Elizabeth Hong-Geller

Pivotal role of phosphoinositide-3 kinase in regulation of cytotoxicity in natural killer cells.

The mitogen-activated protein kinase–extracellular signal–regulated kinase signaling element (MAPK-ERK) plays a critical role in natural killer (NK) cell lysis of tumor cells, but its upstream effectors were previously unknown. We show that inhibition of phosphoinositide-3 kinase (PI3K) in NK cells blocks p21-activated kinase 1 (PAK1), MAPK kinase (MEK) and ERK activation by target cell ligation, interferes with perforin and granzyme B movement toward target cells and suppresses NK cytotoxicity. Dominant-negative N17Rac1 and PAK1 mimic the suppressive effects of PI3K inhibitors, whereas constitutively active V12Rac1 has the opposite effect. V12Rac1 restores the activity of downstream effectors and lytic function in LY294002- or wortmannin-treated, but not PD98059-treated, NK cells. These results document a specific PI3K→Rac1→PAK1→MEK→ERK pathway in NK cells that effects lysis.

Syk Regulation of Phosphoinositide 3-Kinase-Dependent NK Cell Function

Emerging evidence suggests that NK-activatory receptors use KARAP/DAP12, CD3ζ, and FcεRIγ adaptors that contain immunoreceptor tyrosine-based activatory motifs to mediate NK direct lysis of tumor cells via Syk tyrosine kinase. NK cells may also use DAP10 to drive natural cytotoxicity through phosphoinositide 3-kinase (PI3K). In contrast to our recently identified PI3K pathway controlling NK cytotoxicity, the signaling mechanism by which Syk associates with downstream effectors to drive NK lytic function has not been clearly defined. In NK92 cells, which express DAP12 but little DAP10/NKG2D, we now show that Syk acts upstream of PI3K, subsequently leading to the specific signaling of the PI3K→Rac1→PAK1→mitogen-activated protein/extracellular signal-regulated kinase (ERK) kinase→ERK cascade that we earlier described. Tumor cell ligation stimulated DAP12 tyrosine phosphorylation and its association with Syk in NK92 cells; Syk tyrosine phosphorylation and activation were also observed. Inhibition of Syk function by kinase-deficient Syk or piceatannol blocked target cell-induced PI3K, Rac1, PAK1, mitogen-activated protein/ERK kinase, and ERK activation, perforin movement, as well as NK cytotoxicity, indicating that Syk is upstream of all these signaling events. Confirming that Syk does not act downstream of PI3K, constitutively active PI3K reactivated all the downstream effectors as well as NK cytotoxicity suppressed in Syk-impaired NK cells. Our results are the first report documenting the instrumental role of Syk in control of PI3K-dependent natural cytotoxicity.

The bioinorganic chemistry and associated immunology of chronic beryllium disease

Chronic beryllium disease (CBD) is a debilitating, incurable, and often fatal disease that is caused by the inhalation of beryllium particulates. The growing use of beryllium in the modern world, in products ranging from computers to dental prosthetics (390 tons of beryllium in the US in the year 2000) necessitates a molecular based understanding of the disease in order to prevent and cure CBD. We have investigated the molecular basis of CBD at Los Alamos National Laboratory during the past six years, employing a multidisciplinary approach of bioinorganic chemistry and immunology. The results of this work, including speciation, inhalation and dissolution, and immunology will be discussed.

Small RNA-mediated regulation of host–pathogen interactions

The rise in antimicrobial drug resistance, alongside the failure of conventional research to discover new antibiotics, will inevitably lead to a public health crisis that can drastically curtail our ability to combat infectious disease. Thus, there is a great global health need for development of antimicrobial countermeasures that target novel cell molecules or processes. RNA represents a largely unexploited category of potential targets for antimicrobial design. For decades, control of cellular behavior was thought to be the exclusive purview of protein-based regulators. The recent discovery of small RNAs (sRNAs) as a universal class of powerful RNA-based regulatory biomolecules has the potential to revolutionize our understanding of gene regulation in practically all biological functions. In general, sRNAs regulate gene expression by base-pairing with multiple downstream target mRNAs to prevent translation of mRNA into protein. In this review, we will discuss recent studies that document discovery of bacterial, viral, and human sRNAs and their molecular mechanisms in regulation of pathogen virulence and host immunity. Illuminating the functional roles of sRNAs in virulence and host immunity can provide the fundamental knowledge for development of next-generation antibiotics using sRNAs as novel targets.

Design of Chimeric Receptor Mimics with Different TcRVβ Isoforms TYPE-SPECIFIC INHIBITION OF SUPERANTIGEN PATHOGENESIS

The Staphylococcus aureus enterotoxins (S.E.) A-I, and toxic-shock syndrome toxin TSST-1 act as superantigens to cause overstimulation of the host immune system, leading to the onset of various diseases including food poisoning and toxic shock syndrome. SAgs bind as intact proteins to the DRα1 domain of the MHC class II receptor and the TcRVβ domain from the T cell receptor and cause excessive release of cytokines such as IL-2, TNF-α, and IFN-γ, and hyperproliferation of T cells. In addition, different SAgs bind and activate different TcRVβ isoforms during pathogenesis of human immune cells. These two properties of SAgs prompted us to design several chimeric DRα1-linker-TcRVβ proteins using different TcRVβ isoforms to create chimeras that would specifically inhibit the pathogenesis of SAgs against which they were designed. In this study, we compare the design, interaction, and inhibitory properties of three different DRα1-linker-TcRVβ chimeras targeted against three different SAgs, SEB, SEC3, and TSST-1. The inhibitory properties of the chimeras were tested by monitoring IL-2 release and T cell proliferation using a primary human cell model. We demonstrate that the three chimeras specifically inhibit the pathogenesis of their target superantigen. We performed molecular modeling to analyze the structural basis of the type specificity exhibited by different chimeras designed against their target SAgs, examine the role of the linker in determining binding and specificity, and suggest site-specific mutations in the chimera to enhance binding affinity. The fact that our strategy works equally well for SEB and TSST-1, two widely different phylogenic variants, suggests that the DRα1-linker-TcRVβ chimeras may be developed as a general therapy against a broad spectrum of superantigens released during Staphylococcal infection.

