Immunostimulatory CpG oligonucleotides form defined three-dimensional structures: results from an NMR study

Single Stranded DNA Immune Modulators with Unmethylated CpG Motifs: Structure and Molecular Recognition by Toll-Like Receptor 9

Single stranded microbial DNA fragments with unmethylated deoxycytidylyldeoxyguanosine dinucleotide (CpG) motifs are interpreted as danger signals by the innate immune system via recognition by the Toll-like Receptor 9 (TLR9). Their synthetic analogues, Oligodeoxynucleotides (ODN) comprise a promising class of immune modulators with potential applications in the treatment of multiple diseases, such as cancer, autoimmune diseases or allergy. ODN molecules contain a core hexamer sequence, which is species specific consisting of GACGTT and AACGT for mouse and GTCGTT in humans. Assessment of structural features of different type of ODNs is highly challenging. NMR spectroscopic insights were gained for a short, single CpG motif containing ODN 1668. The structural basis of ODN recognition by TLR9 recently started to unravel as crystal structures of TLR9 orthologues in complex with ODN 1668 were solved. Systematic investigations of ODN sequences revealed that ODNs with a single CpG motif are capable of activating mouse TLR9, but two closely positioned CpG motifs are necessary for activation of human TLR9. Furthermore, longer ODNs with TCC and TCG sequences at the 5' end were shown to activate TLR9 with higher efficiency. It was revealed that 5'-xCx motif containing short ODNs (sODN) are able to augment the immune response of short, single CpG containing ODNs, which are incapable of activating of TLR9 alone. All these observations pointed to the existence of a second binding site on TLR9, which was characterized in crystal structures that delivered further insights of the nucleic acid recognition of the innate immune system by TLR9.

Activation of Rac1 GTPase by nanoparticulate structures in human macrophages

Inflammatory activation of alveolar macrophages by ambient particles can be facilitated via Toll-like receptors (TLR). The action of TLR agonists and antagonists has been reported to depend on the formation of nanoparticulate structures. Aim of the present study was to identify the signaling pathways induced by nanoparticulate structures in human macrophages, which might be critical for inflammatory cell activation.

METHODS

Studies were performed in primary human alveolar macrophages or in differentiated THP-1 macrophages. Silica nanoparticles were prepared by Stöber synthesis and characterized by dynamic light scattering and scanning electron microscopy. Mycobacterial DNA was isolated from Mycobacterium bovis BCG, and nanoparticle formation was assessed by atomic force microscopy and dynamic light scattering. Actin polymerization was measured by phalloidin-TRITC staining, and cell activation was determined by reverse transcription quantitative PCR analysis, L929 cytotoxicity assay (cytokine induction), and pull-down assays (Rho GTPases).

RESULTS

In contrast to immune stimulatory sequence ISS 1018, BCG DNA spontaneously formed nanoparticulate structures and induced actin polymerization as did synthetic silica nanoparticles. Co-incubation with silica nanoparticles amplified the responsiveness of macrophages toward the TLR9 ligand ISS 1018. The activation of Rac1 was induced by silica nanoparticles as well as BCG DNA and is suggested as the critical signaling event inducing both cytoskeleton changes as well as inflammatory cell activation.

CONCLUSION

Nanoparticles can induce signaling pathways, which amplify an inflammatory response in macrophages.

Newly identified CpG ODNs, M5-30 and M6-395, stimulate mouse immune cells to secrete TNF-alpha and enhance Th1-mediated immunity

Bacterial CpG motifs are known to induce both innate and adaptive immunity in infected hosts via toll-like receptor 9 (TLR9). Because small oligonucleotides (ODNs) mimicking bacterial CpG motifs are easily synthesized, they have found use as immunomodulatory agents in a number of disease models. We have developed a novel bioinformatics approach to identify effective CpG ODN sequences and evaluate their function as TLR9 ligands in a murine system. Among the CpG ODNs we identified, M5-30 and M6-395 showed significant ability to stimulate TNF-alpha and IFN-gamma production in a mouse macrophage cell line and mouse splenocytes, respectively. We also found that these CpG ODNs activated cells through the canonical NF-kappa B signaling pathway. Moreover, both CpG ODNs were able to induce Th1-mediated immunity in Mycobacterium tuberculosis (Mtb)-infected mice. Our results demonstrate that M5-30 and M6-395 function as TLR9-specific ligands, making them useful in the study of TLR9 functionality and signaling in mice.

