RT Journal Article
T1 Biomarker potential of repetitive-element transcriptome in lung cancer.
A1 Arroyo, Macarena
A1 Bautista, Rocio
A1 Larrosa, Rafael
A1 Cobo, Manuel Angel
A1 Claros, M Gonzalo
K1 Biomarker
K1 Differential expression
K1 Lung cancer
K1 Repetitive element
K1 Transcriptome
AB Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
PB PeerJ, Ltd.
SN 2167-8359
YR 2019
FD 2019-12-19
LK https://hdl.handle.net/10668/27792
UL https://hdl.handle.net/10668/27792
LA en
NO Arroyo M, Bautista R, Larrosa R, Cobo MÁ, Claros MG. Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ. 2019 Dec 19;7:e8277
NO This work was supported by Neumosur (grants 12/2015, 14/2016, and 5/2017), and co-funded by the European Union through the European Regional Development Fund (ERDF) 2014-2020 Programa Operativo de Crecimiento Inteligente together with Spanish Agencia Estatal de Investigación (TIN2017-88728-C2-1-R). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
DS RISalud
RD Apr 18, 2025