensification for improved quality of life or pursuit of novel treatments/approaches, which are desperately needed.

The Prognostic Significance of Early Tumor Volume Change in Rhabdomyosarcoma

Purpose: To describe early tumor volume change in patients with rhabdomyosarcoma (RMS) and investigate its association with overall survival (OS) and local failure. Methods: This retrospective study included patients diagnosed with Group III/IV RMS with available CT and/or MRI scans at two-time points: 1) pre-therapy and 2) early therapy (acquired during weeks 8 – 12 of chemotherapy). Relative volumetric change (RVC) was calculated as the percentage of: (early therapy – pre-therapy volume)/ (pre-therapy volume). Cox regression was used to identify variables associated with overall survival (OS). The Fine-Gray model was used to estimate local failure. Results: Eligible patients (n=55) had the following characteristics: median age at diagnosis: 9.6 years and median follow-up: 30.4 months. Most tumors were alveolar (61.8%) followed by embryonal (34.6%) and spindle cell/sclerosing (4%). The median RVC was -86.4% with larger decreases observed in alveolar vs. non-alveolar RMS (-89.4 vs. -69.8%, p=0.043). For embryonal and spindle cell/sclerosing RMS, all of which were FOXO1 fusion negative, RVC was independently associated with OS (Hazard Ratio for every 50% reduction in RVC [HRRVC]: 0.5, 95% Confidence Interval [CI]: 0.26 – 0.96, p=0.037) and local failure (HRRVC: 0.57, 95% CI: 0.33 – 0.99, p=0.049). The predominant pattern of failure in embryonal and spindle cell/sclerosing RMS was local and most were Group III. Conclusion: There was a greater reduction in tumor volume in alveolar vs. non-alveolar RMS. Early tumor volume reduction was associated with OS and local failure in embryonal or spindle cell/sclerosing RMS, all of which were confirmed FOXO1 fusion negative and had higher incidence of local compared to distant failures.

Targeted immunotherapy and nanomedicine for rhabdomyosarcoma: The way of the future.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. Histology separates two main subtypes: embryonal RMS (eRMS; 60%-70%) and alveolar RMS (aRMS; 20%-30%). The aggressive aRMS carry one of two characteristic chromosomal translocations that result in the expression of a PAX3::FOXO1 or PAX7::FOXO1 fusion transcription factor; therefore, aRMS are now classified as fusion-positive (FP) RMS. Embryonal RMS have a better prognosis and are clinically indistinguishable from fusion-negative (FN) RMS. Next to histology and molecular characteristics, RMS risk groupings are now available defining low risk tumors with excellent outcomes and advanced stage disease with poor prognosis, with an overall survival of about only 20% despite intensified multimodal treatment. Therefore, development of novel effective targeted strategies to increase survival and to decrease long-term side effects is urgently needed. Recently, immunotherapies and nanomedicine have been emerging for potent and effective tumor treatments with minimal side effects, raising hopes for effective and safe cures for RMS patients. This review aims to describe the most relevant preclinical and clinical studies in immunotherapy and targeted nanomedicine performed so far in RMS and to provide an insight in future developments.

Outcome of children and young adults with localized extremity rhabdomyosarcoma treated on Children's Oncology Group trials.

