# Patent

## Title
Screening assay for TLR7, TLR8 and TLR9 agonists and antagonists

## Abstract

The present invention relates to novel screening methods for identifying agonists and antagonists of toll-like receptor (TLR) 7, TLR8 or TLR9. Methods are disclosed for identifying agonists and antagonists of TLR7, TLR8 or TLR9 using mutant TLR proteins containing deletions in one or more extracellular leucine rich regions (LRRs). Such agonists and antagonists have utility in the prevention, treatment and/or cure of various diseases and conditions, including cancer, virus infection, allergy, asthma, and chronic obstructive pulmonary disease (COPD).

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims priority benefit of U.S. provisional application No. 60/665,068, filed Mar. 24, 2005, which is incorporated by reference in its entirety.


FIELD OF THE INVENTION
The present invention relates to the field of screening methods for identification of compounds that potentiate immune response mechanisms to treat various diseases, such as cancer, virus infection, allergy, asthma, and chronic obstructive pulmonary disease (COPD).
BACKGROUND OF THE INVENTION
Toll-like receptors (TLRs) are type-I transmembrane proteins which are responsible for initiation of innate immune responses in vertebrates. They recognize a variety of pathogen-associated molecular patterns (PAMPS) from bacteria, viruses and fungi and act as a first line of defense against invading pathogens. There are ten human TLRs that elicit overlapping yet distinct biological responses due to differences in cellular expression and signaling pathways they initiate.
TLRs possess 19-25 contiguous copies of an extracellular N-terminal motif known as the leucine-rich repeat (LRR) motif, followed by a cysteine-rich region and an intracellular region. (Bell et al., Trends Immunol. 24:528 (2003)). The LRR region is a common feature among the TLRs and is important for ligand binding and cellular signaling. (Modlin, R. L., Ann. Allergy Asthma Immunol. 88:543 (2002); Kobe and Diesenhofer, Curr. Opin. Struct. Biol. 5:409 (1995)).
In humans, TLR7 is expressed mostly in human plasmocytoid dendritic cells (pDCs) and B cells. TLR8 is expressed mostly in cells of myeloid origin, i.e., monocytes, granulocytes and myeloid dendritic cells. TLR9, like TLR7, is expressed in B cells and dendritic cells. (Zarember and Godowski, J. Immunol. 168:554 (2002); Hornung et al., J. Immunol. 168:4 (2002); Rehli, Trends Immunol. 23:375 (2002).
TLR9, which appears to be localized intracellularly, is involved in the inflammatory response to bacterial DNA and oligonucleotides that contain unmethylated CpG sequences. (Shirota, H. et al., J. Immunol. 167:1882 (2001); Takeda, K. et al., Annu. Rev. Immunol. 21:335 (2003)). The role of TLR7, and of its close homologue TLR8, is to detect the presence of “foreign” single-stranded RNA within a cell, as a means to respond to viral invasion. (Heil et al., Science 303:1526 (2004); Diebold et al., Science 303:1529 (2004)). Single-stranded RNA derived from HIV-1 or the influenza virus was shown to induce the production of proinflammatory cytokines in pDCs. The distinguishing features of viral RNAs might be either their high U or G/U content, or the absence of a long poly-A tail at the 3′ terminus of messenger RNA.
Certain compounds of the imidazoquinoline family, notably R848, act as agonists for TLR7 and TLR8. (Heine and Lein, Int. Arch. Allergy Immunol. 130:180 (2003); Dunne and O'Neill, Sci. STKE 2003:re3 (2003)). Once engaged, TLRs initiate a signal transduction cascade leading to activation of NFκB via the adapter protein myeloid differentiation primary response gene 88 (MyD88) and recruitment of the IL-1 receptor associated kinase (IRAK). Phosphorylation of IRAK then leads to recruitment of TNF-receptor associated factor 6 (TRAF6), which then results in the phosphorylation of the NFκB inhibitor I-κB. As a result, NFκB enters the cell nucleus and initiates transcription of genes whose promoters contain NFκB binding sites, such as cytokines (Singh et al., Curr. Sci. 85:1156 (2003)). Indeed, treatment of TLR8-expressing cells, such as PBMCs, with R848 results in production of high levels of IL-12, IFN-γ, IL-1, TNF-α, IL-6 and other inflammatory cytokines. Similarly, stimulation of TLR7-expressing cells, such as pDCs, results in production of very high levels of interferon-α and low levels of inflammatory cytokines.
Through activation of dendritic cells and other antigen-presenting cells, TLR7, TLR8 or TLR9 engagement and cytokine production is expected to activate diverse innate and acquired immune response mechanisms leading to the destruction of pathogens, infected cells or tumor cells. Thus, there is a need for agonists of TLR7, TLR8 or TLR9 for the treatment of cancer, virus infections, allergy, asthma, and COPD. TLR7, TLR8 or TLR9 and agonists thereof, however, require relatively high concentrations of compounds (in the double digit μg/ml range), and such concentrations are often difficult to achieve with complex chemical compounds due to solubility and/or cytotoxicity issues. As a result, screening is usually performed under conditions of low compound concentrations where possible agonists might not give activation levels readily detectable using standard cellular assays for screening. Thus, there is an immediate need for improved screening methods for identifying TLR7, TLR8 or TLR9 agonists.
