Jonas C. Schupp

Multiscale mapping of venous remodelling in idiopathic pulmonary fibrosis

This study maps venous remodelling in IPF using multiscale imaging and molecular data, showing venous enlargement correlates with disease severity and poor survival.

Single-cell and spatial transcriptomics resolve airway obliteration in bronchiolitis obliterans syndrome

This study uses single-cell and spatial transcriptomics to identify structural cell circuits in BOS lungs and their spatial organization during airway obliteration.

Aberrant and Ectopic Cell Populations of the Fibrotic Pushing Border in Restrictive Allograft Syndrome after Lung Transplantation

This study identifies aberrant cell populations in RAS lungs using snRNA-seq and histology, revealing a fibrotic niche composed of specific cell types with potential therapeutic targets.

Alveolar niche disruption and aberrant epithelial reprogramming are early hallmarks of idiopathic pulmonary fibrosis

This study identifies early alveolar niche disruption and aberrant epithelial reprogramming in IPF using multi-modal analyses of patient cohorts.

The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis

This paper presents the first single-nucleus RNA sequencing atlas of pleuroparenchymal fibroelastosis, identifying novel cell states and their spatial organization in lung fibrosis.

Clonal Hematopoiesis Instructs Maladaptive Tissue Repair to Promote Fibrosis

This study shows clonal hematopoiesis promotes fibrosis by altering macrophage behavior and tissue repair processes in lung disease.

Spatial transcriptomics uncovers hybrid, pro-inflammatory and pro-fibrotic cellular niches in pulmonary granuloma of patients with chronic sarcoidosis

This study uses spatial transcriptomics to identify hybrid pro-inflammatory and pro-fibrotic cellular niches in sarcoidosis granulomas, linking them to fibrosis and immune responses.

A multicenter spatial transcriptomics atlas of human tuberculosis and non-tuberculous mycobacterial disease

This study creates a spatial transcriptomics atlas of human tuberculosis and non-tuberculous mycobacterial granulomas, identifying distinct niches and immune signatures.

Spatial and Single-cell Transcriptomics Reveal Programs Governing Fibroblastic Foci Fibroblasts

The paper identifies transcriptional programs in fibroblastic foci fibroblasts using spatial and single-cell transcriptomics, revealing MMP11 as a prognostic biomarker and potential therapeutic target.

Alveolar epithelial cell plasticity and injury memory in human pulmonary fibrosis

Single-nucleus multiomic and ex vivo lung slice profiling of human idiopathic pulmonary fibrosis identifies Alveolar Intermediate cells bridging alveolar and Aberrant Basaloid states and reveals AP-1 chromatin injury memory.

Single-cell RNA Sequencing Analysis of Sputum Cell Transcriptomes Reveals Pathways and Communication Networks That Contribute to the Pathogenesis of Asthma

This study uses single-cell RNA sequencing to analyze sputum cells from asthma patients and controls, identifying dysregulated pathways and communication networks involved in asthma pathogenesis.

Engineered Whole Lungs for Tissue Biology

This study develops an engineered whole-lung tissue model to study tissue organization and alveolar barrier function, showing improved barrier function with alveolar macrophages.

Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration

The paper identifies cell-to-cell communication between mesothelial cells and alveolar tuft cells that regulates lung regeneration after pneumonectomy.

Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases

This study uses single-cell RNA sequencing to identify common and distinct immune aberrations in IPF and FHP, revealing shared monocyte features and disease-specific lymphocyte and receptor repertoires.

iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects

iDESC identifies differential expression in scRNA-seq data with multiple subjects by separating subject effects from disease effects, showing better performance than existing methods.

CINS: Cell Interaction Network inference from Single cell expression data

CINS infers differential cell-cell interactions between conditions using scRNA-Seq data and identifies the proteins involved in these interactions.

Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data

Connectome quantifies and visualizes cell-cell signaling networks from single-cell RNA-sequencing data using a software package for R.

Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in In Vitro, In Vivo and Ex Vivo Models of Pulmonary Fibrosis

This study identifies saracatinib as a potential anti-fibrotic drug effective in multiple models of pulmonary fibrosis, showing equal or superior efficacy compared to existing treatments.

Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis

This study uses single-cell RNA-seq to identify aberrant cell populations in IPF lungs, revealing novel basaloid cells and vascular endothelial changes.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.