Repeat expression is linked to patient survival and exhibits single nucleotide variation in pancreatic cancer revealing LTR70:r.879A>G

Yandim C., KARAKÜLAH G.

GENE, vol.822, 2022 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 822
  • Publication Date: 2022
  • Doi Number: 10.1016/j.gene.2022.146344
  • Journal Name: GENE
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Aquatic Science & Fisheries Abstracts (ASFA), Artic & Antarctic Regions, BIOSIS, CAB Abstracts, Chemical Abstracts Core, EMBASE, Food Science & Technology Abstracts, MEDLINE, Veterinary Science Database
  • Keywords: Repetitive DNA, Pancreatic cancer, RNA-seq, Transcriptome, Survival, Single nucleotide variation, REPETITIVE DNA, TRANSPOSABLE ELEMENTS, RNA, CELLS, HETEROCHROMATIN, METHYLATION, ACTIVATION, PACKAGE, GENES, MECP2
  • Dokuz Eylül University Affiliated: Yes

Abstract

Despite an overwhelming number of cancer literature reporting the links between patient survival and the expression levels of genes or mutations/single nucleotide variations (SNVs) on them, there is only limited information on repeat elements, which make at least half the human genome. Here, we analysed RNA-seq data obtained from primary pancreatic cancer tissues of 51 patients and revealed that two transposons, HERVI-int and X6A_LINE, showed an upregulation trend in the patients who lived shorter, along with 56 other potential repeats which were linked to survival. We also detected expressed single nucleotide variations (SNVs) on repeats, among which LTR70:r.879A>G stands out with the effect of its presence on this particular repeat's expression levels and a significant link to overall patient survival. Interestingly, the expression of LTR70:r.879A>G correlated with different cancer genes in comparison to its reference version highlighting the involvement of BRAF and Fumerate Hydratase with this expressed SNV. This is one of the first studies revealing possible links between repeat expression and survival in cancer and it warrants further research in this avenue.