SUMMARY OF THE INVENTION
The present invention fills the foregoing need by providing a screening method for identifying TLR7, TLR8 or TLR9 agonists and antagonists using low concentrations of compounds, as well as compositions and reagents for performing such a screening method. Applicants have found that mutant TLR7, TLR8 or TLR9 proteins comprising deletions in one or more LRRs makes these receptors more sensitive to low concentrations of agonists, thereby providing more efficient screening methods for identifying TLR7, TLR8 or TLR9 agonists and antagonists as compared to wild-type TLR7, TLR8 or TLR9 proteins.
Accordingly, one aspect of the present invention is directed to an isolated TLR7, TLR8 or TLR9 protein comprising deletions in one or more LRRs. Preferably, the TLR7, TLR8 or TLR9 protein comprises a deletion in the second LRR. In some embodiments, the TLR7 protein comprises the amino acid sequence set forth in SEQ ID NO: 2. In other embodiments, the TLR8 protein comprises the amino acid sequence set forth in SEQ ID NO: 6. In further embodiments, the TLR proteins lack their associated signal peptides.
Another aspect of the present invention is directed to an isolated nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising deletions in one or more LRRs. Preferably, the nucleic acid sequence encodes a TLR7, TLR8 or TLR9 protein comprising a deletion in the second LRR. In some embodiments, the nucleic acid sequence encoding a TLR7 protein comprising deletions in one or more LRRs comprises the nucleotide sequence set forth in SEQ ID NO: 1. In other embodiments, the nucleic acid sequence encoding a TLR8 protein comprising deletions in one or more LRRs comprises the nucleotide sequence set for the in SEQ ID NO: 5.
Another aspect of the present invention is directed to a recombinant vector comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs. Preferably, the recombinant vector is an expression vector in which the nucleic acid sequence is operably linked to a genetic control element capable of directing expression of the nucleic acid sequence in a host cell.
Another aspect of the present invention is directed to a host cell comprising a recombinant vector comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRS. The host cell can be prokaryotic or eukaryotic, but is preferably eukaryotic. In some embodiments, the host cell is a eukaryotic cell transiently transfected with a recombinant vector capable of directing expression of the TLR7, TLR8 or TLR9 protein comprising deletions in one or more LRRs. In other embodiments, the host cell is a eukaryotic cell stably transfected with the recombinant vector.
Another aspect of the present invention is directed to a method for producing a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs comprising culturing a host cell comprising a recombinant vector comprising a nucleic acid molecule sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs operably linked to a promoter sequence under conditions in which the nucleic acid sequence is expressed and TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is produced. In some embodiments, the host cell is a transiently transfected eukaryotic cell. In other embodiments, the host cell is a stably transfected eukaryotic cell.
Another aspect of the present invention is directed to a screening method for identifying an agonist of TLR7, TLR8 or TLR9. According to one embodiment, the method comprises: (a) providing a host cell expressing NFκB comprising a recombinant expression vector comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs; (b) culturing the host cell under conditions in which the nucleic acid sequence is expressed and TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is produced; (c) contacting the host cell with a candidate agent to be tested for TLR7, TLR8 or TLR9 agonistic activity; and (d) measuring the level of an indicator of TLR7, TLR8 or TLR9 activation, whereby a TLR7, TLR8 or TLR9 agonist is identified by measurement of an increase in the level of indicator as compared to the level produced in the absence of such agonist. Preferably, the host cell is a eukaryotic cell. In some embodiments, the indicator is cytokine production. In other embodiments, the indicator is reporter molecule expression.
Another aspect of the present invention is directed to a screening method for identifying an antagonist of TLR7, TLR8 or TLR9. In one embodiment, the method comprises: (a) providing a host cell expressing NFκB comprising a recombinant expression vector comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs; (b) culturing the host cell under conditions in which the nucleic acid sequence is expressed and TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is produced; (c) contacting the host cell with a candidate agent to be tested for TLR7, TLR8 or TLR9 antagonistic activity in the presence of a known TLR7, TLR8 or TLR9 agonist; and (d) measuring the level of an indicator of TLR7, TLR8 or TLR9 activation, whereby a TLR7, TLR8 or TLR9 antagonist is identified by measurement of a decrease in the level of indicator as compared to the level produced in the absence of such antagonist. Preferably, the host cell is a eukaryotic cell. In some embodiments, the indicator is cytokine production. In other embodiments, the indicator is reporter expression.
An additional embodiment of the invention involves the use of an agonist or antagonist in the screening methods of the invention for the prevention or treatment of a disease.



BRIEF DESCRIPTION OF THE FIGS
FIG. 1 provides the location of leucine-rich repeats (LRRs) in TLR7. Residue ranges correspond to the Genbank sequence having accession number NP—057646 (SEQ ID NO: 4). Undefined refers to a region in TLR7 that contains no LRR or other known protein motif. The C-terminal (CT) motif ends at the last conserved Cys residue.



DETAILED DESCRIPTION OF THE INVENTION
The methods of the present invention can be performed utilizing routine techniques in the field of molecular biology. Basic texts disclosing general molecular biology methods include Sambrook et al., Molecular Cloning, A Laboratory Manual (3d ed. 2001) and Ausubel et al., Current Protocols in Molecular Biology (1994).
