Drug repositioning in SLE: crowd-sourcing, literature-mining and Big Data analysis.

Lupus patients are in need of modern drugs to treat specific manifestations of their disease effectively and safely. In the past half century, only one new treatment has been approved by the US Food and Drug Administration (FDA) for systemic lupus erythematosus (SLE). In 2014-2015, the FDA approved 71 new drugs, only one of which targeted a rheumatic disease and none of which was approved for use in SLE. Repositioning/repurposing drugs approved for other diseases using multiple approaches is one possible means to find new treatment options for lupus patients. "Big Data" analysis approaches this challenge from an unbiased standpoint whereas literature mining and crowd sourcing for candidates assessed by the CoLTs (Combined Lupus Treatment Scoring) system provide a hypothesis-based approach to rank potential therapeutic candidates for possible clinical application. Both approaches mitigate risk since the candidates assessed have largely been extensively tested in clinical trials for other indications. The usefulness of a multi-pronged approach to drug repositioning in lupus is highlighted by orthogonal confirmation of hypothesis-based drug repositioning predictions by "Big Data" analysis of differentially expressed genes from lupus patient samples. The goal is to identify novel therapies that have the potential to affect disease processes specifically. Involvement of SLE patients and the scientists that study this disease in thinking about new drugs that may be effective in lupus though crowd-sourcing sites such as LRxL-STAT (www.linkedin.com/in/lrxlstat) is important in stimulating the momentum needed to test these novel drug targets for efficacy in lupus rapidly in small, proof-of-concept trials conducted by LuCIN, the Lupus Clinical Investigators Network (www.linkedin.com/in/lucinstat).

Comparative characteristics of mu chain and alpha chain transcripts expressed by individual tonsil plasma cells.

Plasma cells (PCs) are one of the two major cell types generated during germinal center reactions. To test the hypothesis that PCs express a unique repertoire of immunoglobulin (Ig) genes resulting from intensive antigenic stimulation and selection, the mutational pattern and distribution of V(H) gene segments within 178 transcripts amplified from individual IgM and IgA secreting tonsil PCs were analyzed. The results demonstrated that both mu and alpha transcripts expressed repertoires with limited diversity. Moreover, both mu and alpha transcripts were heavily mutated, with a significantly increased mutational frequency noted for alpha compared to mu transcripts (5.0 x 10(-2) vs 1.8 x 10(-2), P<0.001). In addition, both mu and alpha transcripts showed significantly greater targeting of mutations to RGYW motifs (purine/guanine/pyrimidine/A or T) compared to memory B cells. Finally, clonally expanded cells were detected in alpha but not mu PC compartments. These results indicate that antigen driven stimulation and selection shape the entire expressed PC repertoire, but the impact is greater in alpha expressing PCs.

RAG1 and RAG2 expression by B cell subsets from human tonsil and peripheral blood.

It has been suggested that B cells acquire the capacity for secondary V(D)J recombination during germinal center (GC) reactions. The nature of these B cells remains controversial. Subsets of tonsil and blood B cells and also individual B cells were examined for the expression of recombination-activating gene (RAG) mRNA. Semiquantitative analysis indicated that RAG1 mRNA was present in all tonsil B cell subsets, with the largest amount found in naive B cells. RAG2 mRNA was only found in tonsil naive B cells, centrocytes, and to a lesser extent in centroblasts. Neither RAG1 nor RAG2 mRNA was routinely found in normal peripheral blood B cells. In individual tonsil B cells, RAG1 and RAG2 mRNAs were found in 18% of naive B cells, 22% of GC founder cells, 0% of centroblasts, 13% of centrocytes, and 9% of memory B cells. Individual naive tonsil B cells containing both RAG1 and RAG2 mRNA were activated (CD69(+)). In normal peripheral blood approximately 5% of B cells expressed both RAG1 and RAG2. These cells were uniformly postswitch memory B cells as documented by the coexpression of IgG mRNA. These results indicate that coordinate RAG expression is not found in normal peripheral naive B cells but is up-regulated in naive B cells which are activated in the tonsil. With the exception of centroblasts, RAG1 and RAG2 expression can be found in all components of the GC, including postswitch memory B cells, some of which may circulate in the blood of normal subjects.

