# Patent

## Title
Polynucleotides encoding Toll-Like Receptor 3 antagonists

## Abstract

Toll Like Receptor 3 (TLR3) antibody antagonists, polynucleotides encoding TLR3 antibody antagonists or fragments thereof, and methods of making and using the foregoing are disclosed.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 13/751,718, filed 28 Jan. 2013, currently pending, which is a divisional of U.S. application Ser. No. 12/609,675, filed 30 Oct. 2009, now U.S. Pat. No. 8,409,567, granted 24 Sep. 2013, which claims the benefit of U.S. Provisional Application No. 61/109,974, filed 31 Oct. 2008 and U.S. Provisional Application No. 61/161,860, filed 20 Mar. 2009 and U.S. Provisional Application No. 61/165,100, filed 31 Mar. 2009 and U.S. Provisional Application No. 61/173,686, filed 29 Apr. 2009, the entire contents of which are incorporated herein by reference.


FIELD OF THE INVENTION
The present invention relates to Toll-Like Receptor 3 (TLR3) antibody antagonists, polynucleotides encoding TLR3 antibody antagonists or fragments thereof, and methods of making and using the foregoing.
BACKGROUND OF THE INVENTION
Toll-like receptors (TLRs) regulate activation of the innate immune response and influence the development of adaptive immunity by initiating signal transduction cascades in response to bacterial, viral, parasitic, and in some cases, host-derived ligands (Lancaster et al., J. Physiol. 563:945-955, 2005). The plasma membrane localized TLRs, TLR1, TLR2, TLR4 and TLR6 recognize ligands including protein or lipid components of bacteria and fungi. The predominantly intracellular TLRs, TLR3, TLR7 and TLR9 respond to dsRNA, ssRNA and unmethylated CpG DNA, respectively. Dysregulation of TLR signaling is believed to cause a multitude of problems, and therapeutic strategies are in development towards this axis (Hoffman et al., Nat. Rev. Drug Discov. 4:879-880, 2005; Rezaei, Int. Immunopharmacol. 6:863-869, 2006; Wickelgren, Science 312:184-187, 2006). For example, antagonists of TLR4 and TLRs 7 and 9 are in clinical development for severe sepsis and lupus, respectively (Kanzler et al., Nat. Med. 13:552-559, 2007).
TLR3 signaling is activated by dsRNA, mRNA or RNA released from necrotic cells during inflammation or virus infection. TLR3 activation induces secretion of interferons and pro-inflammatory cytokines and triggers immune cell activation and recruitment that are protective during certain microbial infections. For example, a dominant-negative TLR3 allele has been associated with increased susceptibility to Herpes Simplex encephalitis upon primary infection with HSV-1 in childhood (Zheng et al., Science 317:1522-1527 2007). In mice, TLR3 deficiency is associated with decreased survival upon coxsackie virus challenge (Richer et al., PLoS One 4:e4127, 2009). However, uncontrolled or dysregulated TLR3 signaling has been shown to contribute to morbidity and mortality in certain viral infection models including West Nile, phlebovirus, vaccinia, and influenza A (Wang et al., Nat. Med. 10:1366-1373, 2004; Gowen et al., J. Immunol. 177:6301-6307, 2006; Hutchens et al., J. Immunol. 180:483-491, 2008; Le Goffic et al., PloS Pathog. 2:E53, 2006).
TLR3 has also been shown to drive pathogenic mechanisms in a spectrum of inflammatory, immune-mediated and autoimmune diseases including, for example, septic shock (Cavassani et al., J. Exp. Med. 205:2609-2621, 2008), acute lung injury (Murray et al., Am. J. Respir. Crit. Care Med. 178:1227-1237, 2008), rheumatoid arthritis (Kim et al., Immunol. Lett. 124:9-17, 2009; Brentano et al., Arth. Rheum. 52:2656-2665, 2005), asthma (Sugiura et al., Am. J. Resp. Cell Mol. Biol. 40:654-662, 2009; Morishima et al., Int. Arch. Allergy Immunol. 145:163-174, 2008; Stowell et al., Respir. Res. 10:43, 2009), inflammatory bowel disease such as Crohn's disease and ulcerative colitis (Zhou et al., J. Immunol. 178:4548-4556, 2007; Zhou et al., Proc. Natl. Acad. Sci. (USA) 104:7512-7515, 2007), autoimmune liver disease (Lang et al., J. Clin. Invest. 116:2456-2463, 2006) and type I diabetes (Dogusan et al. Diabetes 57:1236-1245, 2008; Lien and Zipris, Curr. Mol. Med. 9:52-68, 2009). Furthermore, organ-specific increases in TLR3 expression have been shown to correlate with a number of pathological conditions driven by dysregulated local inflammatory responses such as primary biliary cirrhosis of liver tissues (Takii et al., Lab Invest. 85:908-920, 2005), rheumatoid arthritis joints (Ospelt et al., Arthritis Rheum. 58:3684-3692, 2008), and nasal mucosa of allergic rhinitis patients (Fransson et al., Respir. Res. 6:100, 2005).
In necrotic conditions, the release of intracellular content including endogenous mRNA triggers secretion of cytokines, chemokines and other factors that induce local inflammation, facilitate clearance of dead cell remnants and repair the damage. Necrosis often perpetuates inflammatory processes, contributing to chronic or exaggerated inflammation (Bergsbaken et al., Nature Reviews 7:99-109, 2009). Activation of TLR3 at the site of necrosis may contribute to these aberrant inflammatory processes and generate a further pro-inflammatory positive feedback loop via the released TLR3 ligands. Thus, TLR3 antagonism may be beneficial in a variety of disorders involving chronic or exaggerated inflammation and/or necrosis.
Down-modulation of TLR3 activation may also represent a novel treatment strategy for oncologic indications including renal cell carcinomas and head and neck squamous cell carcinomas (Morikawa et al., Clin. Cancer Res. 13:5703-5709, 2007; Pries et al., Int. J. Mol. Med. 21: 209-215, 2008). Furthermore, the TLR3L423F allele encoding a protein with reduced activity has been associated with protection against advanced “dry” age-related macular degeneration (Yang et al., N. Engl. J. Med. 359:1456-1463, 2008), indicating that TLR3 antagonists may be beneficial in this disease.
Pathologies associated with inflammatory conditions and others, such as those associated with infections, have significant health and economic impacts. Yet, despite advances in many areas of medicine, comparatively few treatment options and therapies are available for many of these conditions.
Thus, a need exists to suppress TLR3 activity to treat TLR3-associated conditions.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the effect of anti-human TLR3 (huTLR3) mAbs in an NF-κB reporter gene assay.
FIGS. 2A and 2B show the effect (% inhibition) or anti-huTLR3 mAbs in a BEAS-2B assay.
FIGS. 3A and 3B show the effect of anti-huTLR3 mAbs in a NHBE assay.
FIG. 4 shows the effect of anti-huTLR3 mAbs in a PBMC assay.
FIGS. 5A and 5B show the effect of anti-huTLR3 mAbs in a HASM assay.
FIGS. 6A, 6B and 6C show the binding of anti-huTLR3 mAbs to TLR3 mutants.
FIG. 7A shows epitopes for mAb 15EVQ (black) and C1068 mAb (grey) (top image) and epitope for mAb 12QVQ/QS (black, bottom image) superimposed on the structure of human TLR3 ECD. FIG. 7B shows localized H/D/exchange perturbation map of TLR3 ECD protein complexed with mAb 15EVQ. Residue numbering of TLR3 ECD is according to SEQ ID NO: 2
FIGS. 8A and 8B show the effect of rat/mouse anti-mouse TLR3 mAb mAb 5429 (surrogate) in A) NF-κB and B) ISRE reporter gene assays.
FIG. 9 shows the effect of the surrogate mAbs (mAb 5429, mAb c1811) in the MEF CXCL10/IP-10 assay.
FIG. 10 shows specificity of binding of the surrogate mAb to TLR3. Top panel: isotype control; bottom panel: mAb c1811.
FIG. 11 shows effect of the surrogate mAbs on penH level in an AHR model.
FIG. 12 shows effect of the surrogate mAbs on total neutrophil numbers in BAL fluid in an AHR model.
FIG. 13 shows effect of the surrogate mAbs on CXCL10/IP-10 levels in BAL fluid in an AHR model.
FIG. 14 shows effect of the surrogate mAb on histopathology scores in a DSS model.
FIG. 15 shows effect of the surrogate mAb on A) histopathology scores and B) neutrophil influx in a T-cell transfer model.
FIG. 16 showns effect of the surrogate mAb on clinical scores in a CIA model.
FIG. 17 shows effect of the surrogate mAb on the clinical AUC scores in a CIA model.
FIG. 18 shows effect of the surrogate mAb on the survival of C57BL/6 mice following intranasal administration of influenza A/PR/8/34.
FIG. 19 shows effect of the surrogate mAb on clinical scores following influenza A/PR/8/34 administration.
FIG. 20 shows effect of the surrogate mAb on body weight over 14 days after administration of influenza A/PR/8/34.
FIG. 21 shows effect of the surrogate mAbs on blood glucose levels in (A) WT DIO and (B) TLR3KO DIO animals after glucose challenge.
FIG. 22 shows effect of the surrogate mAb on insulin levels in WT DIO animals.
FIG. 23 shows effect of mAb 15EVQ on (A) NTHi and (B) rhinovirus induced CXCL10/IP-10 and CCL5/RANTES levels in NHBE cells.
FIG. 24 shows effect of mAb 15EVQ on (A) sICAM-1 levels and (B) viability in HUVEC cells.



