Precision medicine approaches for the management of Ewing sarcoma: current perspectives

Advancements in bone malignancy research through next-generation sequencing focussed on osteosarcoma, chondrosarcoma, and Ewing sarcoma

Next-generation sequencing (NGS) technologies have revolutionized bone cancer research, enabling detailed insights into the genetic, transcriptional, and epigenetic layers of these malignancies. This overview discusses the pivotal role of NGS in enhancing the diagnosis, prognosis, and treatment of primary bone cancers such as osteosarcoma, chondrosarcoma, and Ewing sarcoma. By facilitating the identification of novel genetic mutations, gene fusions, and epigenetic alterations, NGS supports the development of personalized medicine approaches and targeted therapies, significantly impacting clinical outcomes. The utilization of various NGS platforms, including Illumina, SOLiD, and Ion Torrent, has provided comprehensive genomic profiles that inform targeted treatment strategies and enable early detection through liquid biopsies and circulating tumor DNA (ctDNA) analysis. Despite the profound clinical benefits, the integration of NGS into routine practice faces challenges such as technical limitations, complex data interpretation, and substantial infrastructure requirements. Future directions involve technological improvements, combinatorial omics approaches, and extensive validation through clinical trials to confirm the efficacy of NGS-guided interventions. These advancements promise to further enhance the precision and effectiveness of bone cancer management, offering hope for more tailored and effective therapeutic outcomes.

Ewing Sarcoma Developed at the Site of Previous Mast Cell Proliferation

KIT gene mutations in Ewing sarcomas are rare; however, they are much more frequent in other neoplasms, namely mastocytosis. We describe a case of an adult male with a one-year duration of recurrent episodes of pain, swelling, and redness on the proximal phalanx of the third finger of his right hand. A core biopsy suggested a possible mastocytosis. After four years of recurrent episodes and worsening symptoms, an incisional biopsy revealed an Ewing sarcoma with a KIT gene mutation (M541L, on exon 10). KIT gene mutations with gain-of-function were identified in 2.6% of Ewing sarcomas. In this case, the detection of a KIT mutation in an Ewing sarcoma developed at the site of previous mast cell proliferation raises the hypothesis of a possible sarcomatous evolution of the original lesion. To the best of our knowledge, similar cases are not described in the current literature. This is also the first report describing the KIT M541L mutation (exon 10) in Ewing sarcoma.

The oncogenic fusion landscape in pediatric CNS neoplasms

Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.

Screening of Potential Key Biomarkers for Ewing Sarcoma: Evidence from Gene Array Analysis

Background

Ewing’s sarcoma (ES) is a common bone cancer in children and adolescents. There are ethnic differences in the incidence and treatment effects. People have made great efforts to clarify the cause; however, the molecular mechanism of ES is still poorly understood.

Methods

We download the microarray datasets GSE68776, GSE45544 and GSE17674 from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) of the three datasets were screened and enrichment analysis was performed. STRING and Cytoscape were used to carry out module analysis, building a protein–protein interaction (PPI) network. Finally, a series of analyses such as survival analysis and immune infiltration analysis were performed on the selected genes.

Results

A total of 629 differentially expressed genes were screened, including 206 up-regulated genes and 423 down-regulated genes. The pathways and rich-functions of DEGs include protein activation cascade, carbohydrate binding, cell-cell adhesion junctions, mitotic cell cycle, p53 pathway, and cancer pathways. Then, a total of 10 hub genes were screened out. Biological process analysis showed that these genes were mainly enriched in mitotic nuclear division, protein kinase activity, cell division, cell cycle, and protein phosphorylation.

Conclusion

Survival analysis and multiple gene comparison analysis showed that CDCA8, MAD2L1 and FANCI may be involved in the occurrence and prognosis of ES. The purpose of our study is to clarify the DEG and key genes, which will help us know more about the molecular mechanisms of ES, provide potential pathway or targets for the diagnosis and treatment.

Role of immunotherapy in Ewing sarcoma

Ewing sarcoma (ES) is thought to arise from mesenchymal stem cells and is the second most common bone sarcoma in pediatric patients and young adults. Given the dismal overall outcomes and very intensive therapies used, there is an urgent need to explore and develop alternative treatment modalities including immunotherapies. In this article, we provide an overview of ES biology, features of ES tumor microenvironment (TME) and review various tumor-associated antigens that can be targeted with immune-based approaches including cancer vaccines, monoclonal antibodies, T cell receptor-transduced T cells, and chimeric antigen receptor T cells. We highlight key reasons for the limited efficacy of various immunotherapeutic approaches for the treatment of ES to date. These factors include absence of human leukocyte antigen class I molecules from the tumor tissue, lack of an ideal surface antigen, and immunosuppressive TME due to the presence of myeloid-derived suppressor cells, F2 fibrocytes, and M2-like macrophages. Lastly, we offer insights into strategies for novel therapeutics development in ES. These strategies include the development of gene-modified T cell receptor T cells against cancer–testis antigen such as XAGE-1, surface target discovery through detailed profiling of ES surface proteome, and combinatorial approaches. In summary, we provide state-of-the-art science in ES tumor immunology and immunotherapy, with rationale and recommendations for future therapeutics development.