Expression, regulation, and function of B cell-expressed CD154 in germinal centers.

Activated B cells and T cells express CD154/CD40 ligand in vitro. The in vivo expression and function of B cell CD154 remain unclear and therefore were examined. Tonsillar B and T cells expressed CD154 at a similar density both in situ and immediately ex vivo, whereas a significantly higher percentage of the former expressed CD154. CD154-expressing B cells were most frequent in the CD38positiveIgD+ pre-germinal center (GC)/GC founder, CD38positive GC and CD38-IgD- memory populations, and were also found in the CD38-IgD+ naive and CD38brightIgD+ plasmablast subsets, but not in the CD38brightIgD- plasma cell subset. B cell expression of CD154 was induced by engaging surface Ig or CD40 by signals that predominantly involved activation of AP-1/NF-AT and NF-kappaB, respectively. The functional importance of CD154-mediated homotypic B cell interactions in vivo was indicated by the finding that mAb to CD154 inhibited differentiation of CD38positiveIgD- GC B cells to CD38-IgD- memory cells. In addition, mAb to CD154 inhibited proliferation induced by engaging sIg or CD40, indicating the role of up-regulation of this molecule in facilitating B cell responsiveness. Of note, CD154 itself not only functioned as a ligand but also as a direct signaling molecule as anti-CD154-conjugated Sepharose beads costimulated B cell responses induced by engaging surface Ig. These results indicate that CD154 is expressed by human B cells in vivo and plays an important role in mediating B cell responses.

TNF receptor-associated factor-3 signaling mediates activation of p38 and Jun N-terminal kinase, cytokine secretion, and Ig production following ligation of CD40 on human B cells.

CD40 engagement induces a variety of functional outcomes following association with adaptor molecules of the TNF receptor-associated factor (TRAF) family. Whereas TRAF2, -5, and -6 initiate NF-kappaB activation, the outcomes of TRAF3-initiated signaling are less characterized. To delineate CD40-induced TRAF3-dependent events, Ramos B cells stably transfected with a dominant negative TRAF3 were stimulated with membranes expressing recombinant CD154/CD40 ligand. In the absence of TRAF3 signaling, activation of p38 and control of Ig production were abrogated, whereas Jun N-terminal kinase activation and secretion of IL-10, lymphotoxin-alpha, and TNF-alpha were partially blocked. By contrast, induction of apoptosis, activation of NF-kappaB, generation of granulocyte-macrophage CSF, and up-regulation of CD54, MHC class II, and CD95 were unaffected by the TRAF3 dominant negative. Together, these results indicate that TRAF3 initiates independent signaling pathways via p38 and JNK that are associated with specific functional outcomes.

Bidirectional regulation of human B cell responses by CD40-CD40 ligand interactions.

Positive and negative effects of CD40 ligation on human B cell function were suggested by the observation that mAb to CD40 ligand partially blocked the suppressive influences of anti-CD3-stimulated control CD4+ T cells, as well as the B cell stimulatory effects of anti-CD3 activated mitomycin C-treated CD4+ T cells. To examine the negative effects of CD40 ligation in greater detail, B cells were cultured with anti-CD3 activated mitomycin C-treated CD4+ T cells that expressed optimal levels of CD40 ligand; additional recombinant human CD40 ligand significantly suppressed Ig production, but not proliferation. In contrast, when B cells were stimulated with SAC (formalinized Cowan I strain Staphylococcus aureus) and IL-2 in the absence of T cells, small amounts of recombinant CD40 ligand-stimulated Ig production, whereas larger quantities directly suppressed Ig secretion. The suppressive action of CD40 ligation on Ig production was most apparent after initial B cell activation. Moreover, IgD-memory B cells were significantly more sensitive to inhibition by CD40 ligation than IgD+ naive B cells. Engagement of CD40 not only suppressed Ig secretion by IgD- memory B cells, but also expression of CD38. Finally, activated B cells acquired the capacity to down-regulate CD40 ligand expression by stimulated CD4+ T cells more effectively than resting B cells. These results indicate that during T cell-B cell collaboration, engagement of CD40 can influence Ig production both positively and negatively, depending on the density of CD40 ligand as well as the stage of B cell activation and differentiation.

