RT Journal Article
T1 Biomarker potential of repetitive-element transcriptome in lung cancer
A1 Claros-Díaz, Manuel Gonzalo
A1 Arroyo, Macarena
A1 Bautista-Moreno, Rocío
A1 Larrosa-Jiménez, Rafael
A1 Cobo, Manuel Ángel
K1 Marcadores bioquímicos
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
YR 2019
FD 2019
LK https://hdl.handle.net/10630/29267
UL https://hdl.handle.net/10630/29267
LA eng
NO Arroyo M, Bautista R, Larrosa R, Cobo MÁ, Claros MG. 2019. Biomarker potential of repetitive-element tran- scriptome in lung cancer. PeerJ 7:e8277 http://doi.org/10.7717/peerj.8277
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 20 ene 2026