Overexpression of transcripts containing LINE-1 in the synovia of patients with rheumatoid arthritis.

OBJECTIVE: To identify novel diagnostic markers by comparing gene expression in rheumatoid (RA) and reactive arthritis (ReA) synovium. METHODS: Synovial biopsy specimens were obtained by needle arthroscopy from the knees of 10 patients with either RA or ReA. RNA was isolated from the biopsy specimens and cDNA synthesised for analysis using a customised cDNA macroarray. Confirmatory analysis was performed using in situ hybridisation on a second set of synovial samples. RESULTS: Two unique transcripts (ReXS1 and fibronectin) were consistently more abundant in ReA and three homologous transcripts were more abundant in RA. The latter all mapped within long interspersed nucleotide elements (LINE-1), that form one of the families of repetitive sequences in the human genome. CONCLUSIONS: The abundance of transcripts containing LINE-1 in the RA synovium may be an epiphenomenon or may have pathogenic significance. Further work is required to determine the identity of the full length transcript(s) before its use as a diagnostic marker in RA can be assessed.

Industrial-scale, genomics-based drug design and discovery.

The demands on drug discovery organizations have increased dramatically in recent years, partly because of the need to identify novel targets that are both relevant to disease and chemically tractable. This is leading to an industrial approach to traditional biology and chemistry, inspired in part by the revolution in genomics. The purpose of this article is to highlight the flow of investigation from gene sequence of potential therapeutic targets, through mRNA and protein expression, to protein structure and drug design. To deal with this scale of activity, many commercial and public organizations have been established and some of the key players will be listed in this article.

Use of two-dimensional gel electrophoresis to measure changes in synovial fluid proteins from patients with rheumatoid arthritis treated with antibody to CD4.

Synovial fluid proteins from microliter volumes of synovial fluid were resolved by two-dimensional polyacrylamide gel electrophoresis and detected by silver staining to investigate the feasibility of using two-dimensional (2D) electrophoresis in the clinical research setting and provide global disease information of disease progression. Several hundred proteins could be resolved as spots, many of which displayed the characteristic pattern of plasma-derived glycoproteins. The lowest level of detection was approximately 0.2 ng from a total of 50 microg of protein loaded. Most of the proteins could be identified on the basis of pI and molecular weight when compared with plasma protein maps on the World Wide Web. Unknown proteins were characterized by mass spectrometry of tryptic digests and by comparison with peptide databases. Synovial fluids from patients with rheumatoid arthritis were analyzed using this technique. Each subject received a fixed dose of antibody to CD4 as part of a phase II clinical trial to determine the efficacy of this immunosuppressive treatment in modifying disease activity. Synovial fluid was removed at day 0, followed by administration of antibody. Subsequent removal of synovial fluid and additional administration of antibody were carried out at different times thereafter. Changes in levels of acute-phase proteins were quantified by densitometry of silver-stained 2D polyacrylamide gels. Other parameters of disease progression such as serum C-reactive protein and physician's global assessment of clinical condition were used for comparison. In this way, changes in acute-phase proteins towards normal levels, as measured by 2D polyacrylamide gel electrophoresis, could be correlated with clinical improvement and conventional clinical chemistry measurements. Thus, the system can be used for quantitative analysis of protein expression in sites of autoimmune disease activity such as the synovial fluid of rheumatoid arthritis patients.

Cambridge Healthtech Institute's 5th Annual Conference: impact of genomics on medicine.

