Effect of molecular cartography on recurrence-specific drivers through analysis of matched primary and recurrent rhabdomyosarcoma tumors.

Abstract

e23546 Background: Despite intensive treatment, the chance of cure for patients with recurrent rhabdomyosarcoma (RMS) is very low, highlighting the need for an improved understanding of recurrent RMS. As most studies to date have focused on diagnosis, our understanding of the molecular and clonal dynamics of pre- and postrecurrence pairs is limited. Methods: We collected critical clinical data from patients with RMS and performed targeted next-generation sequencing on paired tissue and blood samples obtained pre- and postrecurrence. At OrigiMed, which accredited by the College of American Pathologists and certified under the Clinical Laboratory Improvement Amendments, we conducted a thorough examination of a targeted gene panel that included 706 DNA-level and 649 RNA-level cancer-associated genes. Additionally, we executed whole-transcriptome sequencing (WTS) to determine the changes in gene expression and immune infiltration associated with disease recurrence. Cox univariate and multivariate analyses were applied to identify prognostic indicators of progression-free survival (PFS). Results: Paired pre- and post-recurrent tissue and blood samples from15 RMS patients were subjected to targeted gene panel sequencing. Of the 15 patients, 4 underwent WTS. The histological types included nine embryonal RMSs, three alveolar RMSs, and three spindle cell/sclerosing RMSs. Analysis of genome-wide mutation landscapes revealed distinct mutational patterns pre- and postrecurrence. MYOD1 (26.7%), BCOR (20.0%), CDKN2A (20.0%), and TP53 (20.0%) were the most common gene alterations detected at pre-recurrence, whereas TP53 (40.0%), BCOR (20.0%), CDKN2A (20.0%), and COL1A1 (13.3%) were the most common gene alterations observed at post-recurrence. Notably, compared with prerecurrence TP53 mutation was more common in postrecurrent tumors (40.0% vs. 20.0%), which plays an essential role in the pathogenesis of RMS. Pathway analysis between pre- and postrecurrence revealed that the P53 pathway (53.3% vs. 26.7%) was more activated postrecurrence. In particular, after recurrence, alterations in three genes, BCOR (p = 0.024), CDKN2A (p = 0.024), and TP53 (p = 0.036), demonstrated a significant association with the risk groups. These findings imply that these gene alterations may have a substantial connection to recurrence and could act as predictive biomarkers for risk stratification purposes. Cox multivariate analysis revealed that KDM5C (p = 0.015) was an independent poor prognostic factor for PFS. According to the WTS analysis, the expression level of transcripts per million in CAMLG (p = 0.049), GAN (p = 0.049), and HSPA4 (p = 0.049) was higher in postrecurrent tumors than in prerecurrent tumors. Conclusions: Our study reveals multiple potential drivers of recurrent disease in RMS, improving our understanding of tumor evolution and suggesting potential biomarkers. Clinical trial information: NCT05076071 .