Transcription factors drive B cell development

Reciprocal patterns of methylation of H3K36 and H3K27 on proximal vs. distal IgVH genes are modulated by IL-7 and Pax5

The usage of >100 functional murine Ig heavy chain V(H) genes, when rearranged to D(H)J(H) genes, generates a diverse antibody repertoire. The V(H) locus encompasses 2.5 Mb, and rearrangement of V(H) genes in the D(H)-distal half of the locus are controlled very differently from the V(H) genes in the proximal end of the locus. The rearrangement of distal but not proximal V(H) genes is impaired in mice deficient in the cytokine IL-7 or its receptor, in the transcription factor Pax5, or in Ezh2, a histone methyltransferase for Lys-27 of histone H3 (H3K27). The relative role of IL-7, Pax5, and Ezh2 in regulating distal vs. proximal V(H) rearrangement is not clear. Here, we show by ChIP and ChIP-on-chip that the active histone modification H3K36me2 is most highly associated with distal V(H) segments and the repressive histone modification H3K27me3 is exclusively present on proximal V(H) segments. We observed an absence of H3K27me3 in fetal pro-B cells, which predominantly rearrange proximal V(H) genes. Absence of IL-7 signaling reduces H3K36me2, and overexpression of IL-7 increases H3K36me2. In contrast, the major effect of the absence of Pax5 is the reduction in H3K27me3. Our data indicate that the cytokine IL-7 and the transcription factor Pax5 influence the rearrangement of the two regions of the V(H) locus by differentially modulating two reciprocal histone modifications during B lymphocyte development.

Evolving views on the genealogy of B cells

Many fundamental concepts about immune system development have changed substantially in the past few years, and rapid advances with animal models are presenting prospects for further discovery. However, continued progress requires a clearer understanding of the relationships between haematopoietic stem cells and the progenitors that replenish each type of lymphocyte pool. Blood-cell formation has traditionally been described in terms of discrete developmental branch points, and a single route is given for each major cell type. As we discuss in this Review, recent findings suggest that the process of B-cell formation is much more dynamic.

Identification and analysis of mammalian KLK6 orthologue genes for prediction of physiological substrates

Human kallikrein-related peptidase 6 (KLK6) is a novel serine protease that is aberrantly expressed in human cancers and represents a serum biomarker for the molecular diagnosis and monitoring of ovarian cancer. Here, we report the cloning and analysis of human kallikrein-related peptidase 6 gene (KLK6) orthologues in model organisms and farm animals. The corresponding full-length cDNAs were assembled from partial sequences retrieved from EST and genomic databases. Alignment of inferred protein sequences indicated a high degree of conservation of the encoded enzyme. We found that, similarly to (HUMAN)KLK6, monkey, cattle, mouse and rat orthologue genes encode for multiple transcript variants. This strengthens our previously published data showing that (HUMAN)KLK6 transcription is coordinately regulated by alternative promoters. Analysis of the KLK6 upstream genomic region led to the identification of multiple conserved regulatory regions with motifs for nuclear receptor transcription factors. Interestingly, we found that specific CpG dinucleotides in the proximal promoter, that were shown to regulate (HUMAN)KLK6 gene expression via DNA methylation, are conserved in orthologue genes, indicating epigenetic regulation of the KLK6 gene. Construction of a protein-protein interaction network indicated that KLK6 likely acts on the TGF-b1 signal transduction pathway to regulate certain cytoskeletal proteins, such as vimentin and keratin 8, thus, KLK6 may control cell shape that, in turn, regulates cell migration and motility.

An EBF3-mediated transcriptional program that induces cell cycle arrest and apoptosis

In a genome-wide screen for putative tumor suppressor genes, the EBF3 locus on the human chromosome 10q26.3 was found to be deleted or methylated in 73% of the examined cases of brain tumors. EBF3 is expressed in normal brain but is silenced in brain tumors. Therefore, it is suggested that EBF3 is a tumor suppressor. However, it remains unknown whether inactivation of EBF3 locus also occurs in other types of tumors and what functions of EBF3 underlie EBF3-mediated tumor suppression. We show here that expression of EBF3 resulted in cell cycle arrest and apoptosis. The expression of cyclin-dependent kinase inhibitors was profoundly affected with early activation and then repression of p21(cip1/waf1) and persistent activation of both p27(kip1) and p57(kip2), whereas genes involved in cell survival and proliferation were suppressed. EBF3 bound directly to p21(cip1/waf1) promoter and regulated transcription from both p21(cip1/waf1) and p27(kip1) promoters in reporter assays. Apoptosis occurred 48 hours after EBF3 expression with caspase-3 activation. Silencing of the EBF3 locus was observed in brain, colorectal, breast, liver, and bone tumor cell lines and its reactivation was achieved on treatment with 5-aza-2'-deoxycytidine and trichostatin A in a significant portion of these tumor cells. Therefore, EBF3 regulates a transcriptional program underlying a putative tumor suppression pathway.

