Effect of culture conditions on microRNA expression in primary adult control and COPD lung fibroblasts in vitro

In Vitro Cell Dev Biol Anim. 2015 Apr;51(4):390-9. doi: 10.1007/s11626-014-9820-8. Epub 2015 Jan 1.

Abstract

In vitro cell cultures, including lung fibroblasts, have been used to identify microRNAs (miRNAs) associated with chronic obstructive pulmonary disease (COPD) pathogenesis. However, culture conditions may affect miRNA expression. We examined whether miRNA expression in primary adult lung fibroblasts varies with cell density or passage in vitro and whether culture conditions confound the identification of altered miRNA expression in COPD lung fibroblasts. Primary adult control and COPD lung fibroblasts were cultured until passage 3 or 8, after which cells were further cultured for 3 or 7 d (low vs. high density). Then, cells at low density were cultured with serum-free media, and those at high density were cultured with serum-free media in the absence or presence of interleukin-1β (IL-1β) and tumor necrosis factor alpha (TNF-α) for 24 h. RNA was extracted to perform miRNA microarray from which 1.25-fold differential expression and 10% false discovery rate were applied to identify "invariant" and "variant" miRNA for the various culture conditions. Of the 2226 miRNAs evaluated, 39.0% for cell density, 40.7% for cell passage, and 29.4% for both conditions were identified as "invariant" miRNAs. Furthermore, 38.1% of the evaluated miRNAs were "invariant" for cell passage with IL-1β and TNF-α. Differentially expressed miRNAs between control and COPD lung fibroblasts were identified with and without IL-1β and TNF-α, and of these, 32 out of the 34 top-ranked miRNAs exceeded the differences due to culture conditions. Thus, culture conditions may affect miRNA expression of adult human lung fibroblasts. Nevertheless, in vitro cultures can be used to assess differential miRNA expression in COPD lung fibroblasts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Case-Control Studies
  • Cell Count
  • Cells, Cultured
  • Culture Media, Serum-Free / pharmacology
  • Female
  • Fibroblasts / cytology*
  • Fibroblasts / drug effects
  • Fibroblasts / physiology
  • Humans
  • Interleukin-1beta / pharmacology
  • Lung / cytology
  • Lung / pathology
  • Male
  • MicroRNAs / genetics*
  • Middle Aged
  • Pulmonary Disease, Chronic Obstructive / pathology*
  • Tumor Necrosis Factor-alpha / pharmacology

Substances

  • Culture Media, Serum-Free
  • Interleukin-1beta
  • MIRN146 microRNA, human
  • MicroRNAs
  • Tumor Necrosis Factor-alpha