Methods to study primary cilia and autophagy in the brain

Autophagy is an intracellular catabolic pathway that allows proteins, organelles, and pathogens to be recycled. Thus, it is crucial to maintain cell homeostasis, especially important in post-mitotic cells as neurons that cannot dilute cellular damage through mitosis. In the last decade, autophagy has been connected to the primary cilium (PC), a small organelle that acts as a sensory hub and is present in most cell types, including astrocytes and neurons. In this chapter, we briefly describe the state-of-the-art of the interplay between autophagy, PC, and its implications for the brain, in healthy and pathophysiological conditions. Deregulations in autophagy can be monitored by numerous assays, both in vivo and in vitro, and so do changes in PC length/number. Here, we relate a practical and user-friendly description of immunofluorescence methods to study autophagy and PC changes in brain slices, including the tissue preparation, confocal microscopy, image analysis, and deconvolution process.