Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors

Abstract

BackgroundChondrosarcomas are malignant cartilage tumors that do not respond to traditional chemotherapy or radiation. The 5-year survival rate of histologic grade III chondrosarcoma is less than 30%. An animal model of chondrosarcoma has been established - namely, the Swarm Rat Chondrosarcoma (SRC) - and shown to resemble the human disease. Previous studies with this model revealed that tumor microenvironment could significantly influence chondrosarcoma malignancy.MethodsTo examine the effect of the microenvironment, SRC tumors were initiated at different transplantation sites. Pyrosequencing assays were utilized to assess the DNA methylation of the tumors, and SAGE libraries were constructed and sequenced to determine the gene expression profiles of the tumors. Based on the gene expression analysis, subsequent functional assays were designed to determine the relevancy of the specific genes in the development and progression of the SRC.ResultsThe site of transplantation had a significant impact on the epigenetic and gene expression profiles of SRC tumors. Our analyses revealed that SRC tumors were hypomethylated compared to control tissue, and that tumors at each transplantation site had a unique expression profile. Subsequent functional analysis of differentially expressed genes, albeit preliminary, provided some insight into the role that thymosin-β4, c-fos, and CTGF may play in chondrosarcoma development and progression.ConclusionThis report describes the first global molecular characterization of the SRC model, and it demonstrates that the tumor microenvironment can induce epigenetic alterations and changes in gene expression in the SRC tumors. We documented changes in gene expression that accompany changes in tumor phenotype, and these gene expression changes provide insight into the pathways that may play a role in the development and progression of chondrosarcoma. Furthermore, specific functional analysis indicates that thymosin-β4 may have a role in chondrosarcoma metastasis.

Aberrant DNA Methylations in Chondrosarcoma

“…Results showed that the SRC tumor tissues exhibited a lower methylation level than normal cartilage. Specifically, statistically significant differences of methylation levels were revealed among SRC tumors tissues in different transplantation sites [20]. These findings indicated that DNA methylation may be regulated by microenvironment changes, providing insight into the influence of environmental factors on DNA methylation alterations in CS.…”

“…It can occur at normally methylated DNA sequences as repetitive DNA sequences and gene regulatory regions, and can be classified into two subtypes: global hypomethylation (loss of total DNA methylation content) and individual gene hypomethylation (e.g., hypomethylation of an oncogene) [17]. Since repetitive DNA sequences, such as satellite 2 and LINE-1, make up approximately 50% of the genome, their hypomethylation always acts as a marker for evaluating global hypomethylation that is a frequent event in human malignancies, including Swarm rat CS (SRC), which has been shown to resemble the human disease [17][18][19][20]. In a 2009 study, global hypomethylation was induced by using decitabine in SRC, a rat model of human CS [18,[20][21][22][23].…”

“…Since repetitive DNA sequences, such as satellite 2 and LINE-1, make up approximately 50% of the genome, their hypomethylation always acts as a marker for evaluating global hypomethylation that is a frequent event in human malignancies, including Swarm rat CS (SRC), which has been shown to resemble the human disease [17][18][19][20]. In a 2009 study, global hypomethylation was induced by using decitabine in SRC, a rat model of human CS [18,[20][21][22][23]. This study used rat-specific pyrosequencing assays to compare the methylation status of satellite 1 and LINE-1 between SRC cells with decitabine treatment and without treatment [18].…”

“…Repetitive DNA elements Global hypomethylation [18,20] LINE-1 Rat CS cells Repetitive DNA elements Global hypomethylation [18] Maspin Human CS cell lines Epithelial-specific marker Hypomethylation [39] …”

“…A correlation between changes in the microenvironment and DNA methylation alteration was evaluated in 2010 [20]. SRC tumors were transplanted in different locations of Sprague-Dawley rats, including subcutaneous tissue and the tibia.…”