SUMMARY OF THE INVENTION
One aspect of the invention is an isolated polynucleotide encoding an antibody heavy chain variable region (VH) comprising the heavy chain complementarity determining regions (HCDR) 1, 2 and 3 (HCDR1, HCDR2 and HCDR3) amino acid sequences as shown in SEQ ID NOs: 82, 196 and 84, wherein the HCDR2 of SEQ ID NO: 196 is further defined as shown in Formula (V): Xaa24-I-D-P-S-D-S-Y-T-N-Y-Xaa25-P-S-F-Q-G, wherein Xaa24 may be Phe or Arg; and Xaa25 may be Ala or Ser.
Another aspect of the invention is an isolated polynucleotide encoding an antibody light chain variable region (VL) comprising the light chain complementarity determining regions (LCDR) 1, 2 and 3 (LCDR1, LCDR2 and LCDR3) amino acid sequences as shown in SEQ ID NOs: 79, 80 and 195, wherein the LCDR3 of SEQ ID NO: 193 is further defined as shown in Formula (VI): Q-Q-Xaa18-Xaa19-Xaa20-Xaa21-Xaa22-Xaa23-T, wherein Xaa18 may be Tyr, Gly or Ala; Xaa19 may be Gly, Glu or Asn; Xaa20 may be Ser or Thr; Xaa21 may be Val, Ile or Leu; Xaa22 may be Ser or Leu; and Xaa23 may be Ile, Ser, Pro or Tyr.
Another aspect of the invention is an isolated polynucleotide encoding an antibody heavy chain variable region (VH) comprising the heavy chain complementarity determining regions (HCDR) 1, 2 and 3 (HCDR1, HCDR2 and HCDR3) amino acid sequences as shown in SEQ ID NOs: 70, 194 and 72, wherein the HCDR2 of SEQ ID NO: 194 is further defined as shown in Formula (III): I-1-Q-Xaa15-R—S-K-W-Y—N-Xaa16-Y-A-Xaa17-S-V-K-S, wherein Xaa15 may be Lys, Thr or Ile; Xaa16 may be Asn or Asp; and Xaa17 may be Val or Leu.
Another aspect of the invention is an isolated polynucleotide encoding an antibody light chain variable region (VL) comprising the light chain complementarity determining regions (LCDR) 1, 2 and 3 (LCDR1, LCDR2 and LCDR3) amino acid sequences as shown in SEQ ID NOs: 67, 68 and 193, wherein the LCDR3 of SEQ ID NO: 193 is further defined as shown in Formula (IV): Xaa10-S-Y-D-Xaa1′-P-Xaa12-Xaa13-Xaa14-V, wherein Xaa10 may be Gln or Ser; Xaa11 may be Thr, Glu or Asp; Xaa12 may be Val or Asn; Xaa13 may be Tyr or Phe; and Xaa14 may be Ser, Asn or Gln.
Another aspect of the invention is an isolated polynucleotide encoding an antibody VL or VH having certain amino acid sequences.
Another aspect of the invention is a vector comprising the isolated polynucleotide of the invention.
Another aspect of the invention is a host cell comprising the vector of the invention.
Another aspect of the invention is a method of making an antibody that binds toll-like receptor 3 (TLR3) comprising culturing the host cell of the invention and recovering the antibody produced by the host cell.
DETAILED DESCRIPTION OF THE INVENTION
All publications, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference as though fully set forth.
The term “antagonist” as used herein means a molecule that partially or completely inhibits, by any mechanism, an effect of another molecule such as a receptor or intracellular mediator.
As used herein, a “TRL3 antibody antagonist” or an antibody “reactive with TLR3” describes an antibody that is capable of, directly or indirectly, substantially counteracting, reducing or inhibiting TLR3 biological activity or TLR3 receptor activation. For example, an antibody reactive with TLR3 can bind directly to TLR3 and neutralize TLR3 activity, i.e, block TLR3 signaling to reduce cytokine and chemokine release or NF-κB activation.
The term “antibodies” as used herein is meant in a broad sense and includes immunoglobulin or antibody molecules including polyclonal antibodies, monoclonal antibodies including murine, human, human-adapted, humanized and chimeric monoclonal antibodies and antibody fragments.
In general, antibodies are proteins or peptide chains that exhibit binding specificity to a specific antigen. Intact antibodies are heterotetrameric glycoproteins, composed of two identical light chains and two identical heavy chains. Typically, each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies between the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at one end (VL) and a constant domain at its other end; the constant domain of the light chain is aligned with the first constant domain of the heavy chain and the light chain variable domain is aligned with the variable domain of the heavy chain. Antibody light chains of any vertebrate species can be assigned to one of two clearly distinct types, namely kappa (κ) and lambda (λ), based on the amino acid sequences of their constant domains.
Immunoglobulins can be assigned to five major classes, namely IgA, IgD, IgE, IgG and IgM, depending on the heavy chain constant domain amino acid sequence. IgA and IgG are further sub-classified as the isotypes IgA1, IgA2, IgG1, IgG2, IgG3 and IgG4.
The term “antibody fragments” means a portion of an intact antibody, generally the antigen binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab′, F(ab′)2 and Fv fragments, diabodies, single chain antibody molecules and multispecific antibodies formed from at least two intact antibodies.
An immunoglobulin light or heavy chain variable region consists of a “framework” region interrupted by three “antigen-binding sites”. The antigen-binding sites are defined using various terms as follows: (i) the term Complementarity Determining Regions (CDRs) is based on sequence variability (Wu and Kabat, J. Exp. Med. 132:211-250, 1970). Generally, the antigen-binding site has six CDRs; three in the VH(HCDR1, HCDR2, HCDR3), and three in the VL (LCDR1, LCDR2, LCDR3) (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991). (ii) The term “hypervariable region”, “HVR”, or “HV” refers to the regions of an antibody variable domain which are hypervariable in structure as defined by Chothia and Lesk (Chothia and Lesk, Mol. Biol. 196:901-917, 1987). Generally, the antigen-binding site has six hypervariable regions, three in VH (H1, H2, H3) and three in VL (L1, L2, L3). Chothia and Lesk refer to structurally conserved HVs as “canonical structures”. (iii) The “IMGT-CDRs” as proposed by Lefranc (Lefranc et al., Dev. Comparat. Immunol. 27:55-77, 2003) are based on the comparison of V domains from immunoglobulins and T-cell receptors. The International ImMunoGeneTics (IMGT) database (http://www_imgt_org) provides a standardized numbering and definition of these regions. The correspondence between CDRs, HVs and IMGT delineations is described in Lefranc et al., Dev. Comparat. Immunol. 27:55-77, 2003. (iv) The antigen-binding site can also be delineated based on Specificity Determining Residue Usage (SDRU), according to Almagro (Almagro, Mol. Recognit. 17:132-143, 2004), where Specificity Determining Residues (SDR), refers to amino acid residues of an immunoglobulin that are directly involved in antigen contact. SDRU as defined by Almargo is a precise measure of a number and distribution of SDR for different types of antigens as defined by analyses of crystal structures of antigen-antibody complexes.
The term “composite sequences” as used herein means an antigen-binding site defined to include all amino acid residues delineated individually by Kabat, Chothia or IMGT, or any other suitable antigen-binding region delineation.
“Framework” or “framework sequences” are the remaining sequences of a variable region other than those defined to be antigen-binding site. Because the antigen-binding site can be defined by various terms as described above, the exact amino acid sequence of a framework depends on how the antigen-binding site was defined.
The term “antigen” as used herein means any molecule that has the ability to generate antibodies either directly or indirectly. Included within the definition of “antigen” is a protein-encoding nucleic acid.
The term “homolog” means protein sequences having between 40% and 100% sequence identity to a reference sequence. Homologs of human TLR3 include polypeptides from other species that have between 40% and 100% sequence identity to a known human TLR3 sequence. Percent identity between two peptide chains can be determined by pairwise alignment using the default settings of the AlignX module of Vector NTI v.9.0.0 (Invitrogen, Carslbad, Calif.). By “TLR3” is meant human TLR3 (huTLR3) and its homologs. The nucleotide and amino acid sequences of the full length huTLR3 are shown in SEQ ID NOs: 1 and 2, respectively. The nucleotide and amino acid sequences of the huTLR3 extracellular domain (ECD) are shown in SEQ ID NOs: 3 and 4, respectively.
The term “substantially identical” as used herein means that the two antibody or antibody fragment amino acid sequences being compared are identical or have “insubstantial differences”. Insubstantial differences are substitutions of 1, 2, 3, 4, 5 or 6 amino acids in an antibody or antibody fragment amino acid sequence. Amino acid sequences substantially identical to the sequences disclosed herein are also part of this application. In some embodiments, the sequence identity can be about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or higher. Percent identity can be determined as described above. Exemplary peptide chains being compared are heavy or light chain variable regions.
The term “in combination with” as used herein means that the described agents can be administered to an animal together in a mixture, concurrently as single agents or sequentially as single agents in any order.
The term “inflammatory condition” as used herein means a localized response to cellular injury that is mediated in part by the activity of cytokines, chemokines, or inflammatory cells (e.g., neutrophils, monocytes, lymphocytes, macrophages) which is characterized in most instances by pain, redness, swelling, and loss of tissue function. The term “inflammatory pulmonary condition” as used herein means an inflammatory condition affecting or associated with the lungs.
The term “monoclonal antibody” (mAb) as used herein means an antibody (or antibody fragment) obtained from a population of substantially homogeneous antibodies. Monoclonal antibodies are highly specific, typically being directed against a single antigenic determinant. The modifier “monoclonal” indicates the substantially homogeneous character of the antibody and does not require production of the antibody by any particular method. For example, murine mAbs can be made by the hybridoma method of Kohler et al., Nature 256:495-497, 1975. Chimeric mAbs containing a light chain and heavy chain variable region derived from a donor antibody (typically murine) in association with light and heavy chain constant regions derived from an acceptor antibody (typically another mammalian species such as human) can be prepared by the method disclosed in U.S. Pat. No. 4,816,567. Human-adapted mAbs having CDRs derived from a non-human donor immunoglobulin (typically murine) and the remaining immunoglobulin-derived parts of the molecule being derived from one or more human immunoglobulins can be prepared by techniques known to those skilled in the art such as that disclosed in U.S. Pat. No. 5,225,539. Human framework sequences useful for human-adaptation can be selected from relevant databases by those skilled in the art. Optionally, human-adapted mAbs can be further modified by incorporating altered framework support residues to preserve binding affinity by techniques such as those disclosed in Queen et al., Proc. Natl. Acad. Sci. (USA), 86:10029-10032, 1989 and Hodgson et al., Bio/Technology, 9:421, 1991.
Fully human mAbs lacking any non-human sequences can be prepared from human immunoglobulin transgenic mice by techniques referenced in, e.g., Lonberg et al., Nature 368:856-859, 1994; Fishwild et al., Nature Biotechnology 14:845-851, 1996; and Mendez et al., Nature Genetics 15:146-156, 1997. Human mAbs can also be prepared and optimized from phage display libraries by techniques referenced in, e.g., Knappik et al., J. Mol. Biol. 296:57-86, 2000; and Krebs et al., J. Immunol. Meth. 254:67-84 2001.
The term “epitope” as used herein means a portion of an antigen to which an antibody specifically binds. Epitopes usually consist of chemically active (such as polar, non-polar or hydrophobic) surface groupings of moieties such as amino acids or polysaccharide side chains and can have specific three-dimensional structural characteristics, as well as specific charge characteristics. An epitope can be linear in nature or can be a discontinous epitope, e.g., a conformational epitope, which is formed by a spatial relationship between non-contiguous amino acids of an antigen rather than a linear series of amino acids. A conformational epitope includes epitopes resulting from folding of an antigen, where amino acids from differing portions of the linear sequence of the antigen come in close proximity in 3-dimensional space.
The term “specific binding” as used herein refers to antibody binding to a predetermined antigen with greater affinity than for other antigens or proteins. Typically, the antibody binds with a dissociation constant (KD) of 10−7 M or less, and binds to the predetermined antigen with a KD that is at least twofold less than its KD for binding to a non-specific antigen (e.g., BSA, casein, or any other specified polypeptide) other than the predetermined antigen. The phrases “an antibody recognizing an antigen” and “an antibody specific for an antigen” are used interchangeably herein with the term “an antibody which binds specifically to an antigen” or “an antigen specific antibody” e.g. a TLR3 specific antibody. The dissociation constant can be measured using standard procedures as described below.
The term “TLR3 biological activity” or “TLR3 activation” as used herein refers to any activity occurring as a result of ligand binding to TLR3. TLR3 ligands include dsRNA, poly(I:C), and endogenous mRNA, e.g., engodenous mRNA released from necrotic cells. An exemplary TLR3 activation results in activation of NF-κB in response to the TLR3 ligand. NF-κB activation can be assayed using a reporter-gene assay upon induction of the receptor with poly(I:C) (Alexopoulou et al., Nature 413:732-738, 2001; Hacker et al., EMBO J. 18:6973-6982, 1999). Another exemplary TLR3 activation results in activation of interferon response factors (IRF-3, IRF-7) in response to TLR3 ligand. TLR3-mediated IRF activation can be assayed using a reporter gene driven by an interferon-stimulated response element (ISRE). Another exemplary TLR3 activation results in secretion of pro-inflammatory cytokines and chemokines, for example TNF-α, IL-6, IL-8, IL-12, CXCL5/IP-10 and RANTES. The release of cytokines and chemokines from cells, tissues or in circulation can be measured using well-known immunoassays, such as an ELISA immunoassay.
Conventional one and three-letter amino acid codes are used herein as follows:














Amino acid
Three-letter code
One-letter code








Alanine
ala
A



Arginine
arg
R



Asparagine
asn
N



Aspartate
asp
D



Cysteine
cys
C



Glutamate
glu
E



Glutamine
gln
Q



Glycine
gly
G



Histidine
his
H



Isoleucine
ile
I



Leucine
leu
L



Lysine
lys
K



Methionine
met
M



Phenylalanine
phe
F



Proline
pro
P



Serine
ser
S



Threonine
thr
T



Tryptophan
trp
W



Tyrosine
tyr
Y



Valine
val
V









Compositions of Matter

The present invention provides antibody antagonists capable of inhibiting TLR3 biological activity and uses of such antibodies. Such TLR3 antagonists may have the properties of binding TLR3 and inhibiting TLR3 activation. Exemplary mechanisms by which TLR3 activation may be inhibited by such antibodies include in vitro, in vivo or in situ inhibition of ligand binding to TLR3, inhibition of receptor dimerization, inhibition of TLR3 localization to the endosomal compartment, inhibition of kinase activity of downstream signaling pathways, or inhibition of TLR3 mRNA transcription. Other antibody antagonists capable of inhibiting TLR3 activation by other mechanisms are also within the scope of the various aspects and embodiments of the invention. These antagonists are useful as research reagents, diagnostic reagents and therapeutic agents.
Antibody diversity is created by use of multiple germline genes encoding variable regions and a variety of somatic events. The somatic events include recombination of variable (V) gene segments and diversity (D) and joining (J) gene segments to make a complete VH region and the recombination of variable and joining gene segments to make a complete VL region. Antibodies and compositions having identical or similar CDR sequence to those disclosed herein are not likely to have been independently generated. The sequence of antibody genes after assembly and somatic mutation is highly varied, and these varied genes are estimated to encode 1010 different antibody molecules (Immunoglobulin Genes, 2nd ed., eds. Jonio et al., Academic Press, San Diego, Calif., 1995).
The invention provides novel antigen-binding sites derived from human immunoglobulin gene libraries. The structure for carrying an antigen-binding site is generally an antibody heavy or light chain or portion thereof, where the antigen-binding site is located to a naturally occurring antigen-binding site as determined as described above.
The invention provides an isolated antibody or fragment thereof reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises the heavy chain complementarity determining regions (CDR) amino acid sequences 1, 2 and 3 (HCDR1, HCDR2 and HCDR3) and the light chain complementarity determining regions (CDR) amino acid sequences 1, 2 and 3 (LCDR1, LCDR2 and LCDR3) as shown in Table 1a.








