The activation of natural killer cell effector functions by cetuximab-coated, epidermal growth factor receptor positive tumor cells is enhanced by cytokines

PURPOSE

Natural killer (NK) cells express an activating Fc receptor (FcgammaRIIIa) that mediates antibody-dependent cellular cytotoxicity (ADCC) and production of immune modulatory cytokines in response to antibody-coated targets. Cetuximab is a therapeutic monoclonal antibody directed against the HER1 antigen. We hypothesized that the NK cell response to cetuximab-coated tumor cells could be enhanced by the administration of NK cell-stimulatory cytokines.

EXPERIMENTAL DESIGN

Human NK cells stimulated with cetuximab-coated tumor cells and interleukin-2 (IL-2), IL-12, or IL-21 were assessed for ADCC and secretion of IFN-gamma and T cell-recruiting chemokines. IL-21 and cetuximab were given to nude mice bearing HER1-positive xenografts.

RESULTS

Stimulation of human NK cells with cetuximab-coated tumor cells and IL-2, IL-12, or IL-21 resulted in 3-fold to 10-fold higher IFN-gamma production than was observed with either agent alone. NK cell-derived IFN-gamma significantly enhanced monocyte ADCC against cetuximab-coated tumor cells. Costimulated NK cells also secreted elevated levels of chemokines (IL-8, macrophage inflammatory protein-1alpha, and RANTES) that could direct the migration of naive and activated T cells. IL-2, IL-12, and IL-21 enhanced NK cell ADCC against tumor cells treated with cetuximab. The combination of cetuximab, trastuzumab (an anti-HER2 monoclonal antibody), and IL-21 mediated greater NK cell cytokine secretion and ADCC than any agent alone. Furthermore, administration of IL-21 enhanced the effects of cetuximab in a murine tumor model.

CONCLUSIONS

These results show that cetuximab-mediated NK cell activity can be significantly enhanced in the presence of NK cell-stimulatory cytokines. These factors, therefore, may be effective adjuvants to administer, in combination with cetuximab, to patients with HER1-positive malignancies.

An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum

A DNA microarray, comprising 70-mer oligonucleotides, representing 8,453 open reading frames (ORFs), was constructed based on the Bradyrhizobium japonicum strain USDA110 genomic sequence. New annotation predicted 199 additional genes, which were added to the microarray and were shown to be transcribed. These arrays were used to profile transcription in cells under a variety of conditions, including growth in minimal versus rich medium, osmotic stress, and free-living cells versus bacteroids. Increased expression was seen for genes involved in translation, motility, and cell envelope synthesis in rich medium whereas expression increased in minimal medium for genes involved in vitamin biosynthesis and stress responses. Treatment with 50 mM NaCl activated stress-inducible genes but repressed genes involved in chemotaxis and motility. Strikingly, no known transport systems for accumulation of compatible solutes or osmoprotectants were induced in response to osmotic stress. A number of nif, fix, and hup genes, but not all, were upregulated in bacteroids. The B. japonicum type III secretion system, known to be important in early nodulation, was downregulated in bacteroids. The availability of a reliable, low-cost B. japonicum microarray provides a useful tool for functional genomic studies of one of the most agriculturally important bacteria.

Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress

The growth and persistence of rhizobia and bradyrhizobia in soils are negatively impacted by drought conditions. In this study, we used genome-wide transcriptional analyses to obtain a comprehensive understanding of the response of Bradyrhizobium japonicum to drought. Desiccation of cells resulted in the differential expression of 15 to 20% of the 8,453 [corrected] B. japonicum open reading frames, with considerable differentiation between early (after 4 h) and late (after 24 and 72 h) expressed genes. While 225 genes were universally up-regulated at all three incubation times in response to desiccation, an additional 43 and 403 up-regulated genes were common to the 4/24- and 24/72-h incubation times, respectively. Desiccating conditions resulted in the significant induction (>2.0-fold) of the trehalose-6-phosphate synthetase (otsA), trehalose-6-phosphate phosphatase (otsB), and trehalose synthase (treS) genes, which encode two of the three trehalose synthesis pathways found in B. japonicum. Gene induction was correlated with an elevated intracellular concentration of trehalose and increased activity of trehalose-6-phosphate synthetase, collectively supporting the hypothesis that this disaccharide plays a prominent and important role in promoting desiccation tolerance in B. japonicum. Microarray data also indicated that sigma(54)- and sigma(24)-associated transcriptional regulators and genes encoding isocitrate lyase, oxidative stress responses, the synthesis and transport of exopolysaccharides, heat shock response proteins, enzymes for the modification and repair of nucleic acids, and the synthesis of pili and flagella are also involved in the response of B. japonicum to desiccation. Polyethylene glycol-generated osmotic stress induced significantly fewer genes than those transcriptionally activated by desiccation. However, 67 genes were commonly induced under both conditions. Taken together, these results suggest that B. japonicum directly responds to desiccation by adapting to changes imparted by reduced water activity, such as the synthesis of trehalose and polysaccharides and, secondarily, by the induction of a wide variety of proteins involved in protection of the cell membrane, repair of DNA damage, stability and integrity of proteins, and oxidative stress responses.

