Gene expression profiling in immune cells using microarray

Negatively charged liposomes show potent adjuvant activity when simply admixed with protein antigens

Liposomes have been investigated extensively as a vaccine delivery system. Herein the adjuvant activities of liposomes with different net surface charges (neutral, positive, or negative) were evaluated when admixed with protein antigens, ovalbumin (OVA, pI = 4.7), Bacillus anthracis protective antigen protein (PA, pI = 5.6), or cationized OVA (cOVA). Mice immunized subcutaneously with OVA admixed with different liposomes generated different antibody responses. Interestingly, OVA admixed with net negatively charged liposomes prepared with DOPA was as immunogenic as OVA admixed with positively charged liposomes prepared with DOTAP. Immunization of mice with the anthrax PA protein admixed with the net negatively charged DOPA liposomes also induced a strong and functional anti-PA antibody response. When the cationized OVA was used as a model antigen, liposomes with net neutral, negative, or positive charges showed comparable adjuvant activities. Immunization of mice with the OVA admixed with DOPA liposomes also induced OVA-specific CD8(+) cytotoxic T lymphocyte responses and significantly delayed the growth of OVA-expressing B16-OVA tumors in mice. However, not all net negatively charged liposomes showed a strong adjuvant activity. The adjuvant activity of the negatively charged liposomes may be related to the liposome's ability (i) to upregulate the expression of molecules related to the activation and maturation of antigen-presenting cells and (ii) to slightly facilitate the uptake of the antigens by antigen-presenting cells. Simply admixing certain negatively charged liposomes with certain protein antigens of interest may represent a novel platform for vaccine development.

Manipulation of dendritic cell functions by human cytomegalovirus

Dendritic cells are the most potent antigen-presenting cells of the mammalian immune system and are central to the initiation and maintenance of the adaptive immune response. They are crucial for the presentation of antigen to T cells and B cells, as well as the induction of chemokines and proinflammatory cytokines, which orchestrate the balance of the cell-mediated (Th1) and antibody (Th2) response. This ability of dendritic cells to present antigen and release chemokines and cytokines also bridges the innate and adaptive immune responses by driving T cell activation. These cells thus possess key immunological functions that make them the front line of defence for the targeting and clearance of any invading pathogen and, as such, they underpin the host immune response to infection. For efficient infection, invading pathogens often need to overcome these sentinel immune functions. It is therefore not surprising that pathogens have evolved numerous mechanisms to target dendritic cell functions directly or indirectly during infection, and at least one herpesvirus--human cytomegalovirus--has evolved a life cycle that hijacks dendritic cells for its long-term persistence in the infected host.

Dendritic cells as sensors of environmental perturbations

Dendritic cells were discovered 25 years ago as professional antigen presenting cells bridging together innate and adaptive immunity. Recently additional functions of dendritic cells have been uncovered indicating a relevant role of dendritic cells in immune system regulation. Indeed, they are the professional sensors of the immune system that can detect perturbations caused by non-self infectious as well as self non-infectious signals in most tissues. Dendritic cells discriminate both antigen amounts and antigen persistence through their receptor repertoire via the integration of different signaling pathways. The environment plays an essential role in conditioning the effector functions of dendritic cells leading either to the activation or suppression of adaptive immunity.

Commercially available recombinant sonic hedgehog up-regulates Ptc and modulates the cytokine and chemokine expression of human macrophages: an effect mediated by endotoxin contamination?

The Sonic hedgehog (Shh) signalling pathway plays an important role in developmental patterning and proliferation. Recent evidence suggests that Shh also plays a role in the development of the immune system. Here, we demonstrate that components of the Shh signalling pathway are expressed in human macrophages and that the receptor for Shh, Ptc, is up-regulated by a commercially available recombinant preparation of Shh (CArShh). Further, we report that the addition of CArShh up-regulates the production of IL-6, IL-8, MCP-1, IP-10, MIG and RANTES by macrophages, an effect enhanced by the presence of fetal calf serum in the culture medium. In contrast, TGF-beta, TNF-alpha, IL-1b, IL-12 and IL-10 production were not modulated by CArShh and VEGF was minimally up-regulated even in the presence of serum. The up-regulation of these cytokines and chemokines was abrogated by CD14 inhibition and polymixin B, but not reliably inhibited by the specific Shh pathway inhibitor cyclopamine. These results suggest that, although components of the Shh signalling pathway are expressed in macrophages, the modulation of macrophage cytokine and chemokine effector function seen in response to commercially available rShh results from low levels of endotoxin contained within the CArShh preparations employed to explore the effects of Shh in vitro.