B cell activator PAX5 promotes lymphomagenesis through stimulation of B cell receptor signaling

The presumed involvement of paired box gene 5 (PAX5) in B-lymphomagenesis is based largely on the discovery of Pax5-specific translocations and somatic hypermutations in non-Hodgkin lymphomas. Yet mechanistically, the contribution of Pax5 to neoplastic growth remains undeciphered. Here we used 2 Myc-induced mouse B lymphoma cell lines, Myc5-M5 and Myc5-M12, which spontaneously silence Pax5. Reconstitution of these cells with Pax5-tamoxifen receptor fusion protein (Pax5ER(TAM)) increased neoplastic growth in a hormone-dependent manner. Conversely, expression of dominant-negative Pax5 in murine lymphomas and Pax5 knockdown in human lymphomas negatively affected cell expansion. Expression profiling revealed that Pax5 was required to maintain mRNA levels of several crucial components of B cell receptor (BCR) signaling, including CD79a, a protein with the immunoreceptor tyrosine-based activation motif (ITAM). In contrast, expression of 2 known ITAM antagonists, CD22 and PIR-B, was suppressed. The key role of BCR/ITAM signaling in Pax5-dependent lymphomagenesis was corroborated in Syk, an ITAM-associated tyrosine kinase. Moreover, we observed consistent expression of phosphorylated BLNK, an activated BCR adaptor protein, in human B cell lymphomas. Thus, stimulation of neoplastic growth by Pax5 occurs through BCR and is sensitive to genetic and pharmacological inhibitors of this pathway.

Negotiation of the T lineage fate decision by transcription-factor interplay and microenvironmental signals

Notch-Delta signaling of hematopoietic precursors sets in motion a train of events that activates expression of T lineage genes. Even so, through many cell generations the pro-T cells remain uncommitted to the T cell fate, preserving alternative potentials as divergent as monocyte or dendritic cell fates. This plasticity can be explained by the tenacious expression of stem- and progenitor-associated regulatory genes in the cells, and by the combinatorial coding of T cell identity by factors that are not intrinsically T lineage specific in their spectra of activity. T lineage developmental success depends on precise temporal and quantitative regulation of these factors and on the continuing modulating influence of Notch-Delta signals that buffer the cells against mechanisms promoting non-T outcomes. An additional mechanism, still not fully defined, is required just prior to T cell receptor-mediated selection to end plasticity and make T lineage commitment irreversible.

Selective expression of Knot/Collier, a transcriptional regulator of the EBF/Olf-1 family, endows the Drosophila sensory system with neuronal class-specific elaborated dendritic patterns

Dendritic tree morphology is a hallmark of cellular diversity in the nervous system, and Drosophila dendritic arborization (da) neurons provide an excellent model system to study its molecular basis. The da neurons are classified into four classes I-IV in the order of increasing branching complexity. A transcriptional regulator of the early B-cell factor (EBF)/olfactory 1 (Olf-1) family, Knot (Kn)/Collier (Col) is expressed selectively in class IV neurons, which generate the most expansive and complicated dendritic trees in the four classes. Loss of kn function in class IV neurons greatly reduced the number of their dendritic branches. Conversely mis-expression of kn in classes I and II produced supernumerary higher-order branches, whereas class III-specific short and straight terminal branches was hardly formed by kn mis-expression. Neither kn loss of function nor mis-expression were associated with dramatic alterations in the expression patterns of two other transcriptional regulators, Abrupt (Ab) and Cut (Ct), which play important roles in shaping dendritic trees with distinct class specificity from Kn. In contrast, Kn was necessary and sufficient to drive expression of a gene that encodes a class IV-specific channel protein. Collectively, all of our results suggest that Kn exerts its cell-autonomous function to control the formation, and possibly the function, of class IV-like elaborated dendritic arbors.

Cell lineage regulators in B and T cell development

This special issue highlights a pivotal set of regulatory molecules that have emerged as central controllers of cell-type identity in the immune system. Each in its own way has been considered as a kind of 'master' regulator of a particular cell fate choice, but the actual modes of action of these factors vary widely. The comparison among them sheds light on the different ways that an essential regulatory input can affect cellular identity.

Regulatory factors for initial T lymphocyte lineage specification

PURPOSE OF REVIEW

Initiation of T lymphocyte development depends on balanced regulatory inputs from multiple essential transcription factors. This review highlights contributions of E2A, hematopoietic transcription factor PU.1, growth factor independence (Gfi)-1, T cell factor (TCF)-1, and Runx factors and their interactions with the Notch pathway to promote T cell development.

RECENT FINDINGS

E2A and Runx family factors have been implicated in establishing competent precursors in which Notch signaling can induce the T cell program. An early role was also indicated for PU.1. Later PU.1 activities are antagonistic to pro-T cell factors, however, including E proteins, Myb, Gfi-1, and TCF-1. Diversion to a non-T lineage can be promoted by PU.1, CCAAT/enhancer binding protein, or even GATA and TCF, but these diversion mechanisms are blocked by Notch signaling. An emergent gene network summarizes the cross-regulatory relationships among these factors.