To aid in the understanding of the invention, the following non-limiting definitions are provided:
The term “agonist” refers to a compound that can combine with a TLR7, TLR8 or TLR9 receptor to produce or increase a cellular activity. An agonist may be a ligand that directly binds to the receptor. Alternatively, an agonist may combine with a receptor indirectly by, for example, (a) forming a complex with another molecule that directly binds to the receptor, or (b) otherwise results in the modification of another compound so that the other compound directly binds to the TLR7, TLR8 or TLR9 receptor.
The term “activate”, and variations thereof, refers to any measurable increase in cellular activity.
The term “antagonist” refers to a compound that can combine with a TLR7, TLR8 or TLR9 receptor to reduce or inhibit a cellular activity. An antagonist may be a ligand that directly binds to the receptor. Alternatively, an antagonist may combine with a receptor indirectly by, for example, (a) forming a complex with another molecule that directly binds to the receptor, or (b) otherwise results in the modification of another compound so that the other compound directly binds to the TLR7, TLR8 or TLR9 receptor.
The term “cellular activity” refers to a biological activity (e.g., cytokine production), that results from an agonist-receptor interaction.
The term “wild-type” refers to a nucleic acid or protein that has the characteristics of that nucleic acid or protein when isolated from a naturally occurring source. A wild-type nucleic acid or protein is that which is most frequently observed in a population and is thus arbitrarily designed the “normal” or “wild-type” form of that molecule. In contrast, the term “modified” or “mutant” refers to a nucleic acid or protein that displays modifications in sequence and/or functional properties (i.e., altered characteristics) when compared to the wild-type nucleic acid or protein.
The term “transfection” refers to the uptake of DNA by a cell. A cell has been “transfected” when exogenous (i.e., foreign) DNA has been introduced inside the cell membrane. Transfection can be either transient (i.e., the introduced DNA remains extrachromosomal and is diluted out during cell division) or stable (i.e., the introduced DNA integrates into the cell genome or is maintained as a stable episomal element).
“Co-transfection” refers to the simultaneous or sequential transfection of two or more nucleic acids or vectors into a given cell.
The terms “promoter element” or “promoter” refer to a DNA regulatory region capable of binding an RNA polymerase in a cell (e.g., directly or through other promoter-bound proteins or substances) and initiating transcription of a coding sequence. A promoter sequence is, in general, bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at any level. Within the promoter sequence may be found a transcription initiation site (conveniently defined, for example, by mapping with nuclease S1), as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. The promoter may be operably associated with other expression control sequences, including enhancer and repressor sequences.
The terms “in operable combination”, “in operable order” or “operably linked” refer to the linkage of nucleic acid sequences in such a manner that a nucleic acid molecule capable of directing the transcription of a given gene and/or the synthesis of a desired protein molecule is produced. The term also refers to the linkage of amino acid sequences in such a manner so that a functional protein is produced.
The terms “selectable marker” or “selectable gene product” refer to the use of a nucleic acid sequence that encodes an enzymatic activity that confers resistance to an antibiotic or drug upon the cell in which the selectable marker is expressed. Selectable markers may be “positive”; positive selectable markers typically are dominant selectable markers, i.e., genes that encode an enzymatic activity that can be detected in a living cell or cell line. Selectable markers may also be “negative”; negative selectable markers encode an enzymatic activity (e.g., HSV thymidine kinase) whose expression is cytotoxic to the cell when grown in an appropriate selective medium (e.g., gancyclovir).
The term “vector” refers to a nucleic acid assembly capable of transferring gene sequences to target cells (e.g., viral vectors, non-viral vectors, particulate carriers, and liposomes). The term “expression vector” refers to a nucleic acid assembly containing a promoter that is capable of directing the expression of a sequence or gene of interest in a cell. Vectors typically contain nucleic acid sequences encoding selectable markers for selection of cells that have been transfected by the vector. Generally, “vector construct,” “expression vector,” and “gene transfer vector,” refer to any nucleic acid construct capable of directing the expression of a gene of interest and which can transfer gene sequences to target cells. Thus, the term includes cloning and expression vehicles, as well as viral vectors.
The term “reporter gene” refers to a nucleotide sequence included in an expression vector that confers a detectable phenotype. For example, the reporter gene may cause expression of a “reporter molecule”, which confers a detectable phenotype on a cell.
The term “agent” or “compound” describes any molecule, e.g. protein or pharmaceutical, that is screened for the capability of acting as an agonist or antagonist of TLR7, TLR8 or TLR9. An agent may also be identified as an agonist or antagonist by utilizing the screening methods of the invention.
The terms “treating” or “treatment” of a disease refer to executing a protocol, which may include administering one or more drugs to a patient (human or otherwise), in an effort to alleviate signs or symptoms of the disease. Thus, “treating” or “treatment” does not require complete alleviation of signs or symptoms, does not require a cure, and specifically includes protocols that have only a marginal effect on the patient.