The recent publications in Nature and Science by the Human Genome Consortium and Celera Genomics, respectively, while being landmark achievements in themselves, have also given pause for thought. A definitive catalogue of human genes is still not available but the broad picture of how humans compare with lower organisms at the genomic level is becoming clearer. The full impact of these findings on the practice of medicine is hard to predict, but research being conducted now, in the early years of the 21st century, will form the basis of future advances in the diagnosis and treatment of disease. Exactly what this will entail is the subject of intense debate, but there are some common starting points that were discussed at this meeting in Munich. The main theme to emerge was the need to move beyond the human genome sequence towards an understanding of proteins and their interactions in complex biological pathways, thereby increasing opportunities for drug discovery through the identification of new targets. The majority of the talks were therefore devoted to the description of technological advances in the analysis of gene and protein expression (and interaction) and in the use of various methods of gene deletion in order to validate individual proteins as drug targets. Perhaps it will still be a few years before it will be possible to report on the application of genomic analyses to routine medical practice at the first point of care for patients but when that happens, the research efforts described here will have been worthwhile.

Reverse transcriptase-PCR analysis of bacterial rRNA for detection and characterization of bacterial species in arthritis synovial tissue.

Onset of rheumatoid arthritis (RA) is widely believed to be preceded by exposure to some environmental trigger such as bacterial infectious agents. The influence of bacteria on RA disease onset or pathology has to date been controversial, due to inconsistencies between groups in the report of bacterial species isolated from RA disease tissue. Using a modified technique of reverse transcriptase-PCR amplification, we have detected bacterial rRNA in the synovial tissue of late-stage RA and non-RA arthritis controls. This may be suggestive of the presence of live bacteria. Sequencing of cloned complementary rDNA (crDNA) products revealed a number of bacterial sequences in joint tissue from each patient, and from these analyses a comprehensive profile of the organisms present was compiled. This revealed a number of different organisms in each patient, some of which are common to both RA and non-RA controls and are probably opportunistic colonizers of previously diseased tissue and others which are unique species. These latter organisms may be candidates for a specific role in disease pathology and require further investigation to exclude them as causative agents in the complex bacterial millieu. In addition, many of the detected bacterial species have not been identified previously from synovial tissue or fluid from arthritis patients. These may not be easily cultivable, since they were not revealed in previous studies using conventional in vitro bacterial culture methods. In situ hybridization analyses have revealed the joint-associated bacterial rRNA to be both intra- and extracellular. The role of viable bacteria or their nucleic acids as triggers in disease onset or pathology in either RA or non-RA arthritis controls is unclear and requires further investigation.

Analysis of immune system gene expression in small rheumatoid arthritis biopsies using a combination of subtractive hybridization and high-density cDNA arrays.

Subtractive hybridization of cDNAs generated from synovial RNA which had been isolated from patients with rheumatoid arthritis (RA) or normal controls was used in conjunction with high-density array hybridization to identify genes of immunological interest. The method was designed to detect gene expression in small needle biopsy specimens by means of a prior amplification of nanogram amounts of total RNA to full-length cDNA using PCR. The latter was cut with Rsa I, ligated with adapters, hybridized with unmodified driver cDNA, and subjected to suppression subtraction PCR. Differentially expressed products were cloned into E. coli and picked into 384 well plates. Inserts were obtained by PCR across the multiple cloning site, and the products arrayed at high density on nylon filters. The subtracted cDNAs were also labelled by random priming for use as probes for library screening. The libraries chosen were the subtracted one described above and a set of 45,000 ESTs from the I.M. A.G.E consortium. Clones showing positive hybridization were identified by sequence analysis and homology searching. The results showed that the subtracted hybridization approach could identify many gene fragments expressed at different levels, the most abundant being immunoglobulins and HLA-DR. The expression profile was characteristic of macrophage, B cell and plasma cell infiltration with evidence of interferon induction. In addition, a significant number of sequences without matches in the nucleotide databases were obtained, this demonstrates the utility of the method in finding novel gene fragments for further characterisation as potential members of the immune system. Although RA was studied here, the technology is applicable to any disease process even in cases where amounts of tissue may be limited.

Gene expression analysis as an aid to the identification of drug targets.

