Thanks, Gennady! If you email me, I can connect you with Andy who performed the data analysis.

Thanks, Kilian!

This massive project was led by my excellent postdoc @andysonchan.bsky.social.
This work would not have been possible without all our fantastic collaborators, in particular, the groups of Peter Kohl and Franziska Schneider-Warme who provided essential experimental in vivo methods.

Our data provide a rich basis for the identification of molecular targets for novel therapeutic approaches to improve heart healing after myocardial infarction.

Unexpectedly, our data reveal a rare population of progenitor-like cardiomyocytes that up-regulate proliferation gene programs. NiCo predicted rare immune cells (ILC2) together with myeloid and endothelial cells as synergistic inducers of dedifferentiation via BMP7, TWEAK, and IL1B signalling.

Based on NiCo’s covariation analysis, we predict signalling pathways mediating mutual suppression of proliferation between myofibroblasts and macrophages that could be an essential molecular break limiting excessive scar formation. We provide extensive in vitro validation of these pathways.

Using our published NiCo algorithm, we infer cellular niche networks and molecular drivers of cell state dynamics. In particular, we predict and validate signalling pathways that control cell state changes of monocytes into pro-inflammatory and subsequently into immune-regulatory macrophages.

We dissected dynamics of cellular states across all cell populations, including rare cell types underrepresented in available resources. In particular, we resolve dynamics of a broad spectrum of immune cell types.

We generated a large resource of single-cell transcriptome and single-cell resolution spatial transcriptomics (Xenium) data for two common models of cardiac repair (cryoinjury and LAD). We demonstrate very similar responses in both models.

Join us for a series of presentations from leading data science experts, including @francescafinotello.bsky.social, @dominicgrun.bsky.social, Johanna Klughammer, Malte Lücken, @fabiantheis.bsky.social and @jwrth.genomic.social.ap.brid.gy.

Congrats, Shalin and team! Really looking forward to read this!