Aspects of the present invention provide novel materials and methods useful for identifying TLR7, TLR8 or TLR9 agonists and antagonists. The present invention is based on applicants' discovery that mutant TLR7, TLR8 or TLR9 proteins comprising deletions in one or more LRRs makes these receptors more sensitive to low concentrations of agonists, thereby providing more efficient screening methods for identifying TLR7, TLR8 or TLR9 agonists as compared to wild-type TLR7, TLR8 or TLR9 proteins. Such agonists find use in potentiating immune response mechanisms to treat or prevent various diseases, such as cancer, virus infection, allergy, asthma, and chronic obstructive pulmonary disease (COPD).
In one or more embodiments, the TLR7, TLR8 or TLR9 mutation can delete any or all of the amino acids comprising one or more LRRs. Preferably, the deletion occurs in at least the second LRR. The numbering of LRRs in various TLRS, as well as their amino acid sequences, is set forth in, e.g., Bell et al., Trends Immunol. 24:528 (2003). The amino acid sequence of a TLR7 protein comprising a deletion in the second LRR comprises the amino acid sequence set forth in SEQ ID NO: 2. The amino acid sequence of a TLR8 protein comprising a deletion in the second LRR comprises the amino acid sequence set forth in SEQ ID NO: 6.
When expressed in cells, the mutant TLR7, TLR8 or TLR9 proteins comprising deletions in one or more LRRs will typically lack their associated signal peptides. For example, a TLR7 protein comprising a deletion in the second LRR can comprise the amino acid sequence set forth in SEQ ID NO: 2 lacking the first 25 amino acids. Similarly, a TLR8 protein comprising a deletion in the second LRR can comprise the amino acid sequence set forth in SEQ ID NO: 6 lacking the first 44 amino acids. Various predictive methods exist for determining the amino acid sequences of mature secretory proteins lacking their signal peptides, including weight matrix algorithms and neural networking (Chou, Protein Engineering 14:75 (2001), which can then be verified by experimental methods, such as, e.g., N-terminal sequencing of the purified mature TLR proteins.
The nucleic acid sequences encoding the mutant TLR7, TLR8 or TLR9 proteins can be produced using methods well known in the art, including chemical synthesis, site-directed mutagenesis and PCR. Nucleic acid sequences encoding wild-type TLR7 proteins from various species are publicly available from Genbank and include human (Acc. No. NM—016562), mouse (Acc. No. NM—133211), chimpanzee (Acc. No. NM—016562), chicken (Acc. No. XM—416836), rat (Acc. No. XM—228909), and dog (Acc. No. XM—548863). Nucleic acid sequences encoding wild-type TLR8 proteins from various species are also publicly available from Genbank and include human (Acc. Nos. NM—016610 and NM—138636), chimpanzee (Acc. No. XM—528893), pig (Acc. No. NM—214187), and mouse (Acc. No. NM—133212). Nucleic acid sequences encoding wild-type TLR9 proteins from various species are also publicly available from Genbank and include human (Acc. Nos. NM—017442 and NM—138688), rat (Acc. No. NM—198131), pig (Acc. No. NM—213958), dog (Acc. No. NM—001002998), cow (Acc. No. NM—183081), cat (Acc. No. AY137581) and mouse (Acc. No. NM—031178).
Allelic variants (SNPs, splice variants, translation initiation variants, etc.) and homologues (both paralogues and orthologues) of the sequences described above can also be used so long as they retain the desired structure and/or activity of TLR7, TLR8 or TLR9. For example, both human TLR8 and human TLR9 are each known to exist as two separate isoforms, a long form and short form. Methods for identifying homologous and allelic nucleic acid and amino acid sequences are well known in the art and include both hybridization-based and bioinformatics-based approaches (see Baxevanis and Ouellette, Bioinformatics, A Practical Guide to the Analysis of Genes and Proteins (2001)).
Preferably, the nucleic acid sequences are human in origin and encode a TLR protein comprising a deletion in the second LRR, such as those having amino acid sequences comprising the amino acid sequences set forth in SEQ ID NOs: 2 and 6. One such nucleic acid sequence encoding a TLR7 protein comprising a deletion in the second LRR comprises the nucleotide sequence set forth in SEQ ID NO: 1. One such nucleic acid sequence encoding a TLR8 protein comprising a deletion in the second LRR comprises the nucleotide sequence set for the in SEQ ID NO: 5. Due to the degeneracy of the genetic code, however, many different nucleotide sequences can encode the TLR proteins comprising the amino acid sequences set forth in SEQ ID NOs: 2 and 6. The codons can be selected for optimal expression in prokaryotic or eukaryotic systems.
For proper expression in cells, nucleic acid sequences encoding the mutant TLR7, TLR8 or TLR9 proteins will typically include nucleotides that encode an associated signal peptide. However, nucleic acid sequences lacking nucleotides that encode an associated signal peptide are also included within the scope of the invention. For example, a nucleic acid sequence encoding a TLR7 protein comprising a deletion in the second LRR can comprise the nucleotide sequence set forth in SEQ ID NO: 1 lacking the first 75 nucleotides. Similarly, a nucleic acid sequence encoding a TLR8 protein comprising a deletion in the second LRR can comprise the nucleotide sequence set forth in SEQ ID NO: 5 lacking the first 132 nucleotides. Again, due to the degeneracy of the genetic code, many different nucleotide sequences can encode the TLR proteins comprising the amino acid sequences set forth in SEQ ID NOs: 2 and 6 lacking their associated signal peptides.
