Gene profiling of CD11b+ and CD11b− B1 cell subsets reveals potential cell sorting artifacts

To the Editor: In a recent issue of The Journal of Experimental Medicine, Griffin and Rothstein described two subsets within the human B1 cell compartment: a major CD11b  subset (9/10th of the population) and a minor CD11b + subset (1/10th of the population), with the latter being increased in lupus (Griffin and Rothstein, 2011). Griffin and Rothstein (2011) analyzed these two B1 cell subsets using gene profiling and compared these gene profiles with those of naive and memory blood B cells. A heat map is shown in Fig. 2 of their paper. This figure highlights a distinct expression profile for each of the CD11b + and CD11b  subsets compared with naive and memory B cells. Using the data deposited in the National Center for Biotechnology Information GEO database (GSE29717), we performed the same comparison and found that the gene profile of each of these subsets argues in favor of a different conclusion. For CD11b  B1 cells, the 50 most discriminating genes (comparing this subset to CD11b + B1 cells, naive cells, and memory B cells) include those (Fig. 1 A). This profile resembles that of cytotoxic CD8 + T cells. This subset also expresses CD19, CD22, and other B cell markers, which does not discriminate them from naive and memory B cells. Thus CD11b  B1 cells most likely consist of CD8 + T cell–B cell doublets. For CD11b + B1 cells, overexpressed genes include those encoding SIRP, CD33, CD68, CD163, CD302, IL-1, APRIL (TNFSF13), and CD14 (Fig. 1 B). These genes correspond to a myeloid profile. Underexpressed genes include those encoding CD79A and CD79B, and other B cell markers, including TACI, BAFF-R (TNFRSF13b and TNFRSF13c), BLK, CD19, and CD27 Figure 1. Gene expression profiles of human CD11b + and CD11b  B1 cell subsets. (A) Top 50 overexpressed genes discriminating CD11b  B1 cells from CD11b + , naïve, and memory B cells. Sec_B cells, CD11b  B1 cells. Orc_B cells, CD11b + B1 cells. (B) Top 106 overexpressed genes discriminating CD11b + B1 cells from CD11b  , naïve, and memory B cells. (C) Top 73 underexpressed genes discriminating CD11b + B1 cells from CD11b  , naïve, and memory B cells. The total number of genes displayed, which represent an unbiased list of genes according to their ranking order in the comparison, was selected to include most of the discriminating genes selected by Griffin …