Detection of Ewing sarcoma fusion oncogenes variants using CRISPR/Cas13

P Puig-Serra(1) A Nieto-Sánchez(1) M Martínez-Lage(1) M C Casado-Rosas(1) A Alonso-Yanez(1) P Ojeda-Walczuk(1) S Míguez-Amil(1) M López Valls(2) J Díaz-Martín(3) E de Álava(3,4) B Bot Sanz(2) R Fernández Leiro(1) R Torres-Ruiz(1,2) S Rodríguez-Perales(1)

1:Centro Nacional de Investigaciones Oncológicas; 2:CIEMAT-CIBERER; 3:Instituto de Biomedicina de Sevilla (IBiS); 4:Universidad de Sevilla

Ewing sarcoma is an aggressive tumor type that arises mainly in children and adolescents. It is the second most prevalent bone tumor, with a 70–80% survival rate for individuals with standard-risk and a localized tumor; however, this rate decreases to 30% for those patients with metastatic disease. Ewing sarcoma cells are characterized by a balanced chromosomal translocation in which a member of the FET gene family is fused with an ETS transcription factor. EWSR1–FLI1 is the most prevalent fusion oncogene (FO) (85%), although there are numerous variants of this FO with different partner genes. The detection of FOs associated with Ewing sarcoma by traditional diagnostic methods such as qRT-PCR, FISH, or NGS is a routine in the clinic. However, those techniques are expensive and time-consuming, requiring multiple steps and dedicated equipment and personnel. In this context, the identification of a novel RNA-targeting CRISPR enzyme, Cas13, allows the selective detection of FO transcripts oppening up the possibility of the development of new diagnostic options. The CRISPR/Cas13 system has already been used to develop viral detection systems, providing rapid RNA detection with attomolar sensitivity and single-base mismatch specificity. We have optimized a highly sensitive, specific, affordable, and instrument-free diagnostic test for FO detection by Cas13.