Epigenetic silencing of lncRNA in 16 TCGA cancer types.

We have previously described a hominid-specific long non-coding RNA, (also known as , Gene ID: 100128252), which is expressed in all normal cell types, but epigenetically silenced during cancer-associated immortalization of human mammary epithelial cells.  Initial analysis of The Cancer Genome Atlas (TCGA) showed that 15 of 17 cancer types, which represent the 10 most common cancers in women and men, display DNA methylation associated silencing in a large fraction of their tumors.  In this study we analyzed expression and DNA methylation state in the remaining 16 TCGA cancer types not previously reported.  Seven of the 16 cancer types showed DNA methylation linked silencing in a large fraction of their tumors.  These are carcinomas (cervical cancer, and cancers of esophagus, stomach, and bile duct), and the non-epithelial tumors mesothelioma, sarcoma, and uterine carcinosarcoma.  Together with the findings from our previous report, expression is silenced by aberrant DNA methylation in 22 of 33 of TCGA cancer types.  These 22 cancers include most carcinoma types, blood derived cancers and sarcomas.  In conclusion, results suggest that the gene is one of the most common epigenetic aberrations seen in human cancer.  Coupled with the timing of gene silencing during epithelial cell immortalization and its occurrence early in the temporal arc of human carcinogenesis, this provides strong circumstantial evidence for a tumor suppressor role for .