Spatiotemporal dynamics of the cardioimmune niche during lesion repair [scRNA-seq]

[Important Note: Some files appear to have become corrupted during upload, and we are currently replacing them, which may take a few working days. In the meantime, if you need access to the count matrix or metadata files, please email [e-mail]. We apologize for the inconvenience.] The heart is one of the least regenerative organs in humans, and heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes during cardiac wound healing is an essential prerequisite to reduce health burden and improve cardiac function after myocardial tissue damage. By integrating single-cell RNA-sequencing with imaging-based spatial transcriptomics, we reconstructed the spatiotemporal dynamics of the fibrotic niche after ventricular injury in adult mice. Our analysis revealed dynamic regulation of local cell communication niches over time. We identified interactions that regulate cardiac repair, including fibroblast proliferation silencing by Trem2high macrophages that prevents excessive fibrosis. Moreover, we discovered a rare population of dedifferentiating cardiomyocytes early post-lesioning repair, sustained by signals from myeloid and lymphoid cells. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatiotemporal cell type atlas offers valuable insights into the heterocellular interactions that control cardiac repair. Overall design: We utilized two common mouse models to introduce ventricular lesions: ligation of the left anterior descending coronary artery followed by reperfusion (LAD) and cryoablation of the left ventricle (Cryo). After recovery of animals from lesion induction, we isolate and vibratome-cut the LV into tissue slices of 300µm thickness. Slices had a radius of ~5mm, and the IZ (refers to day 1-7 of the wound)/ fibrotic zone (FZ, refers to day 28-56 of the repaired wound) was placed in the center surrounded by border zone (BZ) tissue. For scRNA-seq, CM and non-myocytes (NM) were isolated from cardiac slices obtained at 1, 3, 7, 28 and 56 days post-surgery. After CM exclusion, we combined unbiasedly-sorted samples with samples enriched for endothelial cells (EC), smooth muscle cells (SMC), pericytes and Schwann cells (SwC) (CD31+/CD146+), dendritic cells (CD45+CD14-CD11c+) and lymphocytes (CD45+CD14-CD11c-). In addition, we isolated DAPI+PCM-1+ nuclei for single-nucleus RNA-sequencing (snRNA-seq) of CM.