10006 Background: Extremity rhabdomyosarcoma (RMS) accounts for 15-20% of patients with localized RMS. The long-term survival and associated prognostic factors of extremity RMS patients treated on the contemporary Children’s Oncology Group (COG) trials have not been reported. Methods: Patients with localized extremity RMS enrolled on the D9602, D9803, ARST0331 and ARST0531 COG trials were analyzed. The Kaplan-Meyer method estimated event-free (EFS) and overall survival (OS). The Log-rank test and Cox regression were used to estimate the prognostic significance of age at diagnosis, sex, race, tumor site &amp; size, IRS group, stage, histology, FOXO1 fusion status, anaplasia, lymph node involvement, delayed primary excision (DPE) and radiation on survival. Results: We identified 159 patients with localized extremity RMS; 108 (68%) were &lt; 10 years at diagnosis, 84(53%) had primary tumor &gt; 5 cm, and 35 (22%) and 98 (62%) had IRS group II and III disease. Histology was alveolar in 106 (67%), and 43 (27%) had regional lymph node involvement on imaging or pathology. Seventeen were treated on low-risk (LR) studies D9602 (N = 10) and ARST0331 (N = 7), whereas 142 were treated on intermediate-risk (IR) trials D9803 (N = 85) and ARST0531 (N = 57). Eighty patients (50%) underwent primary surgical excision and 121 (76%) received radiotherapy. DPE was attempted in 60 patients (38%), resulting in an R0 (microscopically negative) margin in 48 (80%). Relapse/progression occurred in 52 patients: metastatic 26 (50%), local 22 (42%), and combined 3(6%). The 5-year EFS and OS of the whole cohort were 62.6% (95% CI: 54%-71.2%) and 78.7%% (95%CI: 71.4%-85.9%). LR patients treated on D9602 and ARST0331 trials had comparable 5-year EFS (70% vs. 71.4%, p-0.90) and OS (90% vs. 85.7%, p-0.54), respectively, while IR patients had significantly better 5-year EFS (68.9% vs. 51%, p-0.023) and OS (86.2% vs. 64.4%, p-0.007) on D9803 trial than ARST0531 trial. The 5-year EFS and OS of IRS group III patients with DPE with R0 margins were comparable to IRS group II patients (70.4% vs. 66.6%) &amp; (86.5% vs. 84.6%), respectively. On univariable analysis, age at diagnosis and sex were associated with EFS, while age at diagnosis, sex, tumor size, IRS group, stage and fusion status were associated with OS (p &lt; 0.05). None of the analyzed factors demonstrated independent statistical association with EFS, whereas female sex was the only factor independently associated with OS [Hazard ratio (HR): 0.4, 95% CI 0.20-0.85)]. Conclusions: IR localized extremity RMS patients treated on ARST0531 had suboptimal outcome. Survival of IRS group III patients with R0 DPE was comparable to IRS group II patients. Females with localized extremity RMS had better OS than males. Clinical trial information: NCT00354835 ; NCT00003958 ; NCT00075582 ; NCT00002995 .

Effect of oncolytic herpes simplex virus on fusion-positive rhabdomyosarcoma to radiotherapy.

10063 Background: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Despite multimodal interventions including surgery, chemotherapy, and radiotherapy, nearly a third of patients with localized disease will experience tumor recurrence. Patients with tumors harboring an oncogenic FOXO1 fusion are at greater risk of relapse and are most in need of novel therapies. Oncolytic viruses are being explored as treatments for pediatric tumors, and data suggest that oncolytic viruses may enhance responses to chemoradiotherapy. M002 is a genetically engineered oncolytic herpes simplex virus (oHSV) that exhibits aneurovirulence in normal cells. M002 selectively replicates in malignant cells, eliminating these cells through cellular burst during the lytic cycle. In the present study, we explored the efficacy of the M002 virus alone and in combination with low-dose ionizing radiotherapy in a human patient-derived xenograft (PDX) model of fusion-positive RMS (FP-RMS). Methods: A human FP-RMS PDX was established and maintained by injection into the quadriceps femoris muscle of athymic nude mice under Institutional Animal Care and Use Committee guidelines (IACUC-09363). Tumors were dissociated and cells were treated with increasing multiplicity of infection (MOI) of either the oHSV, R3659 or its genetically engineered variant, M002. A colorimetric assay evaluated the cytotoxicity of oHSV treatments on the RMS PDX cells after 24, 48, and 72 hours of infection. In separate experiments, cells treated with vehicle (control) or infected with M002 were exposed to irradiation (2 Gy), and viability was determined at 24, 48, 72, and 96 hours. Results: Treatment with M002 or its parent construct, R3659, significantly reduced RMS PDX cell viability in a dose-dependent manner at all time points. M002 showed slightly higher cytotoxicity than R3659 as measured by lethal dose 50% (LD50, 37±1.25 vs 44±0.95 PFU/cell, M002 vs R3659, at 24 hours, p=0.02). When sub-lethal doses of M002 were combined with low-dose irradiation, RMS PDX cell viability was significantly decreased compared to cells treated with either M002 or irradiation alone (26% decrease at 10 PFU/cell). Conclusions: Our preliminary data highlight that M002 exhibits cytotoxicity in a PDX model of FP-RMS. Treatment with M002 further increased the cytotoxicity of ionizing radiation compared to individual treatments, suggesting that oHSV sensitized the cells to radiotherapy. Future studies in vivo may provide more pre-clinical evidence for the radio-sensitizing and therapeutic potential of M002 in FP-RMS.

