Isolation of Trypanosoma brucei brucei Infection-Derived Splenic Marginal Zone B Cells Based on CD1d

Magnetic- and fluorescent-activated cell sorting (MACS and FACS) are used for isolation of distinct cell populations for subsequent studies including transcriptomics. The latter allows for the analysis of infection-induced alterations in gene expression profiles. MACS and FACS both use antibodies against cell surface molecules to isolate populations of interest. Standardized methods for both approaches exist for use in mouse models. These protocols, however, do not account for the fact that infection-associated immunopathology can significantly modulate the cell surface expression of targeted molecules. This is the case for Trypanosoma brucei brucei infection, where downregulation of CD23 surface expression on B cells has been reported. This hallmark of progressing infection interferes with the commercially available MACS technique for B cell purification, as CD23 expression is the target for the separation between Marginal Zone (MZ) and Follicular (Fo) B cells. Here, we provide a robust alternative method for isolation of infection-derived MZ B cells using CD1d and B220 surface molecules in a two-step MACS-FACS approach. The method yields 99% pure viable infection-derived MZ B cells, allowing extraction of a high quality total RNA suitable for subsequent RNA sequencing.