TABLE 1a








SEQ ID NO:













mAb
HCDR1
HCDR2
HCDR3
LCDR1
LCDR2
LCDR3
















16
52
88
54
49
50
51


17
58
64
60
55
56
57


18
70
77
72
67
68
69


19
82
83
84
79
80
89


 1
46
47
48
43
44
45


 2
52
53
54
49
50
51


 3
58
59
60
55
56
57


 4
61
62
60
55
56
57


 5
61
64
60
55
56
63


 6
61
64
60
55
56
65


 7
61
64
60
55
56
66


 8
70
71
72
67
68
69


 9
70
73
72
67
68
69


10
70
75
72
67
68
74


11
70
77
72
67
68
76


12
70
77
72
67
68
78


13
82
83
84
79
80
81


14
82
86
84
79
80
85


15*
82
86
84
79
80
87


15**
111
112
84
109
110
113


15-1
111
114
84
109
110
113


15-2
115
112
84
109
110
113


15-3
116
112
84
109
110
113


15-4
111
117
84
109
110
113


15-5
116
118
84
109
110
113


15-6
116
112
119
109
110
113


15-7
111
112
84
120
110
113


15-8
111
112
84
121
110
113


15-9
116
118
119
109
110
113


F17
61
192
60
55
56
191


F18
70
194
72
67
68
193


F19
82
196
84
79
80
195









In certain embodiments the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises a HCDR2 amino acid sequence as shown in SEQ ID NO: 192, wherein the HCDR2 of SEQ ID NO: 192 is defined as shown in Formula (I):







(I)


Xaa6-I-Xaa7-Xaa8-R-S-Xaa9-W-Y-N-D-Y-A-V-S-V-K-S,






    
    
        wherein
        Xaa6 may be Arg or Lys;
        Xaa7 may be Tyr, His or Ser;
        Xaa8 may be Met, Arg or Tyr; and
        Xaa9 may be Lys or Arg.
    
    


In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises a HCDR2 amino acid sequence as shown in SEQ ID NO: 194, wherein the HCDR2 of SEQ ID NO: 194 is defined as shown in Formula (III):









(III)



I-I-Q-Xaa15-R-S-K-W-Y-N-Xaa16-Y-A-Xaa17-S-V-K-S,






    
    
        wherein
        Xaa15 may be Lys, Thr or Ile;
        Xaa16 may be Asn or Asp; and
        Xaa17 may be Val or Leu.
    
    


In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises a HCDR2 amino acid sequence as shown in SEQ ID NO: 196, wherein the HCDR2 of SEQ ID NO: 196 is defined as shown in Formula (V):









(V)



Xaa24-I-D-P-S-D-S-Y-T-N-Y-Xaa25-P-S-F-Q-G,






    
    
        wherein
        Xaa24 may be Phe or Arg; and
        Xaa25 may be Ala or Ser.
    
    


In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises a LCDR3 amino acid sequence as shown in SEQ ID NO: 191, wherein the LCDR3 of SEQ ID NO: 191 is defined as shown in Formula (II):









(II)



Xaa1-S-Y-D-Xaa2-Xaa3-Xaa4-Xaa5-T-V,






    
    
        wherein
        Xaa1 may be Ala, Gln, Gly or Ser;
        Xaa2 may be Gly, Glu or Ser;
        Xaa3 may be Asp or Asn;
        Xaa4 may be Glu or Ser; and
        Xaa5 may be Phe, Ala or Leu.
    
    


In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises a LCDR3 amino acid sequence as shown in SEQ ID NO: 193, wherein the LCDR3 of SEQ ID NO: 193 is defined as shown in Formula (IV):









(IV)



Xaa10-S-Y-D-Xaa11-P-Xaa12-Xaa13-Xaa14-V,






    
    
        wherein
        Xaa10 may be Gln or Ser;
        Xaa11 may be Thr, Glu or Asp;
        Xaa12 may be Val or Asn;
        Xaa13 may be Tyr or Phe; and
        Xaa14 may be Ser, Asn or Gln.
    
    


In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises a LCDR3 amino acid sequence as shown in SEQ ID NO: 195, wherein the LCDR3 of SEQ ID NO: 195 is defined as shown in Formula (VI):









(VI)



Q-Q-Xaa18-Xaa19-Xaa20-Xaa21-Xaa22-Xaa23-T,






    
    
        wherein
        Xaa18 may be Tyr, Gly or Ala;
        Xaa19 may be Gly, Glu or Asn;
        Xaa20 may be Ser or Thr;
        Xaa21 may be Val, Ile or Leu;
        Xaa22 may be Ser or Leu; and
        Xaa23 may be Ile, Ser, Pro or Tyr.
    
    


The invention also provides an isolated antibody or fragment reactive with TLR3 having the heavy chain complementarity determining regions (CDR) amino acid sequences 1, 2 and 3 (HCDR1, HCDR2 and HCDR3) and light chain complementarity determining regions (CDR) amino acid sequences 1, 2 and 3 (LCDR1, LCDR2 and LCDR3) as shown in Table 1a.
Antibodies whose antigen-binding site amino acid sequences differ insubstantially from those shown in Table 1a (SEQ ID NOs: 49-121 and 191-196) are encompassed within the scope of the invention. Typically, this involves one or more amino acid substitutions with an amino acid having similar charge, hydrophobic, or stereochemical characteristics. Additional substitutions in the framework regions, in contrast to antigen-binding sites may also be made as long as they do not adversely affect the properties of the antibody. Substitutions may be made to improve antibody properties, for example stability or affinity. One, two, three, four, five or six substitutions can be made to the antigen binding site.
Conservative modifications will produce molecules having functional and chemical characteristics similar to those of the molecule from which such modifications are made. Substantial modifications in the functional and/or chemical characteristics of the molecules may be accomplished by selecting substitutions in the amino acid sequence that differ significantly in their effect on maintaining (1) the structure of the molecular backbone in the area of the substitution, for example, as a sheet or helical conformation, (2) the charge or hydrophobicity of the molecule at the target site, or (3) the size of the molecule. For example, a “conservative amino acid substitution” may involve a substitution of a native amino acid residue with a normative residue such that there is little or no effect on the polarity or charge of the amino acid residue at that position. Furthermore, any native residue in the polypeptide may also be substituted with alanine, as has been previously described for alanine scanning mutagenesis (MacLennan et al., Acta Physiol. Scand. Suppl. 643:55-67, 1998; Sasaki et al., Adv. Biophys. 35:1-24, 1998). Desired amino acid substitutions (whether conservative or non-conservative) can be determined by those skilled in the art at the time such substitutions are desired. For example, amino acid substitutions can be used to identify important residues of the molecule sequence, or to increase or decrease the affinity of the molecules described herein. Exemplary amino acid substitutions are shown in Table 1b.









TABLE 1b







More


Original

Conservative


residue
Exemplary substitutions
substitutions







Ala (A)
Val, Leu, Ile
Val


Arg (R)
Lys, Gln, Asn
Lys


Asn (N)
Gln
Gln


Asp (D)
Glu
Glu


Cys (C)
Ser, Ala
Ser


Gln (Q)
Asn
Asn


Gly (G)
Pro, Ala
Ala


His (H)
Asn, Gln, Lys, Arg
Arg


Ile (I)
Leu, Val, Met, Ala, Phe, Norleucine
Leu


Leu (L)
Norleucine, Ile, Val, Met, Ala, Phe
Ile


Lys (K)
Arg, 1,4 Diamino-butyric Acid, Gln, Asn
Arg


Met (M)
Leu, Phe, Ile
Leu


Phe (F)
Leu, Val, Ile, Ala, Tyr
Leu


Pro (P)
Ala
Gly


Ser (S)
Thr, Ala, Cys
Thr


Thr (T)
Ser
Ser


Trp (W)
Tyr, Phe
Tyr


Tyr (Y)
Trp, Phe, Thr, Ser
Phe


Val (V)
Ile, Met, Leu, Phe, Ala, Norleucine
Leu









In certain embodiments, conservative amino acid substitutions also encompass non-naturally occurring amino acid residues which are typically incorporated by chemical peptide synthesis rather than by synthesis in biological systems. Amino acid substitutions can be done for example by PCR mutagenesis (U.S. Pat. No. 4,683,195). Libraries of variants can be generated using well known methods, for example using random (NNK) or non-random codons, for example DVK codons, which encode 11 amino acids (ACDEGKNRSYW), and screening the libararies for variants with desired properties, as shown in Example 1. Table 1c shows substitutions made to three parent TLR3 antibody antagonists within the LCDR3 and HCDR2 regions to improve antibody properties.
Depending on delineation of the antigen-binding sites, the antigen-binding site residues of the antibodies of the invention and subsequently the framework residues may vary slightly for each heavy and light chain. Table 2a and 2b shows the antigen-binding site residues of exemplary antibodies of the invention delineated according to Kabat, Chothia and IMGT, and their composite sequences.