Abstract 1092: RUNX2 inhibition alters PAX3::FOXO1 driven fusion-positive rhabdomyosarcoma cell state and growth

Abstract Investigation: Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric cancer of skeletal muscle lineage. While the incidence of RMS is ~4.5 patients per million individuals aged &amp;lt;20 years, 5-year survival for high-risk children is &amp;lt;30%, and &amp;lt;8% when metastatic. The PAX3::FOXO1 (P3F) fusion gene, resulting from t(2:13), is the most prominent fusion oncogene that drives FP-RMS. P3F is a fusion transcription factor and supports FP-RMS by keeping it in a persistent myoblastic state. We found P3F functions in part by suppressing MST kinase activity in the Hippo tumor suppressor pathway, a developmental pathway involved in cell fate and organ size. To investigate how this may rewire gene expression to support FP-RMS, we performed ATAC-seq analysis of a myoblast-based model of FP-RMS in which MST was further inhibited and found the RUNX2 gene locus was more accessible. Since RUNX2 is a pioneer transcription factor known to interact with the “WW” domains of Hippo pathway members to support mesenchymal cell fate, we hypothesize that RUNX2 maintains these relationships to support FP-RMS cell state and survival. Methods &amp; Results: Inquiry of in silico databases and previously published literature unveiled that sarcomas including RMS have a high dependency on RUNX2 and that P3F directly binds a RUNX2 enhancer. Interrogation of a proximity labeling proteomics study from our collaborators in the Counter lab found that RUNX2 was part of the protein interactome of 7/7 FP-RMS fusions including P3F. Additionally, Co-IP experiments confirmed that there is a direct protein-protein relationship between RUNX2, P3F, and TAZ. Next, we performed in vitro genetic loss of function (LOF) of RUNX2 using RNAi, which showed that suppression of RUNX2 caused cell death, growth inhibition, increased TAZ expression, and induction of both myogenic and osteogenic markers. We also performed complementary pharmacologic LOF using two available small molecules, AI-14-91 (Bushweller lab) in vitro, and CADD522 (commercially available) in vitro and in vivo. We found that these partially phenocopied the genetic LOF and that CADD522 reduces tumor volume and growth. Conclusions: RUNX2 is a vulnerability in RMS based on in silico, in vitro, and in vivo investigation, and may act to prevent osteogenic and myogenic differentiation via protein-protein relationships in the Hippo pathway. The next step will be assessing mechanistic relationships between the Hippo pathway and RUNX2, as well as the genome wide changes upon RUNX2 LOF by performing ChIP-seq, RNA-seq, and scRNA-seq experiments. Citation Format: Elizabeth A. Mendes, Audrey L. Chambers, Samantha J. Weitzel, Michael Deel, Aanandi Munshi, Christopher M. Counter, Seth Zimmerman, John Bushweller, Corinne M. Linardic. RUNX2 inhibition alters PAX3::FOXO1 driven fusion-positive rhabdomyosarcoma cell state and growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1092.

Abstract 1723: Targeting SMARCA1 in rhabdomyosarcoma: Potential therapeutic implications

