Abstract
Recent studies using high-throughput sequencing technologies have demonstrated that transposable elements seem to be involved not only in some cancer onset but also in cancer development. However, their activity is not easy to assess due to the large number of copies present throughout the genome. In this study NearTrans bioinformatic workflow has been used with RNA-seq data from 16 local patients with lung cancer, 8 with adenocarcinoma and 8 with small cell lung cancer. We have found 16 TE-gene pairs significantly expressed in the first disease, and 32 TE-gene pairs the second. Interestingly, some of the genes have been previously described as oncogenes, indicating that normal lung cell compromised on an oncogenic change displays some transposon expression reprogramming that seems to be genome-location dependent. Supporting this is the finding that most differentially expressed transposons change their expression in the same direction than their adjacent genes, and with a similar level of change. The analysis of adjacent genes may reveal or confirm important lung cancer biomarkers as well as new insights in its molecular basis.
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Acknowledgements
This work was funded by the NeumoSur grants 12/2015 and 14/2016. The authors also thankfully acknowledge the computer resources and the technical support provided by the Plataforma Andaluza de Bioinformatica of the University of Malaga.
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Arroyo, M., Larrosa, R., Claros, M.G., Bautista, R. (2019). Expression Change Correlations Between Transposons and Their Adjacent Genes in Lung Cancers Reveal a Genomic Location Dependence and Highlights Cancer-Significant Genes. In: Rojas, I., Valenzuela, O., Rojas, F., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2019. Lecture Notes in Computer Science(), vol 11465. Springer, Cham. https://doi.org/10.1007/978-3-030-17938-0_8
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DOI: https://doi.org/10.1007/978-3-030-17938-0_8
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