Multi-Omics Integration Reveals Macrophage Lysosomal Remodeling as a Signature of Reparative Immunity in Human Lung Ischemia-Reperfusion Injury.

Primary graft dysfunction (PGD) after lung transplantation is driven by ischemia-reperfusion injury (IRI), yet the early myeloid programs bridging inflammatory damage to reparative immunity remain incompletely defined. We integrated proteomic profiling of paired human lung allograft biopsies obtained after cold ischemia and early reperfusion (n = 8 pairs) with a public single-cell RNA-sequencing atlas, followed by functional validation in THP-1-derived macrophages. Reperfusion increased innate immune and extracellular matrix programs while decreasing lysosome- and phagosome-associated proteins. The downregulated signature mapped predominantly to macrophages and monocytes. Myeloid reclustering identified a transitional lipid-associated macrophage (LAM)/phagocytic state characterized by a prominent lysosome-associated transcriptional program. Cathepsin L (CTSL) emerged as a candidate lysosomal effector associated with this reparative state. Cellular origin analysis indicated this dynamic myeloid response involved both donor-resident macrophages and recipient-recruited monocytes. CTSL overexpression enhanced enzymatic activity, partially restored macrophage function, and dampened IRI-associated cytokine responses. These findings support a contributory role for CTSL in macrophage adaptation during early lung allograft reperfusion.