The genopolis microarray database

Background

Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood.

Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of the Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions.

Results

The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip^® platform. It supports dynamical definition of controlled vocabularies and provides automated and supervised steps to control the coherence of data and annotations. It allows a precise control of the visibility of the database content to different sub groups in the community and facilitates exports of its content to public repositories. It provides an interactive users interface for data analysis: this allows users to visualize data matrices based on functional lists and sample characterization, and to navigate to other data matrices defined by similarity of expression values as well as functional characterizations of genes involved. A collaborative environment is also provided for the definition and sharing of functional annotation by users.

Conclusion

The Genopolis Database supports a community in building a common coherent knowledge base and analyse it. This fills a gap between a local database and a public repository, where the development of a common coherent annotation is important. In its current implementation, it provides a uniform coherently annotated dataset on dendritic cells and macrophage differentiation.

The NR4A nuclear receptor family in eosinophils

It is well-known that many members of the family of nuclear receptors have been implicated in human diseases, and metabolic disorders in particular. The NR4A nuclear receptor family consists of three members, Nur77, Nurr1, and NOR1. All of these are orphan receptors, and Nur77 and NOR1 exert possible pathological roles in immune diseases through the modulation of leukocyte functions. CD30 stimulation, which induces eosinophil-specific apoptosis, markedly enhances expression of Nur77 and NOR1 in eosinophils. This suggests the possibility of pharmacological modulation of Nur77- or NOR1-specific apoptotic pathways via receptor-dependent transactivation. In this review, we discuss treatment of allergic diseases by low molecular weight compounds acting through the NR4A receptor family to cause eosinophil apoptosis. NR4A nuclear receptor genes were selected following comprehensive analysis of differentially expressed genes in eosinophils of atopic dermatitis patients compared with healthy volunteers.

Transcriptional profiling reveals a possible role for the timing of the inflammatory response in determining susceptibility to a viral infection

Using a novel cDNA microarray prepared from sources of actively responding immune system cells, we have investigated the changes in gene expression in the target tissue during the early stages of infection of neonatal chickens with infectious bursal disease virus. Infections of two lines of chickens previously documented as genetically resistant and sensitive to infection were compared in order to ascertain early differences in the response to infection that might provide clues to the mechanism of differential genetic resistance. In addition to major changes that could be explained by previously described changes in infected tissue, some differences in gene expression on infection, and differences between the two chicken lines, were observed that led to a model for resistance in which a more rapid inflammatory response and more-extensive p53-related induction of apoptosis in the target B cells might limit viral replication and consequent pathology. Ironically, the effect in the asymptomatic neonatal infection is that more-severe B-cell depletion is seen in the more genetically resistant chicken. Changes of expression of many chicken genes of unknown function, indicating possible roles in the response to infection, may aid in the functional annotation of these genes.

The future of microarray technology: networking the genome search

In recent years microarray technology has been increasingly used in both basic and clinical research, providing substantial information for a better understanding of genome-environment interactions responsible for diseases, as well as for their diagnosis and treatment. However, in genomic research using microarray technology there are several unresolved issues, including scientific, ethical and legal issues. Networks of excellence like GA(2)LEN may represent the best approach for teaching, cost reduction, data repositories, and functional studies implementation.

