Jonathan A. Kropski

A 4D GelMA-Cad/Gelatin Hydrogel for High-Resolution DMD Bioprinting of Vascularized Soft Tissue Models

This paper develops a 4D GelMA-Cad/gelatin hydrogel for vascularized soft tissue bioprinting, showing improved print fidelity and matrix mechanics for tissue modeling.

IPF distal lung epithelial cells acquire a DNA methylation signature consistent with activation of basal cell transcriptional programs

The paper identifies DNA methylation changes in IPF lung epithelial cells linked to dysregulated transcriptional programs and impaired repair.

Inflammatory Fibroblasts Promote Repair After Injury Through Epithelial Proliferation

The paper identifies inflammatory fibroblasts that promote lung repair by enhancing epithelial proliferation through BMP signaling, validated across multiple models and human disease.

Fishing with Two Lines: A Hybrid Approach to Spatial Transcriptomic Discovery

The paper combines two spatial transcriptomic chemistries to improve both sensitivity and coverage in a single tissue section, showing high concordance and enabling more comprehensive analysis.

Sustained Yap/Taz activation promotes aberrant alveolar epithelial cell differentiation and drives persistent fibrotic remodeling

This study shows sustained Yap/Taz activation in alveolar epithelial cells leads to fibrotic remodeling and impaired repair, with potential therapeutic implications.

AlveolEye: Rapid and precise lung morphometry guided by computer vision

AlveolEye improves lung morphometry by using computer vision to rapidly and reproducibly calculate MLI and ASVD from H&E images, reducing variability and increasing precision across observers.

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomicsdataset

The paper introduces SpatialRNA, a Python package enabling the application of Graph Neural Networks to spatial transcriptomics data for domain detection.

T-cell Multiomic Analysis Identifies Subsets and Mechanisms of Interaction with Epithelial Cells in Idiopathic Pulmonary Fibrosis

The paper identifies T-cell subsets and their interactions with epithelial cells in IPF using multiomic profiling, revealing novel signaling pathways and activation patterns.

Denoising image-based spatial transcriptomics data with DenoIST

DenoIST improves spatial transcriptomics data by removing contaminating transcripts, enhancing gene expression specificity and cell type annotation.

Loss of Regulator of telomere elongation helicase (Rtel1) impairs alveolar epithelial cell progenitor function but does not exacerbate experimental fibrosis

This study shows RTEL1 regulates alveolar epithelial cell progenitor function but does not worsen experimental lung fibrosis in mice.

A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity

This paper creates a spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity using 1.2 million cells from 17 human infant lungs.

Accelerated Biological Aging in Familial Pulmonary Fibrosis

This study finds accelerated epigenetic aging in individuals at-risk for familial pulmonary fibrosis and patients, independent of telomere-related genetic variants or telomere length.

Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis

Xenium profiling of 343 genes in 1,126,820 nuclei from 19 human lungs maps fibrosis niches and orders alveolar remodeling from alveolar-capillary disruption to SPP1+ macrophage accumulation.

Rare variants and survival of patients with idiopathic pulmonary fibrosis

This study investigates the impact of rare variants and polygenic risk scores on survival in idiopathic pulmonary fibrosis patients, finding that rare variants are associated with worse outcomes.

Bronchopulmonary Dysplasia with Pulmonary Hypertension Associates with Loss of Semaphorin Signaling and Functional Decrease in FOXF1 Expression

The paper identifies loss of semaphorin signaling and reduced FOXF1 expression in BPD and BPD+PH using single-cell RNA sequencing and validates findings in a murine model.

Association between mosaic loss of chromosome Y and pulmonary fibrosis susceptibility and severity

This study investigates the association between mosaic loss of chromosome Y (mLOY) and pulmonary fibrosis, finding mLOY correlates with age and telomere length but not disease severity, and suggests a potential link between telomere shortening and mLOY.

Cell type-specific and disease-associated eQTL in the human lung

The paper identifies cell-type-specific and disease-associated eQTL in the human lung using single-cell RNA-sequencing data from PF and unaffected donors.

PCSK6 and Survival in Idiopathic Pulmonary Fibrosis

The paper identifies four novel genetic variants associated with IPF survival, including a PCSK6 variant, and suggests PCSK6 as a prognostic biomarker and therapeutic target.

Epithelial Outgrowth Through Mesenchymal Rings Drives Alveologenesis

The paper observes alveoli formation through epithelial outgrowth and mesenchymal rings in live lung slices, challenging the existing model of airspace subdivision.

A Single Cell Atlas of Lung Development

The paper constructs a single-cell RNA sequencing atlas of lung development in mice, revealing cellular dynamics and transcriptional changes during the saccular to alveolar transition.

Age-related expression of SARS-CoV-2 priming protease TMPRSS2 in the developing lung

The paper identifies TMPRSS2 expression patterns in developing lungs and links them to SARS-CoV-2 infection susceptibility in different age groups.

Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

Single-cell RNA-sequencing identifies distinct epithelial and mesenchymal cell types and their roles in pulmonary fibrosis.