Altered Histone Mark Deposition and DNA Methylation at Homeobox Genes in Human Oral Squamous Cell Carcinoma

Abstract

We recently reported a role of Polycomb repressive complex 2 (PRC2) and PRC2 trimethylation of histone 3 lysine 27 (H3K27me3) in the regulation of homeobox (HOX) (Marcinkiewicz and Gudas, 2013) gene transcript levels in human oral keratinocytes (OKF6-TERT1R) and tongue squamous cell carcinoma (SCC) cells. Here, we assessed both the levels of various histone modifications at a subset of homeobox genes and genome wide DNA methylation patterns in OKF6-TERT1R and SCC-9 cells by using ERRBS (enhanced reduced representation bisulfite sequencing). We detected the H3K9me3 mark at HOXB7, HOXC10, HOXC13 and HOXD8 at levels higher in OKF6-TERT1R than in SCC-9 cells; at IRX1 and SIX2 the H3K9me3 levels were conversely higher in SCC-9 than in OKF6-TERT1R. The H3K79me3 mark was detectable only at IRX1 in OKF6-TERT1R and at IRX4 in SCC-9 cells. The levels of H3K4me3 and H3K36me3 marks correlate with the transcript levels of the assessed homeobox genes in both OKF6-TERT1R and SCC-9. We detected generally lower CpG methylation levels on DNA in SCC-9 cells at annotated genomic regions which were differentially methylated between OKF6-TERT1R and SCC-9 cells; however, some genomic regions, including the HOX gene clusters, showed DNA methylation at higher levels in SCC-9 than OKF6-TERT1R. Thus, both altered histone modification patterns and changes in DNA methylation are associated with dysregulation of homeobox gene expression in human oral cavity SCC cells, and this dysregulation potentially plays a role in the neoplastic phenotype of oral keratinocytes.

Clinical implications of epigenetic regulation in oral cancer

“…Further, Chromatin immunoprecipitation (ChIP) studies for H3K9me3 in keratinocyte cell line (OKF6-TERTIR) and tongue carcinoma cell line (SCC-9) corroborated differential expression in the normal and cancer cell lines. Besides, the downstream processes were associated with HOX genes (HOXB7, HOXC10, HOXC13 and HOXD8) in the cancer cell line and IRX1 and IRX4 genes in the keratinocytes [101,102]. The presence of Histone 2 variant c-H2A.X was reported in 30% oral cancer tissue (n = 42), and 61% oral dysplastic tissue (n = 34) [103].…”

HOXC13 promotes proliferation of esophageal squamous cell carcinoma via repressing transcription ofCASP3

“…HOXC13, a member of the homeobox HOXC gene family, has been reported to be overexpressed in human liposarcomas, squamous cell carcinoma, skin tumors and prostate cancer . As a transcription factor, HOXC13 synergistically regulates the expression of Zfp521, which has been identified as a B‐cell proto‐oncogene causing leukemia .…”

The role of HOX genes in head and neck squamous cell carcinoma

“…The mechanism of this widespread dysregulation of HOX genes in HNSCC has not been clearly established. The alterations in promoter methylation and histone modifications mentioned earlier play a role , as do changes in microRNA expression, such as miR‐196 , and other transcription factors, such as POU2F1 . There are numerous reports of more widespread effects of alterations in the expression of miRNAs and lincRNAs encoded within the HOX gene cluster.…”