CITE-seq of cardiac CD45+ leukocytes in mice with myocardial infarction and NK cell depletion

Myocardial infarction triggers an inflammatory response which plays a crucial role in repair and remodelling of the infarcted heart. In this study we examined the role of Natural Killer cells (NK cells), a specific type of inflammatory cells, in controlling the inflammatory response and cardiac repair after myocardial infarction. To assess effects on local inflammation, we used single-cell RNA-seq and CITE-seq to profile cardiac CD45+ leukocytes in infarcted mice with or without NK cell depletion. Biological replicates from the different experimental conditions were pooled using cell hashing as follows: hashtag 1 to 5 control mice; hashtags 6 to 10: NK-depleted mice. Overall design: 8-12 week old male C57BL6J mice underwent permanent coronary ligation to induce myocardial infarction and were injected i.p. with a depleting mouse anti-mouse NK1.1 monoclonal antibody or with and isotype control antibody 1 hour after coronary artery ligation. Five days after the induction of myocardial infarction, CD45+ cells were extracted from the infarcted heart and processed for single-cell RNA-seq with CITE-seq and cell hashing.