Analysis of CD40-CD40 ligand interactions in the regulation of human B cell function.

CD40-CD40 ligand interactions play an essential role in T cell/B cell collaboration. The data presented in this review have served to widen the scope of CD40-CD40 ligand interactions to include initial activation, proliferation, differentiation, and isotype switching of B cells, as well as subsequent downregulation of B cell function. Moreover, CD40 ligand expression by activated B cells is likely to play an essential role in facilitating ongoing responses of stimulated B cells maturing in germinal centers. Finally, CD40 expression by activated T cells may also play an important role in regulating the function of helper T cells within germinal centers. In summary, emerging data have expanded the role of CD40-CD40 ligand interaction during T cell/B cell collaboration and have emphasized its potential to regulate many of the functions of both partners in this essential interaction involved in antibody production.

Ligation of CD40 influences the function of human Ig-secreting B cell hybridomas both positively and negatively.

The effect of ligation of CD40 on the proliferation and Ig secretion of a battery of human Ig-secreting hybridomas was examined to determine the regulatory activity of this surface molecule on B cells after initial activation. B cell hybridomas were generated by fusing activated peripheral blood B cells with SPAZ-4, a non-Ig-secreting fusion partner, and were cloned before analysis. All hybridomas expressed CD40 comparably. These hybridomas were stimulated with either recombinant baculovirus-expressed membrane-bound CD40L or a soluble murine CD40L/CD8 construct in the presence or the absence of various cytokines. Concentrations of CD40L that saturated 40 to 100% of CD40 induced initial homotypic aggregation followed by Fas (CD95)-independent apoptosis, with resultant decreases in growth and Ig secretion. Concentrations of CD40L that saturated 15 to 25% of CD40 also stimulated aggregation of all hybridomas. However, proliferation and Ig secretion of 9 of 13 IgM-secreting hybridomas, but none of 14 IgG- or IgA-secreting hybridomas, were enhanced by these concentrations of CD40L. These responses were independent of interactions mediated by the adhesion pair CD1la/CD18-CD54. These results indicate that the impact of CD40 ligation on human Ig-secreting hybridomas varies with the extent of CD40 engagement and depending on whether the hybridoma derived from an activated B cell that had previously undergone switch recombination.

The CD40 ligand expressed by human B cells costimulates B cell responses.

The possibility that activated B cells might express a ligand for CD40 that was of functional importance for B cell responses was examined by using highly purified human peripheral blood B cells, as well as a variety of B lymphoblastoid cell lines and hybridomas. Following stimulation with the combination of a calcium ionophore and a phorbol ester, human B cells bound a soluble fusion protein containing the extracellular portion of CD40 and the Fc region of IgG1 (CD40.Ig). A variety of B cell lines and hybridomas also bound CD40.Ig, either constitutively or after activation. In addition, CD40.Ig specifically immunoprecipitated a 33-kDa glycoprotein from surface 125I-labeled activated B cells. The nucleotide sequence of the coding region of the CD40 ligand mRNA amplified by RT-PCR from activated T cells and B cell lines was identical. The CD40 ligand expressed on human B cells was important functionally because homotypic aggregation of CD40 ligand-expressing B cells was inhibited by the CD40.Ig construct. Additionally, RNA and DNA synthesis as well as Ig production by polyclonally activated, highly purified peripheral B cells and a variety of B cell lines were inhibited significantly by the CD40.Ig construct. Finally, B cell lines expressing the CD40 ligand induced Ig production from resting normal B cells in a CD40-dependent manner. These results indicate that human B cells express a ligand for CD40 that is identical with that expressed by activated T cells and that the B cell-expressed CD40 ligand plays an important role in facilitating responses of activated B cells.