Many drug targets are components of complex signalling pathways, and in order to understand the true biological consequences of modulating these targets it is necessary to understand the biology of the system in great detail. Genomics research can contribute some of the tools to achieve this, for example through the use of cDNA microarrays. Since activation of signalling pathways leads to mRNA expression, microarray technology can be used to provide a detailed quantitative assessment of the consequences of this activation, often providing a completely new biological perspective on well established cellular systems. This review will discuss some of the results obtained using mRNA profiling of yeast and mammalian cells to analyse signalling pathways of relevance to inflammation and cancer, and will point towards the future applications of this exciting approach to drug target evaluation.

Interleukin-5 receptor alpha chain mRNA is down-regulated by transforming growth factor beta 1.

Interleukin-5 is a T cell-derived cytokine with actions restricted to the eosinophil/basophil lineage and a subset of murine B cells. High affinity receptors have been identified and shown to comprise an IL-5-specific alpha chain (IL-5R alpha) in association with a beta chain which is shared with the receptors for IL-3 and GM-CSF. Nothing is currently known of the factors which regulate the transcription and subsequent expression of the IL-5 receptor alpha chain; this study was undertaken, therefore, in order to identify agents which modulate IL-5R alpha mRNA levels, with the goal of understanding the regulation of this gene in vivo. The human IL-5-dependent erythroleukemia TF-1 was used as a source of mRNA which was analysed by northern blotting using a cDNA probe for IL-5R alpha. A range of cytokines and pharmacological agents were used in 20 hour cultures of TF-1 followed by northern analysis. Of these, only TGF-beta 1 and PMA showed any effect, which was a selective downregulation, although the PMA displayed some cytotoxicity over the long culture period. The remainder (interleukins 1 to 11, G-CSF, GM-CSF, LIF, SCF, erythropoetin, IFN-gamma, RANTES, MIP-1 alpha, FGF, EGF, PDGF, dexamethasone, forskolin, retinoic acid and cyclosporin A) failed to alter expression.(ABSTRACT TRUNCATED AT 250 WORDS)

Secondary immunoglobulin responses of BALB/c mice previously stimulated with goat anti-mouse IgD.

Intravenous injection of goat antibodies to mouse IgD (GAMD) into BALB/c mice has been shown to induce vigorous T-cell dependent immunoglobulin responses, particularly of the IgG1 and IgE isotypes. We have confirmed these findings and show that IgA responses are also triggered in this model. Since the study of IgE regulation in allergic individuals is concerned with secondary and subsequent T- and B-cell responses, we boosted GAMD-primed mice with goat antibodies to IgE or IgA in an attempt to specifically retrigger IgE- and IgA-bearing memory B cells. However, we found that secondary IgG1, IgE and IgA production could be elicited equally well by either antibody preparation or by normal goat IgG (GIg). As with the primary response, GIg primed and boosted mice produced very low or undetectable IgG1, IgE and IgA responses. These data suggest that GAMD is very efficient at priming T cells specific for GIg epitopes and that once primed they can be readily re-triggered by GIg. Spleen cells taken 7 days after boosting GAMD-primed mice were found to spontaneously produce much higher levels of interleukin-6 (IL-6) in culture than cells from unboosted or GIg primed and boosted mice. In contrast to primary responses, where IgE levels return to background (less than 40 ng/ml) very quickly, circulating IgE levels in boosted mice initially declined before reaching a plateau level (approximately 1 microgram/ml) which was maintained for at least 148 days. IgG1 and IgA levels continued to fall over this same time period. Mice which had been primed (but not boosted) 10 months earlier were all found to have detectable IgE in their blood, despite the fact that following priming IgE becomes undetectable within 2-3 weeks. Since only a part of the IgE response was directed towards the antigen (GIg), these observations suggest the possibility that B cells initially primed to make IgE can be non-specifically retriggered in vivo.

Immunoregulation in the common marmoset, Calithrix jaccus: functional properties of T and B lymphocytes and their response to human interleukins 2 and 4.

