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Integrated genetic and epigenetic analysis of myxofibrosarcoma

ABSTRACT: Myxofibrosarcoma (MFS) is a common histological subtype of adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high propensity for local recurrence. We underwent whole exome sequencing, RNA sequencing, and methylation analysis of MFS.

PROVIDER: EGAS00001002889 | EGA |

REPOSITORIES: EGA

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Integrated genetic and epigenetic analysis of myxofibrosarcoma

Project description:Myxofibrosarcoma (MFS) is a common adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high local recurrence rate and high propensity for local recurrence. Using 41 MFSs as a discovery set, we underwent whole exome sequencing (N=41), RNA sequencing (N=29), and methylation analysis (N=41). We subsequently performed targeted sequencing of 140 genes in the entire cohort of 99 MFSs to validate the results in the discovery samples. We also combined 17 MFSs data from TCGA to characterize the molecular features of MFS. Fourteen driver genes were identified, including potentially actionable therapeutic targets seen in 37% of cases. There were frequent alterations in p53 signaling (51%; TP53 and MDM2) and cell cycle checkpoint genes (43%; RB1, CDKN2A/CDKN2B, CDK6, and CCND1) genes. Other conceivably actionable driver genes including ATRX, JAK1, NF1, NTRK1 and novel oncogenic BRAF fusion gene were identified and a novel oncogenic BRAF fusion gene, SLC37A3-BRAF, which could potentially be targeted with BRAF inhibitors, and other conceivably actionable driver genes (ATRX, JAK1, NF1, and NTRK1) were identified. Methylation patterns clustered into three subtypes associated with unique combinations of MFS driver mutations. This cluster was also associated with clinical outcomes, and immune cell compositions. Our results provide a valuable genomic resource to enable the design of precision medicine for MFS. Here, based on these analyses, we identified recurrent driver genes, including novel BRAF fusion gene, and novel methylation clusters associated with unique combinations of driver mutations, clinical outcomes, and immune cell compositions.

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Integrated genetic and epigenetic analysis of myxofibrosarcoma

Project description:Integrated genetic and epigenetic analysis of myxofibrosarcoma

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Profiling DNA copy number alterations of myxofibrosarcomas with NimbleGen array CGH chips

Project description:Characterized by a wide histological spectrum, myxofibrosarcoma ranges from deceptively bland-appearing lesions to frankly pleomorphic sarcomas, representing a suitable model to elucidate the molecular aberrations in multistep disease progression. To explore cancer-associated genes of myxofibrosarcoma, ultrahigh-resolution array comparative genomic hybridization (aCGH) was used to profile DNA copy number alterations in myxofibrosarcoma tumor samples and cell lines. Along with normal reference DNA, 12 tumor samples and 2 cell lines (NMFH-1, OH931) of human myxofibrosarcoma were extracted for genomic DNAs, which were subjected to manufacturer’s (NimbleGen Inc) outsourcing service of DNA labeling, hybridization, and normalization of data obtained from 385K oligonucleotide array CGH chips.

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Trancription profiling of human soft tissue sarcomas: characterization & reclassification of malignant fibrous histiocytoma

Project description:In soft tissue sarcomas, diagnosis of malignant fibrous histiocytoma (MFH) has been a very controversial issue, and MFH is now considered to be reclassified into pleomorphic subtypes of other sarcomas. To characterize and reclassify MFH genetically, we analyzed gene expression in 105 samples from ten types of soft tissue tumors. Experiment Overall Design: Gene expression of 105 soft tissue tumor samples consisting of synovial sarcoma (n=16), myxoid liposarcoma (n=19), lipoma (n=3), well-differentiated liposarcoma (n=3), dedifferentiated liposarcoma (n=15), myxofibrosarcoma (n=15), leiomyosarcoma (n=6), malignant peripheral nerve sheath tumor (n=3), fibrosarcoma (n=4) and malignant fibrous histiocytoma (n=21) were analyzed using an Affymetrix HG-U133A array.

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Gene expression profiling of low-grade fibromyxoid sarcoma (LGFMS)

Project description:Analysis of gene expression in 17 low-grade fibromyxoid sarcoma (LGFMS) samples compared to that of histologically similar tumors. LGFMS is characterized by the specific translocations t(7;16)(q33;p11) or t(11;16)(p11;p11) and corresponding fusion genes FUS-CREB3L2 or FUS-CREB3L1. The results identifies a LGFMS-specific gene expression profile and provide insight into FUS-CREB3L2 regulated gene expression. RNA was extracted from 17 LGFMS tumor biopsies and hybridized to Affymetrix arrays. RNA from 6 myxofibrosarcoma (MFS), 6 desmoid fibromatosis (DFM), 5 solitary fibrous tumor (SFT) and 6 extraskeletal myxoid chondrosarcoma (EMCS) tumor biopsies was used as comparison. Two pools of skeletal muscle RNA was also included in the comparison.

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FOSL1 as a candidate target gene for 11q12 rearrangements in desmoplastic fibroblastoma

Project description:Global gene expression analysis of desmoplastic fibroblastoma (DF) and histologically similar tumors. FOSL1 is identified as a candidate target gene for the 11q12 rearrangments in DF. RNA was extracted from 3 frozen desmoplastic fibroblastoma (DF) biopsies and hybridized onto Affymetrix Human Gene 1.0 ST arrays. RNA from 6 myxofibrosarcoma (MFS), 6 desmoid fibromatosis (DFM), 5 solitary fibrous tumor (SFT) and 17 low-grade fibromyxoid sarcomas (LGFMS) were used as controls. The control dataset has been previously published and is available in the GEO database under Series accession GSE24369. The complete dataset representing: (1) the 3 desmoplastic fibroblastoma Samples and (2) the 34 control Samples from Series GSE24369 (re-processed using RMA), is linked below as a supplementary file.

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Targeted-capture sequencing (bam files) of 81 samples of myxofibrosarcoma and 44 matched pairs

Project description:Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the Targeted-capture sequencing was performed.

| EGAS00001005443 | EGA

Whole exome sequencing (bam files) of 55 samples of myxofibrosarcoma and 44 matched pairs

Project description:Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole exome sequence was performed.

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