Sequential genomic analysis using a multisample/multiplatform approach to better define rhabdomyosarcoma progression...

Area of Science:

• Oncology
• Genomics
• Molecular Biology

Background:

• The genomic landscape of rhabdomyosarcoma (RMS) progression from primary to relapsed disease remains incompletely characterized.
• Understanding genomic alterations is crucial for developing effective therapeutic strategies and monitoring treatment response in RMS.

Purpose of the Study:

• To evaluate the sensitivity of various next-generation sequencing (NGS) platforms for genomic profiling of RMS.
• To assess the feasibility of using liquid biopsy for monitoring treatment response and relapse in RMS patients.
• To investigate genomic differences between primary and relapsed fusion-positive (FP-RMS) and fusion-negative (FN-RMS) rhabdomyosarcoma.

Main Methods:

• Paired primary/relapsed tumor samples from 35 RMS patients (18 FP-RMS, 17 FN-RMS) were analyzed using targeted DNA and whole exome sequencing (WES).
• Circulating tumor DNA (ctDNA) from 10 patients was analyzed using a targeted 36-gene RMS panel and shallow whole-genome sequencing (WGS) for copy number variation.
• NGS platforms were compared for sensitivity in detecting single-nucleotide variations, fusions, and copy number alterations.

Main Results:

• Fusion-positive RMS exhibited genomic stability at relapse, with common secondary alterations (CDKN2A/B, MYCN, CDK4) impacting survival.
• Fusion-negative RMS acquired a higher number of new alterations, notably SMARCA2 missense mutations, at relapse.
• ctDNA analysis successfully detected pathognomonic variants at diagnosis in all RMS patients and confirmed relapse in 86% of FP-RMS and 100% of FN-RMS.
• Increased fusion reads in ctDNA correlated with higher disease burden and predicted fatal outcomes.

Conclusions:

• Genomic profiling of paired primary and relapsed RMS samples reveals distinct progression patterns between FP-RMS and FN-RMS.
• Liquid biopsy using ctDNA is a feasible and sensitive approach for detecting RMS alterations and monitoring disease progression and relapse.
• These findings provide a strong rationale for incorporating liquid biopsy into future clinical trials for RMS treatment monitoring.