Cellular phenotypes are determined by the differential activity of networks linking coregulated genes. Available methods for the reverse engineering of such networks from genome-wide expression profiles have been successful only in the analysis of lower eukaryotes with simple genomes. Using a new method called ARACNe (algorithm for the reconstruction of accurate cellular networks), we report the reconstruction of regulatory networks from expression profiles of human B cells. The results are suggestive a hierarchical, scale-free network, where a few highly interconnected genes (hubs) account for most of the interactions. Validation of the network against available data led to the identification of MYC as a major hub, which controls a network comprising known target genes as well as new ones, which were biochemically validated. The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells.

SummaryImmunoglobulin (Ig)M ϩ IgD ϩ B cells are generally assumed to represent antigen-inexperienced, naive B cells expressing variable (V) region genes without somatic mutations. We report here that human IgM ϩ IgD ϩ peripheral blood (PB) B cells expressing the CD27 cell surface antigen carry mutated V genes, in contrast to CD27-negative IgM ϩ IgD ϩ B cells. IgM ϩ IgD ϩ CD27 ϩ B cells resemble class-switched and IgM-only memory cells in terms of cell phenotype, and comprise ‫ف‬ 15% of PB B lymphocytes in healthy adults. Moreover, a very small population ( Ͻ 1% of PB B cells) of highly mutated IgD-only B cells was detected, which likely represent the PB counterpart of IgD-only tonsillar germinal center and plasma cells. Overall, the B cell pool in the PB of adults consists of ‫ف‬ 40% mutated memory B cells and 60% unmutated, naive IgD ϩ CD27 Ϫ B cells (including CD5 ϩ B cells). In the somatically mutated B cells, V H region genes carry a two-to threefold higher load of somatic mutation than rearranged V genes. This might be due to an intrinsically lower mutation rate in light chain genes compared with heavy chain genes and/or result from light chain gene rearrangements in GC B cells. A common feature of the somatically mutated B cell subsets is the expression of the CD27 cell surface antigen which therefore may represent a general marker for memory B cells in humans.

Humoral immunity depends on the germinal centre (GC) reaction during which somatically mutated high-affinity memory B cells and plasma cells are generated. Recent studies have uncovered crucial cues that are required for the formation and the maintenance of GCs and for the selection of high-affinity antibody mutants. In addition, it is now clear that these events are promoted by the dynamic movements of cells within and between GCs. These findings have resolved the complexities of the GC reaction in greater detail than ever before. This Review focuses on these recent advances and discusses their implications for the establishment of humoral immunity.

Over the past several years, studies on normal and malignant B cells have provided new insights into the unique physiology of the germinal centre (GC). In particular, advances in technology have allowed a more precise dissection of the phenotypes of GC B cells and the specific transcriptional programmes that are responsible for this phenotype. Furthermore, substantial progress has been made in the understanding of the mechanism controlling the exit of B cells from the GC and the decision to become a memory B cell or plasma cell. This Review focuses on these recent advances and discusses their implications for the pathogenesis of B-cell lymphomas.

