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Dissecting the genomic profile of persistently infecting oncolytic Newcastle disease virus (NDVpi) from cancer RNA-Seq data
Poster Title: Dissecting the genomic profile of persistently infecting oncolytic Newcastle disease virus (NDVpi) from cancer RNA-Seq data
Submitted on 08 Dec 2019
Author(s): Ahmad U1, Chan SC2, Chau DM1, Chia SL5, Abdullah S1,3, Yusoff K5 & Veerakumarasivam A1,4*
Affiliations: 1Medical Genetics Laboratory, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. 2School of Foundation Studies, Perdana University, MAEPS Building, MARDI Complex, Jalan MAEPS Perdana, 43400 Serdang, Selangor, Malaysia. 3Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.4Department of Biological Sciences, Sunway School of Science and Technology, Sunway University, Jalan Universiti, Bandar Sunway, 47500 Selangor, Malaysia. 5Virology Laboratory, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. *
This poster was presented at Asean Emerging Researchers Conference (AERC2019)
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Poster Information
Abstract: Background and Objectives: Newcastle disease virus (NDV) is a natural oncolytic virus with non-segmented negative single stranded ssRNA (−) genome of 15kb in size that contains six genes which encodes six major structural proteins arranged in the sequence order of 3’-NP-P-M-F-HN-L-5’. It selectively replicate and kills many different human cancer cells, however, it has been found to persistently infect a subset of bladder cancer cells that resist NDV-mediated oncolysis. This study aims to utilise bioinformatics tools to analyse genome of the established NDV persistently infected TCCSUP bladder cancer cells obtained from RNA-Seq experiment. Methods: Transcriptome profiles of TCCSUP bladder cancer cell lines persistently infected with oncolytic Newcastle disease virus (NDV) AF2240 strain were generated in triplicate by deep sequencing using Illumina HiSeq 2000. Reads were then aligned to a human genome reference hg19 using HISAT2 and BAM files containing the viral and human sequences were generated. To separate these data from each other, we concatenated the corresponding reference genomes (human + viral) and map the reads against this concatenated reference genome. The viral and human reads were separated to obtain their individual BAM files. Integrative Genomic Viewer (IGV) software was then used to visualize the viral BAM file and manually inspected to detect any mutations in the viral sequences. Results: Spanning and inspecting through the viral genome (3’-NP-P-M-F-HN-L-5’) in IGV identified many bases that do not match the viral reference sequence as highlighted by different colours as well as low quality bases that were mostly semi-transparent and faint. Three different nucleotide changes were identified at nucleotide position 359AdelC (deletion) and 1,653C->T in the region encoding for the viral NP protein, and 3,338CinsT (insertion) in the region encoding for M protein. In addition, there was insertion of GGG bases detected in the P gene at 2,290bp position. The alignments also demonstrated viral genome truncations that were mapped to nucleotide positions from 8,263 to 8,390 in the HN protein and nucleotide positions from 6,203 to 6,342 in the L protein regions respectively. Conclusion: Changes in nucleotide sequences of the viral genome may have significant impact on the development of persistence infection in bladder cancer cells. Summary: Dissecting the genomic profile of persistently infecting oncolytic Newcastle disease virus (NDVpi) from RNA-Seq data of bladder cancer cell lines persistently infected with NDV.
References: Alexander, D. J., Manvell, R. J., Lowings, J. P. et al., (1997). Avian Pathology: Journal of the W.V.P.A 26, 399–418.
Rangaswamy, U. S., Wang, W., Cheng, X., et al., (2017). Journal of Virology, 91(16), e00770-17.
Stojdl, D. F., Lichty, B., Knowles, S., Marius, R., Atkins, H., Sonenberg, N., & Bell, J. C. (2000). Nature medicine, 6(7), 821.
Chia, S. L., Yusoff, K., &, N. (2014).  Virology journal, 11(1), 91.
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