Non-human primates have been used to study immune function to a much lesser extent than readily available strains of inbred rodents. Nevertheless, in situations where it might be desirable, but impossible, to study human immune responses in vivo, lower primates could provide an acceptable alternative. In order to extent the knowledge of T- and B-lymphocyte function in lower primates, the common marmoset Callithrix jaccus was used as an experimental model. The functional similarities between this species and humans at the level of T-B co-operation in the antibody response were examined, and xenoreactive T-lymphocyte clones were obtained from marmoset spleen cells using Epstein-Barr virus (EBV)-transformed human B cells as stimulators. These clones could act as helper cells when co-cultured with human B lymphocytes, inducing the secretion of both IgM and IgG. Lymphokine production by mitogen-stimulated marmoset T-cell clones was also examined. Interleukins (IL) 2 and 4 activities were detected in clone supernatants using bioassays and interferon-gamma (IFN-gamma) was detected using a solid-phase ELISA system. However, SDS-PAGE analysis of biosynthetically labelled marmoset and human T-cell clone supernatant proteins revealed major differences between the soluble T-cell products of the two species. The proliferative responses of marmoset T and B cells to recombinant human IL-2 and IL-4 were also examined. Stimulation of [3H]thymidine uptake was detected in both T cell- and anti-IgM-stimulated B-cell cultures with both of the lymphokines. These results suggests that the key components of the antibody response are functionally conserved between lower primates and man and that the common marmoset may be useful as an in vivo model of immune function, particularly with regard to the role of interleukins such as IL-2 and IL-4.

In vitro and in vivo studies with purified recombinant human interleukin 5.

The functional activities of highly purified recombinant human IL 5 (hIL 5) have been characterized on a number of cell types in vitro and in BALB/c mice in vivo. In vitro, hIL 5 could induce the differentiation of eosinophils from precursors in both human and mouse bone marrow with approximately the same efficiency. A mouse IL 5/3-dependent B cell line, LyH7.B13, was found to proliferate in response to hIL 5 but not human interleukin 1 (IL 1), interleukin 2 (IL 2), interleukin 3 (IL 3), interleukin 4 (IL 4), interleukin 6 (IL 6), interferon-gamma (IFN-gamma), or granulocyte macrophage-colony stimulating factor (GM-CSF) and was at least 10-fold more sensitive than BCL1 mouse lymphoma cells. We have successfully used this cell line to demonstrate the production of IL 5 by human T cell clones. In marked contrast to its effects on murine B cell lines, hIL 5 had no demonstrable activity on CD23 expression, anti-mu costimulated proliferation or IgM, IgG, or IgE production by tonsillar B cells and did not influence such responses triggered by IL 4. BALB/c mice injected with hIL 5 for 7 consecutive days were shown to develop an eosinophilia comparable to that induced by infection with the parasite Mesocestoid corti.

Functional and phenotypic properties of T-cell clones which regulate IgE synthesis.

We have generated a panel of T-lymphocyte clones from a patient suffering from the hyper IgE syndrome, and have attempted to correlate the ability of each to help IgE responses in vitro with the profile of lymphokines secreted after mitogenic stimulation. Clones which showed positive IgE helper activity released larger amounts of interleukin-4 (IL-4) than the non-helpers, which tended to release more interleukin-2 (IL-2). Surprisingly, all clones released moderate amounts of gamma interferon (IFN), which has been shown to inhibit the action of IL-4 on B cells. The clones were analysed by indirect immunofluorescence using monoclonal antibodies to CDw29 and CD45R (4B4 and 2H4 respectively). Those T cells which could provide strong helper activity for all isotypes, expressed high levels of CDw29 and low CD45R. These data suggest that these CD4-positive T cells expressing surface antigen of the 'memory' subset i.e. CDw29, are involved in IgE isotype regulation by virtue of their ability to secrete IL-4 upon antigenic stimulation.

Functional and phenotypic analysis of human T-cell clones which stimulate IgE production in vitro.

