Morphologically and functionally distinct subpopulations of human memory B (B(Mem)) cells are identifiable by either their expression of CD27 or Fc receptor-like 4 (FCRL4), an immunoglobulin domain containing a receptor with strong inhibitory potential. We have conducted comparative transcriptome and proteome analyses of FCRL4(+) and FCRL4(-) B(Mem) cells and found that these two subsets have very distinctive expression profiles for genes encoding transcription factors, cell-surface proteins, intracellular signaling molecules, and modifiers of the cell-cycle status. Among the differentially expressed transcription factors, runt-related transcription factor 1 (RUNX1) transcript levels were up-regulated in FCRL4(-) cells, whereas RUNX2 transcripts were preferentially detected in FCRL4(+) cells. In vitro evidence for FCRL4 promoter responsiveness and in vivo promoter occupancy suggested that RUNX transcription factors are involved in the generation of these B(Mem) cell subpopulations. A distinctive signature profile was defined for the FCRL4(+) B(Mem) cells by their expression of CD11c, receptor activator for nuclear factor kappaB ligand, and FAS cell-surface proteins, in combination with increased levels of SOX5, RUNX2, DLL1, and AICDA expression. We conclude that this recently identified subpopulation of B(Mem) cells, which normally resides in epithelial tissue-based niches, may serve a unique role in mucosal defense and, conversely, as a target for neoplastic transformation events.