Stability of multiple testing procedures, defined as the standard deviation of total number of discoveries, can be used as an indicator of variability of multiple testing procedures. Improving stability of multiple testing procedures can help to increase the consistency of findings from replicated experiments. Benjamini-Hochberg’s and Storey’s q-value procedures are two commonly used multiple testing procedures for controlling false discoveries in genomic studies. Storey’s q-value procedure has higher power and lower stability than Benjamini-Hochberg’s procedure. To improve upon the stability of Storey’s q-value procedure and maintain its high power in genomic data analysis, we propose a new multiple testing procedure, named Bon-EV, to control false discovery rate (FDR) based on Bonferroni’s approach. Simulation studies show that our proposed Bon-EV procedure can maintain the high power of the Storey’s q-value procedure and also result in better FDR control and higher stability than Storey’s q-value procedure for samples of large size(30 in each group) and medium size (15 in each group) for either independent, somewhat correlated, or highly correlated test statistics. When sample size is small (5 in each group), our proposed Bon-EV procedure has performance between the Benjamini-Hochberg procedure and the Storey’s q-value procedure. Examples using RNA-Seq data show that the Bon-EV procedure has higher stability than the Storey’s q-value procedure while maintaining equivalent power, and higher power than the Benjamini-Hochberg’s procedure. For medium or large sample sizes, the Bon-EV procedure has improved FDR control and stability compared with the Storey’s q-value procedure and improved power compared with the Benjamini-Hochberg procedure. The Bon-EV multiple testing procedure is available as the BonEV package in R for download at https://CRAN.R-project.org/package=BonEV .

Polyclonal antithymocyte globulin (ATG) is widely used as an anti–T-cell agent for induction and treatment of acute cellular rejection in solid organ transplantation. The authors recently demonstrated that rabbit (r) ATG can be used in combination with plasmapheresis to effectively treat antibody-mediated renal allograft rejection. This observation suggested that rATG may have anti-B cell activity. The authors tested the complement-independent, apoptosis-inducing properties of rATG on CD27− naive B cells, CD40 ligand-activated B cells, and plasma cells in vitro by annexin V staining, subdiploid DNA content, caspase activation, and loss of mitochondrial membrane polarity. Potential surface targets for rATG were assayed by competitive inhibition of monoclonal antibody binding. Rabbit ATG strongly induced apoptosis in vitro against naive, activated B cells and bone marrow resident plasma cells at clinically relevant concentrations (1–100 ng/mL). The authors found rATG activity against numerous B-cell surface proteins and observed that crosslinking of CD30, CD38, CD95, CD80, and HLA-DR likely accounts for this activity. F(ab)2 fragments of rATG showed 90% of the activity of the intact molecule, suggesting participation of the Fc fragment. Inhibition of caspase- and cathepsin-dependent apoptotic pathways partially inhibits rATG-induced B-cell apoptosis. Immunohistochemical staining of pediatric thymi demonstrated the presence of CD20+ B cells and CD138+ plasma cells within the thymic parenchyma, which accounts for the anti–B-cell activity in rATG. Polyclonal rATG induces complement-independent apoptosis of naive, activated, and plasma B cells. This effect appears to involve the caspase- and cathepsin-mediated apoptosis pathways.

Unmethylated CpG DNA activation of naive CD27− B cells has been reported to require B-cell–receptor (BCR) cross-linking. We describe a culture system using CpG DNA with sequential steps for T-cell–independent activation of naive CD19+CD27− human peripheral blood B cells that induces efficient CD138+ plasma-cell differentiation. CD27+ and CD27− B cells were cultured in a 3-step system: (1) days 0 to 4: CpG, IL-2/10/15; (2) days 4 to 7: IL-2/6/10/15 and anti-CD40L; (3) days 7 to 10: IL-6/15, IFN-α, hepatocyte growth factor, and hyaluronic acid. Both CD27+ and CD27− B cells up-regulated intracytoplasmic TLR-9 following CpG DNA activation. CD27− B-cell activation required cell-cell contact. Both naive and memory B cells progressed to a plasma-cell phenotype: CD19lowCD20lowCD27+CD38+HLA-DRlow. Seventy percent of the CD27−-derived CD138+ cells demonstrated productive V chain rearrangements without somatic mutations, confirming their origin from naive precursors. Plasma cells derived from CD27+ B cells were primarily IgG+, while those from CD27− B cells were IgM+. Our results indicate that under certain conditions, naive B cells increase TLR-9 expression and proliferate to CpG DNA stimulation without BCR signaling. In addition to its immunologic significance, this system should be a valuable method to interrogate the antigenic specificity of naive B cells.

Combined treatment of allograft recipients with anti-CD40 ligand and CTLA-4Ig (costimulation blockade) is a powerful promising albeit not consistently tolerizing therapy. It would be desirable to use an effective conventional immunosuppressive regimen in low doses or for a short course as an adjunct; however, cyclosporine treatment drastically blunts the ability of costimulation blockade to produce long-term engraftment. Short courses of cyclosporine or rapamycin were compared as adjuncts to costimulation blockade in the murine BALB/c to C3H/He heterotopic cardiac allograft model. Although cyclosporine therapy blocked the capacity of costimulation blockade to produce permanent engraftment, combined rapamycin and costimulation blockade treatment produced permanent engraftment. A theoretical basis for the differing effects of cyclosporine and rapamycin upon the outcome of costimulation blockade is forwarded. Combined use of costimulation blockade and rapamycin may provide a means to bring costimulation blockade into the clinic.