Peripheral blood mononuclear cells (PBMC) from a patient suffering from the hyper IgE syndrome were used to generate phytohaemagglutinin (PHA)-expanded T-cell clones (all CD4+, CD8-, CD23-). A selection of the clones was tested for their ability to help IgE secretion by culturing with normal B cells in the presence of solid-phase antibody to CD3. Supernatants were harvested on Day 7 and assayed by ELISA for IgE, IgG and IgM. Lymphokine secretion by the clones was assessed by culturing clones for 24 hr with solid-phase antibody to CD3 followed by assay of the supernatants for IL-2, IL-4 and interferon-gamma (IFN-gamma) production. In addition, clones were analysed by flow cytometry for CDw29 and CD45R expression. Initial experiments with seven clones indicated that those clones that could help IgE secretion also stimulated optimal IgG and IgM responses. All clones appeared to secrete IL-2, IL-4 and IFN-gamma, although the amounts of each varied. These results confirm recent findings that human T-cell clones do not fall into Tinf (Th1) and Th (Th2) type subsets as described in the mouse. There was no clear correlation between the lymphokines secreted by the clones and their capacity to help IgE production. However, the helper function of the clones for all isotypes, including IgE, appeared to be related to the level of expression of the surface antigen CDw29.

An in vitro model of allergen-dependent IgE synthesis by human B lymphocytes: comparison of the response of an atopic and a non-atopic individual to Dermatophagoides spp. (house dust mite).

An allergen-dependent in vitro model of immunoglobulin E (IgE) synthesis by human B cells is reported. Using this model, it is demonstrated that polyclonal T cells and CD4+ Dermatophagoides spp. (house dust mite)-specific T-cell clones derived from an atopic, house dust mite (HDM)-allergic individual are able to support IgE synthesis by autologous B cells. The helper activity was interleukin-4 (IL-4) dependent as only cloned T cells expressing detectable mRNA for IL-4 were able to induce IgE synthesis without the addition of exogenous IL-4. Peripheral and cloned T cells reactive with HDM could also be identified from a non-atopic individual but neither population was able to support IgE production even in the presence of exogenous IL-4.

Functional evidence for a monoclonal antibody that binds to the human IL-4 receptor.

The complex pleiotropic effects of the T-cell derived lymphokine interleukin-4 (IL-4) are becoming increasingly well documented; however, functional studies have been hampered by the lack of reagents directed against the receptor for this factor. In this report, we present data which suggest that the monoclonal antibody MR6 binds to the human interleukin-4 receptor (IL-4R). Addition of MR6 to cultures of T cells proliferating in response to IL-4 inhibited this response in a dose-dependent fashion, giving total inhibition at 10 micrograms/ml. Similarly, the IL-4-dependent production of specific antigen-induced IgE by B-cell populations was completely abrogated by MR6. Flow cytometric studies of the modulation of cell surface molecules after T-cell activation suggest that expression of the molecule detected by MR6 (p145-MR6) correlates inversely with that of the interleukin-2 receptor (IL-2R). These data, together with the previously determined molecular weight and tissue distribution of this molecule, strongly indicate that MR6 binds to the human IL-4R.

Antigen-specific T cell unresponsiveness in cloned helper T cells mediated via the CD2 or CD3/Ti receptor pathways.

We have investigated the role of the CD2 protein in the negative regulation of immune function and report that similar to antigen and anti-CD3, the monoclonal anti-CD2 antibodies (T112 and T113) can induce specific unresponsiveness. Antigen and anti-CD2 tolerogenic signals both down-regulated the phenotypic expression of CD3-Ti. In contrast CD2 surface expression was up-regulated after exposure to peptide and down-regulated after anti-T112 and T113 preincubation. However, in both instances interleukin 2 receptor surface levels were increased. These phenotypic changes could only be partly explained by variations in the levels of the transcripts encoding the CD3-Ti and CD2 molecules.