Abstract Background: Rhabdomyosarcoma (RMS) is the most common soft tissue in pediatric sarcoma, and studies demonstrate that RMS arises from skeletal muscle precursor cells. RMS, genetically divided into two subtypes: PAX-FOXO1 fusion positive RMS (FP-RMS), which is driven by chromosomal translocation involving PAX3 or PAX7 genes with FOXO1 and PAX-FOXO1 fusion negative RMS (FN-RMS), which is marked by mutations in RAS isoforms and some other genes. Chromatin was one of the earliest identified targets for cancer therapy. Several chromatin remodeling proteins are associated with cancer progression processes such as proliferation, differentiation, apoptosis, and tumorigenesis. Components of chromatin remodeling complexes have been classified as both oncogenes and tumor suppressors. The ISWI family protein, SMARCA1 has been implicated in tumorigenesis for several cancer types. ISWI complexes regulate cell differentiation and proliferation in other cell systems, but their impact on myogenesis is not well understood. In this study, we will characterize the function of SMARCA1 in RMS cells and skeletal muscle. We hypothesize that SMARCA1 acts to modulate chromatin accessibility and drive RMS tumorigenic growth. Methods: We employed RNA-seq, ATAC-seq, and CUT&amp;RUN to study the impact of SMARCA1 in RMS cells. Furthermore, phenotypic experiments were performed to determine the influence of SMARCA1 on differentiation and proliferation. Results: SMARCA1 is expressed at a high level in RMS tissues but not in muscle tissues. Our findings show that SMARCA1 is modestly upregulated during differentiation in normal myogenesis. Upon treatment with trametinib, FP-RMS cell lines with SMARCA1 knockout exhibited a dramatic decrease in cell confluency and viability. Intriguingly, the control FP-RMS cell lines demonstrated increased SMARCA1 protein levels in response to trametinib, which could suggest a resistance mechanism to the treatment. Trametinib also affected SMARCA1 mRNA expression in FN-RMS cells. Additionally, it was discovered that the elimination of SMARCA1 not only resulted in a reduction in cell migration but also led to a failure of these cells to develop spheres, unlike the control cells, where the migration gap healed in the usual manner and the spheres were observed. These findings may align with our hypothesis that SMARCA1 regulates chromatin accessibility, potentially impacting adhesion properties and signaling pathways. Analysis of gene clusters in RMS transcriptomic data indicated that SMARCA1 co-expresses with a RAS effector, RALA. SMARCA1 is also clustered with HDAC2. In addition, SMARCA1 interacted with HDAC2 in RMS cells, as determined by co-immunoprecipitation experiments. Conclusions: Our findings suggest that SMARCA1 may influence RMS tumor growth. This study might contribute to a deeper understanding of SMARCA1's role in RMS and support its credentialing as a novel therapeutic avenue. Citation Format: Ashwaq Aljabri, Katie Hebron, Yuliya Kriga, Juan Manuel Caravaca, Aiysha Althobaiti, Stacey Stauffer, Angela Kim, Lauren Stoak, Morgan Porter, Jyoti Shetty, Bao Tran, Matthew Geisler, Judith Davie, Marielle Yohe. Targeting SMARCA1 in rhabdomyosarcoma: Potential therapeutic implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1723.

Abstract 1093: Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma

Abstract Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. It is commonly divided into subtypes based on histopathological appearance. The oncogenic fusion proteins PAX3::FOXO1 or PAX7::FOXO1 are present in the alveolar subtype of RMS (ARMS). These chimeric proteins are formed by reciprocal chromosomal translocations and consist of an N-terminal portion of the PAX3 or PAX7 transcription factor fused to a C-terminal portion of the FOXO1 transcription factor. These fusion proteins have been shown to drive malignant transformation in ARMS, and patients with fusion-positive ARMS have a worse prognosis than patients with fusion-negative ARMS and embryonal RMS. We recently reported that piperacetazine, a phenothiazine derivative and first-generation antipsychotic, is capable of binding to and inhibiting the transcriptional activity of PAX3::FOXO1, reducing the expression of PAX3::FOXO1 target genes, and inhibiting the ability of fusion-positive RMS cells to grow in soft agar. We hypothesize that other phenothiazine derivatives may have stronger binding affinity for PAX3::FOXO1 and greater ability to reduce tumor growth in vivo. We employed a structure-activity relationship campaign to develop new phenothiazine derivatives that may be more potent inhibitors of PAX3::FOXO1 than piperacetazine. We synthesized and tested 10 new compounds, in addition to 9 existing FDA-approved phenothiazine derivatives, for their ability to bind to PAX3::FOXO1 and inhibit its transcriptional activity and target gene expression as well as inhibiting the growth of fusion-positive RMS cells in 3D culture. Seven derivatives inhibited PAX3::FOXO1 reporter activity better than piperacetazine, nine of them performed worse, and three of them showed comparable activity to piperacetazine. We demonstrated that piperacetazine does not alter PAX3::FOXO1 levels, subcellular localization, binding to a PAX3::FOXO1 target DNA sequence, or phosphorylation at Ser256 in the FOXO1 portion of the fusion protein. We therefore hypothesize that piperacetazine may be disrupting interactions between PAX3::FOXO1 and its partner proteins. We are employing a proximity-based biotinylation method to identify proteins that are competed away from PAX3::FOXO1 by piperacetazine. Our data suggest that it is possible to target PAX3::FOXO1 protein using small molecules that can directly bind to it and inhibit its activity in fusion-positive RMS cells. Citation Format: Taryn Shaw, Kay Nakazawa, Purushottam Tiwari, Eryn Nelson, Jeffrey Formen, Christian Wolf, Jeffrey Toretsky, Aykut Üren. Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1093.

