Table 3.

MAP1LC3-based methods to measure autophagy in biopsies.

Method	Advantages	Limitations
Immunohistochemistry	High throughput analysis of MAP1LC3 localization in tissue arrays. Availability of fixed tissues in the clinic. Co-localization with additional autophagy-related proteins can be analyzed.	Availability of MAP1LC3 isoform specific antibodies with sufficient sensitivity for FFPE tissue sections. Quantifying MAP1LC3 punctae needs experienced pathologist.
Western blot analysis (from FFPE tissue) [84]	Distinction between MAP1LC3-I and -II.	A lot of tissue is needed to extract enough protein. Requires protein extraction from a cell mixture. Isolation of pure cell populations from the tissues would be needed to analyze cell-specific levels of MAP1LC3 expression. No information on MAP1LC3 localization.
In-situ hybridization [85]	Highly specific for MAP1LC3 isoforms. Allows to assess MAP1LC3 isoform expression levels in different cell types.	MAP1LC3 mRNA expression is not a “marker” of autophagy activity per se. One needs to assume that MAP1LC3 mRNA levels correlate with protein expression.

See abbreviations in the abbreviations section.