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data

We have developed a new integrated probabilistic method for cellular function prediction by using microarray gene expression profiles, in conjunction with predicted protein-protein interactions and annotations of known proteins through an integrative statistical model. Our approach is based on a novel assessment for the relationship between correlation of two genes' expression profiles and their functional relationship in terms of the gene ontology (GO) hierarchy. We applied the method for function predictions of hypothetical genes in Arabidopsis. We have also extended our computational method using Dijkstra's algorithm to identify the components and topology of a pathway, and we applied it for predicting the signaling pathway of phosphatidic acid as a second messenger in Arabidopsis.

Targeting CD37-positive lymphoid malignancies with a novel engineered small modular immunopharmaceutical

CD37 is a lineage-specific B-cell antigen that to date has been neglected as an attractive therapeutic target. To exploit this, novel CD37-specific small modular immunopharmaceuticals (CD37-SMIP) that include variable regions linked to modified human IgG(1) hinge, CH(2), and CH(3) domains were designed. The lead CD37-SMIP molecule induces potent apoptosis in the presence of a cross-linker, and antibody-dependent cellular cytotoxicity against B-cell leukemia/lymphoma cell lines and primary chronic lymphocytic leukemia (CLL) cells superior to therapeutic antibodies used in these diseases. The CD37-SMIP-dependent ADCC function in vitro was mediated by natural killer (NK) cells but not naive or activated monocytes. Significant in vivo therapeutic efficacy was demonstrated in a SCID mouse xenograft leukemia/lymphoma model. Depletion of NK cells in this mouse model resulted in diminished efficacy further supported the in vivo importance of NK cells in SMIP therapy. These findings provide strong justification for CD37 as a therapeutic target and introduce small modular immunopharmaceuticals as a novel class of targeted therapies for B-cell malignancies.

Single feature polymorphism discovery in rice

The discovery of nucleotide diversity captured as single feature polymorphism (SFP) by using the expression array is a high-throughput and effective method in detecting genome-wide polymorphism. The efficacy of such method was tested in rice, and the results presented in the paper indicate high sensitivity in predicting SFP. The sensitivity of polymorphism detection was further demonstrated by the fact that no biasness was observed in detecting SFP with either single or multiple nucleotide polymorphisms. The high density SFP data that can be generated quite effectively by the current method has promise for high resolution genetic mapping studies, as physical location of features are well-defined on rice genome.

Fcgamma receptor signaling in phagocytes

Fcgamma receptors are among the best-studied phagocytic receptors. The key features of Fcgamma receptor-mediated phagocytosis include phagocytic cup formation by extensive actin cytoskeletal rearrangements, particle engulfment, and the release of proinflammatory mediators such as cytokines and reactive oxygen species. These events are elegantly regulated by the simultaneous engagement of activating and inhibitory Fcgamma receptors and by intracellular signaling molecules. Extensive studies in the past several years have defined the molecular mechanisms of the phagocytic process. The purpose of this review is to revisit some of the well-established signaling pathways as well as to summarize the new findings in this field.

Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats

In order to expand our knowledge of the soybean genome and to create a useful DNA repeat sequence database, over 24 000 DNA fragments from a soybean [Glycine max (L.) Merr.] cv. Williams 82 genomic shotgun library were sequenced. Additional sequences came from over 29 000 bacterial artificial chromosome (BAC) end sequences derived from a BstI library of the cv. Williams 82 genome. Analysis of these sequences identified 348 different DNA repeats, many of which appear to be novel. To extend the utility of the work, a pilot study was also conducted using methylation filtration to estimate the hypomethylated, soybean gene space. A comparison between 8366 sequences obtained from a filtered library and 23 788 from an unfiltered library indicate a gene-enrichment of ~3.2-fold in the hypomethylated sequences. Given the 1.1-Gb soybean genome, our analysis predicts a ~343-Mb hypomethylated, gene-rich space.

Inferring gene regulatory networks from multiple microarray datasets

MOTIVATION

Microarray gene expression data has increasingly become the common data source that can provide insights into biological processes at a system-wide level. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to a large number of genes, which makes the problem of inferring gene regulatory network an ill-posed one. On the other hand, gene expression data generated by different groups worldwide are increasingly accumulated on many species and can be accessed from public databases or individual websites, although each experiment has only a limited number of time-points.

