Molecular Heterogeneity of Ewing Sarcoma as Detected by Ion Torrent Sequencing

Abstract

Ewing sarcoma (ES) is the second most common malignant bone and soft tissue tumor in children and adolescents. Despite advances in comprehensive treatment, patients with ES metastases still suffer poor outcomes, thus, emphasizing the need for detailed genetic profiles of ES patients to identify suitable molecular biomarkers for improved prognosis and development of effective and targeted therapies. In this study, the next generation sequencing Ion AmpliSeq™ Cancer Hotspot Panel v2 was used to identify cancer-related gene mutations in the tissue samples from 20 ES patients. This platform targeted 207 amplicons of 2800 loci in 50 cancer-related genes. Among the 20 tissue specimens, 62 nonsynonymous hotspot mutations were identified in 26 cancer-related genes, revealing the molecular heterogeneity of ES. Among these, five novel mutations in cancer-related genes (KDR, STK11, MLH1, KRAS, and PTPN11) were detected in ES, and these mutations were confirmed with traditional Sanger sequencing. ES patients with KDR, STK11, and MLH1 mutations had higher Ki-67 proliferation indices than the ES patients lacking such mutations. Notably, more than half of the ES patients harbored one or two possible ‘druggable’ mutations that have been previously linked to a clinical cancer treatment option. Our results provided the foundation to not only elucidate possible mechanisms involved in ES pathogenesis but also indicated the utility of Ion Torrent sequencing as a sensitive and cost-effective tool to screen key oncogenes and tumor suppressors in order to develop personalized therapy for ES patients.

Biology of Bone Sarcomas and New Therapeutic Developments

“…At time of diagnosis, 20–25% of patients show clinically detectable metastases [ 33 – 35 ]. Although Ewing sarcoma is the most homogeneous entity among bone sarcomas, composed of undifferentiated round cancer cells characterised by CD99-, FLI1-, HNK1- and CAV1-positive immunostaining associated with limited stromal components [ 36 ], recent work demonstrated in contrast their heterogeneity [ 37 – 40 ]. Previous studies highlighted only a few recurrent somatic mutations in Ewing sarcomas ( TP53, STAG2, CDKN2 ) [ 38 , 41 , 42 ].…”

“…Previous studies highlighted only a few recurrent somatic mutations in Ewing sarcomas ( TP53, STAG2, CDKN2 ) [ 38 , 41 , 42 ]. However, more recent studies by Zhang et al used next-generation sequencing (Ion AmpliSeq™ Cancer Hotspot Panel v2) to identify a series of five new mutations ( KDR, STK11, MLH1, KRAS and PTPN11 ) related to a higher proliferation index and revealing a higher tumour heterogeneity than initially suspected [ 37 ]. This heterogeneity is not restricted to the genetic patterns but can be extended to epigenetic profiles [ 39 ].…”

Role of Next-Generation Sequencing as a Diagnostic Tool for the Evaluation of Bone and Soft-Tissue Tumors

“…In addition to its diagnostic role, NGS may confirm the presence of mutations and translocations, which are potential targets of molecular-based personalized treatment options in ES or desmoplastic small round cell tumor ( Table 2 ) [41][42][43][44][45][46][47][48][49][50] . Histological and IHC features of SBRCT are shown in Figure 1 .…”

PTPN11 hypomethylation is associated with gastric cancer progression

“…PTPN11 mutations have been extensively investigated in the past years. Germline mutations in PTPN11 cause Noonan syndrome (9)(10)(11) and its clinically related Leopard syndrome (12), whereas somatic mutations of PTPN11 contribute to leukemogenesis (13)(14)(15)(16)(17), as well as in the development of specific solid tumors, including neuroblastoma (18,19), metachondromatosis (20,21), brain tumors (22)(23)(24), neurofibromatosis (25), optic nerve pilomyxoid astrocytoma (26), breast carcinoma (27,28), colorectal cancer (29,30) and Ewing sarcoma (31). However, oncogenic mutations of PTPN11 are rare in the majority of solid tumors including GC (32,33).…”