Abstract: Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.
Abstract: Since the discovery of RNAi and microRNAs more than 10 years ago, much research has focused on the development of systems that usurp microRNA pathways to downregulate gene expression in mammalian cells. One of these systems makes use of endogenous microRNA pri-cursors that are expressed from polymerase II promoters where the mature microRNA sequence is replaced by gene specific duplexes that guide RNAi (shRNA-miRs). Although shRNA-miRs are effective in directing target mRNA knockdown and hence reducing protein expression in many cell types, variability of RNAi efficacy in cell lines has been an issue. Here we show that the choice of the polymerase II promoter used to drive shRNA expression is of critical importance to allow effective mRNA target knockdown. We tested the abundance of shRNA-miRs expressed from five different polymerase II promoters in 6 human cell lines and measured their ability to drive target knockdown. We observed a clear positive correlation between promoter strength, siRNA expression levels, and protein target knockdown. Differences in RNAi from the shRNA-miRs expressed from the various promoters were particularly pronounced in immune cells. Our findings have direct implications for the design of shRNA-directed RNAi experiments and the preferred RNAi system to use for each cell type.
Abstract: Leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1), one of the most widely spread immune receptors, attenuates immune cell activation when bound to specific sites in collagen. The collagen-binding domain of LAIR-1 is homologous to that of glycoprotein VI (GPVI), a collagen receptor crucial for platelet activation. Because LAIR-1 and GPVI also display overlapping collagen-binding specificities, a common structural basis for collagen recognition would appear likely. Therefore, it is crucial to gain insight into the molecular interaction of both receptors with their ligand to prevent unwanted cross-reactions during therapeutic intervention. We determined the crystal structure of LAIR-1 and mapped its collagen-binding site by nuclear magnetic resonance (NMR) titrations and mutagenesis. Our data identify R59, E61, and W109 as key residues for collagen interaction. These residues are strictly conserved in LAIR-1 and GPVI alike; however, they are located outside the previously proposed GPVI collagen-binding site. Our data provide evidence for an unanticipated mechanism of collagen recognition common to LAIR-1 and GPVI. This fundamental insight will contribute to the exploration of specific means of intervention in collagen-induced signaling in immunity and hemostasis.
Abstract: Myeloid cells play a crucial role in controlling infection. Activation of these cells needs to be tightly regulated, because their potent effector functions can damage host tissue. Inhibitory receptors expressed by immune cells play an important role in restricting immune cell activation. In this study, we have characterized a hitherto unidentified ITIM-bearing receptor that is highly expressed on human neutrophils and monocytes: signal inhibitory receptor on leukocytes-1 (SIRL-1). The chromosomal location of SIRL-1 is adjacent to the human leukocyte receptor complex on chromosome 19q13.4 and contains two ITIMs in its cytoplasmic tail. As a classical ITIM-bearing receptor, SIRL-1 is capable of inhibiting FcepsilonRI-mediated signaling and can recruit the Src homology 2 domain-containing phosphatases Src homology region 2 domain-containing phosphatases 1 and 2. To investigate the specific involvement of the individual ITIMs in this study, mutational analysis was performed, which revealed that both ITIMs are crucial for SIRL-1 inhibitory function and phosphatase recruitment. When primary cells were stimulated in vitro, SIRL-1(high) monocytes produce less TNF-alpha than SIRL-1(low) monocytes. Thus, SIRL-1 is a novel inhibitory immune receptor belonging to the growing family of ITIM-bearing receptors that is implied in the regulation of phagocytes.
Abstract: Immune responses are tightly controlled by the opposing actions of activating and inhibitory immune receptors. Previously we identified collagens as ligands for the inhibitory leukocyte-associated Ig-like receptor-1 (LAIR-1), revealing a novel mechanism of peripheral immune regulation by inhibitory immune receptors binding to extracellular matrix collagens. This interaction can be blocked by LAIR-2, a secreted member of the LAIR-1 family. LAIR-1 specifically interacts with synthetic trimeric peptides containing 10 repeats of glycine-proline-hydroxyproline (GPO) residues which can directly inhibit immune cell activation in vitro. Here we studied the interaction of human LAIR-1 and LAIR-2 with collagen in more detail by using novel overlapping synthetic trimeric peptides (Toolkits) encompassing the entire triple-helical domain of human collagens II and III. LAIR-1 and LAIR-2 bind several of these collagen-like peptides, with LAIR-2 being able to bind more than LAIR-1. LAIR binding to trimeric collagen peptides was influenced by GPO content of the peptide, although additional non-GPO triplets contributed to the interaction. Furthermore, we identified several trimeric peptides that were potent LAIR-1 ligands and could efficiently induce inhibition of T cell activation and FceRI-induced degranulation of RBL-2H3 cells through binding to LAIR-1. A detailed understanding of the LAIR recognition motifs within collagen may lead to the development of potent reagents that can be used in in vitro, ex vivo, and in vivo functional studies to dissect the biology and function of the collagen/LAIR-1 interaction.