Inositol lipid metabolism in human T lymphocytes activated via the T3 complex.

Cloned human T lymphocytes and a mitogenic monoclonal antibody (UCHT1) that binds to the T3 antigen complex were used to study the role of inositol lipid hydrolysis in T-cell activation. Binding of the T3 molecular complex with anti-T3 antibody induced the generation of inositol trisphosphate after a lag of 1 min. While this is commensurate with the rise in cytosolic Ca2+ in these cells, examination of the inositol lipid revealed that phosphorylation of phosphatidylinositol 4-phosphate to phosphatidylinositol 4,5-bisphosphate occurred before the generation of inositol trisphosphate. Thus, activation of an inositol lipid kinase appears to be one of the primary signals in cellular activation in human T lymphocytes.

Biochemical events initiated by exposure of human T lymphocyte clones to immunogenic and tolerogenic concentrations of antigen.

Interleukin 2-dependent helper T cells, cloned from human peripheral blood lymphocytes activated with strain A influenza virus hemagglutinin, proliferate in response to a 24-residue synthetic peptide (p20) of hemagglutinin, but become unresponsive to a subsequent immunogenic challenge when pretreated with a high concentration of p20. This phenomenon is associated with a loss of the T3 antigen complex, presumably in association with the T cell receptor. We have examined this phenomenon in more detail and show that in addition to changes in the expression of T3 molecules on the cell surface, high doses of p20 cause changes in the expression of certain biosynthetically and surface-labeled proteins, although total DNA and protein synthesis was unaltered. Thus, by examining these biochemical phenomena we can begin to define some of the processes which occur during antigen activation of human T lymphocytes at the clonal level.

Investigation of early T cell activation: analysis of the effect of specific antigen, interleukin 2 and monoclonal antibodies on intracellular free calcium concentration.

The three mitogenic anti-T3 antibodies, UCHT1, anti-Leu-4 and WT-32, all produce a rapid increase in T cell intracellular Ca2+ ( [Ca2+]i) in all individuals, as measured by quin 2 tetra-acetoxymethyl ester fluorescence. This indicates that the lack of responsiveness of approximately 30% of individuals to UCHT1 in proliferation assays is not due to failure of the antibody to elicit Ca2+ mobilization and that a rise in [Ca2+]i is per se not adequate to induce cell division. Another mitogenic antibody, WT-31, which is directed against the constant portion of the T cell receptor, did not, however, produce a rapid calcium rise in peripheral blood T cells. The clone HA1.7 gave a similar Ca2+ response to UCHT1. WT-31 did not induce a rise in [Ca2+]i, nor did the specific antigen to which the clone responded. Accessory cells may be required to induce Ca2+ mobilization with these ligands. There was no response to IL2, or an antibody (anti-Tac) to the IL2 receptor. In contrast to peripheral blood T cells treatment of HA1.7 with WT-31 led to an enhancement of the calcium response to subsequent UCHT1 addition. Furthermore, cross-linking of WT-31 on the surface of HA1.7 cells did produce a small rise in [Ca2+]i. The IL2-independent malignant T cell line, HUT78, exhibited a calcium response to both UCHT1 and WT-32. Both of these responses occurred without cross-linking. The T cell receptor is closely associated with cell-surface proteins, including the T3 antigen and these studies confirm the importance of the T3 antigen in T cell activation. They also suggest that the relationship between the T cell receptor and the T3 antigen may vary in T cells in different proliferative states.

Tolerance in T-cell clones.

The interaction of antigen with immunologically competent cells may lead either to the induction of an immune response or to a state of antigen specific unresponsiveness complete orpartial, which is often called immunological 'tolerance'. This is believed to be a major mechanism of discrimination between self and non-self(1-3). In this review Marc Feldmann and his colleagues discuss new insights into T-cell tolerance in vivo and in vitro, and discuss their significance for our understanding of mechanisms of immune activation and regulation.