Researchers at the University of Liège have used imaging-based spatial single-cell transcriptomics to map the cellular organization of lungs from people who died with severe COVID-19. Their findings identify distinct macrophage-associated tissue neighborhoods linked with fibrotic remodeling, inflammatory injury, and alveolar regions.
The study, published in Myeloid Cells , provides a detailed view of how immune and structural cells are arranged within severely damaged lungs. Rather than treating all macrophages as a single population, the work suggests that their molecular features and potential roles may depend strongly on where they are located in the tissue and the local stage of lung injury.
Severe COVID-19 can produce markedly different lung pathologies, including diffuse alveolar damage, inflammation, airway remodeling, and fibrosis. Although previous studies have described individual cell types associated with severe disease, less is known about how these cells are organized in relation to one another within affected tissue.
The researchers analyzed post-mortem lung samples from three patients with severe COVID-19 and three control subjects who died from non-pulmonary causes. Using the CosMx Spatial Molecular Imager platform, they profiled 76,973 cells across 80 fields of view and identified 20 distinct cell populations.
The COVID-19 samples showed substantial differences from one another, consistent with distinct pathological states. One sample displayed an acute inflammatory pattern; another showed extensive fibrotic remodeling; and a third had an intermediate profile characterized by immune-cell infiltration and milder fibrosis.
Spatial neighborhood analysis identified 10 cellular niches. Several of these were largely restricted to the COVID-19 samples. In the tissue with extensive fibrosis, the researchers identified neighboring regions enriched in collagen-producing COL1A1-positive fibroblasts and CHI3L1/MMP9-high macrophages. These macrophages were positioned close to the fibroblasts and expressed genes associated with pro-fibrotic signaling.
Computational ligand-receptor analysis identified TGF-beta 1, TGF-beta 2, and galectin-3 as candidate signals through which these macrophages might influence fibroblast gene programs involved in extracellular-matrix remodeling. The spatial proximity between CHI3L1/MMP9-high macrophages and COL1A1-positive fibroblasts was also observed when the team reanalyzed an independent COVID-19 spatial-transcriptomics dataset.
In a different COVID-19 sample, the researchers found an alveolar-associated niche containing SPP1-high macrophages alongside alveolar epithelial cells and resident macrophages. Analysis of this niche highlighted WNT ligands and the macrophage-regulating factors M-CSF and GM-CSF as candidate local signals that may shape macrophage identity in alveolar regions.
The findings do not show that the predicted signaling pathways cause fibrosis or lung repair. The researchers emphasize that the study was designed to generate hypotheses about cell-cell interactions, rather than establish causal mechanisms.
“This study shows how spatial molecular methods can connect conventional pathology with the local cellular interactions that may shape lung injury,” the authors conclude. “The results point to specific macrophage states and candidate signaling networks that can now be tested in larger and functional studies.”
The study has important limitations. It examined tissue from only three patients with severe COVID-19, with one anatomical region analyzed per person. The samples were collected after death, and the pathological diversity observed may not represent all people with severe COVID-19. The control tissues also showed pre-existing histological alterations. In addition, the spatial platform measured a restricted gene panel and detected a limited number of RNA molecules per cell.
The results should therefore not be interpreted as identifying a new treatment target or demonstrating that macrophage-directed therapies would prevent COVID-19-related fibrosis. Larger cohorts, additional anatomical regions, longitudinal samples, and experimental validation will be needed to determine whether the observed cellular niches recur across patients and contribute directly to disease progression or recovery.
Commentary/editorial
Human tissue samples
Spatial single-cell profiling reveals macrophage niches in severe COVID-19 lungs
15-Sep-2026
Cecilia Ruscitti and Maude Liégeois are postdoctoral fellows of the F.R.S.-FNRS. Coraline Radermecker is a Research Associate of the F.R.S.-FNRS. The other authors declare no conflicts of interest.