Insertion of a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs into a vector is readily accomplished when the termini of the nucleic acid sequence and the vector comprise compatible restriction sites. If this cannot be done, it may be necessary to modify the termini of the nucleic acid and/or vector by digesting back single-stranded DNA overhangs generated by restriction endonuclease cleavage to produce blunt ends, or to achieve the same result by filling in the single-stranded termini with an appropriate DNA polymerase. Alternatively, desired sites may be produced, e.g., by ligating nucleotide sequences (linkers) onto the termini. Such linkers may comprise specific oligonucleotide sequences that define desired restriction sites. Restriction sites can also be generated by the use of PCR. The cleaved vector and the DNA fragments may also be modified if required by homopolymeric tailing.
Recombinant expression vectors used in this invention are typically self-replicating DNA constructs comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs operably linked to a suitable genetic control element that is capable of regulating expression of the nucleic acids in a compatible host cell. Genetic control elements may include a prokaryotic promoter system or a eukaryotic promoter expression control system, and typically include a transcriptional promoter, an optional operator to control the onset of transcription, transcription enhancers to elevate the level of mRNA expression, a sequence that encodes a suitable ribosome binding site, and sequences that terminate transcription and translation. Expression vectors also may contain an origin of replication that allows the vector to replicate independently of the host cell.
Suitable prokaryotic promoters include the β-lactamase and lactose promoter systems, the tryptophan (trp) promoter system, the lambda PL promoter system and the tac promoter. Numerous expression vectors containing such control sequences are known in the art and available commercially. Suitable eukaryotic promoters include the cytomegalovirus (CMV) promoter, the SV40 early promoter region, the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (RSV), the herpes TK promoter, the adenoviral promoter of an early or late (ElA, MLP, etc.) gene, the regulatory sequences of the metallothionein (MT) and phosphoglycerokinase (PGK) genes, as well as the TLR7, TLR8 or TLR9 promoters themselves. Inducible promoters and tissue specific promoters may also be used.
Suitable host cells for expressing a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs include prokaryotes and lower eukaryotes. Suitable prokaryotes include both gram negative and positive organisms, e.g., E. coli and B. subtilis, S. typhimurium, or any bacterial strain capable of expressing heterologous proteins. Suitable lower eukaryotes include yeast strains such S. cerevisiae, S. pombe, Kluyveromyces strains, Candida, or any yeast strain capable of expressing heterologous proteins. If the protein is made in yeast or bacteria, it may be necessary to modify the protein produced therein, for example by phosphorylation or glycosylation of the appropriate sites, or by introduction of the targeting sequences, in order to obtain a functional protein. Such covalent attachments may be accomplished using known chemical or enzymatic methods.
The host cell is preferably a higher eukaryote cell line. Suitable higher eukaryote cell lines include both primary and established cell lines from animal cells, both of non-mammalian origin, e.g., insect cells and birds, and of mammalian origin, e.g., human, primates, and rodents.
Higher eukaryotic tissue culture cells are preferred hosts for the recombinant production of a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs. Although any higher eukaryotic tissue culture cell line might be used, including insect baculovirus expression systems, mammalian cells are preferred. Suitable mammalian cell lines include HeLa cells, Chinese hamster ovary (CHO) cells, baby rat kidney (BRK) cells, baby hamster kidney (BHK) cells, African green monkey kidney (COS and CV-1) cells, human embryonic kidney (HEK 293) cells, A431 cells, Colo2O5 cells, 3T3 cells, mouse L cells, HL-60 cells, U937 cells, HaK cells and Jurkat cells.
Methods for the transformation or transfection of such cells are well known in the art and include electroporation, calcium phosphate co-precipitation, protoplast or spheroplast fusion, lipofection, DEAE-dextran-mediated transfection, biolistics, and viral infection. The transfected expression vector can be maintained transiently in the cell. Alternatively, if the expression vector contains a selectable marker, cells can be selected in which the vector has stably integrated into the genome by culturing the transfected cells in the appropriate antibiotic or drug. Suitable dominant selectable markers include the bacterial aminoglycoside 3′ phosphotransferase gene (also referred to as the neo gene) which confers resistance to the drug G418 in mammalian cells, the bacterial hygromycin G phosphotransferase (hyg) gene which confers resistance to the antibiotic hygromycin, and the bacterial xanthine-guanine phosphoribosyl transferase gene (also referred to as the gpt gene) which confers the ability to grow in the presence of mycophenolic acid.
Once transformed or transfected, the host cells can be cultured under conditions in which the nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is expressed and a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is produced. Generally, the resulting TLR protein will lack its associated signal peptide.
Host cells expressing a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs find utility in screening methods for identifying agonists of TLR7, TLR8 or TLR9. As described below, a TLR7 or TLR8 protein comprising a deletion in the second LRR decreases 5-10 fold the agonist concentration required to achieve maximum activation levels of genes whose expression is induced by NFκB. These deletion mutants convey a significant advantage over the wild-type proteins because they can be used in screening assays to detect TLR7, TLR8 or TLR9 agonists in small compound concentrations, thereby avoiding solubility or cytotoxicity problems known to occur in solutions with a high concentration of compounds.