NR4A orphan nuclear receptor family in peripheral blood eosinophils from patients with atopic dermatitis and apoptotic eosinophils in vitro

To identify novel genes related to the clinical signs of atopic dermatitis (AD), differentially expressed genes were sought in peripheral blood eosinophils from both AD patients and healthy volunteers. RNA was prepared from eosinophils, expression of various genes was monitored using the Affymetrix GeneChip, and expression was quantified by real-time RT-PCR. Two genes, Nur77 and NOR1, members of NR4A orphan nuclear receptor family, were expressed at a significantly higher level in AD patients than in healthy volunteers. Expression of another gene in the NR4A receptor family, Nurr1, was also higher in AD patients than in healthy volunteers. When peripheral blood leukocytes from healthy volunteers were fractionated, NOR1 expression was highest in eosinophils, but expression of Nur77 and Nurr1 genes was not eosinophil-specific. Extremely intense apoptosis was induced in both eosinophils and an eosinophil cell line, AML14.3D10, by treatment with antibody (Ab) to both CD30 and Fas. Rapid expression of the genes for the NR4A receptor family was observed with anti-CD30 Ab treatment but not with anti-Fas Ab. The NR4A orphan nuclear receptor family gene expression and the subsequent eosinophil apoptosis were downregulated by the MAPK inhibitor, U0126. These results suggest that the expression of the NR4A receptor family genes through CD30 signaling may regulate eosinophil apoptosis in allergic conditions such as AD.

Human interleukin-19 and its receptor: a potential role in the induction of Th2 responses

Interleukin-19 (IL-19) is a newly discovered member of the IL-10 family of ligands whose function is presently undefined. We recently described its cloning and initial characterization and in so doing, noted that the induction of IL-19 by LPS in human monocytes was down-regulated by interferon-gamma (IFN-gamma) and up-regulated by IL-4. This preliminary observation led us to speculate that IL-19 may play a role in the Th1/Th2 system and we examined this hypothesis further. Our results suggested that IL-19 is able to influence the maturation of human T-cells. CD4+ T-cells resulting from SEB stimulation in the presence of IL-19 contained a higher proportion of IL-4 producing cells than those developing in the absence of IL-19. This observation was complimented by the observation that fewer IFN-gamma cells accrued in the presence of IL-19, thereby suggesting that IL-19 altered the balance of Th1/Th2 cells in favour of Th2. Furthermore, in whole PBMC cultures, IL-19 up-regulated IL-4 and down-regulated IFNgamma in a dose-dependent manner. These results are presented here in review format, in the context of an overall discussion of IL-19 and its receptor.

Optimization of dendritic cell maturation and gene transfer by recombinant adenovirus

Dendritic cells (DC) have vast potential for immunotherapy. Transferring therapeutic genes to DC may enhance their inherent T cell-stimulatory capacity. Recombinant adenovirus is the most efficient vehicle for DC gene transfer and can alone mature DC. We sought to define the parameters of adenovirus infection of murine bone marrow-derived DC (BMDC) and the concomitant impact on BMDC maturation. The efficiency of adenoviral gene transfer to DC depended on the mouse strain, the organ source of DC, and the level of DC maturation. C57BL/6 BMDC consistently had higher transgene expression than BALB/c DC. While BMDC had considerable GFP expression after AdGFP infection, adenovirus was relatively ineffective in accomplishing transgene expression in freshly isolated hepatic or splenic DC. BMDC that were relatively immature because of a shorter duration of culture had higher transgene expression after infection. Nevertheless, pretreatment of DC with exogenous stimulants such as LPS or TNF-alpha resulted in higher transgene expression. Maturation of BMDC depended only on virus entry but not viral gene or transgene expression. Therefore, DC maturation was disproportionately high compared to the percentage of DC that actually expressed the adenoviral transgene. Maturation by adenovirus was only seen in BMDC, but not in liver or splenic DC, and was more pronounced in DC from later in culture (day 12 versus day 6). There was a dose-response relationship, up to a threshold dose, between adenovirus infection and both DC maturation and enhancement of DC activation of antigen-specific T cells. Our findings underscore the importance of optimizing gene transfer to DC in designing strategies for immunotherapy.

[Array technology in skin pharmacology and allergology]

Because of their variable application, microarrays are currently used in different areas of research and development, such as skin pharmacology and allergology. Microarrays are plane carriers, on whose surface a variety of known DNA-molecules and proteins were immobilised. Transcripts can be detected by cDNA- and oligonucleotid-arrays and proteins of activated genes can be discovered using antibody microarrays. Detection of allergen-specific IgE from human serum can be performed using allergen chips. Since many details of the molecular mechanism and pathogenesis of skin cancer and inflammatory skin diseases and the effect of xenobiotics on cells of the human skin are still not known, array-technologies are a powerful tool to identify novel marker genes and offer the possibility of develop new therapeutic strategies as well as prognosis- and diagnosis-systems.