Reappraisal of prognostic factors used in the European Pediatric Soft Tissue Sarcoma Study Group RMS 2005 study for localized rhabdomyosarcoma to optimize risk stratification and generate a prognostic nomogram.

The objective of this study was to investigate the role of clinical factors together with FOXO1 fusion status in patients with nonmetastatic rhabdomyosarcoma (RMS) to develop a predictive model for event-free survival and provide a rationale for risk stratification in future trials. The authors used data from patients enrolled in the European Pediatric Soft Tissue Sarcoma Study Group (EpSSG) RMS 2005 study (EpSSG RMS 2005; EudraCT number 2005-000217-35). The following baseline variables were considered for the multivariable model: age at diagnosis, sex, histology, primary tumor site, Intergroup Rhabdomyosarcoma Studies group, tumor size, nodal status, and FOXO1 fusion status. Main effects and significant second-order interactions of candidate predictors were included in a multiple Cox proportional hazards regression model. A nomogram was generated for predicting 5-year event-free survival (EFS) probabilities. The EFS and overall survival rates at 5years were 70.9% (95% confidence interval, 68.6%-73.1%) and 81.0% (95% confidence interval, 78.9%-82.8%), respectively. The multivariable model retained five prognostic factors, including ageat diagnosis interacting with tumor size, tumor primary site, Intergroup Rhabdomyosarcoma Studies clinical group, and FOXO1 fusion status. Based on each patient's total score in the nomogram, patients were stratified into four groups. The 5-year EFS rates were 94.1%, 78.4%, 65.2%, and 52.1% in the low-risk, intermediate-risk, high-risk, and very-high-risk groups, respectively, and the corresponding 5-year overall survival rates were 97.2%, 91.5%, 74.3%, and 60.8%, respectively. The results presented here provide the rationale to modify the EpSSG stratification, with the most significant change represented by the replacement of histology with fusion status. This classification was adopted in the new international trial launched by the EpSSG.

Abstract LB_A23: The role of SMARCA1 in Rhabdomyosarcoma and skeletal muscle differentiation

Abstract Background: Rhabdomyosarcoma (RMS) is the most common soft tissue of pediatric sarcoma, and studies demonstrate that RMS arises from skeletal muscle precursor cells. RMS, genetically and histologically, is divided into two subtypes: PAX-FOXO1 fusion positive (alveolar) RMS (aRMS), which is driven by chromosomal translocation involving PAX3 or PAX7 genes with FOXO1 and PAX-FOXO1 fusion negative (embryonal) RMS (eRMS), which is marked by mutations in RAS isoforms and some genes such as TP53, PIK3CA, CTNNB1 and FGFR4. Chromatin was one of the earliest identified targets for cancer therapy. Several chromatin remodeling proteins are associated with cancer progression processes such as proliferation, differentiation, apoptosis, and tumorigenesis. Components of chromatin remodeling complexes, such as the imitation switch (ISWI) complex, have been classified as both oncogenes and tumor suppressors. The ISWI family protein, SMARCA1 (also known as SNF2L), has been implicated in tumorigenesis for several cancer types. ISWI complexes regulate cell differentiation and proliferation in other cell systems, but their impact in myogenesis is not well understood. In this study, we will characterize the function of SMARCA1 in RMS cells and skeletal muscle. We hypothesize that SMARCA1 acts to modulate chromatin accessibility, and drive RMS tumorigenic growth. Methods: We will use RNA-seq, ATAC-seq, and CUT&amp;RUN to study the impact of SMARCA1 deletion in RMS cells. Furthermore, phenotypic experiments will be performed to determine the influence of SMARCA1 on differentiation. Results: SMARCA1 is expressed at a high level in RMS tissues but not in muscle tissues. Furthermore, our findings show that SMARCA1 is modestly upregulated during the differentiation in normal myogenesis. Curiously, eRMS cell lines show no change in the protein level of SMARCA1 when treated with a MEK inhibitor, trametinib. Analysis of gene clusters in RMS transcriptomic data of indicated that SMARCA1 co-expresses with a RAS effector, RALA. SMARCA1 also clustered with HDAC2. In addition, SMARCA1 interacted with HDAC2 in RMS cells as determined by co-immunoprecipitation experiments. Conclusions: This study will deepen our understanding of how SMARCA1 impacts RMS differentiation and proliferation and may credential SMARCA1 as a novel therapeutic target in rhabdomyosarcoma. Citation Format: Ashwaq K Aljabri, Katie E Hebron, Yuliya Kriga, Juan Manuel Caravaca, Aiysha Althobaiti, Alex Emmons, Stacey Stauffer, Angela Kim, Lauren Stoak, Morgan Porter, Jyoti Shetty, Peter Fitzgerald, Bao Tran, Matthew Geisler, Judith K Davie, Marielle E Yohe. The role of SMARCA1 in Rhabdomyosarcoma and skeletal muscle differentiation [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A23.

