Cardiac resident macrophages (crMΦs) constitute up to 5% of the non-myocyte population in the murine heart and were shown to play key roles in cardiac homeostasis and disease. Long non-coding RNAs (lncRNAs) are regulatory molecules that impact characteristics such as cell identity, proliferation or cell migration. However, the function of lncRNAs in crMΦ remains enigmatic. Using RNASeq (>100 million reads/sample) of purified murine crMΦs and single cell sequencing (scSeq) of total murine myocardium in health and disease, we could identify the lncRNA Schlafenlnc as a highly enriched and abundant lncRNA in crMΦs. 

Using the CRISPR-Cas system we successfully deleted the full Schlafenlnc locus in a macrophage progenitor cell line. Next, we performed RNASeq of unstimulated as well as LPS-treated (inflammatory stimulus) Schlafenlnc-deficient macrophages. We could show that Schlafenlnc impacted on the expression level of genes which are associated with chemotaxis and migration, including Galectin-3 and MMP-14, two proteins which are also known to play an important role in cardiac disease. In line with these findings, we could show that Schlafenlnc-deficient macrophages display decreased chemotaxis as well as adhesion using cell-based assays. To analyze potential binding partners, we performed RNA-pulldown experiments followed by mass spectrometry analysis. Indeed, we could identify 27 interaction partners of Schlafenlnc. The function of these potential binding partners includes mRNA processing, transcriptional regulation and alternative splicing. 

Finally, to analyze the function of Schlafenlnc in vivo, we generated Schlafenlnc -deficient mice by gene targeting and employed cardiac function measurements as well as scSeq during health and a model of pressure overload of the left ventricle (transverse aortic constriction, TAC). Consistent with our in vitro data, we identified a macrophage migration defect in Schlafenlnc -deficient mice, which showed reduced macrophage infiltration 6 days after TAC. 

Collectively, our data show that the lncRNA Schlafenlnc is a critical regulator of macrophage migratory functions and might play an important role during cardiac disease.