Establishment of Rapid and Accurate Screening System for Molecular Target Therapy of Osteosarcoma

Abstract

Introduction Comprehensive analyses using clinical sequences subcategorized osteosarcoma (OS) into several groups according to the activated signaling pathways. Mutually exclusive co-occurrences of gene amplification ( PDGFRA/KIT/KDR, VEGFA/CCND3, and MDM2/CDK4) have been identified in approximately 40% of OS, representing candidate subsets for clinical evaluation of additional therapeutic options. Thus, it would be desirable to evaluate the specific gene amplification before starting therapy in patients with OS. Materials and Methods This is a retrospective study. We examined 13 cases of clinical OS samples using NanoString-based copy number variation (CNV) analysis. Decalcification and chemotherapeutic effects on this analysis were also assessed. Results First, the accuracy of this system was validated by showing that amplification/deletion data obtained from this system using various types of cancer cell lines almost perfectly matched to that from the Cancer Cell Line Encyclopedia (CCLE). We identified potentially actionable alterations in CDK4/MDM2 amplification in 10% of samples and potential additional therapeutic targets ( PDGFRA/KIT/KDR and VEGFA/CCND3) in 20% of samples, which is consistent with the reported frequencies. Furthermore, this assay could identify these potential therapeutic targets regardless of the sample status (frozen vs formalin-fixed paraffin-embedded [FFPE] tissues). Conclusion We established a NanoString-based rapid and cost-effective method with a short turnaround time (TAT) to examine gene amplification status in OS. This CNV analysis using FFPE samples is recommended where the histological evaluation of viable tumor cells is possible, especially for tumors after chemotherapy with higher chemotherapeutic effects.

NTRK2 expression in gastrointestinal stromal tumors with a special emphasis on the clinicopathological and prognostic impacts

“…NanoString-based CNV analysis was performed using nCounter (NanoString Technologies, Seattle, WA, USA) as previously described 16 . The probe list used in this assay is described in Supplementary Table 3 .…”

Tyrosine kinase alterations in colorectal cancer with emphasis on the distinct clinicopathological characteristics

“…For ALK and ROS1 IHC‐positive cases, an imbalanced gene expression assay using the NanoString nCounter system (NanoString Technologies, Inc., Seattle, WA, USA) was performed as previously described 11,18,19 to confirm the imbalanced expression of ALK and ROS1 . A NanoString copy number variation (CNV) assay (NanoString Technologies, Inc.) was performed for c‐MET IHC 3+ cases to evaluate MET amplification status, as previously described 20 . Data analysis was performed using the nSolver software version 4.0.…”

“…A NanoString copy number variation (CNV) assay (NanoString Technologies, Inc.) was performed for c-MET IHC 3+ cases to evaluate MET amplification status, as previously described. 20 Data analysis was performed using the nSolver software version 4.0. The copy number calculations were performed according to the manufacturer's instructions.…”

Clinicopathological and molecular pathological characteristics in tamoxifen‑related endometrial cancer

“…A total of 30 samples, including 10 TAM-related ECs and 20 sporadic ECs, underwent CNV analysis using the NanoString nCounter gene expression system (NanoString Technologies, Seattle, WA). A customized panel including 28 genes encoding receptor tyrosine kinases which we previously established ( 13 ) was employed. The copy number for these genes for each EC lesion compared to the nonneoplastic lesion were determined in nSolver according to the manufacturer's instructions.…”