Deletion of the Long Non-coding <i>RNA</i><i>ANRIL</i> In Addition to the Protein-Coding Genes of the INK4-ARF Locus in the A549 Cell Line: An Existing Phenomenon or a Novel Genetic Alteration?

A549, a human lung adenocarcinoma cell line, is a KRAS mutant cell used for over 5 decades as a type II alveolar cell and non-small cell lung adenocarcinoma model. Cyclin-dependent kinase inhibitor 2 A ( CDKN2A ) and cyclin-dependent kinase inhibitor 2 B ( CDKN2B ) are protein-coding genes in the INK4-ARF locus and function as tumor suppressors and negative regulators of the cell cycle. These genes have been reported to be deleted in the A549 cell line. The Long non-coding RNA ANRIL is located in the antisense direction of CDKN2B and shares a bidirectional promoter with CDKN2A . ANRIL is a negative regulator of the INK4-ARF locus genes and has an oncogenic role in cancers. ANRIL deletion in the A549 cell line has not been reported to date.

Herein, the presence of ANRIL was investigated in the A549 cell line.

In this study, the A549 cell line from 2 different sources was tested for the presence of the INK4-ARF locus genes by polymerase chain reaction (PCR) using specific primers at both DNA and RNA levels. We compared our findings with Calu-6, MRC-5, and HepG2 cell lines.

Our analysis revealed that all protein-coding genes in the INK4-ARF locus, including CDKN2A and CDKN2B , were deleted in the A549 cell lines. Furthermore, we observed that ANRIL was entirely deleted in the A549 cells. The evaluated locus and all of its genes are present and expressed in other investigated cell lines.

For the deletion of ANRIL in the A549 cell line, 2 scenarios are possible: First, from a structural point of view, the deletion of the protein-coding genes in the antisense of ANRIL in the INK4-ARF locus implies the possibility of a concurrent loss of ANRIL with the deletion of these genes in the A549 cell line. Second, as cancer cell lines are genetically unstable and are always susceptible to the acquisition of new mutations, ANRIL loss may have occurred later, following a novel genetic alte RNA tion in a population derived from a mutated cell.