Human B-1 cells are not preplasmablasts: analysis of microarray data and other issues

To the editor:

We recently reported that human B-1 cells express the phenotype CD20⁺CD27⁺CD43⁺CD70⁻.^1,2  Covens et al³  now assert that B cells with this phenotype resemble plasmablasts and thus represent preplasmablasts. Their conclusion rests to a large extent on microarray data that they interpret as positioning B-1 cells closer to plasmablasts than to memory (or naïve) B cells.

Any similarity analysis of microarray datasets depends on several critical choices regarding: (1) how “closeness” between gene profiles is measured; (2) how many genes are considered; and (3) how genes are selected for inclusion. Covens et al chose: (1) Pearson’s correlation coefficient; (2) 100 top-ranked genes; and (3) genes ranked by plasmablast-over-memory or plasmablast-over-B-1 1-sided fold-change.

We found these choices to be unusual and we examined how the outcome may be altered with other choices. In particular, we calculated the distance (either Euclidean or Manhattan distance) to measure closeness, then varied the number of genes, and considered several other gene selection approaches. Our results clearly indicate that when distance is used to measure closeness, B-1 cells are closer to memory B cells than to plasmablasts regardless of number of genes analyzed or selection criteria for analysis (Figure 1A-B). When correlation coefficient is used to measure closeness, B-1 cells are again closer to memory B cells than to plasmablasts, regardless of number of genes analyzed, for all other gene selection methods except the 1-sided fold-change selection (Figure 1C-D). Our analysis reproduces the conclusion of Covens et al, but only for their specific choices, including the choice of using 100 genes. When the number of genes analyzed is increased beyond 200-1000 even with the 1-sided fold-change gene selection, B-1 cells are closer to memory B cells than to plasmablasts. This conclusion is alternatively confirmed by evaluating the number of genes that differ by 2-fold or more (and 0.5 or less) and P value < .05 in 2-way comparisons involving all genes examined (Table 1). Here, many more genes differ between B-1 cells and plasmablasts as compared with B-1 cells and memory B cells.

The fundamental difference between using correlation and using distance as a measure of closeness is illustrated in Figure 1E-F, which is the 100-gene set used in Figure 4B of Covens et al to show B-1 cells being closest to plasmablast cells. Indeed, the Pearson correlation coefficient between B-1 cells and plasmablasts (0.951) is slightly larger than that between B-1 cells and memory B cells (0.892). However, the scattering of the samples is much closer to the diagonal line between B-1 and memory B cells, indicating a closer distance. If the gap between the scattering of points and the diagonal line for B-1 cells vs plasmablasts is not due to a batch effect,⁴  there is no reason to believe that the B-1 cell expression profile of these 100 genes is not closer to that of memory B cells. The 2 correlation coefficients in Figure 1E-F are not significantly different, and minor changes in detail (eg, use of 2-sided fold-change, P value, or combinations of P value and fold-change as the selection criterion⁵ ; inclusion of larger number of genes; removal of a few outlier genes) could switch the order of the two.

Thus, the similarity between B-1 cells and plasmablasts suggested by Covens et al relates to a highly restricted set of analytical parameters and is contradicted by analyzing closeness according to distance rather than correlation and/or by considering more genes and/or by gene selection criteria other than the 1-sided fold-change. Our analysis of their data indicates instead that human B-1 cells are closer to memory B cells than to plasmablasts, which fits well with the memory function recently reported for mouse B-1 cells.⁶ 

Other criteria by which Covens et al propose that CD20⁺CD27⁺CD43⁺CD70⁻ B cells are preplasmablasts include: spontaneous secretion of immunoglobulin A; induction of CD43 expression on CD43⁻ B cells without expression of exclusionary CD69 and CD70; response to T-dependent tetanus toxoid antigen vaccination; and loss of CD20 expression by a fraction of CD20⁺CD27⁺CD43⁺CD70⁻ B cells after stimulation by a Toll-like receptor agonist and cytokine cocktail. These observations are not persuasive for several reasons. B-1 cells are known to isotype switch, in mouse and human, especially to immunoglobulin A,^7,8  so this property cannot determine lineage. The lack of positive controls for CD69 and CD70 makes it difficult to evaluate negative staining results, and upregulated CD69 expression might have declined by 5 days.⁹  Further, CD43 is an activation antigen¹  so its inducible expression, like CD5 in mouse,¹⁰  does not obviate its utility as a lineage marker. The lack of prevaccination enzyme-linked immunospots mars interpretation of B-1 cell immunoglobulin that is known to be polyreactive. But beyond that, these authors and, separately, Westerink and colleagues, recently reported that the same CD20⁺CD27⁺CD43⁺ B-1 cells are responsive to pneumococcal polysaccharide vaccination, a function attributed to B-1 cells,^6,11-13  which raises the possibility that Covens et al isolated a predominant population of B-1 cells that inadvertently contained a small number of (tetanus-responsive) non–B-1 cells. B-1 cells are known to be capable of further differentiation, including acquisition of CD138¹⁴  (less than 1% of all B cells in Covens et al’s Figure 5), so induction of plasma cell phenotype is no more an argument for B-2 lineage than for B-1 lineage. Further, the gates used to identify CD20⁺ B cells appear to have included some CD20lo B cells that may have later, after stimulation, been counted as CD20⁻, and, importantly, the vast majority of B-1 cells did not change phenotype (lose CD20 and/or express CD38) after vigorous stimulation (Covens et al’s Figure 5).

In sum, the report by Covens et al does not provide substantive evidence of a preplasmablast phenotype for CD20⁺CD27⁺CD43⁺CD69⁻CD70⁻ human B cells; rather, these B cells represent a population with functional similarities to mouse B-1 cells and thus are designated human B-1 cells.