TABLE 1c







Family




17

SEQ


mAb
LCDR3
ID


















17
A
S
Y
D
G
D
E
F
T
V
NO:





3













4













5
Q



E

S
A





6
G



S
N
S
L





7
S



S

S
L





con-
A, Q, G, S
S
Y
D
G, E, S
D, N
E, S
F, A, L
T
V
191


sensus












Family




17

SEQ


mAb
HCDR2
ID


























17
R
I
Y
M
R
S
K
W
Y
N
D
Y
A
V
S
V
K
S
NO:





3


H
R

















4
K

S
Y


R














5





















6





















7





















con-
R, K
I
Y, 
M,
R
S
K, R
W
Y
N
D
Y
A
V
S
V
K
S
192


sensus


H, S
R, Y












Family




18A

SEQ


mAb
LCDR3
ID



















18
Q
S
Y
D
S
Q
F
S
F
G
V
NO:





8














9














Family 














18B














mAb














10
Q
S
Y
D
T
P
V
Y
S
V




11
S



E

N
F
N





12
S



D

N
F
Q





con-
Q, S
S
Y
D
T, E, D
P
V, N
Y, F
S, N, Q
V

193


sensus










*consensus based on mAbs 10, 11, 12












Family 




18A, 




18B

SEQ 


mAb
HCDR2
ID


























18
I
I
Q
K
R
S
K
W
Y
N
N
Y
A
V
S
V
K
S
NO:





8



T






D










9



I






D


L







10





















11





















12





















con-
I
I
Q
K, T, I
R
S
K
W
Y
N
N, D
Y
A
V, L
S
V
K
S
194


sensus












Family




19

SEQ


mAb
LCDR2
ID

















19
Q
Q
Y
G
S
V
S
I
T
NO:





13


G
E
S
I
L
S




14


A
E
T


P




15


G
N
T
L

Y




15-1


G
N
T
L

Y




15-2


G
N
T
L

Y




15-3


G
N
T
L

Y




15-4


G
N
T
L

Y




15-5


G
N
T
L

Y




15-6


G
N
T
L

Y




15-7


G
N
T
L

Y




15-8


G
N
T
L

Y




15-9


G
N
T
L

Y




con-
Q
Q
Y, G, A
G, E, N
S, T
V, I, L
S, L
I, S, P, Y
T
195


sensus












Family




19

SEQ


mAb
HCDR2
ID

























19
F
I
D
P
S
D
S
Y
T
N
Y
A
P
S
F
Q
G
NO:





13




















14




















15




















15.1
R



















15.2




















15.3




















15.4











S








15.5
R










S








15.6




















15.7




















15-8




















15-9
R










S








con-
F, R
I
D
P
S
D
S
Y
T
N
Y
A, S
P
S
F
Q
G
196


sensus




















TABLE 2a









HCDR1
HCDR2
HCDR3














mAb
CDR definition
SEQ ID
Sequence
SEQ ID
Sequence
SEQ ID
Sequence

















14
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


14
Kabat

NYWVG

FIDPSDSYTNYAPSFQ

ELYQGYMDTFDS


 


14
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


14
Consensus
111
GYSFTNYWVG
112
FIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15
Kabat

NYWVG

FIDPSDSYTNYAPSFQ

ELYQGYMDTFDS


 


15
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15
Consensus
111
GYSFTNYWVG
112
FIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15-1
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-1
Kabat

NYWVG

RIDPSDSYTNYAPSFQ

ELYQGYMDTFDS


 


15-1
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-1
Consensus
111
GYSFTNYWVG
114
RIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15-2
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-2
Kabat

NYWIG

FIDPSDSYTNYAPSFQ

ELYQGYMDTFDS


 


15-2
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-2
Consensus
115
GYSFTNYWIG
112
FIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15-3
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-3
Kabat

NYWIS
86
FIDPSDSYTNYAPSFQ
84
ELYQGYMDTFDS


 


15-3
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-3
Consensus
116
GYSFTNYWIS
112
FIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15-4
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-4
Kabat

NYWVG

FIDPSDSYTNYSPSFQ

ELYQGYMDTFDS


 


15-4
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-4
Consensus
111
GYSFTNYWVG
117
FIDPSDSYTNYSPSFQ
84
ARELYQGYMDTFDS


 


15-5
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-5
Kabat

NYWIS

RIDPSDSYTNYSPSFQ

ELYQGYMDTFDS


 


15-5
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-5
Consensus
116
GYSFTNYWIS
118
RIDPSDSYTNYSPSFQ
84
ARELYQGYMDTFDS


 


15-6
IMGT
82
GYSFTNYW
86
IDPSDSYTNY

ARQLYQGYMDTFDS


 


15-6
Kabat

NYWIS

FIDPSDSYTNYAPSFQ

QLYQGYMDTFDS


 


15-6
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-6
Consensus
116
GYSFTNYWIS
112
FIDPSDSYTNYAPSFQ
119
ARQLYQGYMDTFDS


 


15-7
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-7
Kabat

NYWVG

FIDPSDSYTNYAPSFQ

ELYQGYMDTFDS


 


15-7
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-7
Consensus
111
GYSFTNYWVG
112
FIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15-8
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
84
ARELYQGYMDTFDS


 


15-8
Kabat

NYWVG

FIDPSDSYTNYAPSFQ

ELYQGYMDTFDS


 


15-8
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-8
Consensus
111
GYSFTNYWVG
112
FIDPSDSYTNYAPSFQ
84
ARELYQGYMDTFDS


 


15-9
IMGT
82
GYSFTNYW
86
IDPSDSYTNY
119
ARQLYQGYMDTFDS


 


15-9
Kabat

NYWIS

RIDPSDSYTNYSPSFQG

QLYQGYMDTFDS


 


15-9
Chothia

GYSFT

PSDSYT

LYQGYMDTFD


 


15-9
Consensus
116
GYSFTNYWIS
118
RIDPSDSYTNYSPSFQG
119
ARQLYQGYMDTFDS









In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable region and wherein the antibody comprises the amino acid sequences of the heavy chain variable (VH) and the light chain variable (VL) regions and also provides for each isolated heavy chain variable and light chain variable region as shown in Table 3a. F17, F18 and F19 represent antibody variants comprising consensus amino acid sequences for families 17, 18 and 19, respectively (see Example 1).











TABLE 2b









LCDR1
LCDR2
LCDR3
















SEQ ID

SEQ ID

SEQ ID



mAb
CDR definition
NO:
Sequence
NO:
Sequence
NO:
Sequence

















14
IMGT
79
QSIGLY
80
AAS
85
QQAETVSPT


 


14
Kabat

RASQSIGLYLA

AASSLQS

QQAETVSPT


 


14
Chothia

SQSIGLY

AAS

AETVSP


 


14
Consensus
109
RASQSIGLYLA
110
AASSLQS
85
QQAETVSPT


 


15
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15
Chothia

SQSIGLY

AAS

GNTLSY


 


15
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-1
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-1
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-1
Chothia

SQSIGLY

AAS

GNTLSY


 


15-1
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-2
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-2
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-2
Chothia

SQSIGLY

AAS

GNTLSY


 


15-2
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-3
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-3
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-3
Chothia

SQSIGLY

AAS

GNTLSY


 


15-3
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-4
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-4
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-4
Chothia

SQSIGLY

AAS

GNTLSY


 


15-4
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-5
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-5
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-5
Chothia

SQSIGLY

AAS

GNTLSY


 


15-5
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-6
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-6
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-6
Chothia

SQSIGLY

AAS

GNTLSY


 


15-6
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT


 


15-7
IMGT

QSISSY
80
AAS
87
QQGNTLSYT


 


15-7
Kabat

RASQSISSYLA

AASSLQS

QQGNTLSYT


 


15-7
Chothia

SQSISSY

AAS

GNTLSY


 


15-7
Consensus
120
RASQSISSYLA
110
AASSLQS
113
QQGNTLSYT


 


15-8
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-8
Kabat

RASQSIGLYLN

AASSLQS

QQGNTLSYT


 


15-8
Chothia

SQSIGLY

AAS

GNTLSY


 


15-8
Consensus
121
RASQSIGLYLN
110
AASSLQS
113
QQGNTLSYT


 


15-9
IMGT
79
QSIGLY
80
AAS
87
QQGNTLSYT


 


15-9
Kabat

RASQSIGLYLA

AASSLQS

QQGNTLSYT


 


15-9
Chothia

SQSIGLY

AAS

GNTLSY


 


15-9
Consensus
109
RASQSIGLYLA
110
AASSLQS
113
QQGNTLSYT




















TABLE 3a








SEQ ID NO:

SEQ ID NO:













mAb
VH
VL
mAb
VH
VL















16
6
5
15-1
124
41


17
8
7
15-2
125
41


18
10
9
15-3
126
41


19
12
11
15-4
127
41


1
14
13
15-5
128
41


2
16
15
15-6
129
41


3
18
17
15-7
42
122


4
20
19
15-8
42
123


5
22
21
15-9
159
41


6
24
23
F17
198
197


7
26
25
F18
200
199


8
28
27
F19
202
201


9
30
29
c1811
164
163


10
32
31
9QVQ/QSV
212
209


11
34
33
10QVQ/QSV
213
210


12
36
35
12QVQ/QSV
214
211


13
38
37
14EVQ
215
39


14
40
39
15EVQ
216
41


15
42
41









Although the embodiments illustrated in the Examples comprise pairs of variable regions, one from a heavy and one from a light chain, a skilled artisan will recognize that alternative embodiments may comprise single heavy or light chain variable regions. The single variable region can be used to screen for variable domains capable of forming a two-domain specific antigen-binding fragment capable of, for example, binding to TLR3. The screening may be accomplished by phage display screening methods using for example hierarchical dual combinatorial approach disclosed in PCT Publ. No. WO92/01047. In this approach, an individual colony containing either a H or L chain clone is used to infect a complete library of clones encoding the other chain (L or H), and the resulting two-chain specific antigen-binding domain is selected in accordance with phage display techniques as described.
In other embodiments, the invention provides an isolated antibody or fragment reactive with TLR3 comprising both a heavy chain and a light chain variable regions having amino acid sequences at least 95% identical to the variable region amino acid sequence as shown in Table 3a.
In another aspect, the invention provides an isolated antibody having certain heavy chain and light chain amino acid sequences as shown in Table 3b.
Another aspect of the invention is isolated polynucleotides encoding any of the antibodies of the invention or their complement. Certain exemplary polynucleotides are disclosed herein, however, other polynucleotides which, given the degeneracy of the genetic code or codon preferences in a given expression system, encode the antibody antagonists of the invention are also within the scope of the invention.
Exemplary antibody antagonists may be antibodies of the IgG, IgD, IgG, IgA or IgM isotypes. Additionally, such antibody antagonists can be post-translationally modified by processes such as glycosylation, isomerization, deglycosylation or non-naturally occurring covalent modification such as the addition of polyethylene glycol (PEG) moieties (pegylation) and lipidation. Such modifications may occur in vivo or in vitro. For example, the antibodies of the invention can be conjugated to polyethylene glycol (PEGylated) to improve their pharmacokinetic profiles. Conjugation can be carried out by techniques known to those skilled in the art. Conjugation of therapeutic antibodies with PEG has been shown to enhance pharmacodynamics while not interfering with function. See Deckert et al., Int. J. Cancer 87:382-390, 2000; Knight et al., Platelets 15:409-418, 2004; Leong et al., Cytokine 16:106-119, 2001; and Yang et al., Protein Eng. 16:761-770, 2003.










TABLE 3b







Heavy chain
Light chain



mAb
SEQ ID NO:
SEQ ID NO:








14
102
155



15
102
156



15-1
130
156



15-2
131
156



15-3
132
156



15-4
133
156



15-5
134
156



15-6
135
156



15-7
102
157



15-8
102
158



15-9
160
156



F17
204
203



F18
206
205



F19
208
207



14EVQ
220
155



15EVQ
220
156



5429
166
165



c1811
168
167









Pharmacokinetic properties of the antibodies of the invention could also be enhanced through Fc modifications by techniques known to those skilled in the art. For example, IgG4 isotype heavy chains contain a Cys-Pro-Ser-Cys (CPSC) motif in the hinge region capable of forming either inter- or intra-heavy chain disulfide bonds, i.e., the two Cys residues in the CPSC motif may disulfide bond with the corresponding Cys residues in the other heavy chain (inter) or the two Cys residues within a given CPSC motif may disulfide bond with each other (intra). It is believed that in vivo isomerase enzymes are capable of converting inter-heavy chain bonds of IgG4 molecules to intra-heavy chain bonds and vice versa (Aalberse and Schuurman, Immunology 105:9-19, 2002). Accordingly, since the heavy:light chain (H:L) pairs in those IgG4 molecules with intra-heavy chain bonds in the hinge region are not covalently associated with each other, they may dissociate into H:L monomers that then reassociate with H:L monomers derived from other IgG4 molecules forming bispecific, heterodimeric IgG4 molecules. In a bispecific IgG antibody the two Fabs of the antibody molecule differ in the epitopes that they bind. Substituting the Ser residue in the hinge region CPSC motif of IgG4 with Pro results in “IgG1-like behavior,” i.e., the molecules form stable disulfide bonds between heavy chains and therefore, are not susceptible to H:L exchange with other IgG4 molecules. In one embodiment, the antibodies of the invention will comprise an IgG4 Fc domain with a S to P mutation in the CPSC motif. The location of the CPSC motif is typically found at residue 228 of a mature heavy chain but can change depending on CDR lengths.
Further, sites can be removed that affect binding to Fc receptors other than an FcRn salvage receptor in the antibodies of the invention. For example, the Fc receptor binding regions involved in ADCC activity can be removed in the antibodies of the invention. For example, mutation of Leu234/Leu235 in the hinge region of IgG1 to L234A/L235A or Phe235/Leu236 in the hinge region of IgG4 to P235A/L236A minimizes FcR binding and reduces the ability of the immunoglobulin to mediate complement dependent cytotoxicity and ADCC. In one embodiment, the antibodies of the invention will comprise an IgG4 Fc domain with P235A/L236A mutations. The location of these residues identified above is typical in a mature heavy chain but can change depending on CDR lengths. Exemplary antibodies having P235A/L236A mutations are antibodies having heavy chains encoded by sequence shown in SEQ ID NOs: 218, 219 or 220.
Fully human, human-adapted, humanized and affinity-matured antibody molecules or antibody fragments are within the scope of the invention as are fusion proteins and chimeric proteins. Antibody affinity towards an antigen may be improved by rational design or random affinity maturation using well-known methods such as random or directed mutagenesis, or employing phage display libraries. For example, variation of Vernier Zone residues that mostly reside in the framework region can be employed to modulate affinity of an antibody as described in U.S. Pat. No. 6,639,055. Recently, Almagro et al. defined “Affinity Determining Residues”, ADRs, that reside in the CDRs, and whose engineering can increase affinity (Cobaugh et al., J Mol. Biol. 378: 622-633, 2008).