RESULTS

This paper proposes a novel method to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory networks. The proposed method is called GNR (Gene Network Reconstruction tool) which is based on linear programming and a decomposition procedure. The method theoretically ensures the derivation of the most consistent network structure with respect to all of the datasets, thereby not only significantly alleviating the problem of data scarcity but also remarkably improving the prediction reliability. We tested GNR using both simulated data and experimental data in yeast and Arabidopsis. The result demonstrates the effectiveness of GNR in terms of predicting new gene regulatory relationship in yeast and Arabidopsis.

AVAILABILITY

The software is available from http://zhangorup.aporc.org/bioinfo/grninfer/, http://digbio.missouri.edu/grninfer/ and http://intelligent.eic.osaka-sandai.ac.jp or upon request from the authors.

Renal transplantation in Indo-Asian patients in the UK

Membership of some ethnic groups has an effect on renal transplant outcome but little is known about the impact of Indo-Asian ethnicity, despite this group's high incidence of renal disease. We compared outcomes in Indo-Asians and Caucasians at the Hammersmith Hospital (Indo-Asians, N = 46; Caucasians, N = 90), in the Long-Term Efficacy and Safety Surveillance (LOTESS) database of cyclosporin-treated renal transplant recipients (Indo-Asians, N = 254; Caucasians, N = 4262) and the National Transplant Database held by UK Transplant (Indo-Asians, N = 459; Caucasians, N = 4831). The baseline demographic and co-morbid characteristics of the two ethnic groups were comparable, save for more diabetes in the Indo-Asian community. Following transplantation, the incidence of delayed graft function and steroid-resistant acute rejection were also comparable, as were graft and patient survival (out to 5 years) and graft function. In addition, post-transplant blood pressure, levels of cholesterol and triglycerides and exposure to corticosteroids and cyclosporin were comparable. However, when patients who were not diabetic before transplantation were studied separately, there was an increased incidence of diabetes in the Indo-Asian community (Hammersmith data: Indo-Asians 10.9% vs. Caucasians 3.3%, p = 0.02; LOTESS data Indo-Asians 5.5% vs. Caucasians 1.6%, p < 0.0001). Subsequent management of this group should pursue immunosuppressive regimens less likely to impair post-transplant glucose tolerance.

FcgammaR-induced production of superoxide and inflammatory cytokines is differentially regulated by SHIP through its influence on PI3K and/or Ras/Erk pathways

Phagocytosis of IgG-coated particles via FcgammaR is accompanied by the generation of superoxide and inflammatory cytokines, which can cause collateral tissue damage in the absence of regulation. Molecular mechanisms regulating these phagocytosis-associated events are not known. SHIP is an inositol phosphatase that downregulates PI3K-mediated activation events. Here, we have examined the role of SHIP in FcgammaR-induced production of superoxide and inflammatory cytokines. We report that primary SHIP-deficient bone marrow macrophages produce elevated levels of superoxide upon FcgammaR clustering. Analysis of the molecular mechanism revealed that SHIP regulates upstream Rac-GTP binding, an obligatory event for superoxide production. Likewise, SHIP-deficient macrophages displayed enhanced IL-1beta and IL-6 production in response to FcgammaR clustering. Interestingly, whereas IL-6 production required activation of both PI3K and Ras/Erk pathways, IL-1beta production was dependent only on Ras/Erk activation, suggesting that SHIP may also regulate the Ras/Erk pathway in macrophages. Consistently, SHIP-deficient macrophages displayed enhanced activation of Erk upon FcgammaR clustering. Inhibition of Ras/Erk or PI3K suppressed the enhanced production of IL-6 in SHIP-deficient macrophages. In contrast, inhibition of Ras/Erk, but not PI3K, suppressed IL-1beta production in these cells. Together, these data demonstrate that SHIP regulates phagocytosis-associated events through the inhibition of PI3K and Ras/Erk pathways.

Molecular analysis of expression and function of hFcgammaRIIbl and b2 isoforms in myeloid cells

The inhibitory receptor FcgammaRIIb becomes tyrosine phosphorylated and associates with the inositol phosphatase SHIP to downregulate phagocytosis. The two splice variants of FcgammaRIIb, b1 and b2, are differentially expressed in hematopoetic cells. Both isoforms of FcgammaRIIb are expressed in human myeloid cells although FcgammaRIIb2 predominates. In murine B cells FcgammaRIIb2 associates with clathrin-coated pits and undergoes endocytosis, whereas FcgammaRIIbl is excluded from the coated pits, indicating that the two isoforms serve partially differing functions. In humans, there are conflicting reports with regard to the ability of FcgammaRIIb2 to become tyrosine phosphorylated, and the functional capacities of the two isoforms are poorly understood. We, and others, have previously reported that the expression of FcgammaRIIb is upregulated in human monocytes by the anti-inflammatory cytokine IL-4. Here, we extend these findings to demonstrate that the IL-4-induced upregulation of FcgammaRIIb is synergistically enhanced by the addition of IL-10, both at the protein and the mRNA level. The upregulated receptors are functional as assessed by their ability to become tyrosine phosphorylated and to downregulate phagocytosis. Interestingly, both b1 and b2 isoforms are upregulated by anti-inflammatory cytokines. Transfection experiments expressing human FcgammaRIIbl or b2 in Raw 264.7 murine macrophage cells revealed that both isoforms are tyrosine phosphorylated and promote SHIP phosphorylation. Finally, both b1 and b2 isoforms of FcgammaRIIb downregulate phagocytosis to a similar extent. Thus we conclude that FcgammaRIIbl and b2 are both functional inhibitory receptors in the phagocytic process.

Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae

Characterizing gene function is one of the major challenging tasks in the post-genomic era. To address this challenge, we have developed GeneFAS (Gene Function Annotation System), a new integrated probabilistic method for cellular function prediction by combining information from protein-protein interactions, protein complexes, microarray gene expression profiles, and annotations of known proteins through an integrative statistical model. Our approach is based on a novel assessment for the relationship between (1) the interaction/correlation of two proteins' high-throughput data and (2) their functional relationship in terms of their Gene Ontology (GO) hierarchy. We have developed a Web server for the predictions. We have applied our method to yeast Saccharomyces cerevisiae and predicted functions for 1548 out of 2472 unannotated proteins.

Sodium butyrate inhibits platelet-derived growth factor-induced proliferation of vascular smooth muscle cells

Sodium butyrate (SB), a naturally occurring short-chain fatty acid, was investigated for its therapeutic value as an antiproliferative agent for vascular smooth muscle cells (SMCs). At 5-mmol/L concentration, SB had no significant effect on rat SMC proliferation. However, at the same concentration, SB inhibited platelet-derived growth factor (PDGF)-AA-, -AB-, and -BB-induced proliferation of SMCs. Exposure of SMCs to PDGF-BB resulted in activation of receptor intrinsic tyrosine kinase activity and autophosphorylation of beta-PDGF-receptor (beta-PDGFR). The activated beta-PDGFR physically associated and phosphorylated signaling molecules such as ras-GTPase activating protein (GAP) and phospholipase C gamma (PLC gamma). SB, in the absence of PDGF-BB, caused neither beta-PDGFR tyrosine phosphorylation nor phosphorylation and association of GAP and PLC gamma with beta-PDGFR. PDGF-BB-enhanced activation of receptor intrinsic tyrosine kinase activity and autophosphorylation of tyrosine residues of beta-PDGFR were unaffected by SB irrespective of whether SMCs were preincubated with SB before exposure to PDGF-BB plus SB or incubated concomitantly with PDGF-BB plus SB. Likewise, phosphorylation and association of GAP and PLC gamma with PDGF-BB-activated beta-PDGFR were unaffected. In addition, SB did not block PDGF-BB-stimulated, PLC gamma-mediated production of inositol triphosphate. Similarly, PDGF-BB-induced beta-PDGFR degradation was unaffected when SMCs were exposed to PDGF-BB plus SB, and SB by itself had no influence on beta-PDGFR degradation. Unlike beta-PDGFR kinase activity, mitogen-activated protein kinase (MAP-kinase) activity was stimulated by SB by about 2.7-fold. Exposure of SMCs to PDGF-BB caused an approximately 11.4-fold increase in MAP-kinase activity and this increase in activity was not significantly affected when cells were coincubated with PDGF-BB and SB (10.3-fold). However, pretreatment of SMCs with SB for 30 minutes and subsequent incubation in PDGF-BB plus SB abolished most of the PDGF-BB-induced MAP-kinase activity (4.6-fold). Transcription of growth response genes such as c-fos, c-jun, and c-myc were induced by PDGF-BB, and their induction was suppressed, particularly c-myc, by incubating SMCs with PDGF-BB plus SB. Similarly, preincubation of cells with SB for 30 minutes and subsequent incubation in PDGF-BB plus SB diminished PDGF-BB-induced transcription of c-fos, c-jun, and c-myc. However, SB by itself had no significant effect on c-fos, c-jun, and c-myc transcription.(ABSTRACT TRUNCATED AT 400 WORDS)

Phytochemical investigation of roots of Pterocarpus marsupium. Isolation and structural studies of two new flavanone glycosides

From the roots of Pterocarpus marsupium 7-Hydroxy-6, 8-dimethyl flavanone-7-O-alpha-L-arabinopyranoside and 7,8,4'-trihydroxy-3', 5'-dimethoxy flavanone-4'-O-beta-D-glucopyranoside have been isolated and their structure elucidated.