title: Impact of microRNA-130a on the neutrophil proteome.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are important for the development and function of neutrophils. miR-130a is highly expressed during early neutrophil development and regulates target proteins important for this process. miRNA targets are often identified by validating putative targets found by in silico prediction algorithms one at a time. However, one miRNA can have many different targets, which may vary depending on the context. Here, we investigated the effect of miR-130a on the proteome of a murine and a human myeloid cell line.
  
  
  RESULTS
  Using pulsed stable isotope labelling of amino acids in cell culture and mass spectrometry for protein identification and quantitation, we found 44 and 34 proteins that were significantly regulated following inhibition of miR-130a in a miR-130a-overexpressing 32Dcl3 clone and Kasumi-1 cells, respectively. The level of miR-130a inhibition correlated with the impact on protein levels. We used RAIN, a novel database for miRNA-protein and protein-protein interactions, to identify putative miR-130a targets. In the 32Dcl3 clone, putative targets were more up-regulated than the remaining quantified proteins following miR-130a inhibition, and three significantly derepressed proteins (NFYC, ISOC1, and CAT) are putative miR-130a targets with good RAIN scores. We also created a network including inferred, putative neutrophil miR-130a targets and identified the transcription factors Myb and CBF-β as putative miR-130a targets, which may regulate the primary granule proteins MPO and PRTN3 and other proteins differentially expressed following miR-130a inhibition in the 32Dcl3 clone.
  
  
  CONCLUSIONS
  We have experimentally identified miR-130a-regulated proteins within the neutrophil proteome. Linking these to putative miR-130a targets, we provide an association network of potential direct and indirect miR-130a targets that expands our knowledge on the role of miR-130a in neutrophil development and is a valuable platform for further experimental studies.
authors.affiliation: The Granulocyte Research Laboratory, Department of Hematology, National University Hospital, University of Copenhagen, 9322, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark. corinna.cavan.pedersen@regionh.dk.
authors.forename: Corinna Cavan
authors.initials: CC
authors.lastname: Pedersen
authors.affiliation: Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark. jan.refsgaard@cpr.ku.dk.
authors.forename: Jan Christian
authors.initials: JC
authors.lastname: Refsgaard
authors.affiliation: Department of Autoimmunology & Biomarkers, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark. ooe@ssi.dk.
authors.forename: Ole
authors.initials: O
authors.lastname: Østergaard
authors.affiliation: Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark. lars.juhl.jensen@cpr.ku.dk.
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: Department of Autoimmunology & Biomarkers, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark. nhe@ssi.dk.|Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, J.B. Winsløws Vej 19, DK-5000, Odense C, Denmark. nhe@ssi.dk.
authors.forename: Niels Henrik Helweg
authors.initials: NH
authors.lastname: Heegaard
authors.affiliation: The Granulocyte Research Laboratory, Department of Hematology, National University Hospital, University of Copenhagen, 9322, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark. niels.borregaard@regionh.dk.
authors.forename: Niels
authors.initials: N
authors.lastname: Borregaard
authors.affiliation: The Granulocyte Research Laboratory, Department of Hematology, National University Hospital, University of Copenhagen, 9322, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark. jack.cowland@regionh.dk.
authors.forename: Jack Bernard
authors.initials: JB
authors.lastname: Cowland
mesh_terms: D000818:Animals; D002460:Cell Line; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D022423:Myeloid Cells / Q000378:metabolism; D009504:Neutrophils / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics / Q000379:methods
chemical_list: C582652:MIRN130 microRNA, mouse; D035683:MicroRNAs; D020543:Proteome