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.

Our spatio-temporal map of lesion repair in the heart at single-cell resolution is now published in @natureportfolio.nature.com Cardiovascular Research.
www.nature.com/articles/s44...
We dissected dynamics of multicellular niches that control cardiac repair. See 🧵 for highlights.

The Roadmap of the Human Liver Cell Atlas is out in @natrevgastrohep.nature.com laying out the scope and goals of our Human Liver Cell Atlas emerging from the @cziscience.bsky.social funded Liver Seed Network.
www.nature.com/articles/s41...

Registration for our "Advances in Single-Cell Technologies" meeting is still open and we invite abstract submissions until October 30th. Join us in beautiful Freiburg together with an excellent line-up of single-cell technology experts!
www.uniklinik-freiburg.de/single-cell-...

Join our "Advances in Single-Cell Technologies" meeting in December in Freiburg, co-organised with Marco Prinz and @katrinkierdorf.bsky.social. Excellent line-up of speakers covering spatial technologies, lineage tracing, computational methods, and more.
www.uniklinik-freiburg.de/single-cell-...

New preprint from the lab! Using multiplexed spatial analysis and single-cell multiomics, we resolved the portal liver immune niche and identified crosstalk between cholangiocytes, dendritic cells and gdT cells that controls fibrosis in a mouse cholangitis model.
www.biorxiv.org/content/10.1...

Consider attending the MOPITAS autumn school on Spatial Transcriptomics in Munich with expert lectures and hands-on sessions for all steps of spatial transcriptomics data analysis.
event.sdu.dk/mopitas-scho...

Registration for the upcoming symposium "Imaging the Immune System VI" in Würzburg is still open. Fantastic speaker line-up at a beautiful historic venue in the centre of Würzburg.

imaging-immune-system.wuesi.com

Our new lab coffee machine. What a beauty…

NiCo is out! Our new algorithm for spatial transcriptomics data analysis predicts the crosstalk of cell types co-localized in tissue niches and sheds light on signalling mediators and downstream effects of cell-cell interactions by inferring covarying gene programs.

www.nature.com/articles/s41...

Hiring! I'm looking for a postdoc in machine learning of spatial single-cell data. Exciting project to develop methods for modelling cellular circuits in disease and regeneration of heart, liver and bone marrow using Xenium data from our lab.
tinyurl.com/ymkvk7vn

Excited to share our study on spatio-temporal reconstruction of cardiac scar formation led by Andy Chan. We combine scRNA-seq with spatial transcriptomics to resolve the fibrotic niche and the niche of dedifferentiating cardiomyocytes.
www.biorxiv.org/content/10.1...