Analysis of LC3-Associated Phagocytosis and Antigen Presentation in Macrophages and B Cells

Canonical autophagy and the non-canonical autophagy pathway LC3-associated phagocytosis (LAP) play crucial roles in the immune system by processing antigens for major histocompatibility complex (MHC) class II restricted presentation to CD4⁺ T cells. Recent studies offer insight into the relationship between LAP, autophagy, and antigen processing in macrophages and dendritic cells; however their involvement during antigen processing in B cells is less well understood. In this chapter, we describe how to monitor, manipulate, and understand the role of LAP and classical autophagy during MHC-restricted antigen presentation by human monocyte-derived macrophages as well as in B cell lymphoblastoid cell lines (LCLs). It includes an explanation on how to generate LCLs and monocyte-derived macrophages from primary human cells. Then we describe two different approaches to manipulate the autophagy pathways: silencing of the atg4b gene using CRISPR/Cas9 technology and a lentivirus delivery system for specific ATG4B overexpression. We also propose a method for triggering LAP and measuring different ATG proteins using Western blot and immunofluorescence. Finally, we show an approach to investigate MHC class II antigen presentation by an in vitro co-culture assay that uses the measurement of secreted cytokines, released by activated CD4⁺ T cells, as readout.