Gerard J. Nau

Human macrophage activation programs induced by bacterial pathogens.

Understanding the response of innate immune cells to pathogens may provide insights to host defenses and the tactics used by pathogens to circumvent these defenses. We used DNA microarrays to explore the responses of human macrophages to a variety of bacteria. Macrophages responded to a broad range of bacteria with a robust, shared pattern of gene expression. The shared response includes genes encoding receptors, signal transduction molecules, and transcription factors. This shared activation program transforms the macrophage into a cell primed to interact with its environment and to mount an immune response. Further study revealed that the activation program is induced by bacterial components that are Toll-like receptor agonists, including lipopolysaccharide, lipoteichoic acid, muramyl dipeptide, and heat shock proteins. Pathogen-specific responses were also apparent in the macrophage expression profiles. Analysis of Mycobacterium tuberculosis-specific responses revealed inhibition of interleukin-12 production, suggesting one means by which this organism survives host defenses. These results improve our understanding of macrophage defenses, provide insights into mechanisms of pathogenesis, and suggest targets for therapeutic intervention.

Clustering short time series gene expression data

MOTIVATION Time series expression experiments are used to study a wide range of biological systems. More than 80% of all time series expression datasets are short (8 time points or fewer). These datasets present unique challenges. On account of the large number of genes profiled (often tens of thousands) and the small number of time points many patterns are expected to arise at random. Most clustering algorithms are unable to distinguish between real and random patterns. RESULTS We present an algorithm specifically designed for clustering short time series expression data. Our algorithm works by assigning genes to a predefined set of model profiles that capture the potential distinct patterns that can be expected from the experiment. We discuss how to obtain such a set of profiles and how to determine the significance of each of these profiles. Significant profiles are retained for further analysis and can be combined to form clusters. We tested our method on both simulated and real biological data. Using immune response data we show that our algorithm can correctly detect the temporal profile of relevant functional categories. Using Gene Ontology analysis we show that our algorithm outperforms both general clustering algorithms and algorithms designed specifically for clustering time series gene expression data. AVAILABILITY Information on obtaining a Java implementation with a graphical user interface (GUI) is available from http://www.cs.cmu.edu/~jernst/st/ SUPPLEMENTARY INFORMATION Available at http://www.cs.cmu.edu/~jernst/st/

Regulation of T‐Cell Activation; Differences among T‐Cell Subsets

Four regulatory phenomena appear to regulate differentially the activation of TH1, TH2, and CTL clones. First, IFN-gamma selectively inhibits proliferation of TH2 but not TH1 cells; lymphokine production by TH2 cells is not affected by IFN-gamma. In addition, when fresh OVA-specific HTL clones are derived in the presence of rIL-2 TH2 cells are preferentially obtained, whereas TH1 cells predominate if cloning is performed in rIL-2 plus rIFN-gamma. These results suggest that the presence of IFN-gamma during the course of an immune response would result in the preferential expansion of HTL of the TH1 phenotype. Proliferation of CTL clones is not influenced by IFN-gamma. Second, different APC populations appear to differentially activate TH1 and TH2 clones. Purified splenic B cells stimulate optimal proliferation of TH2 but not TH1 cells, whereas macrophage/dendritic cells appear to stimulate optimal proliferation of TH1 but not TH2 cells. Since both APC types stimulate lymphokine production by each of the HTL subsets, these results suggest the existence of TH1- and TH2-specific cofactors for growth. Third, high doses of immobilized anti-CD3 mAb inhibit IL-2-dependent proliferation of TH1 but not TH2 clones. Since this effect appears to require calcium, this observation suggests that TCR-mediated signalling events might differ between the two HTL subsets. Indeed, little or no increase in [Ca++]i can be detected in TH2 clones stimulated with Con-A, while such an increase is easily discernible in TH1 cells. Although high concentrations of immobilized anti-CD3 mAb inhibit IL-2-dependent proliferation of CTL clones, proliferation of these cells in response to immobilized anti-CD3 alone reaches a plateau. Since activation with anti-CD3 is thought to mimic antigenic stimulation, these results suggest that antigen concentration may play a role in determining which predominant T-cell types proliferate in a particular immunological situation. Fourth, pretreatment of TH1 cells, but not TH2 cells or CTL, with IL-2 results in decreased lymphokine production and proliferation in response to subsequent stimulation via the TCR. This antigen-responsive state appears to involve a defect in calcium-dependent signalling, providing additional evidence for different signalling mechanisms in TH1 and TH2 clones.(ABSTRACT TRUNCATED AT 400 WORDS)

Osteopontin (Eta-1) in cell-mediated immunity: teaching an old dog new tricks

Abstract Previously regarded as an adhesive bone matrix protein, recent studies suggest that osteopontin (Eta-1) is also a novel RGD-containing cytokine that regulates early cell-mediated immunity. Proteins related to the extracellular matrix may function as important modulators of immune responses.