Abstract: The cell surface receptor tyrosine kinase HER2/neu enhances tumor metastasis. Recent studies suggest that deregulated microRNA (miRNA) expression promotes invasion and metastasis of cancer cells; we therefore explored the possibility that HER2/neu signaling induces the expression of specific miRNAs involved in this process. We identified a putative oncogenic miRNA, miR-21, whose expression is correlated with HER2/neu up-regulation and is functionally involved in HER2/neu-induced cell invasion. We show that miR-21 is up-regulated via the MAPK (ERK1/2) pathway upon stimulation of HER2/neu signaling in breast cancer cells, and overexpression of other ERK1/2 activators such as RASV12 or ID-1 is sufficient to induce miR-21 up-regulation in HER2/neu-negative breast cancer cells. Furthermore, the metastasis suppressor protein PDCD4 (programmed cell death 4) is down-regulated by miR-21 in breast cancer cells expressing HER2/neu. Our data reveal a mechanism for HER2/neu-induced cancer cell invasion via miRNA deregulation. In addition, our results identify miR-21 as a potential therapeutic target for the prevention of breast cancer invasion and metastasis.
Abstract: Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per gene) that are analyzed by deep sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of true hits.
Abstract: Leukocyte-associated Ig-like receptor (LAIR)-1 is a collagen-receptor that inhibits immune cell function upon collagen binding. Next to LAIR-1, the human genome encodes LAIR-2, a putative soluble homolog. In this study we show, for the first time, that the LAIR-2 gene is broadly transcribed in human PBMC, mirroring the expression profile of LAIR-1. LAIR-2 protein is expressed as a soluble receptor exhibiting high affinity for various collagen molecules to which it binds in a hydroxyproline-dependent manner. In vitro stimulation of PBMC induces secretion of LAIR-2. We detect high amounts of LAIR-2 in urine of pregnant women, indicating that the soluble receptor is indeed produced in vivo and can be cleared from the body via urine. Furthermore, LAIR-2 levels are increased in synovial fluid of patients with rheumatoid arthritis as compared with osteoarthritis patients. We hypothesize that soluble LAIR-2 may function as a natural competitor for LAIR-1, thereby regulating its inhibitory potential. Indeed, LAIR-2 prevents binding of human LAIR-1 to collagens and LAIR-1 cross-linking in vitro, suggesting that the protein has an immunoregulatory function in vivo. Hence, we reveal a novel mechanism of immune regulation by a soluble LAIR receptor regulating the inhibitory potential of the membrane-bound LAIR-1 via competition for ligands.
Abstract: Leukocyte-associated Ig-like receptor-1 (LAIR-1) is a cell-surface molecule that functions as an inhibitory receptor on various immune cells. We developed mAbs to study the expression of mouse leukocyte-associated Ig-like receptor-1 (mLAIR-1) on primary immune cells and established that it is expressed on the majority of cells of the immune system, including T cells, NK cells, monocytes and dendritic cells. Furthermore, mLAIR-1 is inducibly expressed on blood granulocytes in vivo and is differentially expressed upon T cell activation in vitro. Unexpectedly, mLAIR-1 was not expressed on splenic and blood B220(+) B cells. Similar to its human homolog, mLAIR-1 interacted with high affinity with a wide range of collagen molecules. Furthermore, mLAIR-1 specifically interacted in a hydroxyproline-dependent manner with synthetic collagen Gly-Pro-Hyp peptides. We show, for the first time, that mLAIR-1 cross-linking with its ligands inhibits CD3-induced T cell stimulation in vitro. Given the similarities between the mouse and human receptors, mLAIR-1 may serve as a good model to assess the role of the LAIR-1 receptors in regulation of immune responses.