Comprehensive modeling and functional analysis of Toll-like receptor ligand-recognition domains

Toll-like receptors (TLRs) are innate immune pattern-recognition receptors endowed with the capacity to detect microbial pathogens based on pathogen-associated molecular patterns. The understanding of the molecular principles of ligand recognition by TLRs has been greatly accelerated by recent structural information, in particular the crystal structures of leucine-rich repeat-containing ectodomains of TLR2, 3, and 4 in complex with their cognate ligands. Unfortunately, for other family members such as TLR7, 8, and 9, no experimental structural information is currently available. Methods such as X-ray crystallography or nuclear magnetic resonance are not applicable to all proteins. Homology modeling in combination with molecular dynamics may provide a straightforward yet powerful alternative to obtain structural information in the absence of experimental (structural) data, provided that the generated three-dimensional models adequately approximate what is found in nature. Here, we report the development of modeling procedures tailored to the structural analysis of the extracellular domains of TLRs. We comprehensively compared secondary structure, torsion angles, accessibility for glycosylation, surface charge, and solvent accessibility between published crystal structures and independently built TLR2, 3, and 4 homology models. Finding that models and crystal structures were in good agreement, we extended our modeling approach to the remaining members of the TLR family from human and mouse, including TLR7, 8, and 9.

Homology modeling of human Toll-like receptors TLR7, 8, and 9 ligand-binding domains

Toll-like receptors (TLRs) play a key role in the innate immune system. The TLR7, 8, and 9 compose a family of intracellularly localized TLRs that signal in response to pathogen-derived nucleic acids. So far, there are no crystallographic structures for TLR7, 8, and 9. For this reason, their ligand-binding mechanisms are poorly understood. To enable first predictions of the receptor-ligand interaction sites, we developed three-dimensional structures for the leucine-rich repeat ectodomains of human TLR7, 8, and 9 based on homology modeling. To achieve a high sequence similarity between targets and templates, structural segments from all known TLR ectodomain structures (human TLR1/2/3/4 and mouse TLR3/4) were used as candidate templates for the modeling. The resulting models support previously reported essential ligand-binding residues. They also provide a basis to identify three potential receptor dimerization mechanisms. Additionally, potential ligand-binding residues are identified using combined procedures. We suggest further investigations of these residues through mutation experiments. Our modeling approach can be extended to other members of the TLR family or other repetitive proteins.

Modifications in small interfering RNA that separate immunostimulation from RNA interference

Synthetic small interfering RNA (siRNA) can suppress the expression of endogenous mRNA through RNA interference. It has been reported that siRNA can induce type I IFN production from plasmacytoid dendritic cells, leading to off-target effects. To separate immunostimulation from the desired gene-specific inhibitory activity, we designed RNA strands with chemical modifications at strategic positions of the ribose or nucleobase residues. Substitution of uridine residues by 2'-deoxyuridine or thymidine residues was found to decrease type I IFN production upon in vitro stimulation of human PBMC. Thymidine residues in both strands of a siRNA duplex further decreased immunostimulation. Fortunately, the thymidine residues did not affect gene-silencing activity. In contrast, 2'-O-methyl groups at adenosine and uridine residues reduced both IFN-alpha secretion and gene-silencing activity. Oligoribonucleotides with 2'-O-methyladenosine residues actively inhibited IFN-alpha secretion induced by other immunostimulatory RNAs, an effect not observed for strands with 2'-deoxynucleosides. Furthermore, neither 5-methylcytidine nor 7-deazaguanosine residues in the stimulatory strands affected IFN-alpha secretion, suggesting that recognition does not involve sites in the major groove of duplex regions. The activity data, together with structure prediction and exploratory UV-melting analyses, suggest that immunostimulatory sequences adopt folded structures. The results show that immunostimulation can be suppressed by suitable chemical modifications without losing siRNA potency by introducing seemingly minor structural changes.

Structural requirements for uptake and recognition of CpG oligonucleotides

Recognition of infectious danger by innate immune cells is a fundamental requirement to directly combat infections and to activate the adaptive immune response of T and B cells. Pathogen-associated molecular patterns (PAMPs) play a fundamental role in this process. PAMPs are sensed by pattern recognition receptors, among which the Toll-like receptors (TLRs) play an important role. Within the TLR ligands, bacterial CpG DNA is peculiar. CpG DNA is recognized by TLR9 and harbors the outstanding propensity to induce a milieu that favors activation of Th1-dominated immune responses. This is mainly due to activation of dendritic cells and subpopulations, thereby inducing an intense interferon and IL-12 response. Therefore, CpG DNA has become a promising candidate for constructing new vaccines as well as for induction of immune responses in cancer and allergy. CpG DNA can be synthesized with high purity, defined base composition and various chemical modifications. We aimed to understand the structural requirements for cellular uptake and activation of CpG DNA, which will improve our means to enhance the intrinsic activity of CpG for therapeutic use. We show that sequence modifications can be utilized to enhance cellular uptake, and that chemical substitutions can confer new qualities to synthetic CpG DNA. Additionally, we propose a model of CpG DNA recognition which occurs by sensing partial duplex forms instead of single-stranded DNA. Moreover, we provide evidence that the propensity of CpG DNA to induce high amounts of IL-12 is due to its unique ability to trigger epigenetic modifications of the IL-12p40 promoter, including acetylation and nucleosomal remodeling. Hence, CpG DNA represents a new and promising class of adjuvant for vaccination.