(P 147) INVESTIGATING THE POTENTIAL OF EXTRACELLULAR VESICLE BIOMARKERS IN SYNOVIAL SARCOMA DETECTION

Objective: Synovial sarcoma (SS) is a rare and aggressive soft tissue cancer with high heterogeneity, low 5- and 10-year survival rates, and a high risk for recurrence and metastasis. Current diagnostic approaches include histology, PCR, and fluorescent in situ hybridization (FISH), however these methods require surgically resected tumor samples. There are currently no viable options for non-invasive detection of SS, which contributes to delays in detecting advanced disease. Recent studies suggest that extracellular vesicles play important roles in various aspects of cancer biology, including tumor growth, progression, tumorigenesis, and metastasis. There have already been efforts in neuroblastoma and osteosarcoma to utilize exosomal biomarkers, a class of extracellular vesicles, as non-invasive diagnostic tools. While the role of extracellular vesicles is becoming increasingly clear in other cancer types, little is known about their value in sarcomas, and even less is known in regard to synovial sarcoma. This project aims to identify transcriptional profiles within extracellular vesicles secreted from SS cells that may be used as diagnostic and prognostic biomarkers for non-invasive detection and disease surveillance using nanopore-integrated optofluidics technology.

Methods: Biomarker identification: SS tumors are characterized by the t(X;18)(p11.2;q11.2) chromosomal translocation that results in the unique SS18-SSX gene fusion. We have performed bulk RNA sequencing (RNA-seq) and successfully identified SS18-SSX fusion transcripts in extracellular vesicular RNA (evRNA) from patient-derived SS cell lines (see abstract by Vasquez et al, CTOS 2024). We will parse our evRNA-Seq data to identify biomarkers for disease detection in addition to the SS18-SSX fusion.
Biomarker detection: To capture secreted evRNA biomarkers from SS cell lines, we will utilize emerging breakthrough technologies in nanopore-integrated optofluidic platforms. This system has been shown to provide a label-free and amplification-free single-molecule detection in the attomolar concentration range, which is commensurate with clinically-relevant biomarker concentrations (Sampad et al, 2024. PNAS). We are currently designing SS18-SSX biomarker probes, with the intention of building a panel of SS-specific biomarker probes, which we hypothesize will allow for highly sensitive quantification of targeted molecules within the sample.

Results: We anticipate that the evRNA from SS cell line media will yield a collection of RNA-based biomarkers characteristic of SS, that can be used for non-invasive detection of SS. We foresee that the amplification and release of RNA molecules in extracellular vesicles will aid in the sensitivity and specificity of developing a liquid biopsy detection technique. We hypothesize that the nanopore-integrated optofluidic platform will provide a low complexity, highly sensitive, and clinically feasible method for SS diagnosis and disease monitoring.

Conclusion: Delayed clinical diagnosis is a significant obstacle in synovial sarcoma, and methods for early disease detection are needed. This work aims to apply innovative new nanopore technology, as well as the Vaske lab’s expertise in RNA genomics, to extracellular vesicles as a method of developing an early detection and disease surveillance technique for SS that can be applied to other fusion-positive cancer types. We anticipate that the secreted biomarkers from SS cell line media will provide a proof-of-concept method that we aim to expand in SS patient blood samples.