Abstract: Regulation of cellular responses by inhibitory receptors is crucial for proper function of the immune system. The prototype inhibitory immune receptors are major histocompatibility complex (MHC) class I binding killer-Ig like receptors (KIRs) present on effector cells such as natural killer (NK) cells and effector T cells. However, the recent identification of non-MHC class I ligands for inhibitory immune receptors, such as KLRG1, KLRB1 and LAIR-1, indicates that also MHC class I-independent inhibitory immune receptors play crucial roles in inducing peripheral tolerance. The presence of these receptors on many other immune cell types besides effector cells suggests that tight regulation of cell activation is necessary in all facets of the immune response in both normal and diseased tissue. Here, we review novel insights and implications of non-MHC class I ligand binding to inhibitory immune receptors. We give an overview of the known ligand-receptor pairs by grouping the ligands according to their properties and discuss implications of these interactions for the maintenance of immune balance and for the defense against tumors and pathogens.
Abstract: Collagens are the most abundant proteins in the human body, important in maintenance of tissue structure and hemostasis. Here we report that collagens are high affinity ligands for the broadly expressed inhibitory leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). The interaction is dependent on the conserved Gly-Pro-Hyp collagen repeats. Antibody cross-linking of LAIR-1 is known to inhibit immune cell function in vitro. We now show that collagens are functional ligands for LAIR-1 and directly inhibit immune cell activation in vitro. Thus far, all documented ligands for immune inhibitory receptors are membrane molecules, implying a regulatory role in cell-cell interaction. Our data reveal a novel mechanism of peripheral immune regulation by inhibitory immune receptors binding to extracellular matrix collagens.
Abstract: Leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1) is a cell-surface molecule that functions as an inhibitory receptor on various immune cells in both humans and mice. We have cloned a LAIR-1 homologue from the rat that we have named rat LAIR-1. The LAIR-1 gene maps to rat chromosome 1q12 in a region showing conserved synteny with human chromosome 19q13.4 and mouse chromosome 7, where the leukocyte receptor cluster is located. Rat LAIR-1 shows 40 and 71% protein sequence identity with human LAIR-1 and mouse LAIR-1, respectively, has a single Ig-like domain and contains two immunoreceptor tyrosine-based inhibitory motif-like sequences in its cytoplasmic tail. Soluble rat LAIR-1 fusion proteins bind to the same adherent cell lines as human LAIR-1 and mouse LAIR-1, indicating that a putative ligand for all the LAIR-1 molecules is expressed on these cells. Furthermore, we show that rat and mouse LAIR-1 bind the same molecule expressed on human HT29 cells. Since many autoimmune diseases are studied in rat models, identification of rat LAIR-1 allows for in vivo studies on the function of LAIR molecules in these systems.
Abstract: We report the molecular cloning and characterization of the first leukocyte-associated Ig-like receptor 1 (LAIR-1) homologue in mice that we have named mouse LAIR-1 (mLAIR-1). The mLAIR-1 gene maps to the proximal end of mouse chromosome 7 in a region syntenic with human chromosome 19q13.4 where the leukocyte receptor cluster is located. The protein shares 40% sequence identity with human LAIR-1, has a single Ig-like domain, and contains two immunoreceptor tyrosine-based inhibitory motif-like structures in its cytoplasmic tail. Mouse LAIR-1 is broadly expressed on various immune cells, and cross-linking of the molecule on stably transfected RBL-2H3 and YT.2C2 cells results in strong inhibition of their degranulation and cytotoxic activities, respectively. Upon pervanadate stimulation, the mLAIR-1 cytoplasmic tail becomes phosphorylated, thereby recruiting Src homology region 2-containing tyrosine phosphatase-2. Interestingly, unlike human LAIR-1, Src homology region 2-containing tyrosine phosphatase-1 is not recruited to the mLAIR-1 cytoplasmic tail. Screening human and mouse cell lines for mLAIR-1 and human LAIR-1 binding partners identified several lines expressing putative ligand(s) for both receptors.
Abstract: Although the archaeal transcription apparatus resembles the eukaryal RNA polymerase II system, many bacterial-like regulators can be found in archaea. Particularly, all archaeal genomes sequenced to date contain genes encoding homologues of Lrp (leucine-responsive regulatory protein). Whereas Lrp-like proteins in bacteria are involved in regulation of amino acid metabolism, their physiological role in archaea is unknown. Although several archaeal Lrp-like proteins have been characterized recently, no target genes apart from their own coding genes have been discovered yet, and no ligands for these regulators have been identified so far. In this study, we show that the Lrp-like protein LysM from Sulfolobus solfataricus is involved in the regulation of lysine and possibly also arginine biosynthesis, encoded by the lys gene cluster. Exogenous lysine is the regulatory signal for lys gene expression and specifically serves as a ligand for LysM by altering its DNA binding affinity. LysM binds directly upstream of the TFB-responsive element of the intrinsically weak lysW promoter, and DNA binding is favored in the absence of lysine, when lysWXJK transcription is maximal. The combined in vivo and in vitro data are most compatible with a model in which the bacterial-like LysM activates the eukarya-like transcriptional machinery. As with transcriptional activation by Escherichia coli Lrp, activation by LysM is apparently dependent on a co-activator, which remains to be identified.