Cumulative Toll-Like Receptor Activation in Human Macrophages Treated with Whole Bacteria

Purified components from bacteria selectively activate Toll-like receptors (TLR), leading to shared and unique responses in innate immune cells. Whole bacteria contain agonists for multiple TLR and induce a common macrophage activation program of transcription. It is not known, however, whether the stimulation of specific TLR by whole bacteria results in differential activation of the innate immune system. We evaluated gene expression data from human macrophages and found a unique gene expression profile induced by Gram-negative bacteria. In contrast, Gram-positive bacteria evoked few specific alterations in gene expression. LPS, a TLR4-specific ligand, was sufficient to elicit the distinct expression profile observed with Gram-negative bacteria. TLR4 activation regulated gene expression by both an IFN-dependent and an IFN-independent mechanism, illustrated by I-TAC and IL-12 p70, respectively. IL-12 p70 was produced by cells in whole blood exposed to Gram-negative bacteria, demonstrating faithful reproduction of the macrophage response in mixed populations of cells and identifying a potential diagnostic marker of infection. Our results show that the macrophage response to bacteria is dominated by the accumulated input from multiple TLR. For macrophages exposed to Gram-negative bacteria, gene expression changes encompass those induced by Gram-positive bacteria plus a distinct TLR4 response. This distinct TLR4 response may provide the basis to diagnose clinical Gram-negative infections.

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

In innate immune sensing, the detection of pathogen-associated molecular patterns by recognition receptors typically involve leucine-rich repeats (LRRs). We provide a categorization of 375 human LRR-containing proteins, almost half of which lack other identifiable functional domains. We clustered human LRR proteins by first assigning LRRs to LRR classes and then grouping the proteins based on these class assignments, revealing several of the resulting protein groups containing a large number of proteins with certain non-LRR functional domains. In particular, a statistically significant number of LRR proteins in the typical (T) and bacterial + typical (S+T) categories have transmembrane domains, whereas most of the LRR proteins in the cysteine-containing (CC) category contain an F-box domain (which mediates interactions with the E3 ubiquitin ligase complex). Furthermore, by examining the evolutionary profiles of the LRR proteins, we identified a subset of LRR proteins exhibiting strong conservation in fungi and an enrichment for “nucleic acid-binding” function. Expression analysis of LRR genes identifies a subset of pathogen-responsive genes in human primary macrophages infected with pathogenic bacteria. Using functional RNAi, we show that MFHAS1 regulates Toll-like receptor (TLR)–dependent signaling. By using protein interaction network analysis followed by functional RNAi, we identified LRSAM1 as a component of the antibacterial autophagic response.

Osteopontin Expression Correlates with Clinical Outcome in Patients with Mycobacterial Infection

Osteopontin (OPN) is a protein that is expressed in chronic inflammatory diseases including tuberculosis, and its deficiency predisposes to more severe mycobacterial infections in mice. However, no reports have identified altered OPN expression in, or correlated these alterations to, infections in humans. The data presented herein identify alterations in the tissue expression of OPN protein and describe an inverse correlation between these levels and disease progression after inoculation of Mycobacterium bovis bacillus Calmette-Guérin vaccine in humans. Patients with regional adenitis and good clinical outcomes had abundant OPN in infected lymph nodes. This pattern of OPN accumulation was also observed in patients infected by M. avium-intracellulare. In contrast, patients with disseminated infection and histologically ill-defined granulomas had no significant osteopontin accumulation in infected lymph nodes; these patients had either deficiencies in the interferon-gamma receptor 1 or idiopathic immune defects. The level of OPN protein expression was inversely correlated with disseminated infection and, of particular interest, with death of the patient. We conclude that osteopontin expression correlates with an effective immune and inflammatory response when humans are challenged by a mycobacterial infection and that osteopontin contributes to human resistance against mycobacteria.

