title: Effect of culture conditions on microRNA expression in primary adult control and COPD lung fibroblasts in vitro.
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.
authors.affiliation: Pulmonary, Critical Care, Sleep and Allergy Medicine, University of Nebraska Medical Center, Omaha, NE, USA, junijunieight@yahoo.co.jp.
authors.forename: Jun
authors.initials: J
authors.lastname: Ikari
authors.forename: Lynette M
authors.initials: LM
authors.lastname: Smith
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Nelson
authors.forename: Shunichiro
authors.initials: S
authors.lastname: Iwasawa
authors.forename: Yoko
authors.initials: Y
authors.lastname: Gunji
authors.forename: Maha
authors.initials: M
authors.lastname: Farid
authors.forename: Xingqi
authors.initials: X
authors.lastname: Wang
authors.forename: Hesham
authors.initials: H
authors.lastname: Basma
authors.forename: Carol
authors.initials: C
authors.lastname: Feghali-Bostwick
authors.forename: Xiangde
authors.initials: X
authors.lastname: Liu
authors.forename: Dawn L
authors.initials: DL
authors.lastname: DeMeo
authors.forename: Stephen I
authors.initials: SI
authors.lastname: Rennard
mesh_terms: D000368:Aged; D016022:Case-Control Studies; D002452:Cell Count; D002478:Cells, Cultured; D016895:Culture Media, Serum-Free / Q000494:pharmacology; D005260:Female; D005347:Fibroblasts / Q000166:cytology* / Q000187:drug effects / Q000502:physiology; D006801:Humans; D053583:Interleukin-1beta / Q000494:pharmacology; D008168:Lung / Q000166:cytology / Q000473:pathology; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D029424:Pulmonary Disease, Chronic Obstructive / Q000473:pathology*; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology
chemical_list: D016895:Culture Media, Serum-Free; D053583:Interleukin-1beta; C542542:MIRN146 microRNA, human; D035683:MicroRNAs; D014409:Tumor Necrosis Factor-alpha