SUMMARY

Entry into the T-cell pathway is controlled by a dynamic balance among essential regulatory factors that depend on Notch signaling not only to trigger initiation of the T-cell program but also to maintain the lineage fidelity of their collective action.

Immunological systems biology: Gene expression analysis of B-cell development in Ramos B-cells

B-cell development into antibody producing cells is a complex process that relies on the tightly controlled production of hundreds of genes and proteins. A B-cell is activated through the B-cell receptor (BCR) and this activation is modified by different co-stimulatory or inhibitory co-receptors. The concerted action of signals from BCR and from co-receptors decides the fate of the B-cells. The majority of B-cells enter apoptosis, while some of them progress through the cell cycle and become, for example, antibody producing plasma cells. We studied BCR stimulated Ramos B-cells to explore the expression of BCR pathway, cell cycle and apoptosis related genes. We followed, using microarrays, the gene expression for several days after BCR engagement. Several bioinformatics methods were used to investigate the properties and common features of co-expressed genes. Certain gene ontologies have statistically significant enrichment into clusters of similarly expressed genes. The cell signaling pathways and gene expression data were combined to reveal detailed information about biological processes and B-cell systems biology. The results provide knowledge of the development of adaptive immunity and clues about how the pathways are affected by regulation of the expression of genes.

High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression

Gross cytogenetic anomalies are traditionally being used as diagnostic, prognostic and therapeutic markers in the clinical management of cancer, including childhood acute lymphoblastic leukemia (ALL). Recently, it has become increasingly clear that genetic lesions driving tumorigenesis frequently occur at the submicroscopic level and, consequently, escape standard cytogenetic observations. Therefore, we profiled the genomes of 40 childhood ALLs at high resolution. We detected multiple de novo genetic lesions, including gross aneuploidies and segmental gains and losses, some of which were subtle and affected single genes. Many of these lesions involved recurrent (partially) overlapping deletions and duplications, containing various established leukemia-associated genes, such as ETV6, RUNX1 and MLL. Importantly, the most frequently affected genes were those controlling G1/S cell cycle progression (e.g. CDKN2A, CDKN1B and RB1), followed by genes associated with B-cell development. The latter group includes microdeletions of the B-lineage transcription factors PAX5, EBF, E2-2 and IKZF1 (Ikaros), as well as genes with other established roles in B-cell development, that is RAG1 and RAG2, FYN, PBEF1 or CBP/PAG. The fact that we frequently encountered multiple lesions affecting genes involved in cell cycle regulation and B-cell differentiation strongly suggests that both these processes need to be targeted independently and simultaneously to trigger ALL development.

PU.1 activates transcription of SHP-1 gene in hematopoietic cells

Protein-tyrosine phosphatase SHP-1 is the key negative regulator of numerous signaling pathways. SHP-1 is expressed in the hematopietic and epithelial cells as two structurally similar mRNA transcripts controlled by two different promoters designated P2 and P1, respectively. Whereas the transcriptional regulation of the SHP-1 gene P1 promoter has been partially elucidated, the structure and functional control of the P2 promoter remain unknown despite the critical role played by SHP-1 in the normal and malignant lymphoid and other hematopoetic cells. Using luciferase reporter assays with the set of constructs that contained a gradually truncated intron 1 of the SHP-1 gene, we identified the minimal (<120 bp) fragment that is able to fully activate expression of the reporter gene. Furthermore, we found that PU.1 (a member of the Ets transcription factor family that plays a crucial role in differentiation and function of the lymphoid and myeloid cells) binds to the identified P2 promoter both in vitro and in vivo. PU.1 also activates the promoter in the sequence specific manner and is critical for its expression as evidenced by the profound supression of the SHP-1 gene transcription upon the siRNA-mediated depletion of PU.1. These findings provide an insight into the structure of the hematopoietic cell-specific P2 promoter of the SHP-1 gene and identify PU.1 as the transcriptional activator of the P2 promoter.

Fate decisions regulating bone marrow and peripheral B lymphocyte development

In adult mammals, bone marrow pluripotent hematopoietic stem cells generate B lymphoid-specified progeny that progress through a series of well-characterized stages before generating B-cell receptor expressing B lymphocytes. These functionally immature B lymphocytes then migrate to the spleen wherein they differentiate through transitional stages into follicular or marginal zone B lymphocytes capable of responding to T-dependent and -independent antigens, respectively. During the terminal stages of B lymphocyte development in the bone marrow, as well as immediately following egress into the peripheral compartments, B lymphocytes are counterselected to eliminate B lymphocytes with potentially dangerous self-reactivity. These developmental and selection events in the bone marrow and periphery are dependent on the integration of intrinsic genetic programs with extrinsic microenvironmental signals that drive progenitors toward increasing B lineage commitment and maturation. This chapter provides a comprehensive overview of the various stages of primary and secondary B lymphocyte development with an emphasis on the selection processes that affect decisions at critical checkpoints. Our intent is to stress the concept that at many steps in the developmental process leading to a mature immunocompetent B lymphocyte, B lineage cells are integrating multiple and different signaling inputs that are translated into specific and appropriate cell fate decisions.