FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis

Mirolyuba Ilieva, Henry E. Miller, Arav Agarwal, Gabriela K. Paulus, Jens Hedelund Madsen, Alexander J.R. Bishop, Sakari Kauppinen, Shizuka Uchida

Research output: Contribution to journalArticlepeer-review

Abstract

Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on fibroblasts, a common cell type in various organs and tissues. Using fibroblasts and changes in their expression profiles during fibrosis as a model system, we show that the overall expression level of lncRNA genes is significantly lower than that of protein-coding genes. Furthermore, we identified lncRNA genes whose expression is upregulated during fibrosis. Using dermal fibroblasts as a model, we performed loss-of-function experiments and show that the knockdown of the lncRNAs LINC00622 and LINC01711 result in gene expression changes associated with cellular and inflammatory responses, respectively. Since there are no lncRNA databases focused on fibroblasts and fibrosis, we built a web application, FibroDB, to further promote functional and mechanistic studies of fibrotic lncRNAs.

Original languageEnglish (US)
Article number13
JournalNon-coding RNA
Volume8
Issue number1
DOIs
StatePublished - Feb 2022

Keywords

  • Fibroblast
  • Fibrosis
  • Gene expression
  • LncRNA
  • RNA-seq

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics

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