Identification and analysis of novel lung cancer RNAs by using Alu-PCR

Lung cancer is the leading cause of cancer-related death worldwide where tobacco smoking is considered as the main cause of the disease. However, the carcinogenesis of lung cancer is yet to be fully elucidated. Thus, our study proposed that Alu elements can be used to identify novel genomic alterations without the knowledge of the sequences. As the Alu elements are widely dispersed in human genome, they can be used as universal primer for the detection of genomic alteration in lung cancer. The aim of this study is to clone novel RNA transcripts, validate these genes by using real-time PCR and obtain the full length sequence of the selected gene. This study also aims to validate the expression of the selected gene by using MTT assay. Total of 4 fragments named as C11, C12, C13 and C20 which are 791 bp, 601 bp, 719 bp and 583 bp in length, respectively, were successfully isolated using Alu-PCR. BLAST search revealed no significant match to Ref_Seq mRNA database, indicating they are novel transcripts. The expression of C11, C12 and C20 was identified to be donwregulated by 0.32, 0.022 and 0.611 fold, respectively in lung cancer. Meanwhile C13 was upregulated by 10.25 fold in lung cancer. Full-length amplification of C13 sequence resulted in 2176 bp with open reading frame of 302 amino acids. Based on the full length sequence of C13 transcript, it could be classified as a novel gene or non coding RNA. Meanwhile, in-vitro assessment showed that the C13 transcript act as an oncogenic. Therefore, this study concluded that the C13 transcript can be a potential biomarker for lung cancer.