To create a comprehensive picture of alterations in sarcoma, we have undertaken an integrated, genome-wide sequencing and microarray analysis, focusing on a few common sarcoma subtypes: myxofibrosarcoma, pleomorphic malignant fibrous histiocytoma, myxoid/round cell liposarcoma, and well-differentiated and dedifferentiated liposarcoma. The sequencing and microarray analyses are capable of detecting many types of alterations, including aberrant DNA methylation, mutations, gene fusions, novel transcripts, aberrant splice forms, and altered expression of mRNAs and microRNAs.
The tumor-specific alterations we discover are analyzed computationally to identify individual genes and pathways that are commonly affected in the tumors. The alterations are also tested for association with outcomes such as tumor recurrence and patient survival. The alterations that show associations can be used to build models to better predict individual patients’ outcomes. Finally, to assess the functional significance of individual alterations, the genes and microRNAs of interest are tested for effects on cell proliferation, apoptosis, and differentiation in vitro and tumor growth in vivo.
Through these methods, we have assembled the largest dataset of genomic alterations in sarcoma to date, and we have shown that some of these alterations may be useful therapeutic targets. In myxoid/round cell liposarcoma, these alterations include PIK3CA mutations, which are found in 18 percent of tumors and may be targeted with PI3 kinase inhibitors. In myxofibrosarcoma, we have identified NF1 mutations, which might be possible to target with MEK or mTOR inhibitors. In dedifferentiated liposarcoma, our results implicate several microRNAs and several effectors of cytokinesis (PRC1, PLK1), as well as CEBP-alpha, a regulator of differentiation. Interestingly, some of these genes, including those encoding CEBP-alpha and one of the microRNAs, appear to be downregulated by aberrant methylation. This suggests that demethylating agents may have a role in the treatment of dedifferentiated liposarcoma. Consistent with this, treating DDLS cells with a demethylating agent and the histone deacetylase inhibitor SAHA increased CEBPa expression, decreased proliferation, induced apoptosis, and reduced tumor growth in DDLS mice by 50 to 70 percent.
The results from our research will ultimately enable the identification of new targets based on a better understanding of the molecular genetics of solid tumors.