Fully human, human-adapted, humanized, affinity-matured antibody molecules or antibody fragments modified to improve stability, selectivity, cross-reactivity, affinity, immunogenicity or other desirable biological or biophysical property are within the scope of the invention. Stability of an antibody is influenced by a number of factors, including (1) core packing of individual domains that affects their intrinsic stability, (2) protein/protein interface interactions that have impact upon the HC and LC pairing, (3) burial of polar and charged residues, (4) H-bonding network for polar and charged residues; and (5) surface charge and polar residue distribution among other intra- and inter-molecular forces (Worn et al., J. Mol. Biol., 305:989-1010, 2001). Potential structure destabilizing residues may be identified based upon the crystal structure of the antibody or by molecular modeling in certain cases, and the effect of the residues on antibody stability can be tested by generating and evaluating variants harboring mutations in the identified residues. One of the ways to increase antibody stability is to raise the thermal transition midpoint (Tm) as measured by differential scanning calorimetry (DSC). In general, the protein Tm is correlated with its stability and inversely correlated with its susceptibility to unfolding and denaturation in solution and the degradation processes that depend on the tendency of the protein to unfold (Remmele et al., Biopharm., 13:36-46, 2000). A number of studies have found correlation between the ranking of the physical stability of formulations measured as thermal stability by DSC and physical stability measured by other methods (Gupta et al., AAPS PharmSci. 5E8, 2003; Zhang et al., J. Pharm. Sci. 93:3076-3089, 2004; Maa et al., Int. J. Pharm., 140:155-168, 1996; Bedu-Addo et al., Pharm. Res., 21:1353-1361, 2004; Remmele et al., Pharm. Res., 15:200-208, 1997). Formulation studies suggest that a Fab Tm has implication for long-term physical stability of a corresponding mAb. Differences in amino acids in either framework or within the CDRs could have significant effects on the thermal stability of the Fab domain (Yasui, et al., FEBS Lett. 353:143-146, 1994).
The antibody antagonists of the invention may bind TLR3 with a Kd less than or equal to about 10−7, 10−8, 10−9, 10−10, 10−11 or 10−12 M. The affinity of a given molecule for TLR3, such as an antibody can be determined experimentally using any suitable method. Such methods may utilize Biacore or KinExA instrumentation, ELISA or competitive binding assays known to those skilled in the art.
Antibody antagonists binding a given TLR3 homolog with a desired affinity can be selected from libraries of variants or fragments by techniques including antibody affinity maturation. Antibody antagonists can be identified based on their inhibition of TLR3 biological activity using any suitable method. Such methods may utilize reporter-gene assays or assays measuring cytokine production using well known methods and as described in the application.
Another embodiment of the invention is a vector comprising at least one polynucleotide of the invention. Such vectors may be plasmid vectors, viral vectors, vectors for baculovirus expression, transposon based vectors or any other vector suitable for introduction of the polynucleotides of the invention into a given organism or genetic background by any means.
Another embodiment of the invention is a host cell comprising any of the polynucleotides of the invention such as a polynucleotide encoding a polypeptide comprising an immunoglobulin heavy chain variable region having the amino acid sequence shown in SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 124, 125, 126, 127, 128, 129, 159, 198, 200, 202, 164, 212, 213, 214, 215 or 216 or an immunoglobulin light chain variable region having the amino acid sequence shown in SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 122, 123, 197, 199, 201, 163, 209 or 210.
Another embodiment of the invention is a host cell comprising a polynucleotide encoding a polypeptide comprising an immunoglobulin heavy chain having the amino acid sequence shown in SEQ ID NO: 102, 130, 131, 132, 133, 134, 135, 160, 204, 206, 208, 220, 166 or 168, or an immunoglobulin light chain having the amino acid sequence shown in SEQ ID NO: 155, 156, 157, 158, 203, 205, 207, 165 or 167. Such host cells may be eukaryotic cells, bacterial cells, plant cells or archeal cells. Exemplary eukaryotic cells may be of mammalian, insect, avian or other animal origins. Mammalian eukaryotic cells include immortalized cell lines such as hybridomas or myeloma cell lines such as SP2/0 (American Type Culture Collection (ATCC), Manassas, Va., CRL-1581), NS0 (European Collection of Cell Cultures (ECACC), Salisbury, Wiltshire, UK, ECACC No. 85110503), FO (ATCC CRL-1646) and Ag653 (ATCC CRL-1580) murine cell lines. An exemplary human myeloma cell line is U266 (ATTC CRL-TIB-196). Other useful cell lines include those derived from Chinese Hamster Ovary (CHO) cells such as CHO-K1SV (Lonza Biologics, Walkersville, Md.), CHO-K1 (ATCC CRL-61) or DG44.
Another embodiment of the invention is a method of making an antibody reactive with TLR3 comprising culturing a host cell of the invention and recovering the antibody produced by the host cell. Methods of making antibodies and purifying them are well known in the art.
Another embodiment of the invention is a hybridoma cell line that produces an antibody of the invention.
Another embodiment of the invention is an isolated antibody or fragment thereof that is reactive with TLR3, wherein the antibody binds at least one TLR3 amino acid residue selected from a group consisting of (a) residues K467, R488, or R489 of SEQ ID NO: 2; (b) residue K467 of SEQ ID NO: 2; (c) residue R489 of SEQ ID NO: 2; (d) residues K467 and R489 of SEQ ID NO: 2; and (e) residues K467, R488, and R489 of SEQ ID NO: 2. The isolated antibody may further bind at least one TLR3 amino acid residue selected from the residues Y465, Y468, N517, D536, Q538, H539, N541, E570 or K619 of SEQ ID NO:2.
Another embodiment of the invention is isolated antibody or fragment thereof, wherein the antibody binds at least on TLR3 amino acid residue selected from a group consisting of residues D116 or K145 of SEQ ID NO: 2.
Several well known methodologies can be employed to determine the binding epitope of the antibodies of the invention. For example, when the structures of both individual components are known, in silico protein-protein docking can be carried out to identify compatible sites of interaction. Hydrogen-deuterium (H/D) exchange can be carried out with the antigen and antibody complex to map regions on the antigen that may be bound by the antibody. Segment and point mutagenesis of the antigen can be used to locate amino acids important for antibody binding. For large proteins such as TLR3, point mutagenesis mapping is simplified when the binding site is first localized to a region on the protein, such as by docking, segment mutagenesis or H/D exchange.
Another aspect of the invention is an isolated antibody or fragment thereof reactive with TLR3 that competes for TLR3 binding with a monoclonal antibody, wherein the monoclonal antibody comprises the amino acid sequences of certain heavy chain complementarity determining regions (CDRs) 1, 2 and 3, the amino acid sequences of certain light chain CDRs 1, 2 and 3, the amino acid sequences of certain heavy chain variable regions (VH) or the amino acid sequence of certain light chain variable regions (VL). Exemplary monoclonal antibodies of the invention are an isolated antibody comprising a heavy chain variable region having an amino acid sequence shown in SEQ ID NO: 216 and a light chain variable region amino acid sequence shown in SEQ ID NO: 41, and an antibody comprising a heavy chain variable region having an amino acid sequence shown in SEQ ID NO: 214 and a light chain variable region amino acid sequence shown in SEQ ID NO: 211.
Competition between binding to TLR3 can be assayed in vitro using well known methods. For example, binding of MSD Sulfo-TagTM NHS-ester-labeled antibody to TLR3 in the presence of an unlableled antibody can be assessed by ELISA. Exemplary antibodies of the invention are mAb 12, mAb 15 and mAb c1811 (see Table 3a). Previously described anti-TLR3 antibodies c1068 and its derivatives (described in PCT Publ. No. WO06/060513A2), TLR3.7 (eBiosciences, cat no 14-9039) and Imgenex IMG-315A (Imgenex IMG-315A; generated against human TLR3 amino acids amino acids 55-70, VLNLTHNQLRRLPAAN, residues 55-70 of SEQ ID NO: 2) do not compete with binding to TLR3 with mAbs 12, 15 or c1811 as shown in Example 5.
Another aspect of the invention is an isolated antibody reactive with TLR3, wherein the antibody has at least one of the following properties:

