Spatial and Single-cell Transcriptomics Reveal Programs Governing Fibroblastic Foci Fibroblasts https://www.biorxiv.org/content/10.1101/2025.09.26.678416v1

2025 Lasker–DeBakey Clinical Medical Research Award Transformative Research in Cystic Fibrosis An illustrated diagram showing advances in the understanding and treatment of cystic fibrosis.

Drs. Michael Welsh, Jesús González, and Paul Negulescu have won the 2025 Lasker–DeBakey Clinical Medical Research Award for their roles in developing treatments for cystic fibrosis. Learn more: nej.md/41L3UCI

#MedSky #PulmSky #Genetics

Macrophage-derived oncostatin M repairs the lung epithelial barrier during inflammatory damage Tissue repair programs must function alongside antiviral immunity to restore the lung epithelial barrier following infection. We found that macrophage-derived oncostatin M (OSM) counteracted the patho...

#WeekendRead! #InterferonsFriendsOrFoes?! @ruthfranklinlab.bsky.social, Medzhitov, Hoagland, Rodriguez-Morales &co show @science.org that macrophage-derived oncostatin M overcomes type I IFN detrimental responses during severe influenza lung infection by driving AT-II epithelial cell proliferation!

This is remarkable

Intruiging preprint using #singlecell genomic profiles of treated and untreated #IPF patients to identify a "therapeutic gap" of established anti-fibrotic treatments and implicating STAT3 in IPF pathogenesis. Have a look 👇
www.biorxiv.org/content/10.1...

Finally out as reprint!!!
"Alveolar epithelial cell plasticity & injury memory in human pulmonary fibrosis".
Glad to share the results of our single nuc-seq & single cell ATAC-seq analyses of human IPF & PCLS before peer review - see the key findings in 🧵👇🏽
www.biorxiv.org/content/10.1...

Finally! The Pulmonary Fibrosis Drug Connectome is on #IPFCellAtlas!! If you want to know if a drug is antifibrotic, which cells it targets, or what drugs target a gene you like, in what cells - go to ipfcellatlas.com click on the Connectome tab. Enjoy - It's Free!!!
#DataSharing
#CurePF4All

Huge personal milestone today: thesis submitted 🎉 @lmumuenchen.bsky.social @www.helmholtz-munich.de — and first day of clinical training @ University Hospital Basel 🇨🇭! Grateful and excited for what’s ahead 🙌

Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment Lung-resident immune cells, spanning both innate and adaptive compartments, preserve the integrity of the respiratory barrier, but become pathogenic if dysregulated[1][1]. Current in vitro organoid mo...

I enjoyed reading this very cool preprint over the weekend - congratulations @graycamplab.bsky.social and Laurian Cabon, should be a very powerful tool for the field 😍
www.biorxiv.org/content/10.1...

Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis - Nature Biotechnology Human pluripotent cells are differentiated into lung progenitors and alveolar type 1 cells.

On my reading list for the weekend:

Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis | @naturebiotech.bsky.social

With some intruiging insights into Heřmanský–Pudlák Syndrome

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

RUNX2 promotes fibrosis via an alveolar-to-pathological fibroblast transition - Nature The use of two mouse models of pulmonary fibrosis helped the identification of the transcription factor RUNX2 as a regulator of the transition of alveolar fibroblasts to pathological fibroblasts.

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

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - Nature Genetics Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.

Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!

Front cover of the current issue of the EMBO journal featuring microscope images of organoid models of alveoli

Great to be front page news! Congratulations @jennydickens41.bsky.social Read the paper here: www.embopress.org/doi/full/10....

Super cool an intriguing work by the group of @hansclevers.bsky.social - A human organoid model of alveolar regeneration reveals distinct epithelial response to interferon-gamma

www.biorxiv.org/content/10.1...

Awesome and super helpful - thank you so very much!

I am aware of he amazing work of @andreasmoor.bsky.social and his group - but I didn’t find anything comparable in humans!

#MedSky
#ImmunoSky

Looking for sc or snRNA-seq datasets/studies in humans that specifically profile #eosinophils or contain a substantial number of them!

If you have any leads, please share! And if you don’t but know someone who might, please re-post so it reaches the right people :)
Many, many thanks!

Congratulations!

Mapping cells through time and space with moscot - Nature Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...

Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep

Precision-Cut Lung Slices: Emerging Tools for Preclinical and Translational Lung Research: An Official American Thoracic Society Workshop Report
@atscommunity.bsky.social #medsky

🔓 Open Access

🔗 tinyurl.com/mwxrej45

Imperfect wound healing sets the stage for chronic diseases Although the age of the genome gave us much insight about how our organs fail with disease, it also suggested that diseases do not arise from mutations alone; rather, they develop as we age. In this R...

Thought-provoking review by Paul Martin et al. including @ipfdoc.bsky.social on how imperfect epithelial repair sets the stage for chronic disease 🧪

www.science.org/doi/10.1126/...

The marsilea logo with a cross layout in the center and gray background saying "Transform your data landscape".

Yimin's paper on a a novel visualization paradigm and implementation of cross-layout visualizations is now published in the journal Genome Biology (genomebiology.biomedcentral.com/articles/10....). Check it out at github.com/Marsilea-viz...

Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...

To all interested in all things related to Pulmonary Fibrosis - the #CureFibrosis starter pack is ready for 2025 - please let me know if you wish to be included and ofcourse follow - use #CurePF4All #CureIPF #CureFibrosis etc
#HappyNewYear
go.bsky.app/6hgNDdr

Would love to join, if possible!

Multiscale single-cell assessment of the fibrotic niche in idiopathic pulmonary fibrosis Background: Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal disease characterized by excessive extracellular matrix deposition within the lung. Recent advances in single-cell ...

Delighted 2 share latest preprint evaluating fibrotic niche in #IPF using spatial transcriptomics & Hyperion mass cytometry. We believe it raises some interesting questions about IPF pathogenesis IPF.
@nebanovich.bsky.social @kaminskimed.bsky.social

www.biorxiv.org/content/10.1...

Dynamic behavior and lineage plasticity of the pulmonary venous endothelium - Nature Cardiovascular Research Wong et al. identify Slc6a2 as a marker of pulmonary venous endothelial cells and demonstrate that these cells differentiate into capillary endothelial cells during vascular regeneration after lung in...

Exciting paper in Nature CVR: venous ECs branch and differentiate into capillary ECs to regenerate the alveolar gas exchange unit following lung injury - but NOT in fibrotic (KRT5+) or AT1 depleted regions - food for thought and of potential relevance for #cureIPF

www.nature.com/articles/s44...

1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.

Would love to be added!

Herzlichen Glückwunsch, Kilian!!!