A Serratia marcescens OxyR Homolog Mediates Surface Attachment and Biofilm Formation

OxyR is a conserved bacterial transcription factor with a regulatory role in oxidative stress response. From a genetic screen for genes that modulate biofilm formation in the opportunistic pathogen Serratia marcescens, mutations in an oxyR homolog and predicted fimbria structural genes were identified. S. marcescens oxyR mutants were severely impaired in biofilm formation, in contrast to the hyperbiofilm phenotype exhibited by oxyR mutants of Escherichia coli and Burkholderia pseudomallei. Further analysis revealed that OxyR plays a role in the primary attachment of cells to a surface. Similar to what is observed in other bacterial species, S. marcescens OxyR is required for oxidative stress resistance. Mutations in oxyR and type I fimbrial genes resulted in severe defects in fimbria-associated phenotypes, revealing roles in cell-cell and cell-biotic surface interactions. Transmission electron microscopy revealed the absence of fimbria-like surface structures on an OxyR-deficient strain and an enhanced fimbrial phenotype in strains bearing oxyR on a multicopy plasmid. The hyperfimbriated phenotype conferred by the multicopy oxyR plasmid was absent in a type I fimbrial mutant background. Real-time reverse transcriptase PCR indicated an absence of transcripts from a fimbrial operon in an oxyR mutant that were present in the wild type and a complemented oxyR mutant strain. Lastly, chromosomal P(lac)-mediated expression of fimABCD was sufficient to restore wild-type levels of yeast agglutination and biofilm formation to an oxyR mutant. Together, these data support a model in which OxyR contributes to early stages of S. marcescens biofilm formation by influencing fimbrial gene expression.

IL-1β-Driven ST2L Expression Promotes Maturation Resistance in Rapamycin-Conditioned Dendritic Cells

Maturation resistance and tolerogenic properties can be conferred on human and murine dendritic cells (DC), crucial regulators of T cell responses, by exposure to rapamycin (RAPA), a “tolerance-sparing” immunosuppressive agent. Mechanisms underlying this acquired unresponsiveness, typified by diminished functional responses to TLR or CD40 ligation, have not been identified. We report that in vitro and in vivo conditioning of murine myeloid DC with RAPA elicits the de novo production of IL-1β by otherwise phenotypically immature DC. Interestingly, IL-1β production promotes overexpression of the transmembrane form of the IL-1R family member, IL-1R-like 1, also know as ST2 on RAPA-conditioned DC (RAPA-DC). ST2 is the recently identified receptor for IL-33, a cytokine favoring Th2 responses. In addition, transmembrane ST2, or ST2L, has been implicated as a potent negative regulator of TLR signaling. RAPA-DC generated from ST2−/− mice exhibited higher levels of costimulatory molecules (CD86) than wild-type RAPA-DC. Consistent with its regulatory function, IL-1β-induced ST2L expression suppressed the responsiveness of RAPA-DC to TLR or CD40 ligation. Thus, as a result of their de novo production of IL-1β, RAPA-DC up-regulate ST2L and become refractory to proinflammatory, maturation-inducing stimuli. This work identifies a novel mechanism through which a clinically important immunosuppressant impedes the capacity of DC to mature and consequently stimulate effector/adaptive T cell responses.

Interleukin-12 and Interleukin-27 Regulate Macrophage Control of Mycobacterium tuberculosis

Mycobacterium tuberculosis is an intracellular pathogen that persists within macrophages and remains a considerable global threat to human health. The purpose of this study was to investigate how interleukin (IL)-12 and IL-27 regulate human macrophage interactions with M. tuberculosis. Quantitative measurement of transcripts showed that IL-12 or M. tuberculosis induced IL-27 gene expression in human macrophages. Furthermore, IL-27 receptor subunits were shown by reverse transcription-polymerase chain reaction and flow cytometry to be expressed and present at the cell surface. Neutralization of IL-27 in the presence of IL-12 reduced viable M. tuberculosis recovered from macrophages. Antimycobacterial activity was accompanied by a heightened inflammatory response that included tumor necrosis factor, IL-6, interferon-gamma, and a subset of chemokines. These results implicate IL-12 and IL-27 in regulating human macrophages, and IL-27 derived from macrophages during infection impedes control of M. tuberculosis growth.