A5012234490- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Neonatal Respiratory Health Research
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Congenital Diaphragmatic Hernia Studies
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Tumors and Oncological Cases
- Cancer Cells and Metastasis
- Microfluidic and Bio-sensing Technologies
- Hedgehog Signaling Pathway Studies
- Epigenetics and DNA Methylation
- Biosensors and Analytical Detection
- 3D Printing in Biomedical Research
- Head and Neck Surgical Oncology
- Medical Imaging and Pathology Studies
- Pulmonary Hypertension Research and Treatments
- Congenital heart defects research
- IL-33, ST2, and ILC Pathways
Stockholm University
2020-2024
Science for Life Laboratory
2020-2024
Wenner-Gren Foundations
2023
Abstract The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins mechanisms generating heterogeneity, we created a comprehensive topographic atlas of early human development. Here report 83 states several spatially resolved developmental trajectories predict interactions within defined niches. We integrated single-cell RNA sequencing transcriptomics into web-based, open platform for interactive exploration. show gene...
Fibroblast-to-myofibroblast conversion is a major driver of tissue remodelling in organ fibrosis. Distinct lineages fibroblasts support homeostatic niche functions, yet their specific activation states and phenotypic trajectories during injury repair have remained unclear.
Changes in cell identities and positions underlie tissue development disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of states, spatially resolved mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), sensitive, multiplex RNA approach. Direct hybridization padlock probes on is followed by circularization with SplintR ligase rolling circle amplification (RCA) the...
ABSTRACT The tracheal epithelium is a primary target for pulmonary diseases as it provides conduit air flow between the environment and lung lobes. cellular molecular mechanisms underlying airway epithelial cell proliferation differentiation remain poorly understood. Hedgehog (HH) signaling orchestrates communication mesenchymal cells in lung, where modulates stromal proliferation, back to epithelium. Here, we reveal previously unreported autocrine function of HH cells. Epithelial depletion...
Abstract Fibroblast to myofibroblast conversion is a major driver of tissue remodeling in organ fibrosis. Several distinct lineages fibroblasts support homeostatic niche functions, yet, specific activation states and phenotypic trajectories during injury repair have remained unclear. Here, we combined spatial transcriptomics, longitudinal single-cell RNA-seq genetic lineage tracing study fibroblast fates mouse lung regeneration. We discovered transitional state characterized by high Sfrp1...
Summary The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins mechanisms generating cell heterogeneity, we created a first comprehensive topographic atlas of early human development. We report 83 states, several spatially-resolved developmental trajectories predict interactions within defined niches. integrated scRNA-Seq spatial transcriptomics into web-based, open platform for interactive exploration. illustrate...
<title>Abstract</title> Integration of single cell mRNA sequencing data from millions cells revealed a high diversity types in the healthy and diseased human lung. In large complex organ, which is also constantly exposed to external agents, it crucial understand influence lung tissue topography or factors on gene expression variability within each type. Here, we applied three spatial transcriptomics approaches, to: (i) localize majority types, including rare epithelial topography, (ii)...
Abstract Changes in cell identities and positions underlie tissue development disease progression. Although, single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell-states, spatially resolved mapping presents a challenging task. We developed SCRINSHOT ( S ingle C ell R esolution IN itu H ybridization O n T issues), sensitive, multiplex RNA approach. Direct hybridization padlock probes on is followed by circularization with SplintR ligase rolling circle...
Abstract Secretory cells are major structural and functional constituents of the lung airways. Their spatial organization specification mechanisms partially understood. Here, we labelled secretory airway cell types analysed them at single-cell resolution. We found opposing, overlapping gene-expression gradients along proximal-distal axis superimposed on a general gene program encoding detoxification. One graded is elevated proximally relates to innate immunity, whereas other enriched...
Epithelial cells receive multiple signals from the surrounding mesenchymal niche, which controls homeostasis and activation of stem upon injury. Along airway tree respiratory unit numerous specialized epithelial cell types are surrounded by a poorly defined heterogeneous mesenchyme. This includes smooth muscle, endothelium, stromal cells, such as pericytes populations different fibroblast subtypes. To use an unbiased method for classification subtypes, we used single transcriptomics on whole...
Abstract The tracheal epithelium is a primary target for pulmonary diseases as it provides conduit air flow between the environment and lung lobes. cellular molecular mechanisms underlying airway epithelial cell proliferation differentiation remain poorly understood. Hedgehog (Hh) signaling orchestrates communication mesenchymal cells in lung, where modulates stromal proliferation, back to epithelium. Here, we reveal new, autocrine function of Hh cells. Epithelial depletion ligand Sonic...
SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues) is a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA followed by circularization with SplintR ligase and rolling circle amplification (RCA) the hybridized probes. Sequential detection RCA-products using fluorophore-labeled oligonucleotides profiles thousands cells in tissue sections. We evaluated specificity sensitivity murine human organ quantification marker gene expression shows...
SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues) is a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA followed by circularization with SplintR ligase and rolling circle amplification (RCA) the hybridized probes. Sequential detection RCA-products using fluorophore-labeled oligonucleotides profiles thousands cells in tissue sections. We evaluated specificity sensitivity murine human organ quantification marker gene expression shows...