Project description:We used the Infinium HumanMethylation27 platform to profile DNA methylation in 80 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 14 representative sarcoma cell lines. Marcus, Renner
Project description:We used the Infinium HumanMethylation27 platform to profile DNA methylation in 80 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 14 representative sarcoma cell lines.
Project description:DNA methylation and copy number variation (CNV) profiling has emerged as a promising tool for the classification of bone and soft tissue tumors. We evaluated its utility in cartilage tumors, where distinguishing low-grade from high-grade conventional central chondrosarcoma (CS) as well as atypical cartilaginous tumors (ACT) from enchondromas are frequent diagnostic challenges, particularly on biopsy material. We analyzed 214 chondrogenic tumors, including enchondromas, ACT, conventional central, dedifferentiated, and clear cell chondrosarcomas, and determined their IDH1/2 mutation status. Unsupervised dimensionality reduction of genome-wide DNA methylation patterns revealed four clusters among IDH-mutant tumors (IDH-MUT-1: mostly enchondromas and ACT and some high-grade CS; IDH-MUT-2: predominantly high-grade CS; IDH-MUT-3: largely dedifferentiated CS; IDH-MUT-HN: distinct head and neck group with markedly different methylation pattern) and two clusters among IDH-wildtype tumors (IDH-WT-1 and IDH-WT-2: both primarily high-grade CS, with IDH-WT-2 showing higher tumor grade and more extensive CNVs). Clear cell chondrosarcomas formed a separate cluster (CC). The amount of CNVs, including loss of CDKN2A, increased with tumor grade, reflecting increased genomic instability during chondrosarcoma progression. Supervised classifiers trained separately, both on methylation and CNV data, distinguished low- and high-grade cartilaginous tumors with AUC values of 0.87–0.97 and 85–90% accuracy. Furthermore, we tested whether dedifferentiated chondrosarcoma (DDCS) can be distinguished from metastatic carcinomas and other high-grade sarcomas of bone. Across 246 reference samples, a supervised classifier achieved 97.2% accuracy (AUC 99.8%) and correctly identified 30/32 (93.8%) DDCS. These results indicate that DNA methylation and CNV data analysis provide a valuable tool for distinguishing most low- and high-grade chondrosarcomas, with additional utility also in differentiating DDCS from morphologic mimics.
Project description:Interventions: Nucleic acid from tumor tissues and serum SNPs
Primary outcome(s): 1. Tissue biomarkers including mutation, gene expression, and DNA methylation that correlate with efficacy from trifluridine/tipiracil hydrochloride therapy 2. Serum biomarkers including mutation, gene expression, and DNA methylation that correlate with efficacy from trifluridine/tipiracil hydrochloride therapy 3. SNPs that correlate with toxicities from trifluridine/tipiracil hydrochloride therapy
Study Design: Single arm Non-randomized
Project description:Soft tissue sarcoma diagnostics and prognostics are challenging, particularly in highly malignant and pleomorphic subtypes such as undifferentiated pleomorphic sarcoma (UPS) and leiomyosarcoma (LMS). We applied 32K BAC-arrays and gene expression profiling to 18 extremity soft tissue LMS and 31 extremity soft tissue UPS with the aim to identify molecular subtype signatures and genomic prognostic markers. Both the gains/losses and gene expression signatures revealed striking similarities between UPS and LMS, which were indistinguishable using unsupervised hierarchical cluster analysis and significance analysis for microarrays. Gene expression analysis revealed just 9 genes, among them Tropomyosin beta, that were differentially expressed. Loss of 4q31 (encompassing the SMAD1 locus), loss of 18q22 and tumor necrosis were identified as independent predictors of metastasis in multivariate stepwise Cox regression analysis. Combined analysis applying loss of 4q31 and 18q22 and presence of necrosis improved the area under receiver operating characteristic curve for metastasis prediction from 0.64 to 0.86. The extensive genetic similarities between extremity soft tissue UPS and LMS suggest a shared lineage of these STS subtypes and the new and independent genetic prognosticators identified hold promise for refined prognostic determination in high-grade, genetically complex STS. Genomic DNA was extracted from a total of 49 samples, 31 Undifferentiated pleomorphic Sarcomas and 18 Leiomyosarcomas. The DNA was labeled using Bioprime array CGH labeling kit (Invitrogen). Promega pooled male DNA was used as reference. Labeled DNA was hybridized onto BAC arrays containing ~32 000 BAC clones printed in singlets. BAC arrays were produced at the SWEGENE DNA Microarray Facility at Lund University.
