The significant correlations of proteins in the phagosome- and LTM pathways with activated cytotoxic T-cells (CD69+) and the level of obstruction (FEV1/FVC) in smokers, both hallmarks of COPD, suggest that dysregulation of these two pathways may play an important role in the molecular events preceding the development of COPD in susceptible smokers. The gene discussed is CD69; the disease is chronic obstructive pulmonary disease.