Among the 39 predictions that were common to the five strains/genotypes investigated, we identified mechanisms known to be associated with emphysema including NF-κB signaling, Toll-like receptor (TLR4) signaling, and increased protein abundance of inflammatory mediators such as tumor necrosis factor (TNF)-α, colony stimulating factor 2 (granulocyte–macrophage) (CSF2), as well as several interleukins. Here, NFKB1 is linked to pulmonary emphysema.