A Functional Genomic Approach Identifies FAL1 as an Oncogenic Long Noncoding RNA that Associates with BMI1 and Represses p21 Expression in Cancer

In a genome-wide survey on somatic copy-number alterations (SCNAs) of long noncoding RNA (IncRNA) in 2,394 tumor specimens from 12 cancer types, we found that about 21.8% of IncRNA genes were located in regions with focal SCNAs. By integrating bioinformatics analyses of IncRNA SCNAs and expression with functional screening assays, we identified an oncogene, focally amplified IncRNA on chromosome 1 (FAL1), whose copy number and expression are correlated with outcomes in ovarian cancer. FAL1 associates with the epigenetic repressor BMI1 and regulates its stability in order to modulate the transcription of a number of genes including CDKN1A. The oncogenic activity of FAL1 is partially attributable to its repression of p21. FAL1-specific siRNAs significantly inhibit tumor growth in vivo.