Microanatomical Labeling of Germinal Center Structures for Flow Cytometry Using Photoactivation

Germinal centers (GCs) are inducible microanatomical structures required for the generation of high-affinity antibodies. Migration of B and T cells within and into/out of GCs plays a key role in the evolutionary process that underlies affinity maturation, and thus microanatomical location of cells is an important variable when studying GC processes. We describe a protocol in which in situ photoactivation by multiphoton microscopy can be used to add microanatomical information to flow cytometry, allowing for identification and isolation of GC cells based on their location. Cells in different microanatomical compartments can then be sorted and analyzed for surface marker and mRNA expression.