NK cell cytotoxicity is controlled by numerous NK inhibitory and activating receptors. Most of the inhibitory receptors bind MHC class I proteins and are expressed in a variegated fashion. It was recently shown that TIGIT, a new protein expressed by T and NK cells binds to PVR and PVR-like receptors and inhibits T cell activity indirectly through the manipulation of DC activity. Here, we show that TIGIT is expressed by all human NK cells, that it binds PVR and PVRL2 but not PVRL3 and that it inhibits NK cytotoxicity directly through its ITIM. Finally, we show that TIGIT counter inhibits the NK-mediated killing of tumor cells and protects normal cells from NK-mediated cytoxicity thus providing an ''alternative self'' mechanism for MHC class I inhibition.inhibitory receptors ͉ natural killers I n contrast to T cells, that possess a single dominant antigen receptor (1), NK cells rely on a vast combinatorial array of receptors to initiate effector functions (2). Both activating and inhibitory receptors expressed on NK cells regulate their activity when interacting with tumors, virus infected cells and bacteria, as well as normal self-cells (2). MHC class I-expressing cells are protected from NK-mediated lysis due to the recognition of various MHC class I proteins by the inhibitory receptors KIR, LIR and CD94-NKG2A (3). Other NK inhibitory receptors which do not interact with MHC class I also exist, such as CEACAM1 and IRp60 (4-8). The significance, however, of these non-MHC class I inhibitory receptors in normal conditions is still unclear. All of the inhibitory receptors share a common immune receptor tyrosinebased inhibitory motif (ITIM) in their cytoplasmic regions, which delivers the inhibitory signal (3).The NK cell-mediated killing is extracted by specific receptors, among which are the natural cytotoxicity receptors (NCRs), which include the NKp30 that interacts with pp65 of human cytomegalovirus (CMV), BAT3 and the recently identified B7-family member B7-H6 (9-11), and the NKp46/NKp44 receptors, which interact with various viral hemagglutinins (12, 13). The NKG2D receptor interacts with MICA, MICB and ULBP 1-5 (14) and NKp80 interacts with AICL (15). In addition, two other receptors, DNAM-1 and CD96, enhance NK cytotoxicity (16,17). Both DNAM-1 and CD96 recognize PVR (CD155), whereas DNAM-1 also recognizes PVRL2 (CD112) (16,17). It was recently shown that a new receptor, named TIGIT, for T cell Ig and ITIM domain, interacts with PVR and its related proteins and that TIGIT inhibits T cell activity indirectly through the manipulation of DC activity (18). Here, we show that TIGIT, through its ITIM, can directly inhibit NK cytotoxicity. ResultsTIGIT Inhibits YTS Killing Through Its ITIM Motif. While searching for new CD28 family-like receptors, based on bioinformatics analysis, we observed that a protein named VSIG9 or VSTM3 in the databases expresses an ITIM motif. We continued to work on this protein and found that it interacts with PVR (CD155) but not with any other NK ligands tested (supporting information (...

G-protein-coupled receptors (GPCRs) represent an important group of targets for pharmaceutical therapeutics. The completion of the human genome revealed a large number of putative GPCRs. However, the identification of their natural ligands, and especially peptides, suffers from low discovery rates, thus impeding development of therapeutics based on these potential drug targets. We describe the discovery of novel GPCR ligands encrypted in the human proteome. Hundreds of potential peptide ligands were predicted by machine learning algorithms. In vitro screening of selected 33 peptides on a set of 152 GPCRs, including a group of designated orphan receptors, was conducted by intracellular calcium measurements and cAMP assays. The screening revealed eight novel peptides as potential agonists that specifically activated six different receptors in a dose-dependent manner. Most of the peptides showed distinct stimulatory patterns targeted at designated and orphan GPCRs. Further analysis demonstrated a significant in vivo effect for one of the peptides in a mouse inflammation model.

