Table 1.

Difficulties in assessing the contribution of autophagy to cell death

Category	Examples	Refs
Misdiagnosed ‘autophagy’	Ras-induced vacuolization of glioblastoma cells, which was initially interpreted as a sign of autophagy, actually results from large-scale macropinocytosis	11,12
Discrepancy in results of different assays used to measure cell death	A partial inhibition of plasma membrane permeabilization by knockdown of ATG genes is not accompanied by an inhibition of DNA degradation	35
Increased numbers of autophagosomes might represent increased or decreased autophagy	Accumulation of autophagosomes in the muscle from patients with Danon disease,in Lamp2−/− mice or after chloroquine intoxication; this accumulation is due to the failure to remove autophagosomes (through fusion with lysosomes) and hence reflects an inhibition of autophagy	80,81
Quantitative discrepancy between the magnitude of autophagy inhibition and cell death inhibition	Complete inhibition of signs of autophagy (such as Lc3 lipidation and GFP–Lc3 aggregation in cytoplasmic dots) leads to only partial inhibition of cell death	18,32,33
Lack of specificity of autophagy inhibitors	Pharmacological inhibitors of autophagy are nonspecific, whereas specific knockout or knockdown of ATG genes can affect autophagy-unrelated functions	46,50,52
Autophagy for optimal corpse clearance by phagocytes	Failure to provide engulfment signals causes dying autophagy-deficient cells to persist in tissues, owing to inefficient clearance by phagocytic cells; lack of tissue regression can be misinterpreted as a block in cell death	36
Autophagy inhibition results in changes in morphology or rate of degradation of dead cells	Genetic inactivation of ATG genes in Drosophila melanogaster results in the persistence of vacuolated salivary gland cell fragments with active caspase-3 and DNA fragmentation	20

ATG, autophagy-related; GFP, green fluorescent protein.