Congenic mice: cutting tools for complex immune disorders

Autoimmune diseases are, in general, under complex genetic control and subject to strong interactions between genetics and the environment. Greater knowledge of the underlying genetics will provide immunologists with a framework for study of the immune dysregulation that occurs in such diseases. Ascertaining the number of genes that are involved and their characterization have, however, proven to be difficult. Improved methods of genetic analysis and the availability of a draft sequence of the complete mouse genome have markedly improved the outlook for such research, and they have emphasized the advantages of mice as a model system. In this review, we provide an overview of the genetic analysis of autoimmune diseases and of the crucial role of congenic and consomic mouse strains in such research.

Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes

We used microarray technology to measure mRNA decay rates in resting and activated T lymphocytes in order to better understand the role of mRNA decay in regulating gene expression. Purified human T lymphocytes were stimulated for 3 h with medium alone, with an anti-CD3 antibody, or with a combination of anti-CD3 and anti-CD28 antibodies. Actinomycin D was added to arrest transcription, and total cellular RNA was collected at discrete time points over a 2 h period. RNA from each point was analyzed using Affymetrix oligonucleotide arrays and a first order decay model was used to determine the half-lives of approximately 6000 expressed transcripts. We identified hundreds of short-lived transcripts encoding important regulatory proteins including cytokines, cell surface receptors, signal transduction regulators, transcription factors, cell cycle regulators and regulators of apoptosis. Approximately 100 of these short-lived transcripts contained ARE-like sequences. We also identified numerous transcripts that exhibited stimulus-dependent changes in mRNA decay. In particular, we identified hundreds of transcripts whose steady-state levels were repressed following T cell activation and were either unstable in the resting state or destabilized following cellular activation. Thus, rapid mRNA degradation appears to be an important mechanism for turning gene expression off in an activation-dependent manner.

Atopic diseases of childhood

The atopic diseases of childhood consist of the triad of asthma, allergic rhinitis, and atopic dermatitis. All share a common pathogenesis, being mediated by IgE, and are frequently present together in the same individual and family. These disorders and their comorbidities comprise a large component of general pediatric practice and their incidence in developed countries has been increasing over the past few decades. They are a leading reason for clinic and emergency room visits, as well as hospital admissions. They have the potential to interfere with education, physical activity, socialization, and self-esteem. Fortunately, we now have a reasonable armamentarium of maintenance medications available to help control these disorders and improve the quality of life for children suffering from them. In addition, early diagnosis and aggressive management of these disorders seem to offer the possibility of altering their natural history. As such, developing a sensible approach to the diagnosis and treatment of these disorders in an outpatient setting is essential. In this review, I summarize the most current literature and provide a framework for effectively diagnosing and managing these disorders.

High-density oligonucleotide array analysis of mRNA transcripts in peripheral blood cells of severe atopic dermatitis patients

BACKGROUND

There are few laboratory tests for evaluating atopic dermatitis (AD) with the exception of IgE levels or the eosinophil count. We attempted to identify new diagnostic markers by screening the genome-wide expression of transcripts in peripheral blood mononuclear cells (PBMC).

METHODS

For this study, we enrolled 7 nonatopic healthy volunteers, 5 AD patients who responded well to treatment and 6 who responded poorly. We compared genome-wide transcript levels in PBMC derived from patients with severe AD and healthy volunteers using high-density oligonucleotide arrays (GeneChip, Affymetrix). After the first screening with GeneChip, we employed real-time quantitative PCR to confirm differential expression levels.

RESULTS

Screening with GeneChip showed that the levels of a total of 92 transcripts increased at least 3-fold in one population compared to another. After further evaluation of these genes with real-time quantitative PCR, the levels of 4 transcripts were confirmed to be significantly different in PBMC from AD patients compared to controls, namely IFN-gamma, TRAIL (TNF-related apoptosis-inducing ligand), ISGF-3 (STAT1) and defensin-1. With the exception of IFN-gamma, none of these genes has previously been implicated in AD pathology.

CONCLUSION

These 4 transcripts in PBMC are expected to be useful markers for evaluating AD.