Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation.
Jessica Schira-HeinenAgathe CzaplaMarion HendricksAndreas KloetgenWasco WruckJames AdjayeGesine KöglerHans Werner MüllerKai StühlerHans-Ingo TrompeterPublished in: Scientific reports (2020)
The contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.
Keyphrases
- rheumatoid arthritis
- stem cells
- disease activity
- cord blood
- ankylosing spondylitis
- mass spectrometry
- transcription factor
- high resolution
- interstitial lung disease
- binding protein
- systemic lupus erythematosus
- single cell
- endothelial cells
- air pollution
- cell proliferation
- poor prognosis
- magnetic resonance imaging
- liquid chromatography
- gene expression
- cell therapy
- cell cycle arrest
- genome wide
- computed tomography
- newly diagnosed
- bone marrow
- ms ms
- oxidative stress
- long non coding rna
- gas chromatography
- pi k akt