Next-Generation Sequencing Identifies Potential Actionable Targets in Paediatric Sarcomas

Background: Bone and soft-tissue sarcomas represent 13% of all paediatric malignancies. International contributions to introduce next-generation sequencing (NGS) approaches into clinical application are currently developing. We present the results from the Precision Medicine program for children with sarcomas at a reference centre. Results: Samples of 70 paediatric sarcomas were processed for histopathological analysis, reverse transcriptase polymerase chain reaction (RT-PCR) and next-generation sequencing (NGS) with a consensus gene panel. Pathogenic alterations were reported and, if existing, targeted recommendations were translated to the clinic. Seventy paediatric patients with sarcomas from 10 centres were studied. Median age was 11.5 years (range 1–18). Twenty-two (31%) had at least one pathogenic alteration by NGS. Thirty pathogenic mutations in 18 different genes were detected amongst the 22 patients. The most frequent alterations were found in TP53, followed by FGFR4 and CTNNB1. Combining all biological studies, 18 actionable variants were detected and six patients received targeted treatment observing a disease control rate of 78%. Extrapolating the results to the whole cohort, 23% of the patients would obtain clinical benefit from this approach. Conclusions: Paediatric sarcomas have a different genomic landscape when compared to adult cohorts. Incorporating NGS targets into paediatric sarcomas’ therapy is feasible and allows personalized treatments with clinical benefit in the relapse setting.

Epiphyseal Ewing Sarcoma in a skeletally mature patient: A case report and review of the literature

While Ewing sarcoma of bone is the second most common primary osseous malignancy in childhood where it typically involves the diaphysis or metadiaphyses of long bones of skeletally immature patients, primary epiphyseal involvement of the long bone in skeletally mature patients is rare with no cases reported in the literature to our knowledge, rendering this case the first of its kind.

We present the first case of primary Ewing Sarcoma of the epiphyses of the long bones in a skeletally mature 20-year-old male patient. The patient initially presented with left knee stiffness and pain that was empirically treated with non-steroidal anti-inflammatory medications. His pain progressed despite treatment. An x-ray of the left knee was obtained 5 months later demonstrating an irregular lucent lesion in the medial femoral condyle. A subsequent MRI revealed an enhancing lesion in the medial femoral condyle, and when biopsied it was consistent with Ewing sarcoma (positive for EWSR1gene rearrangement by fluorescence in situ hybridization). The lesion was resected surgically, and the patient underwent neoadjuvant chemotherapy with a good clinical outcome.

PDX-Derived Ewing's Sarcoma Cells Retain High Viability and Disease Phenotype in Alginate Encapsulated Spheroid Cultures

Simple Summary

Ewing’s Sarcoma (ES) is the second most frequent bone tumour in children and young adults, with very aggressive behaviour and significant disease recurrence. To better study the disease and find new therapies, experimental models are needed. Recently, patient-derived xenografts (PDX), obtained by implanting patient tumour samples in immunodeficient mice, have been developed. However, when ES cells are extracted from the patient’s tumour or from PDX and placed on plasticware surfaces, they lose their original 3D configuration, cell identity and function. To overcome these issues, we implemented cultures of PDX-derived ES cells, by making them aggregate to form ES cell spheroids and then encapsulating these 3D spheroids into a hydrogel, alginate, to stabilize the culture. We show that this methodology maintained ES cell viability and intrinsic characteristics of the original ES tumour cells for at least one month and that it is suitable for study the effect of anticancer drugs.

Abstract

Ewing’s Sarcoma (ES) is the second most frequent malignant bone tumour in children and young adults and currently only untargeted chemotherapeutic approaches and surgery are available as treatment, although clinical trials are on-going for recently developed ES-targeted therapies. To study ES pathobiology and develop novel drugs, established cell lines and patient-derived xenografts (PDX) are the most employed experimental models. Nevertheless, the establishment of ES cell lines is difficult and the extensive use of PDX raises economic/ethical concerns. There is a growing consensus regarding the use of 3D cell culture to recapitulate physiological and pathophysiological features of human tissues, including drug sensitivity. Herein, we implemented a 3D cell culture methodology based on encapsulation of PDX-derived ES cell spheroids in alginate and maintenance in agitation-based culture systems. Under these conditions, ES cells displayed high proliferative and metabolic activity, while retaining the typical EWSR1-FLI1 chromosomal translocation. Importantly, 3D cultures presented reduced mouse PDX cell contamination compared to 2D cultures. Finally, we show that these 3D cultures can be employed in drug sensitivity assays, with results similar to those reported for the PDX of origin. In conclusion, this novel 3D cell culture method involving ES-PDX-derived cells is a suitable model to study ES pathobiology and can assist in the development of novel drugs against this disease, complementing PDX studies.