Piperacetazine Directly Binds to the PAX3::FOXO1 Fusion Protein and Inhibits Its Transcriptional Activity.

RMS is a malignant soft-tissue tumor mainly affecting the pediatric population. A subgroup of RMS with worse prognosis harbors a unique chromosomal translocation creating an oncogenic fusion protein, PAX3::FOXO1. We identified piperacetazine as a direct inhibitor of PAX3::FOXO1, which may provide a scaffold for designing RMS-specific targeted therapy.

Prognosis of children and young adults with newly diagnosed rhabdomyosarcoma metastatic to bone marrow treated on Children's Oncology Group studies.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Metastatic disease occurs in 16% of all RMS cases and has a poor prognosis. There are limited studies examining the outcomes specific to patients with RMS metastatic to bone marrow despite an incidence of 6% at diagnosis. Our study aims to document the outcomes, prognostic factors, and clinical courses of children presenting with RMS metastatic to bone marrow treated on Children's Oncology Group (COG) cooperative trials. We performed a retrospective analysis of the patients diagnosed with RMS metastatic to bone marrow between 1997 and 2013 enrolled on one of four COG RMS clinical trials of D9802, D9803, ARST0431, and ARST08P1. We identified 179 cases with RMS metastatic to bone marrow. Patients had a median age of 14.8years, 58% were male, predominantly alveolar histology (76%), extremity was the most common primary site (32%), and 87% had metastatic disease to additional sites; 83% (n=149) received radiation as a treatment modality. The 3- and 5-year event-free survival was 9.4% and 8.2%, respectively. The 3- and 5-year overall survival was 26.1% and 12.6%, respectively. Age ≥10years, alveolar histology, FOXO1 fusion presence, unfavorable primary location, higher Oberlin score, and lack of radiation were identified as poor prognostic/predictive characteristics. This study represents the largest analysis of RMS metastatic to bone marrow, defining the poor prognostic outcome for these patients. These patients may be eligible for therapy deintensification or early pursuit of novel treatments/approaches that are desperately needed.

Patterns of Failure in Pediatric and Young Adult Rhabdomyosarcoma

To characterize patterns of failure in pediatric and young adult patients with rhabdomyosarcoma (RMS) from a single institution with over 20 years of experience. Patients diagnosed with RMS from 2000 to 2022 were identified retrospectively. Time to failure was calculated from diagnosis. Local only failure was defined as first failure at the primary site without distant failure. Distant failure was defined as first failure outside of the primary site with or without local failure. Cumulative incidence (CI) of failure was calculated using death as a competing risk. Fine-Gray regression was used to evaluate impact of prognostic factors. Ninety-five patients were eligible. Median age was 7.28 years (range 0 - 35 years), 41% of patients were >10 years old. Median follow up was 33.3 months. Approximately half (n = 47, 49.5%) of the tumors demonstrated alveolar histology. FOXO1 fusion status was available in 76 (80%) patients, of which 7 out of 37 alveolar tumors (18.9%) were FOXO1 fusion negative. The majority of tumors presented with unfavorable primary site (n = 72, 75.8%) and advanced stage (Stage III and IV, n = 72, 75.8%). The 5-yr CI of local only failure and distant failure for the entire cohort was 19.0% (95% CI 11.3, 28.3) and 34.6% (24.0, 45.5%), respectively. The predominant pattern of failure by Group was: Groups 1&2: Local only (5yr CI 14.8%), Group 3: Distant (5yr CI: 25.9%), Group 4: Distant (5yr CI: 67.6%). CI of distant failure by primary site was higher in perianal/gluteal (n = 2/5, 5yr CI 60.0%) and extremity (n = 8/19, 5yr CI 45.9%) sites. Of the 28 distant failures, 10 (36%) also had a local failure component. CI of local only failure by primary site was higher in parameningeal head and neck (n = 6/25, 5yr CI 30%) and bladder/prostate (n = 2/12, 5yr CI 23%) sites. The following were associated with an increased CI of distant failures: increasing age (HR 1.08, p<0.01), alveolar vs. embryonal histology (HR 3.01, p = 0.0095), FOXO1 fusion positive vs. negative (HR 2.8, p = 0.02) and Group IV vs. Groups I/II (HR 7.7, p = 0.0007). FOXO1 fusion and alveolar histology were associated with older age and Group IV, both of which were independently associated with increased distant failure on multivariate analysis. Failures were predominantly distant in older patients and patients with Group IV RMS, both of which were associated with FOXO1 fusion and alveolar histology, highlighting the need to improve therapies in this population. Local only failures were highest in parameningeal head and neck and bladder/prostate primaries, highlighting the need to improve local control strategies at these sites.

