Establishment and proteomic characterization of patient-derived clear cell sarcoma xenografts and cell lines

Abstract

Clear cell sarcoma (CCS) is an aggressive mesenchymal malignancy characterized by the unique chimeric EWS-ATF1 fusion gene. Patient-derived cancer models are essential tools for the understanding of tumorigenesis and the development of anti-cancer drugs; however, only a limited number of CCS cell lines exist. The objective of this study was to establish patient-derived CCS models. We established patient-derived CCS models from a 43-yr-old female patient. We prepared the patient-derived xenografts (PDXs) from tumor tissues obtained through biopsy or surgery and isolated stable cell lines from PDXs and the original tumor tissue. The presence of gene fusions was examined by RT-PCR, and Sanger sequencing. The established cell lines were characterized by short tandem repeat, viability, colony and spheroid formation, and invasion analyses. Differences in gene enrichment between the primary tumor and cell lines were examined by mass spectrometry and KEGG pathway analysis. The cell lines were maintained for more than 80 passages, and had tumorigenic characteristics such as colony and spheroid formation and invasion. Mass spectrometric proteome analysis demonstrated that the cell lines were enriched for similar but distinct molecular pathways, compared to those in the xenografts and original tumor tissue. Next, tyrosine kinase inhibitors were screened for their suppressive effects on viability. We found that ponatinib, vandetanib, and doxorubicin suppressed the growth of cell lines, and had equivalent IC values. Further in-depth investigation and understanding of drug-sensitivity mechanisms will be important for the clinical applications of our cell lines.

Species‐Specific Quantitative Proteomics Profiles of Sarcoma Patient‐Derived Models Closely Reflect Their Primary Tumors

“…In other words, the CCS subtypes were characterized by decreased focal adhesion pathways versus the UPS and plRMS subtypes. Among the CCS subtypes, a cell line derived from NCC‐CCS1 was characterized by decreased focal adhesion pathways, which was consistent with results showing that cell lines derived from NCC‐CCS1B formed spheroids, whereas a cell line derived from NCC‐CCS1 did not, as previously reported …”

“…The sarcoma patient‐derived models that were proteomically profiled in this study (workflow in Figure A, Table S1, Supporting Information) were previously described and represent the UPS, CCS, and plRMS subtypes. All PDXs were passaged until the third generation in mice (X1–X3) and frozen in liquid nitrogen.…”

“…The sources and generation of all PDXs and cell lines from undifferentiated pleomorphic sarcoma (UPS), clear cell sarcoma (CCS), and pleomorphic rhabdomyosarcoma (plRMS) subtypes used in this study were previously reported. Detailed descriptions of these procedures are given in the Supporting Information Materials and Methods.…”

“…It remains however unclear how well these preclinical tumor models recapitulate patient tumor biology. We therefore developed sarcoma patient‐derived models for proteomic and functional studies, and tried to assess whether PDXsretain their proteomic characteristics with successive passaging …”

Characterisation of a Novel Cell Line (ICR-SS-1) Established from a Patient-Derived Xenograft of Synovial Sarcoma

“…The development of matched PDX-derived cell lines is non-trivial due to the relatively high failure rate associated with establishing cell lines from tumour specimens [ 23 , 24 ] and there are only a few reported studies demonstrating success using this approach, including in breast, colorectal, and pancreatic cancers [ 21 , 25 , 26 , 27 ]. In sarcomas, matched PDX-derived lines have been established in osteosarcoma, Ewing’s sarcoma, clear cell sarcoma, and CIC::DUX4 sarcoma [ 23 , 28 , 29 , 30 ].…”