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

Ruwisch, J.; Yilmaz, H.; Christian, L.; Neubert, L.; Leiber, L. M.; Brueggemann, A.; Banerjee, S.; Greer, M.; Rackwitz, W.; Giercke, L.; Werlein, C.; Pawlow, C. A.; Engelhardt, R.; Coppens, A.; Ballmaier, M.; Chichelnitskiy, E.; Simon, S.; Salman, J.; Aburahma, K.; Yildirim, A. O.; Gote-Schniering, J.; Hohlfeld, J.; Vanaudenaerde, B.; Jonigk, D. D.; Dettmer, S.; Ius, F.; Hoeper, M. M.; Gaedcke, S.; Kaminski, N.; Li, Y.; Verleden, S. E.; Gottlieb, J.; Falk, C.; Kamp, J. C.; Schupp, J. C.

doi:10.64898/2026.08.21.746071

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bioRxiv · 10.64898/2026.08.21.746071

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

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Abstract

Background: Chronic lung allograft dysfunction (CLAD) is the leading cause of death beyond the first year after lung transplantation, and its most frequent phenotype is bronchiolitis obliterans syndrome (BOS), a fibrotic small-airway disease. Mechanistic work has focused on the immune compartment, yet intensified immunosuppression does not alter established disease. Aim: To resolve which structural cell states populate the BOS graft and how they are spatially organized during airway obliteration. Methods: We profiled explanted lungs from 33 BOS patients undergoing re-transplantation and 33 controls, combining single-nucleus RNA sequencing (14 BOS, 13 controls) with targeted spatial transcriptomics of 108 regions (27 BOS, 24 controls) and multiplex immunofluorescence validation. Single-nucleus data were integrated with a published restrictive allograft syndrome (RAS) atlas. Results: Across 175,128 nuclei and 1.67 million spatially resolved cells, BOS lungs harbored a profibrotic circuit of Aberrant Basaloid cells and CTHRC1+ fibrotic fibroblasts previously described in fibrotic lung diseases, including RAS. Spatial mapping identified a CXCL14+TNC+ injury-associated basal cell state arising early in the obliterative cascade, identifying basal cells as their major reservoir. CTHRC1+ fibroblasts expanded subepithelially replacing resident peribronchial fibroblasts, alongside a peribronchial vascular shift toward systemic venous endothelium. The circuit extended beyond the airway wall to the alveolar interface, defining two convergent remodeling fronts. Conclusion: BOS engages structural-cell circuits largely shared with RAS and fibrotic lung diseases, but along an airway-centered rather than parenchyma-centered axis. CLAD thus emerges as a spatial rather than cellular spectrum, defined by anatomical distribution more than cell identity. Shared structural programs may therefore be targetable across CLAD phenotypes.

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Ruwisch, J., Yilmaz, H., Christian, L., Neubert, L., Leiber, L. M., Brueggemann, A., Banerjee, S., Greer, M., Rackwitz, W., Giercke, L., Werlein, C., Pawlow, C. A., Engelhardt, R., Coppens, A., Ballmaier, M., Chichelnitskiy, E., Simon, S., Salman, J., Aburahma, K., Yildirim, A. O., Gote-Schniering, J., Hohlfeld, J., Vanaudenaerde, B., Jonigk, D. D., Dettmer, S., Ius, F., Hoeper, M. M., Gaedcke, S., Kaminski, N., Li, Y., Verleden, S. E., Gottlieb, J., Falk, C., Kamp, J. C., Schupp, J. C.. 2026-08-23. Single-cell and spatial transcriptomics resolve airway obliteration in bronchiolitis obliterans syndrome. https://doi.org/10.64898/2026.08.21.746071

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