In the course of infection or autoimmunity, particular transcription factors orchestrate the differentiation of T H 1, T H 2 or T H 17 effector cells, the responses of which are limited by a distinct lineage of suppressive regulatory T cells (T reg ). T reg cell differentiation and function are guided by the transcription factor Foxp3, and their deficiency due to mutations in Foxp3 results in aggressive fatal autoimmune disease associated with sharply augmented T H 1 and T H 2 cytokine production [1][2][3] . Recent studies suggested that Foxp3 regulates the bulk of the Foxp3-dependent transcriptional program indirectly through a set of transcriptional regulators serving as direct Foxp3 targets 4,5 . Here we show that in mouse T reg cells, high amounts of interferon regulatory factor-4 (IRF4), a transcription factor essential for T H 2 effector cell differentiation, is dependent on Foxp3 expression. We proposed that IRF4 expression endows T reg cells with the ability to suppress T H 2 responses. Indeed, ablation of a conditional Irf4 allele in T reg cells resulted in selective dysregulation of T H 2 responses, IL4-dependent immunoglobulin isotype production, and tissue lesions with pronounced plasma cell infiltration, in contrast to the mononuclear-cell-dominated pathology typical of mice lacking T reg cells. Our results indicate that T reg cells use components of the transcriptional machinery, promoting a particular type of effector CD4 + T cell differentiation, to efficiently restrain the corresponding type of the immune response.T reg cell deficiency results in activation and expansion of CD4 + and CD8 + T cells, dendritic cells, granulocytes and macrophages, and greatly increased production of a wide range of cytokines including interleukin (IL)-2, T H 1 and T H 2 cytokines 6,7 . Expression of Foxp3 is required for the establishment and maintenance of T reg lineage identity and suppressor function [8][9][10][11] . Our recent study suggested that in T reg cells Foxp3 might regulate expression of IRF4 (refs 12 -14) a transcription factor that is indispensable for T H 2 effector cell differentiation 15,16 . Furthermore, a recent study suggested a prominent role for IRF4 in T H 17Correspondence and requests for materials should be addressed to A.Y.R. (rudenska@mskcc.org). † Present address: Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.Supplementary Information is linked to the online version of the paper at www.nature.com/nature.Author Information Reprints and permissions information is available at www.nature.com/reprints. Full Methods and any associated references are available in the online version of the paper at www.nature.com/nature. Fig. 1a, b). Irf4 messenger RNA was increased in thymic and peripheral Foxp3 + T reg cells in comparison to CD25 − Foxp3 − CD4 + T cells (data not shown) 8 . Furthermore, Foxp3 knockdown using a retrovirally encoded Foxp3-specific short hairpin RNA resulted in a marked diminution in Irf4 mRNA ( Supplementary Fig. 1c 1...

B cell–derived chronic lymphocytic leukemia (B-CLL) represents a common malignancy whose cell derivation and pathogenesis are unknown. Recent studies have shown that >50% of CLLs display hypermutated immunoglobulin variable region (IgV) sequences and a more favorable prognosis, suggesting that they may represent a distinct subset of CLLs which have transited through germinal centers (GCs), the physiologic site of IgV hypermutation. To further investigate the phenotype of CLLs, their cellular derivation and their relationship to normal B cells, we have analyzed their gene expression profiles using oligonucleotide-based DNA chip microarrays representative of ∼12,000 genes. The results show that CLLs display a common and characteristic gene expression profile that is largely independent of their IgV genotype. Nevertheless, a restricted number of genes (<30) have been identified whose differential expression can distinguish IgV mutated versus unmutated cases and identify them in independent panels of cases. Comparison of CLL profiles with those of purified normal B cell subpopulations indicates that the common CLL profile is more related to memory B cells than to those derived from naive B cells, CD5+ B cells, and GC centroblasts and centrocytes. Finally, this analysis has identified a subset of genes specifically expressed by CLL cells of potential pathogenetic and clinical relevance.

B cells producing high-affinity antibodies are destined to differentiate into memory B cells and plasma cells, but the mechanisms leading to those differentiation pathways are mostly unknown. Here we report that the transcription factor IRF4 is required for the generation of plasma cells. Transgenic mice with conditional deletion of Irf4 in germinal center B cells lacked post-germinal center plasma cells and were unable to differentiate memory B cells into plasma cells. Plasma cell differentiation required IRF4 as well as the transcriptional repressor Blimp-1, which both acted 'upstream' of the transcription factor XBP-1. In addition, IRF4-deficient B cells had impaired expression of activation-induced deaminase and lacked class-switch recombination, suggesting an independent function for IRF4 in this process. These results identify IRF4 as a crucial transcriptional 'switch' in the generation of functionally competent plasma cells.

Chronic lymphocytic leukemia (CLL) is a malignancy of B cells of unknown etiology. Deletions of the chromosomal region 13q14 are commonly associated with CLL, with monoclonal B cell lymphocytosis (MBL), which occasionally precedes CLL, and with aggressive lymphoma, suggesting that this region contains a tumor-suppressor gene. Here, we demonstrate that deletion in mice of the 13q14-minimal deleted region (MDR), which encodes the DLEU2/miR-15a/16-1 cluster, causes development of indolent B cell-autonomous, clonal lymphoproliferative disorders, recapitulating the spectrum of CLL-associated phenotypes observed in humans. miR-15a/16-1-deletion accelerates the proliferation of both human and mouse B cells by modulating the expression of genes controlling cell-cycle progression. These results define the role of 13q14 deletions in the pathogenesis of CLL.