Comparative epigenomics of human and mouse mammary tumors

Abstract

Gene silencing by aberrant epigenetic chromatin alteration is a well-recognized event contributing to tumorigenesis. Although genetically engineered tumor-prone mouse models have proven a powerful tool in understanding many aspects of carcinogenesis, to date few studies have focused on epigenetic alterations in mouse tumors. To uncover epigenetically silenced tumor suppressor genes (TSGs) in mouse mammary tumor cells, we conducted initial genome-wide screening by combining the treatment of cultured cells with the DNA demethylating drug 5-aza-2 0 -deoxycytidine (5-azadC) and the histone deacetylase inhibitor trichostatin A (TSA) with expression microarray. By conducting this initial screen on EMT6 cells and applying protein function and genomic structure criteria to genes identified as upregulated in response to 5-azadC/ TSA, we were able to identify two characterized breast cancer TSGs (Timp3 and Rprm) and four putative TSGs (Atp1B2, Dusp2, FoxJ1 and Smpd3) silenced in this line. By testing a panel of 10 mouse mammary tumor lines, we determined that each of these genes is commonly hypermethylated, albeit with varying frequency. Furthermore, by examining a panel of human breast tumor lines and primary tumors we observed that the human orthologs of ATP1B2, FOXJ1 and SMPD3 are aberrantly hypermethylated in the human disease whereas DUSP2 was not hypermethylated in primary breast tumors. Finally, we examined hypermethylation of several genes targeted for epigenetic silencing in human breast tumors in our panel of 10 mouse mammary tumor lines. We observed that the orthologs of Cdh1, RarB, Gstp1, RassF1 genes were hypermethylated, whereas neither Dapk1 nor Wif1 were aberrantly methylated in this panel of mouse tumor lines. From this study, we conclude that there is significant, but not absolute, overlap in the epigenome of human and mouse mammary tumors. V V C

Forkhead box J1 expression is upregulated and correlated with prognosis in patients with clear cell renal cell carcinoma

“…Thus, FOXJ1 was proposed as a prognostic marker in patients with hepatocellular carcinoma (40). By contrast, a previous study proposed that FOXJ1 was decreased and may function as a tumor suppressor gene in breast cancer (39). The expression of FOXJ1 and its role in RCC has remained to be determined.…”

“…In addition, FOXJ1 inhibits the humoral immune response in B cells, with FOXJ1 deficiency in B cells being associated with germinal center formation and the development of autoantibodies (38). A previous study proposed that FOXJ1 expression was decreased in breast cancer, thus, functioning as a tumor suppressor gene (39). However, FOXJ1 expression was increased in hepatocellular carcinoma and was associated with poor prognosis.…”

Chick Embryo Extract Demethylates Tumor Suppressor Genes in Osteosarcoma Cells

“…Extraction and Sodium Bisulfite Modification of Genomic DNA Genomic DNA was isolated from osteosarcoma cells with a Qiagen Blood and Cell Culture DNA kit (Qiagen, Valencia, VA, USA) and stored at À20°C before use [10]. DNA was modified with an EZ DNA Methylation kit (ZYMO Research Co, Orange, CA, USA) according to the manufacturer's instructions.…”

Boswellic acid induces epigenetic alterations by modulating DNA methylation in colorectal cancer cells

“…Overexpression of SMPD3 leads to an inhibition of cell growth in the human breast cancer cell line MCF7, 25 and the promoter region of SMPD3 has been reported to be hypermethylated in human breast cancers. 26 The demethylation and upregulation of putative tumor suppressor genes could help explain the anticancer effects of AKBA.…”

“…Table 1 shows the primers' sequences and the putative function of genes. [24][25][26][38][39][40][41][42][43][44][45][46] F AGG CGA GAA GGT ATA GTT TC 185 GCC TTG TGC CTT CTC AAT TT 101 Inhibits cell cycle progression 38 R ATT CAC CCT CGA ATC TAA AT TCA GTG TCA TTA ATC TTG GAA TGT T DDIT4 F GAT TTT GGT AGT TGT AGT …”