Treatment of Recurrent Orbital Rhabdomyosarcoma with Exenteration and HDR Brachytherapy in a Custom Mold

Rhabdomyosarcoma (RMS) is the most frequent cancer affecting the orbit in children. The orbit is classified as a favorable site for RMS as treatment with chemotherapy and radiation is effective. Local failure for patients with RMS of the orbit has ranged from 2-16% on IRS and COG protocols. In the event of local recurrence, survival is poor, and management is difficult. We report four patients with local recurrence of orbital RMS managed with orbital exenteration followed by high dose rate (HDR) brachytherapy. Four patients were treated from 2016-2022. HDR brachytherapy with Ir-192 was delivered in a custom mold of the orbit made after the orbital exenteration procedure. Brachytherapy was given in 6-7 twice daily (BID) fractions starting 1 week after the orbital exenteration. At the time of brachytherapy, patient ages were 3, 1, 7, and 7 years. Three patients had embryonal histology and underwent initial systemic therapy with ARST0331 regimen A. The fourth patient had alveolar, FOXO1 fusion positive RMS and was initially treated as per COG D9803 regimen A. All patients had received proton radiotherapy as part of initial treatment. Three received 50.40 Gy and one received 45 Gy. Patients developed biopsy-proven, recurrent disease an average of 56 weeks (range 38-77) after initial diagnosis. All patients received salvage chemotherapy before undergoing orbital exenteration at an average of 12 weeks after recurrence (range 5-16). Three patients received 30 Gy in 6 BID fractions, and one patient received 28 Gy in 7 fractions with HDR brachytherapy using an Ir-192 source. All four patients are alive without evidence of disease at an average of 27 months (range 6-70) from recurrence and 39 months (range 21-78) from initial diagnosis. All patients have acceptable orbit healing. Two patients have asymptomatic evidence of frontal lobe edema (and in one case possible necrosis) extending 1-2 cm above the orbit. This appears to be beyond the range of the brachytherapy dosimetry, but the combination of proton beam and brachytherapy are implicated. No other toxicities have occurred. Orbital RMS has a favorable prognosis, but local failure after initial combined modality therapy can be fatal. Options for successful local salvage are limited. Orbital exenteration with HDR brachytherapy in a custom mold is an effective and safe procedure for local control in these difficult cases.

A systematic review of the prevalence of pathogenic or likely pathogenic germline variants in individuals with FOXO1 fusion-positive rhabdomyosarcoma.

Several cancer predisposition syndromes (CPS) are reported to predispose to rhabdomyosarcoma, most frequently in children with embryonal rhabdomyosarcoma. There are lingering questions over the role of CPS in individuals with alveolar rhabdomyosarcoma (ARMS), which are frequently driven by FOXO1 fusion oncoproteins. We conducted a systematic review to identify patients with FOXO1 fusion-positive ARMS (FP-ARMS) who underwent germline DNA sequencing. We estimated the prevalence of pathogenic/likely pathogenic (P/LP) variants in cancer predisposing genes (CPGs) and of CPSs. We included 19 publications reporting on 191 patients with FP-ARMS. P/LP variants in CPGs were identified in 26/191 (13.6%) patients, nine (4.9%) of which were associated with a CPS diagnosis. Evidence for causal associations between CPSs and FP-ARMS could not be assessed with available data from this review. Only one patient was affected with a CPS known to predispose to rhabdomyosarcoma, Li-Fraumeni syndrome. Typical CPS associations with rhabdomyosarcoma are rare, but not nonexistent, in patients with FP-ARMS. FOXO1 fusion status, alone, is insufficient for clinicians to rely on to distinguish between patients with/without CPS.