I'm trying to figure out if my protein of interest, Protein X, which is a viral protein, causes autophagy. I am probing for human LC3B using a polyclonal rabbit antibody in a human endothelial cell line, SLK cells. I observe that after western blot, LC3-II is not expressed but LC3-I is expressed. The mock and vector control show higher LC3-II than Protein X. What are possibilities for significantly reduced LC3-II?
I suggest you study the Guidelines article:
Klionsky DJ et al, Autophagy. 2016;12(1):1-222.
doi: 10.1080/15548627.2015.1100356.
There you’ll find consensus guidelines re. your question.
I agree with Rafael and would shortly summarize, that depending on incubation time, cell line and context, LC3-II accumulation is indicative of:
a) inhibition of upstream autophagy (ATGs)
b) inhibition of LC3 lipidation
c) induction of autophagy and autolysosomal degradation
The same is true for accumulation of LC3/LC3-II, which in itself should not serve as single evidence for pro-/anti-autophagic effects.
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