In the presence of CS, ceramide has been found to accumulate in p62+ aggresome bodies, indicating autophagy impairment [22]. As CFTR-autophagy becomes impaired in both CF and COPD, cells have chronically elevated intracellular levels of ROS altering cellular homeostasis, causing exacerbations and accelerating the pathogenesis and progression of these respiratory diseases [22,110,182]. Moreover, the deleterious effect of ceramide accumulation on CFTR-autophagy has been demonstrated to directly impair defenses against bacteria [52,184,186,187] and viruses [188]. As such, ceramide accumulation as a result of either inherent or acquired CFTR dysfunction leads to autophagy impairment causing a diminished immune response and bacterial colonization or viral replication. Hence, dysfunctional CFTR and autophagy dysfunction go hand in hand with an increased susceptibility of individuals to pathogens that significantly decrease lung function and cause acute and chronic exacerbations (Figure 1).