# Impact of microRNA-130a on the neutrophil proteome

## TL;DR

This study explores how microRNA-130a affects the protein levels in neutrophils, revealing new insights into its role in neutrophil development.

## Contribution

The study experimentally identifies miR-130a-regulated proteins and constructs an association network of potential targets.

## Key findings

- Inhibition of miR-130a significantly regulated 44 and 34 proteins in murine and human myeloid cell lines.
- Three proteins (NFYC, ISOC1, and CAT) were identified as putative miR-130a targets with high RAIN scores.
- Transcription factors Myb and CBF-β were linked as putative miR-130a targets, potentially regulating granule proteins.

## Abstract

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.

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.

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.

The online version of this article (doi:10.1186/s12865-015-0134-8) contains supplementary material, which is available to authorized users.