Molecular inversion probe analysis detects novel copy number alterations in Ewing sarcoma.

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Ewing sarcoma (ES) is a common pediatric bone cancer with poor outcomes for metastatic or relapsed disease.
• Understanding the molecular drivers of ES is crucial for developing new prognostic markers and therapeutic strategies.

Purpose of the Study:

• To investigate copy number alterations (CNAs) and loss of heterozygosity (LOH) in Ewing sarcoma using molecular inversion probes (MIPs).
• To correlate identified CNAs with clinical features, patient outcomes, and validate findings using immunohistochemistry (IHC).

Main Methods:

• Utilized molecular inversion probes (MIPs) to analyze CNAs and LOH in formalin-fixed paraffin-embedded (FFPE) samples from 40 primary and 12 metastatic ES tumors.
• Correlated CNAs with clinical data and survival outcomes, validating key findings with immunohistochemistry (IHC).

Main Results:

• Identified known and novel CNAs, including homozygous loss and copy-neutral LOH of SMARCB1 (INI1/SNF5) in ES.
• Confirmed SMARCB1 protein loss in 7-10% of ES tumors across multiple cohorts via IHC.
• Developed a multifactor copy number (MCN)-index highly predictive of overall survival (P < 0.001).
• Discovered RELN gene deletions in 25% of metastatic ES samples.

Conclusions:

• MIP technology successfully identified CNAs in FFPE ES samples, providing new insights into molecular pathogenesis.
• CNAs, particularly the MCN-index and SMARCB1 alterations, are significant prognostic markers for ES.
• These findings support the use of CNA analysis for risk stratification in future ES clinical trials.