Recent progress in genomic sequencing, computational biology, and ontology development has presented an opportunity to investigate biological systems from a unique perspective, that is, examining genomes and transcriptomes through the multiple and hierarchical structure of Gene Ontology (GO). We report here our development of GO Engine, a computational platform for GO annotation, and analysis of the resultant GO annotations of human proteins. Protein annotation was centered on sequence homology with GO-annotated proteins and protein domain analysis. Text information analysis and a multiparameter cellular localization predictive tool were also used to increase the annotation accuracy, and to predict novel annotations. The majority of proteins corresponding to full-length mRNA in GenBank, and the majority of proteins in the NR database (nonredundant database of proteins) were annotated with one or more GO nodes in each of the three GO categories. The annotations of GenBank and SWISS-PROT proteins are available to the public at the GO Consortium web site.Biomedical research over the last century has made tremendous progress in our understanding of biology and medicine. The recent genomic sequencing of human, mouse, and other organisms, and high-throughput studies, such as those based on microarray technology, have been yielding massive amounts of data. However, the knowledge accumulated so far is mainly fragmented. Full utilization of this data and its integration with existing knowledge can be facilitated by a systematic representation of knowledge, that is, the development of ontology. Ontology is the formalized specification of knowledge in a certain subject. Great potential exists for ontology-based literature retrieval in biomedical research (McGuinness 1999), ontology-based database integration in drug discovery, and ontology-facilitated biomedical research. Recently, the Gene Ontology (GO) Consortium (www. geneontology.org) has developed a systematic and standardized nomenclature for annotating genes in various organisms. Using three main ontologies-molecular function, biological process, and cellular component-a significant number of genes in yeast, Drosophila, mouse, and other model organisms have been annotated, either manually or automatically (Ashburner et al. 2000; The Gene Ontology Consortium 2001).Association between ontology nodes and proteins, namely, protein annotation through gene ontology, is an integral application of ontology and has many practical uses. For example, designing of microarray probes would be greatly facilitated by a comprehensive understanding of all the genes involved. A microarray aimed to examine a particular process, such as apoptosis, would optimally have probes against all the genes significantly and directly involved in apoptosis. These genes can be chosen using GO annotations.To efficiently annotate proteins, we have developed a software platform, the GO Engine, which combines rigorous sequence homology comparison with text information analysis. During evolution, many ne...

Blocking conformational changes in biologically active proteins holds therapeutic promise. Inspired by the susceptibility of viral entry to inhibition by synthetic peptides that block the formation of helixhelix interactions in viral envelope proteins, we developed a computational approach for predicting interacting helices. Using this approach, which combines correlated mutations analysis and Fourier transform, we designed peptides that target gp96 and clusterin, 2 secreted chaperones known to shift between inactive and active conformations. In human blood mononuclear cells, the gp96-derived peptide inhibited the production of TNF␣, IL-1␤, IL-6, and IL-8 induced by endotoxin by >80%. When injected into mice, the peptide reduced circulating levels of endotoxin-induced TNF␣, IL-6, and IFN␥ by >50%. The clusterin-derived peptide arrested proliferation of several neoplastic cell lines, and significantly enhanced the cytostatic activity of taxol in vitro and in a xenograft model of lung cancer. Also, the predicted mode of action of the active peptides was experimentally verified. Both peptides bound to their parent proteins, and their biological activity was abolished in the presence of the peptides corresponding to the counterpart helices. These data demonstrate a previously uncharacterized method for rational design of protein antagonists.cancer ͉ contact map prediction ͉ cytokines ͉ inflammation ͉ helix C onformational changes in proteins have an essential role in regulating activity. Natural and synthetic molecules that modulate such changes are of considerable biological importance. Such molecules include allosteric effectors that alter the rate of enzymecatalyzed reactions (1), molecules that shift the oligomerization equilibrium of proteins (2), and molecules that interfere with transmembrane helix-helix associations (3).Conformational changes that have been extensively studied are those that take place during viral-induced membrane fusion. This process is required for the propagation of enveloped viruses, and is facilitated by viral encoded type 1 integral membrane proteins (4, 5). Viral entry of enveloped viruses depends on a conformational change involving the formation of helix-helix interactions, i.e., 2 alpha helices that do not interact in the native (nonfusogenic) state, but do interact with each other when the protein folds into its fusion-active (fusogenic) form. Remarkably, synthetic peptides corresponding to some of these helical segments have an antiviral activity (6 -8), of which one has been developed for the treatment of HIV-1 infection (9, 10).We hypothesized that such a mode of inhibition could be also applied on nonviral proteins. The aim of the present study was to develop a computational tool for the detection of intramolecular helix-helix interactions and to use this tool for detecting such interacting helices in proteins of interest. This study focuses on secreted chaperones due to their biological and therapeutic relevance (11-14), and because conformational changes are known to take p...

The B7-like protein family members play critical immunomodulatory roles and constitute attractive targets for the development of novel therapies for human diseases. We identified Ig-like domain-containing receptor (ILDR)2 as a novel B7-like protein with robust T cell inhibitory activity, expressed in immune cells and in immune-privileged and inflamed tissues. A fusion protein, consisting of ILDR2 extracellular domain with an Fc fragment, that binds to a putative counterpart on activated T cells showed a beneficial effect in the collagen-induced arthritis model and abrogated the production of proinflammatory cytokines and chemokines in autologous synovial-like cocultures of macrophages and cytokine-stimulated T cells. Collectively, these findings point to ILDR2 as a novel negative regulator for T cells, with potential roles in the development of immune-related diseases, including autoimmunity and cancer.