Figure S7. TCGA LUAD methylation at the FOXA2 locus. A. Individual CpGs are denoted by their Illumina 450K designation. Scale = 0 (no methylation) to 1 (complete methylation). Hg19-based coordinates for each probe are listed below the cg ascension number. Distance from FOXA2 transcript variant 1 Transcription Start Site (TSS) is also shown. "+" is downstream of TSS (within the gene), "-" is upstream of TSS. B. Luciferase assay for activity of FOXA2 promoter in the presence or absence of in vitro SssI methylation. Data is normalized to CpGLess empty vector values from appropriate treatment group. A paired t-test was performed on N=3 biological replicates, each performed in technical triplicate.
ARTICLE ABSTRACTLung cancer is the leading cause of cancer-related death in the United States. Long noncoding RNAs (lncRNA) are a class of regulatory molecules whose role in lung carcinogenesis is poorly understood. In this study, we profiled lncRNA expression in lung adenocarcinoma (LUAD) cell lines, compared their expression with that of purified alveolar epithelial type II cells (the purported cell of origin for LUAD), cross-referenced these with lncRNAs altered in the primary human tumors, and interrogated for lncRNAs whose expression correlated with patient survival. We identified LINC00261, a lncRNA with unknown function in LUAD, adjacent to the pioneering transcription factor FOXA2. Loss of LINC00261 was observed in multiple tumor types, including liver, breast, and gastric cancer. Reintroduction of LINC00261 into human LUAD cell lines inhibited cell migration and slowed proliferation by inducing G2–M cell-cycle arrest, while upregulating DNA damage pathway genes and inducing phosphorylation-mediated activation of components of the DNA damage pathway. FOXA2 was able to induce LINC00261 expression, and the entire locus underwent hypermethylation in LUAD, leading to loss of expression. We have thus identified an epigenetically deregulated lncRNA, whose loss of expression in LUAD promotes the malignant phenotype and blocks activation of the DNA damage machinery, predisposing lung cells to cancer development.
These findings identify LINC00261 as a tumor suppressor that blocks cellular proliferation by activating the DNA damage response and suggest that epigenetic therapy to inhibit DNA methylation may enhance treatment of LUAD.