Counting Small RNA in Pathogenic Bacteria

Here, we present a modification to single-molecule fluorescence in situ hybridization that enables quantitative detection and analysis of small RNA (sRNA) expressed in bacteria. We show that short (~200 nucleotide) nucleic acid targets can be detected when the background of unbound singly dye-labeled DNA oligomers is reduced through hybridization with a set of complementary DNA oligomers labeled with a fluorescence quencher. By neutralizing the fluorescence from unbound probes, we were able to significantly reduce the number of false positives, allowing for accurate quantification of sRNA levels. Exploiting an automated, mutli-color wide-field microscope and data analysis package, we analyzed the statistics of sRNA expression in thousands of individual bacteria. We found that only a small fraction of either Yersinia pseudotuberculosis or Yersinia pestis bacteria express the small RNAs YSR35 or YSP8, with the copy number typically between 0 and 10 transcripts. The numbers of these RNA are both increased (by a factor of 2.5× for YSR35 and 3.5× for YSP8) upon a temperature shift from 25 to 37 °C, suggesting they play a role in pathogenesis. The copy number distribution of sRNAs from bacteria-to-bacteria are well-fit with a bursting model of gene transcription. The ability to directly quantify expression level changes of sRNA in single cells as a function of external stimuli provides key information on the role of sRNA in cellular regulatory networks.

Functional gene discovery using RNA interference-based genomic screens to combat pathogen infection.

The rampant use of antibiotics in the last half-century has imposed an unforeseen biological cost, the unprecedented acceleration of bacterial evolution to produce drug-resistant strains to practically every approved antibiotic. This rise in antimicrobial drug resistance, alongside the failure of conventional research efforts to discover new antibiotics, may eventually lead to a public health crisis that can drastically curtail our ability to combat infectious disease. To address this public health need for novel countermeasure strategies, research efforts have recently focused on identification of genes in the host, rather than the pathogen, that are essential for successful pathogen infection, as potential targets for drug discovery. In the past decade, RNA interference (RNAi) has emerged as a powerful tool for analyzing gene function by silencing target genes through the specific destruction of their mRNAs. Based on RNAi methodology, high-throughput genome- wide assay platforms have been developed to identify candidate host genes that are manipulated by pathogens during infection. In this review, we will discuss recent strategies for RNAi-based genomic screens to investigate hostpathogen mechanisms in human cell models using both bacterial pathogens, including Salmonella typhimurium, Mycobacterium tuberculosis, and Listeria monocytogenes, and viruses, such as Human Immunodeficiency Virus (HIV), Hepatitis C Virus (HCV) and influenza. These functional genomics studies have begun to elucidate novel pathogen virulence mechanisms and thus, may serve as the basis for the design of novel host-based inhibitor therapeutics that can block or alleviate the downstream effects of pathogen infection.

Targeting Toll-Like Receptor Signaling Pathways for Design of Novel Immune Therapeutics

The Toll-like receptor (TLR) family plays a fundamental role in host innate immunity by mounting a rapid and potent inflammatory response to pathogen infection. TLRs recognize distinct microbial components and activate intracellular signaling pathways that induce expression of host inflammatory genes. Extensive research in the past decade to understand TLR-mediated mechanisms of innate immunity has enabled pharmaceutical companies to begin to develop novel therapeutics for the purpose of controlling inflammatory disease. Initially, extracellular TLR agonists were designed to compete with natural microbial ligands for binding to TLRs. More recently, basic research to identify new targets for drug development has begun to explore modulation of TLR intracellular signaling pathways, in addition to TLR ligand binding. In this review, we will discuss recent strategies, including the use of decoy peptides and mimetics, plant polyphenols, and chemically modified antisense oligonucleotides, that inhibit different molecular events in TLR signaling pathways to modulate the inflammatory response. The molecular mechanisms of these inhibitors range from interference with protein-protein interactions between signaling proteins, to inhibition of transcription factor activity, to perturbation of the plasma membrane, and are derived from host, pathogen, and plant sources and by rational design. Taken together, these studies represent promising avenues for the development of novel tailored immune therapeutics that can relieve the great toll inflicted by inflammatory disease on human health and quality of life.

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.

Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

BackgroundBacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology.ResultsWe profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. In particular, the trans-encoded BTH_s1 and s39 exhibited differential expression profiles dependent on growth phase and cell stimuli, such as antibiotics and serum. Furthermore, knockdown of the highly-expressed BTH_s39 by antisense transcripts reduced B. thailandensis cell growth and attenuated host immune response upon infection, indicating that BTH_s39 functions in bacterial metabolism and adaptation to the host. In addition, expression of cis-encoded BTH_s13 and s19 found in the 5′ untranslated regions of their cognate genes correlated with tight regulation of gene transcript levels. This sRNA-mediated downregulation of gene expression may be a conserved mechanism of post-transcriptional gene dosage control.ConclusionsThese studies provide a broad analysis of differential Burkholderia sRNA expression profiles and illustrate the complexity of bacterial gene regulation in response to different environmental stress conditions.