In summary, apart from mTOR, AMPK and NLRP3, other signals, such as Sphk1, DJ-1, LRRK2 could modulate autophagy to participate in microglia polarization as well as inflammatory mediators’ production, thus affecting neuroinflammatory processes in cerebral ischemia, AD, TBI and other CNS diseases. This evidence concerns the gene MTOR and brain ischemia.