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Updated: Oct 10, 2025
Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
Published on: July 25, 2020
Histopathological and Molecular Profiling of Clear Cell Sarcoma and Correlation with Response to Crizotinib: An
Che-Jui Lee1, Elodie Modave2, Bram Boeckx2
1Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium.
Abstract:
Clear cell sarcoma (CCSA) is characterized by a chromosomal translocation leading to EWSR1 rearrangement, resulting in aberrant transcription of multiple genes, including MET. The EORTC 90101 phase II trial evaluated the MET inhibitor crizotinib in CCSA but resulted in only sporadic responses. We performed an in-depth histopathological and molecular analysis of archival CCSA samples to identify alterations potentially relevant for the treatment outcome. Immunohistochemical characterization of MET signaling was performed using a tissue microarray constructed from 32 CCSA cases. The DNA from 24 available tumor specimens was analyzed by low-coverage whole-genome sequencing and whole-exome sequencing for the detection of recurrent copy number alterations (CNAs) and mutations. A pathway enrichment analysis was performed to identify the pathways relevant for CCSA tumorigenesis. Kaplan-Meier estimates and Fisher's exact test were used to correlate the molecular findings with the clinical features related to crizotinib treatment, aiming to assess a potential association with the outcomes. The histopathological analysis showed the absence of a MET ligand and MET activation, with the presence of MET itself in most of cases. However, the expression/activation of MET downstream molecules was frequently observed, suggesting the role of other receptors in CCSA signal transduction. Using sequencing, we detected a number of CNAs at the chromosomal arm and region levels. The most common alteration was a gain of 8q24.21, observed in 83% of the cases. The loss of chromosomes 9q and 12q24 was associated with shorter survival. Based on exome sequencing, 40 cancer-associated genes were found to be mutated in more than one sample, with SRGAP3 and KMT2D as the most common alterations (each in four cases). The mutated genes encoded proteins were mainly involved in receptor tyrosine kinase signaling, polymerase-II transcription, DNA damage repair, SUMOylation and chromatin organization. Disruption in chromatin organization was correlated with longer progression-free survival in patients receiving crizotinib. Conclusions: The infrequent activation of MET may explain the lack of response to crizotinib observed in the majority of cases in the clinical trial. Our work describes the molecular heterogeneity in CCSA and provides further insight into the biology of this ultra-rare malignancy, which may potentially lead to better therapeutic approaches for CCSA.
Insights
Clear cell sarcoma (CCSA) rarely responds to MET inhibitors like crizotinib due to infrequent MET activation. Molecular analysis reveals significant heterogeneity and potential new therapeutic targets beyond MET signaling.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Clear cell sarcoma (CCSA) is a rare cancer characterized by EWSR1 rearrangement, often leading to MET gene alterations.
- A prior clinical trial showed limited efficacy of the MET inhibitor crizotinib in CCSA patients.
Purpose of the Study:
- To investigate the histopathological and molecular basis for the limited response to crizotinib in clear cell sarcoma.
- To identify potential therapeutic targets and understand the molecular heterogeneity of CCSA.
Main Methods:
- Immunohistochemistry was used to assess MET signaling in 32 CCSA samples.
- Whole-genome and whole-exome sequencing were performed on 24 tumor specimens to detect copy number alterations (CNAs) and mutations.
- Pathway enrichment analysis and correlation of molecular findings with clinical outcomes were conducted.
Main Results:
- MET ligand and activation were largely absent, though MET itself was present in most cases.
- Frequent alterations included gain of 8q24.21 (83%), loss of 9q and 12q24 (associated with shorter survival), and mutations in SRGAP3 and KMT2D.
- Disruptions in chromatin organization correlated with longer progression-free survival in patients treated with crizotinib.
Conclusions:
- The infrequent MET activation explains the poor response to crizotinib in most CCSA patients.
- This study highlights the molecular heterogeneity of CCSA and suggests alternative therapeutic strategies may be needed.
- Further research into identified molecular alterations could lead to improved treatments for this rare cancer.
