A Spatial Map of the Lung Reveals the Cellular Mechanisms Driving Damage and Fibrosis in Severe COVID-19

Lungs affected by fatal forms of COVID-19 lose cells essential for breathing and undergo profound changes in their internal organization and the way their cells communicate with one another. A study involving the Sant Pau Research Institute (IR Sant Pau), published in Nature Communications, has mapped this transformation spatially and identified some of the molecular mechanisms that accompany the progression of lung damage and fibrosis.

The study, led by Dr. Manel Esteller, head of the Cancer Epigenetics group at IR Sant Pau, ICREA Research Professor, and Professor of Genetics at the University of Barcelona (UB), includes researchers from several Spanish and European institutions. The authors analyzed lung tissue from 19 patients who died from COVID-19, seven with acute diffuse alveolar damage (DAD) and twelve with proliferative DAD, alongside control lung samples. DAD is the lung injury that occurs in severe forms of acute respiratory distress syndrome and is one of the main abnormalities observed in fatal cases of COVID-19.

In total, the researchers examined 91,068 microscopic regions of lung tissue and used the Human Lung Cell Atlas as a reference to identify and locate 45 cell types. Unlike conventional transcriptomic analyses, which require tissue dissociation and result in the loss of its original organization, spatial transcriptomics preserves the location of each region analyzed, allowing gene expression to be linked to lung architecture.

“What we see is that severe COVID-19 causes not only cellular damage but also a profound reorganization of lung tissue. The cell populations present, their distribution, and the signals they exchange all change, and this combination helps us better understand how damage progresses and why such extensive fibrosis can ultimately develop,” explains Dr. Esteller.

A Profound Reorganization of Lung Tissue

The analysis indicates that the progression from normal lung tissue to acute and subsequently proliferative DAD is accompanied by a profound transformation in the tissue’s cellular composition. Among epithelial cells, the researchers observed a decrease in alveolar type 1 cells (AT1), which are responsible for much of the exchange of oxygen and carbon dioxide between the lungs and the blood. In contrast, alveolar type 2 cells (AT2) increased in proliferative DAD. These cells can proliferate and act as progenitors of AT1 cells after injury, so this increase reflects the activation of mechanisms to repair the alveolar epithelium.

“As damage progresses, we see the loss of cells essential for normal lung function, such as capillary endothelial cells and natural killer cells, while certain macrophage populations and, particularly, peribronchial fibroblasts increase,” explains Dr. Esteller. “These fibroblasts become much more abundant and reorganize into specific niches within the tissue, a change closely associated with the fibrotic response we observe in the most advanced stages of the disease.”

A Molecular Pathway That Drives Fibrosis

The spatial information allowed the researchers to analyze not only which cells were present but also how they communicated with one another through ligand–receptor interactions. This analysis identified a cell communication signature particularly associated with proliferative DAD and enriched in the transforming growth factor beta (TGF-β) pathway, one of the main mechanisms involved in tissue repair and in the development of fibrosis when its activation is excessive or persistent.

Within this pathway, the study reveals an imbalance between two regulators with opposing functions. In proliferative DAD, the activity of SMAD3, which promotes extracellular matrix production, tissue repair, and fibrosis, increases, while SMAD7, which acts as a brake on profibrotic TGF-β/SMAD3 signaling, decreases.

“What we see is that the lung activates mechanisms to repair the damage, but in the most severe cases this response can ultimately promote the formation of fibrous tissue and hinder the recovery of its normal structure,” notes Dr. Esteller. “Identifying the signals that drive this process helps us better understand why such extensive fibrosis can develop and highlights specific points that could be investigated in the future to try to curb it.”

The researchers also identified the TIMP1-CD63 interaction as one of the main components of this profibrotic signature. Using all these data, they reconstructed a signaling network within peribronchial fibroblasts in which activation of the ITGB1 receptor is linked to changes in SMAD3 and SMAD7 and to the activation of kinases such as ILK, AKT1, MAP2K4, and MAPK14. Some of these components could become targets for future research aimed at limiting pulmonary fibrosis.

The Lung Attempts to Regenerate the Alveoli

The same approach also made it possible to reconstruct another process that occurs alongside inflammation and fibrosis: the lung’s attempt to repair the destroyed alveolar epithelium. The researchers analyzed the transition from AT2 to AT1 cells and, by combining gene expression with the cells’ positions within the tissue, identified different states of differentiation. Some regions contained cells still in intermediate stages, while others displayed markers of more advanced maturation, such as CAV1, which is characteristic of mature AT1 cells. The findings indicate that programs aimed at regenerating the alveolar epithelium remain active even in lungs with very advanced disease, although the process does not occur uniformly throughout the tissue and may be incomplete.

“The lung does not remain passive in the face of injury. We were able to trace, within the tissue itself, the attempt by type 2 alveolar cells to generate new type 1 cells and rebuild the alveolar epithelium,” explains Dr. Esteller. “The problem is that, in these patients, this regeneration process coexists with a profound disruption of cell communication and a very intense fibrotic response, so normal lung architecture is never restored.”

Changes That Differ from Those in Other Lung Diseases

To determine the extent to which the observed alterations were specific to severe COVID-19 or part of a general lung response to injury, the researchers compared their findings with eight cases of diffuse alveolar damage unrelated to COVID-19 and with samples of idiopathic pulmonary fibrosis. The differences were particularly clear in fibroblasts. In proliferative COVID-19, peribronchial fibroblasts predominated and formed specific niches within the tissue, whereas alveolar fibroblasts predominated in alveolar damage from other causes. In idiopathic pulmonary fibrosis, peribronchial fibroblasts did not organize in the same way either.

“The comparison with other lung diseases shows us that fibrosis is not identical in every case,” explains Dr. Esteller. “In severe COVID-19, we find a particular combination of cell types, molecular signals, and patterns of tissue organization. This is important because it helps us distinguish which changes are part of a general response to damage and which appear to be more closely related to this disease.”

This conclusion was further supported by comparing gene regulatory programs with data from more than 1.4 million cells in the Human Lung Cell Atlas, obtained from healthy lungs and from patients with COVID-19, pneumonia unrelated to COVID-19, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. In this analysis, some mechanisms identified in the study, including the pattern of higher SMAD3 activity and lower SMAD7 activity, showed a particularly strong association with COVID-19.

The study was conducted primarily using postmortem samples, and the different stages of lung damage came from different patients, so it cannot directly track disease progression in the same individual. The authors also note that clinical differences between the groups make it difficult to fully separate the specific effects of infection from other factors, such as comorbidities, disease duration, or secondary lung infections.

“This work gives us a much more complete picture of what happens inside the lung in the most severe forms of COVID-19, because we can simultaneously observe which cells are present, where they are located, and how they communicate,” concludes Dr. Esteller. “But beyond this particular disease, it demonstrates the potential of spatial transcriptomics to study how diseased tissue is organized and to identify mechanisms that may remain hidden when we analyze cells in isolation.”

Reference Article:

Garcia-Prieto CA, Musulen E, Grases D, Davalos V, Ferrer G, Pérez-Miés B, Caniego-Casas T, Palacios J, Saenz-Sardà X, Englund E, Porta E, Esteller M. Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19. Nat Commun. 2026. doi:10.1038/s41467-026-78188-3.