Abstract: Understanding the molecular basis of the distinct biological properties of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV), such as its narrow host range and high virulence, requires detailed information on the temporal expression and subcellular localization of SeMNPV gene products. The expression of two unique SeMNPV ORFs, 116 (Se116) and 117 (Se117), which show 45% amino acid similarity, was analyzed. Se116 and Se117 were expressed both in cultured cells and in larvae of S. exigua as polyadenylated transcripts of 0.80 and 0.75 kb, respectively. These transcripts initiated from ATCA(G/T)T promoter motifs, commonly found for baculovirus early genes. Se116 transcripts were detected with increasing abundance from 8 to 48 h p.i., whereas Se117 transcripts were present from 4 h p.i. and most abundantly at 24 h p.i. Western blot analysis of infected Se301 cells revealed 27- and 23-kDa proteins for Se116 and Se117, respectively. C-terminal GFP-fusion proteins of Se116 and Se117 were primarily localized in the nucleus of Se301 cells. When Se301 cells were infected with SeMNPV, both GFP-fusion proteins were localized in the virogenic stroma of the nucleus. While the function of the Se116 protein is still enigmatic, the Se117 protein appeared to be a structural protein associated with nucleocapsids of occlusion-derived SeMNPV virions but not of budded virus.
Abstract: The immune system constantly receives opposing signals that on the one side activate immune cells allowing them to eradicate diseased cells and pathogens, and on the other side inhibit these same cells to limit and ultimately terminate an immune response. A correct balance is crucial for effective defence against pathogens without affecting healthy tissues. One of the mechanisms of negative regulation in the immune system is provided by specialized inhibitory receptors that upon interaction with their ligands attenuate activation signals initiated by activating receptors. Loss of inhibitory signaling is often associated with autoreactivity and unchecked inflammatory responses, illustrating the essential role these systems play in immune regulation. This thesis is focused on the function of such an inhibitory receptor called leukocyte-associated immunoglobulin-like receptor (LAIR)-1, which is expressed on most immune cells in peripheral blood. Although the inhibitory potential and mechanisms of LAIR-1 inhibition are well established, the actual function of the receptor in vivo remains unknown due the lack of animal models and the unknown identity of the LAIR-1 ligand. In the first part we identified and characterized mouse and rat LAIR-1 orthologues of human LAIR-1. Like human LAIR-1, mouse LAIR-1 is expressed on immune cells and functions as an inhibitory receptor. Furthermore we show that human and mouse LAIR-1 bind to similar, but not identical, cytoplasmic signalling effector molecules. In the second part we identified collagens as ligands for the LAIR-1 molecules. Both transmembrane and extracellular matrix collagens interact with LAIR-1 and the interaction results in inhibition of immune cell functions via LAIR-1. Our data reveal a novel mechanism of peripheral immune regulation by inhibitory immune receptors binding to extracellular matrix collagens. Additionally, we studied the functional interaction of LAIR-1 and collagens by using synthetic trimeric collagen peptides overlapping the entire human collagen II and III proteins. We show that LAIR-1 binds to multiple sites on these collagens and that the relative content of collagen-specific glycine-proline-hydroxyproline triplets in the proteins is associated with increased LAIR-1 binding. Besides the transmembrane LAIR-1, humans encode soluble LAIR-2 receptors. For the first time we provide evidence that LAIR-2 is expressed in humans as a soluble collagen receptor and that the molecule can block the collagen/LAIR-1 interaction. Hence, we hypothesize that soluble LAIR-2 may function as a natural competitor for LAIR-1 in vivo, thereby regulating its inhibitory potential. Further studies should aim at dissecting the in vivo role of LAIR-1 and LAIR-2 in normal physiology and disease. Furthermore, detailed studies on the biochemical interaction between collagens and LAIR may allow rational design of new and potent research tools and could result in the development of therapeutics which exploits collagen/LAIR interactions.
