Abstract 84: A discovery on splicing variant patterns of leucine-tRNA synthetase gene based on targeted RNA sequencing
Authors: Song HyoJin , Kim Daeyoon , Park Hyejoo , Cheong Hyun Sub , Kim Sunghoon , Koh Youngil , Yoon Sung-Soo 
Published: July 2016

A leucine-tRNA synthetase, which belongs to the class I aminoacyl-tRNA synthetase family, is encoded by LARS gene. LARS gene functions as an intracellular leucine sensor for mTORC1, mammalian target of rapamycin C1 signaling pathway. This cytosolic gene has a catalytic role of ligating leucine amino acid to its cognate tRNA, in ATP-dependent manner. Accordingly, the protein synthesis regulation, protein translation, cell size, and autophagy are known to be reported by this gene. Therefore, a comprehensive study on LARS gene is necessary for the sake of advanced drug research and precise personalized cancer therapy, in relation to mTOR pathway, which is the root cause of cancer genesis.

We discovered the differently expressed splicing patterns in 16 transcripts in LARS gene. Alternative splicing variants of LARS gene were sequenced of 12 cancer cell lines using targeted RNA sequencing to verify their possibilities as a drug target; 12 cancer cell lines are consist of 8 hematologic cell lines and 4 solid cancer cell lines. Sequencing data of LARS gene is aligned by TopHat, and consequently transcript assembly and coverage percentage calculation are processed by Cufflinks, afterwards.

Our data, observed from the integrated analysis of these values, shows outstanding features on three transcripts: known protein coding transcript LARS-001 (ENST00000394434, known processed transcript LARS-013 (ENST00000511505), and transcript LARS-015 (ENST00000508709), which is known to retain intron sequences. First of all, the coverage percentage value of transcript LARS-001 in a multiple myeloma cell line, KMS-12-BM, was substantially different from the other cell lines. Secondly, an exceptionally high coverage percent value of the transcript LARS-013 in HL-60, an acute promyelocytic leukemia cell line, was shown. Lastly, the transcript LARS-015 showed a considerably high coverage percent value in SK-MES-1, which is a lung squamous cell carcinoma cell line.

Three distinct features of LARS transcripts, transcript LARS-001 in KMS-12-BM, transcript LARS-013 in HL-60, and transcript LARS-015 in SK-MES-1, were characterized. Interestingly, transcript LARS-001 is transcribed with no exon skipping and is only highly expressed in KMS-12-BM. On the other hand, the serial exon skipping from exon 14 to exon 26 in major transcript LARS-201 has shown commonly in 12 cell lines. This implies that LARS gene has unique patterns of alternative splicing variants, which can be consider of taking a significant role in carcinogenesis across diverse cancer types. Hence, additional analysis on exploring the biologically functional correlation between LARS gene and cancer, including cohort validation is to be demonstrated in the future research.

Citation Format: HyoJin Song, Daeyoon Kim, Hyejoo Park, Hyun Sub Cheong, Sunghoon Kim, Youngil Koh, Sung-Soo Yoon. A discovery on splicing variant patterns of leucine-tRNA synthetase gene based on targeted RNA sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 84.