Distinct transcriptional and functional features of regenerative mouse neonatal cardiac macrophages

Abstract Background The myocardium of neonatal mice is able to regenerate after myocardial infarction (MI), whereas in adults the formation of scar predominantly occurs following heart injury. Macrophages are involved in the fibrotic response in adult mouse hearts, but also required for successful regeneration in neonates. Recent work has demonstrated that macrophages directly contribute collagen to scar formation following MI. Furthermore, neonatal and adult cardiac macrophages have divergent transcriptional responses to injury. Here, we describe differential transcriptomes and signalling pathways of these functionally distinct neonatal resident cardiac macrophages. Methods Hearts from neonatal P1, P7 and adult CD1 mice (n=3 per group) were digested with collagenase to produce a single cell suspension. Macrophages were isolated by FACS and identified as Ly6G, F4/80+, LyChi/lo cells. Macrophage whole transcriptomes were measured by Illumina RNA-sequencing. Transcript abundance was quantified from raw reads by Salmon and analysis of differentially expressed (DE) genes was carried out with DESeq2. Gene Ontology (GO) enrichment analysis of DE genes was performed with PANTHER. Genes were ranked according to p-value for differential expression, then these ranked genes were used for Gene Set Enrichment Analysis (GSEA) to detect enriched gene sets from the Molecular Signatures Database. Results RNA-sequencing of transcriptomes from neonatal P1, P7 and adult mouse macrophages from hearts highlighted distinct gene expression profiles. The greatest differences were between P1 vs. adult (4,494 differentially expressed (DE) genes at p