One embodiment of the agonist screening method involves (a) providing a host cell expressing NFκB comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRS; (b) culturing the host cell under conditions in which the recombinant nucleic acid molecule is expressed and TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is produced; (c) contacting the host cell with a candidate agent to be tested for TLR7, TLR8 or TLR9 agonistic activity; and (d) measuring the level of an indicator of TLR7, TLR8 or TLR9 activation, whereby a TLR7, TLR8 or TLR9 agonist is identified by measurement of an increase in the level of indicator as compared to the level produced in the absence of such agonist.
Generally, a plurality of assays can be run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection. In addition, candidate agents are generally contacted with cells not expressing a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs as a control for target specificity. Although the screening method generally is used as an assay to identify previously unknown molecules that can act as a therapeutic agent, the method can also be used to confirm and standardize the desired activity of a known TLR7, TLR8 or TLR9 agonist or to optimize the structure and/or activity of a known TLR7, TLR8 or TLR9 agonist during, e.g., molecular evolution procedures.
The indicator that is measured during the screening method can be an endogenous gene product whose expression is induced by NFκB, such as a cytokine. Such cytokines include IL-12, IFN-γ, IL-1, TNF-α, IL-6 and other inflammatory cytokines. Either the cytokine or the mRNA encoding the cytokine can be measured. Methods for measuring the levels of a cytokine or its mRNA are well known in the art and include, e.g., ELISA, RIA, Western blot, Northern blot, and quantitative PCR.
Alternatively, the indicator that is measured is a reporter molecule whose expression is induced by NFκB. Reporter assays are preferred because they are easily adaptable to high through-put screening procedures. Suitable reporter molecules include, for example, fluorescent polypeptides such as green fluorescent protein, cyan fluorescent protein, red fluorescent protein, or enhanced forms thereof; an antibiotic resistance polypeptide such as puromycin N-acetyltransferase, hygromycin B phosphotransferase, aminoglycoside phosphotransferase, and the Sh ble gene product; a cell surface protein marker such as the cell surface protein marker neural cell adhesion molecule (N-CAM); an enzyme such as β-lactamase, chloramphenicol acetyltransferase, adenosine deaminase, aminoglycoside phosphotransferase, dihydrofolate reductase, thymidine kinase, luciferase or xanthine guanine phosphoribosyltransferase polypeptide; or a tag such as a c-myc peptide, a polyhistidine, a FLAG epitope, or any ligand (or cognate receptor), including any peptide epitope (or antibody, or antigen binding fragment thereof, that specifically binds the epitope).
For example, a host cell expressing a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs can be cotransfected with an expression vector comprising a luciferase gene operably linked to a genetic control element containing one or more NFκB binding sites (e.g., GGGGACTTTCC, SEQ ID NO: 19). Upon engagement of the TLR7, TLR8 or TLR9 deletion mutant by an agonist, NFκB will translocate into the cell nucleus and initiate transcription of the luciferase gene, resulting in expression of luciferase. Expression of luciferase can be detected and measured using the appropriate instrumentation and reagents, for example, by detecting light emission using a luminometer upon addition of luciferin.
Any candidate agent or compound can be screened in the above-described method. Candidate agents encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including, but not limited to, peptides, saccharides, siRNA, antisense, antibodies, fatty acids, steroids, purines, pyrimidines, and various derivatives, structural analogs and combinations thereof.
Candidate agents can be obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc., to produce structural analogs.
Diseases and conditions amenable to treatment with the identified TLR7, TLR8 or TLR9 agonists are those in which an immune response is desired and include the following:
(a) viral diseases such as, for example, diseases resulting from infection by an adenovirus, a herpesvirus (e.g., HSV-I, HSV-II, CMV, or VZV), a poxvirus (e.g., an orthopoxvirus such as variola or vaccinia, or molluscum contagiosum), a picomavirus (e.g., rhinovirus or enterovirus), an orthomyxovirus (e.g., influenza virus), a paramyxovirus (e.g., parainfluenza virus, mumps virus, measles virus, and respiratory syncytial virus (RSV)), a coronavirus (e.g., SARS), a papovavirus (e.g., papillomaviruses, such as those that cause genital warts, common warts, or plantar warts), a hepadnavirus (e.g., hepatitis B virus), a flavivirus (e.g., hepatitis C virus or Dengue virus), or a retrovirus (e.g., a lentivirus such as HIV);
(b) bacterial diseases such as, for example, diseases resulting from infection by bacteria of, for example, the genus Escherichia, Enterobacter, Salmonella, Staphylococcus, Shigella, Listeria, Aerobacter, Helicobacter, Klebsiella, Proteus, Pseudomonas, Streptococcus, Chlamydia, Mycoplasma, Pneumococcus, Neisseria, Clostridium, Bacillus, Corynebacterium, Mycobacterium, Campylobacter, Vibrio, Serratia, Providencia, Chromobacterium, Brucella, Yersinia, Haemophilus, or Bordetella; 
(c) other infectious diseases, such as chlamydia, fungal diseases including but not limited to candidiasis, aspergillosis, histoplasmosis, cryptococcal meningitis, or parasitic diseases including but not limited to malaria, pneumocystis camii pneumonia, leishmaniasis, cryptosporidiosis, toxoplasmosis, and trypanosome infection; and
(d) neoplastic diseases, such as intraepithelial neoplasias, cervical dysplasia, actinic keratosis, basal cell carcinoma, squamous cell carcinoma, renal cell carcinoma, Kaposi's sarcoma, melanoma, renal cell carcinoma, leukemias including but not limited to myelogeous leukemia, chronic lymphocytic leukemia, multiple myeloma, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma, B-cell lymphoma, and hairy cell leukemia, and other cancers;
(e) TH2-mediated, atopic diseases, such as atopic dermatitis or eczema, eosinophilia, asthma, allergy, allergic rhinitis, COPD, and Ommen's syndrome;
(f) certain autoimmune diseases such as systemic lupus erythematosus, essential thrombocythaemia, multiple sclerosis, discoid lupus, alopecia areata; and
(g) diseases associated with wound repair such as, for example, inhibition of keloid formation and other types of scarring (e.g, enhancing wound healing, including chronic wounds).
