Profiling of B cells and their subsets by whole blood gene expression analysis versus flow cytometry in multiple sclerosis

•We provide data of differentially expressed mRNA in B cell populations.•B cell counts correlate with whole blood expression of identified targets.•Whole blood CD19 expression differentiates B cell repletion from complete depletion. We investigated if differentially expressed mRNA targets could be used as surrogate markers for circulating B cells and subsets. In paired blood samples from patients with untreated, anti-CD20-treated, fingolimod-treated, and natalizumab-treated multiple sclerosis, whole blood expression of CD19 correlated with B cell counts determined by flow cytometry, ROR1 with transitional B cells, TCL1A and ZNF727 with naïve B cells, NEXMIF with memory B cells and BCMA with plasmablasts. CD19 expression distinguished patients with B cell repletion and may be used as an alternative to flow cytometry, but NEXMIF was unsuitable for memory B cell monitoring in rituximab-treated patients.