Abstract

As a first line of defense, small airway homeostasis is critical to lung functionality. Pathological changes of the cellular and ECM components in the small airways are often seen in chronic lung diseases such as COPD. Mechanistic understanding of these changes is key to developing novel therapies. Recent single-cell transcriptomic efforts of the Human Lung Cell Atlas working group revealed the cellular landscape of healthy and diseased lungs, yet the associated spatial context and proteomic information remains elusive.

Here, we address this knowledge gap with spatially-resolved proteomics, using a combination of laser-capture microdissection and state-of-the-art mass spectrometry. As our first pilot study, we characterized 62 distinct regions characterized by stereotypical histo(patho)logical patterns of control donors (n=2) and patients with chronic lung diseases (COPD, n=2; IPF, n=2). We microdissected regions along the distal airways (terminal and respiratory bronchioles and alveoli), vasculature (pulmonary arteries, veins and micro vessels), as well as pathological patterns associated with these structures in COPD and IPF. We identified regions enriched in disease-specific cell populations, such as the aberrant basaloid cells in histopathologically staged IPF samples, and characterized the associated ECM niche. We used cell type and state signatures from an integrated single cell atlas of chronic lung disease and identified regional enrichments for specific cell states in the niche proteomes.

In summary, a spatially-resolved proteomics workflow enables correlation of local cell states to the ECM niche signal, providing insights into uncovered instructive tissue niches in distal human lung.