The screening method described above can also be used to identify antagonists of TLR7, TLR8 or TLR9. One embodiment of the antagonist screening method involves (a) providing a host cell expressing NFκB comprising a nucleic acid sequence encoding a TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs; (b) culturing the host cell under conditions in which the recombinant nucleic acid molecule is expressed and TLR7, TLR8 or TLR9 protein comprising a deletion in one or more LRRs is produced; (c) contacting the host cell with a candidate agent to be tested for TLR7, TLR8 or TLR9 antagonistic activity in the presence of a known TLR7, TLR8 or TLR9 agonist; and (d) measuring the level of an indicator of TLR7, TLR8 or TLR9 activation, whereby a TLR7, TLR8 or TLR9 antagonist is identified by measurement of a decrease in the level of indicator as compared to the level produced in the absence of such antagonist. Examples of known agonists of TLR7, TLR8 and TLR8 include R848, loxoribine, uridine, single-stranded viral RNA, and unmethylated bacterial DNA. Identified TLR7, TLR8 or TLR9 antagonists are expected to be useful in the treatment of inflammatory and autoimmune diseases.
Specific embodiments according to the methods of the present invention will now be described in the following examples. The examples are illustrative only, and are not intended to limit the remainder of the disclosure in any way.
EXAMPLES
Example 1
Construction of Human TLR7 and TLR8 Deletion Mutants
A nucleic acid sequence (comprising the nucleotide sequence set forth in SEQ ID NO: 1) encoding a mutant human TLR7 protein having a deletion of the amino acid sequence PIPLG (amino acids 102-106 of the wild-type human TLR7 amino acid sequence set forth in SEQ ID NO: 4) in the second LRR was prepared by PCR. Briefly, a first PCR was performed on the human wild-type TLR7 cDNA (SEQ ID NO: 3 cloned into the expression vector pCMVFlag (a derivative of pCR3.1 (Invitrogen, Carlsbad, Calif.)) (pCMVhuTLR7) using the sense primer 5′-CTA ACT AGA GAA CCC ACT GC-3′ (SEQ ID NO: 9) and the antisense primer 5′-GAT GCA CAT GTT GTT TTT TGA TAC ACA GTT GCA TCT GAA ATC-3′ (SEQ ID NO: 10). A second PCR was performed on the TLR7 cDNA using the sense primer 5′-GAT TTC AGA TGC AAC TGT GTA TCA AAA AAC AAC ATG TGC ATC-3′ (SEQ ID NO: 11) and the antisense primer 5′-CTT CAC TTG AAT CTC CTG AAG-3′ (SEQ ID NO: 12). The bands were gel purified and combined in a third PCR using the primers of SEQ ID NOs: 9 and 12. The band was gel purified, digested with BamHI and PmeI and cloned into pCMVhuTLR7 digested with the same enzymes to produce pCMVhuTLR7Δ2. The mutation was confirmed by DNA sequencing. The resulting mutant TLR7 amino acid sequence (comprising the amino acid sequence set forth in SEQ ID NO: 2) contained a FLAG epitope with an initiation methionine (MDYKDDDDK; SEQ ID NO: 18, encoded by 5′-ATG GAT TAC AAA GAC GAT GAC GAT AAA-3′; SEQ ID NO: 17) followed by a glutamic acid (E) and phenylalanine (F) upstream of the valine (V) at position 1 of SEQ ID NO: 2. The glutamic acid and phenylalanine residues were introduced by addition of an EcoRI restriction during construction of the wild-type pCMVhuTLR7 vector.
Similarly, a nucleic acid sequence (comprising the nucleotide sequence set forth in SEQ ID NO: 5) encoding a mutant TLR8 protein having a deletion of the amino acid sequence VQHQN (amino acids 118-122 of the wild-type human TLR8 isoform 1 amino acid sequence set forth in SEQ ID NO: 8) in the second LRR was prepared by PCR. Briefly, a first PCR was performed on the human wild-type TLR8 isoform 1 cDNA (SEQ ID NO: 7) cloned into the expression vector pcDNATM3.1/Zeo (Invitrogen) (pCMVhuTLR8) using the sense primer 5′-CTA ACT AGA GAA CCC ACT GC-3′ (SEQ ID NO: 13) and the antisense primer 5′-GAT TGT ATA CCG GGA TTT CCA TTG GGG TTG TGG TTT AGA T-3′ (SEQ ID NO: 14). A second PCR was performed on the TLR8 cDNA using the sense primer 5′-ATC TAA ACC ACA ACC CCA ATG GAA ATC CCG GTA TAC AAT C-3′ (SEQ ID NO: 15) and the antisense primer 5′-ATC TTT TAC CAA CGG TGA TAT TCT G-3′ (SEQ ID NO: 16). The bands were gel purified and combined in a third PCR using the primers of SEQ ID NOs: 13 and 16. The band was gel purified, digested with BamHI and ClaI or HindIII and ClaI and cloned into pCMVhuTLR8 digested with the same enzymes to produce pCMVhuTLR8Δ2. The mutation was confirmed by DNA sequencing. The resulting mutant TLR8 amino acid sequence (comprising the amino acid sequence set forth in SEQ ID NO: 6) contained a FLAG epitope with an initiation methionine (MDYKDDDDK; SEQ ID NO: 18, encoded by 5′-ATG GAT TAC AAA GAC GAT GAC GAT AAA-3′; SEQ ID NO: 17) upstream of the methionine (M) at position 1 of SEQ ID NO: 6. Alternatively, the shorter human wild-type TLR8 isoform 2 cDNA (Acc. No. NM—138636) can be used to produce a mutant TLR8 protein having a deletion of the amino acid sequence VQHQN (amino acids 100-104 of the wild-type human TLR8 isoform 2 amino acid sequence disclosed at Acc. No. NP—619542) in the second LRR.
A nucleic acid sequence encoding a human TLR9 protein having a deletion in the second LRR of the amino acid sequence PVGLS (e.g., amino acids 100-104 of the wild-type human TLR9 amino acid sequence disclosed at Acc. No. NP—059138 or amino acids 43-47 of the wild-type human TLR9 amino acid sequence disclosed at Acc. No. NP—619633) can be produced by similar methodologies using, e.g., cDNA encoding either the longer (NM—017442) or shorter (NM—138688) isoform of human TLR9, respectively.
Example 2
Expression and Activation of Human TLR7 and TLR8 Deletion Mutants
A comparison of the response of wild-type and mutant TLR7 and TLR8 proteins to agonist activation was performed. HEK 293 cells were transfected in bulk in 15 cm dishes with a mixture of NFκB-luciferase reporter plasmid (Clontech) and pCMVhuTLR7Δ2 or pCMVhuTLR8Δ2. Six hours after transfection, cells were divided into 96- or 384-well plates at different cell densities to achieve a degree of confluency between 25-100%. The next day, increasing concentrations of the TLR7 agonists R848, loxoribine, and uridine were added to the wells. Wells without agonist served as negative controls. After five hours, the cells were lysed with SteadyGloTM luciferase reagent (Promega) according to the manufacturer's recommendations. After a 10-minute incubation period, luciferase activity was measured using a luminometer. The data were plotted as a fold-induction compared to luciferase activity of cells which received medium alone.
While 10 nM R848 did not result in significant activation of wild-type TLR7, mutant TLR7 containing a deletion in the second LRR mediated a reproducible 6-fold induction of luciferase activity. Close-to-maximum activation of wild-type TLR7 was achieved in the presence of 1 μM R848, while 10-fold lower concentrations were sufficient for full activation of the mutant TLR7. The weak TLR7 agonist loxoribine activated wild-type TLR7 only at levels greater than 0.5 mM, while the same activation was achieved with the mutant TLR7 at a 5-fold lower concentration of 0.1 mM.
Similarly, while at least 0.5 μM R848 was required to achieve 5-fold induction of luciferase with wild-type TLR8, 50 nm of R848 activated mutant TLR8 containing a deletion in the second LRR and stimulated close to 10-fold induction of luciferase. Additionally, 4.5 mM uridine activated mutant TLR8 15-fold, while in the presence of wild-type TLR8 only a marginal 3-fold activation was observed.
Thus, the described deletions in the second LRR of TLR7 and TLR8 increase the sensitivity of these receptors at least 5-10 fold compared to the wild-type receptors. As such, these mutant receptors provide screening methods that can more readily detect agonists and antagonists of TLR7, TLR8 and TLR9 and, therefore, will increase the probability of discovering new such molecules.
All publications cited in the specification, both patent publications and non-patent publications, are indicative of the level of skill of those skilled in the art to which this invention pertains. All these publications are herein fully incorporated by reference to the same extent as if each individual publication were specifically and individually indicated as being incorporated by reference.
Although the invention herein has been described with reference to particular embodiments, it is to be understood that these embodiments are merely illustrative of the principles and applications of the present invention. It is therefore to be understood that numerous modifications may be made to the illustrative embodiments and that other arrangements may be devised without departing from the spirit and scope of the present invention as defined by the following claims.

## Claims

1. An isolated mutant TLR7 protein comprising the amino acid sequence set forth in SEQ ID NO: 2.

2. The isolated mutant TLR7 protein of claim 1 lacking its associated signal peptide.

3. An isolated mutant TLR7 protein comprising the amino acid sequence set forth in residues 26-1043 of SEQ ID NO: 2.