    
    
        a. reduces human TLR3 biological activity in an in vitro poly(I:C) NF-kB reporter gene assay >50% at <1 μg/ml;
        b. inhibits >60% of IL-6 or CXCL5/IP-10 production from BEAS-2B cells stimulated with <100 ng/ml poly(I:C) at <10 μg/ml;
        c. inhibits >50% of IL-6 or CXCL5/IP-10 production from BEAS-2B cells stimulated with <100 ng/ml poly(I:C) at <0.4 μg/ml;
        d. inhibits >50% of IL-6 production from NHBE cells stimulated with 62.5 ng/ml poly(I:C) at <5 μg/ml;
        e. inhibits >50% of IL-6 production from NHBE cells stimulated with 62.5 ng/ml poly(I:C) at <1 μg/ml;
        f. inhibits >20% of poly(I:C)-induced IFN-γ, IL-6 or IL-12 production by PBMC cells at <1 μg/ml.
        g. inhibits cynomologus TLR3 biological activity in an in vitro NF-κB reporter gene assay with IC50<10 μg/ml; or
        h. inhibits cynomologus TLR3 biological activity in an in vitro ISRE reporter gene assay with IC50<5 μg/ml.

Methods of Treatment

    
    


TLR3 antagonists of the invention, for example TLR3 antibody antagonists, can be used to modulate the immune system. While not wishing to be bound by any particular theory, the antagonists of the invention may modulate the immune system by preventing or reducing ligand binding to TLR3, dimerization of TLR3, TLR3 internalization or TLR3 trafficking. The methods of the invention may be used to treat an animal patient belonging to any classification. Examples of such animals include mammals such as humans, rodents, dogs, cats and farm animals. For example, the antibodies of the invention are useful in antagonizing TLR3 activity, in the treatment of inflammation, inflammatory and metabolic diseases and are also useful in the preparation of a medicament for such treatment wherein the medicament is prepared for administration in dosages defined herein.
Generally, inflammatory conditions, infection-associated conditions or immune-mediated inflammatory disorders that may be prevented or treated by administration of the TLR3 antibody antagonists of the invention include those mediated by cytokines or chemokines and those conditions which result wholly or partially from activation of TLR3 or signaling through the TLR3 pathway. Examples of such inflammatory conditions include sepsis-associated conditions, inflammatory bowel diseases, autoimmune disorders, inflammatory disorders and infection-associated conditions. It is also thought that cancers, cardiovascular and metabolic conditions, neurologic and fibrotic conditions can be prevented or treated by administration of the TLR3 antibody antagonists of the invention. Inflammation may affect a tissue or be systemic. Exemplary affected tissues are the respiratory tract, lung, the gastrointestinal tract, small intestine, large intestine, colon, rectum, the cardiovascular system, cardiac tissue, blood vessels, joint, bone and synovial tissue, cartilage, epithelium, endothelium, hepatic or adipose tissue. Exemplary systemic inflammatory conditions are cytokine storm or hypercytokinemia, systemic inflammatory response syndrome (SIRS), graft versus host disease (GVHD), acute respiratory distress syndrome (ARDS), severe acute respiratory distress syndrome (SARS), catastrophic anti-phospholipid syndrome, severe viral infections, influenza, pneumonia, shock, or sepsis.
Inflammation is a protective response by an organism to fend off an invading agent. Inflammation is a cascading event that involves many cellular and humoral mediators. On one hand, suppression of inflammatory responses can leave a host immunocompromised; however, if left unchecked, inflammation can lead to serious complications including chronic inflammatory diseases (e.g. asthma, psoriasis, arthritis, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease and the like), septic shock and multiple organ failure. Importantly, these diverse disease states share common inflammatory mediators, such as cytokines, chemokines, inflammatory cells and other mediators secreted by these cells.
TLR3 activation by its ligands poly(I:C), dsRNA or endogenous mRNA leads to activation of signaling pathways resulting in synthesis and secretion of pro-inflammatory cytokines, activation and recruitment of inflammatory cells, such as macrophages, granulocytes, neutrophils and eosinophils, cell death, and tissue destruction. TLR3 induces secretion of IL-6, IL-8, IL-12, TNF-α, MIP-1, CXCL5/IP-10 and RANTES, and other pro-inflammatory cytokines and chemokines implicated in immune cell recruitment and activation, thus contributing to tissue destruction in autoimmune and other inflammatory diseases. TLR3 ligand endogenous mRNA is released from necrotic cells during inflammation, and may result in a positive feedback loop to activate TLR3 and perpetuate inflammation and further tissue damage. TLR3 antagonists, such as TLR3 antibody antagonists, may normalize cytokine secretion, reduce recruitment of inflammatory cells, and reduce tissue damage and cell death. Therefore, TLR3 antagonists have therapeutic potential to treat inflammation and a spectrum of inflammatory conditions.
One example of an inflammatory condition is sepsis-associated condition that may include systemic inflammatory response syndrome (SIRS), septic shock or multiple organ dysfunction syndrome (MODS). dsRNA released by viral, bacterial, fungal, or parasitic infection and by necrotic cells can contribute to the onset of sepsis. While not wishing to be bound by an particular theory, it is believed that treatment with TLR3 antagonists can provide a therapeutic benefit by extending survival times in patients suffering from sepsis-associated inflammatory conditions or prevent a local inflammatory event (e.g., in the lung) from spreading to become a systemic condition, by potentiating innate antimicrobial activity, by demonstrating synergistic activity when combined with antimicrobial agents, by minimizing the local inflammatory state contributing to the pathology, or any combination of the foregoing. Such intervention may be sufficient to permit additional treatment (e.g., treatment of underlying infection or reduction of cytokine levels) necessary to ensure patient survival. Sepsis can be modeled in animals, such as mice, by the administration of D-galactosamine and poly(I:C). In such models, D-galactosamine is a hepatotoxin which functions as a sepsis sensitizer and poly(I:C) is a sepsis-inducing molecule that mimics dsRNA and activates TLR3. TLR3 antagonist treatment may increase animal survival rates in a murine model of sepsis, and thus TLR3 antagonists may be useful in the treatment of sepsis.
Gastrointestinal inflammation is inflammation of a mucosal layer of the gastrointestinal tract, and encompasses acute and chronic inflammatory conditions. Acute inflammation is generally characterized by a short time of onset and infiltration or influx of neutrophils. Chronic inflammation is generally characterized by a relatively longer period of onset and infiltration or influx of mononuclear cells. Mucosal layer may be mucosa of the bowel (including the small intestine and large intestine), rectum, stomach (gastric) lining, or oral cavity. Exemplary chronic gastrointestinal inflammatory conditions are inflammatory bowel disease (IBD), colitis induced by environmental insults (e.g., gastrointestinal inflammation (e.g., colitis) caused by or associated with (e.g., as a side effect) a therapeutic regimen, such as administration of chemotherapy, radiation therapy, and the like), infections colitis, ischemic colitis, collagenous or lymphocytic colitis, necrotizing enterocolitis, colitis in conditions such as chronic granulomatous disease or celiac disease, food allergies, gastritis, infectious gastritis or enterocolitis (e.g., Helicobacter pylori-infected chronic active gastritis) and other forms of gastrointestinal inflammation caused by an infectious agent.
Inflammatory bowel disease (IBD) includes a group of chronic inflammatory disorders of generally unknown etiology, e.g., ulcerative colitis (UC) and Crohn's disease (CD). Clinical and experimental evidence suggest that the pathogenesis of IBD is multifactorial involving susceptibility genes and environmental factors. In inflammatory bowel disease, the tissue damage results from an inappropriate or exaggerated immune response to antigens of the gut microflora. Several animal models for inflammatory bowel diseases exist. Some of the most widely used models are the 2,4,6-trinitrobenesulfonic acid/ethanol (TNBS)-induced colitis model or the oxazalone model, which induce chronic inflammation and ulceration in the colon (Neurath et al., Intern. Rev. Immunol 19:51-62, 2000). Another model uses dextran sulfate sodium (DSS), which induces an acute colitis manifested by bloody diarrhea, weight loss, shortening of the colon and mucosal ulceration with neutrophil infiltration. DSS-induced colitis is characterized histologically by infiltration of inflammatory cells into the lamina propria, with lymphoid hyperplasia, focal crypt damage, and epithelial ulceration (Hendrickson et al., Clinical Microbiology Reviews 15:79-94, 2002). Another model involves the adoptive transfer of naïve CD45RBhigh CD4 T cells to RAG or SCID mice. In this model, donor naïve T cells attack the recipient gut causing chronic bowel inflammation and symptoms similar to human inflammatory bowel diseases (Read and Powrie, Curr. Protoc. Immunol. Chapter 15 unit 15.13, 2001). The administration of antagonists of the present invention in any of these models can be used to evaluate the potential efficacy of those antagonists to ameliorate symptoms and alter the course of diseases associated with inflammation in the gut, such as inflammatory bowel disease. Several treatment options for IBD are available, for example anti-TNF-α antibody therapies have been used for a decade to treat Crohn's disease (Van Assche et al., Eur. J. Pharmacol. Epub October 2009). However, a significant percentage of patients are refractory to the current treatments (Hanauer et al., Lancet 359:1541-1549, 2002; Hanauer et al., Gastroenterology 130:323-333, 2006), and thus new therapies targeting refractory patient populations are needed.
Another example of an inflammatory condition is an inflammatory pulmonary condition. Exemplary inflammatory pulmonary conditions include infection-induced pulmonary conditions including those associated with viral, bacterial, fungal, parasite or prion infections; allergen-induced pulmonary conditions; pollutant-induced pulmonary conditions such as asbestosis, silicosis, or berylliosis; gastric aspiration-induced pulmonary conditions, immune dysregulation, inflammatory conditions with genetic predisposition such as as cystic fibrosis, and physical trauma-induced pulmonary conditions, such as ventilator injury. These inflammatory conditions also include asthma, emphysema, bronchitis, chronic obstructive pulmonary disease (COPD), sarcoidosis, histiocytosis, lymphangiomyomatosis, acute lung injury, acute respiratory distress syndrome, chronic lung disease, bronchopulmonary dysplasia, community-acquired pneumonia, nosocomial pneumonia, ventilator-associated pneumonia, sepsis, viral pneumonia, influenza infection, parainfluenza infection, rotavirus infection, human metapneumovirus infection, respiratory syncitial virus infection and aspergillus or other fungal infections. Exemplary infection-associated inflammatory diseases may include viral or bacterial pneumonia, including severe pneumonia, cystic fibrosis, bronchitis, airway exacerbations and acute respiratory distress syndrome (ARDS). Such infection-associated conditions may involve multiple infections such as a primary viral infection and a secondary bacterial infection.
Asthma is an inflammatory disease of the lung that is characterized by airway hyperresponsiveness (“AHR”), bronchoconstriction, wheezing, eosinophilic or neutrophilic inflammation, mucus hypersecretion, subepithelial fibrosis, and elevated IgE levels. Patients with asthma experience “exacerbations”, a worsening of symptoms, most commonly due to microbial infections of the respiratory tract (e.g. rhinovirus, influenza virus, Haemophilus influenza, etc.). Asthmatic attacks can be triggered by environmental factors (e.g. ascarids, insects, animals (e.g., cats, dogs, rabbits, mice, rats, hamsters, guinea pigs and birds), fungi, air pollutants (e.g., tobacco smoke), irritant gases, fumes, vapors, aerosols, chemicals, pollen, exercise, or cold air. Apart from asthma, several chronic inflammatory diseases affecting the lung are characterized by neutrophil infiltration to the airways, for example chronic obstructive pulmonary disease (COPD), bacterial pneumonia and cystic fibrosis (Linden et al., Eur. Respir. J. 15:973-977, 2000; Rahman et al., Clin. Immunol. 115:268-276, 2005), and diseases such as COPD, allergic rhinitis, and cystic fibrosis are characterized by airway hyperresponsiveness (Fahy and O'Byrne, Am. J. Respir. Crit. Care Med. 163:822-823, 2001). Commonly used animal models for asthma and airway inflammation include the ovalbumin challenge model and methacholine sensitization models (Hessel et al., Eur. J. Pharmacol. 293:401-412, 1995). Inhibition of cytokine and chemokine production from cultured human bronchial epithelial cells, bronchial fibroblasts or airway smooth muscle cells can also be used as in vitro models. The administration of antagonists of the present invention to any of these models can be used to evaluate the use of those antagonists to ameliorate symptoms and alter the course of asthma, airway inflammation, COPD and the like.
Other inflammatory conditions and neuropathies, which may be prevented or treated by the methods of the invention are those caused by autoimmune diseases. These conditions and neuropathies include multiple sclerosis, systemic lupus erythematous, and neurodegenerative and central nervous system (CNS) disorders including Alzheimer's disease, Parkinson's disease, Huntington's disease, bipolar disorder and Amyotrophic Lateral Sclerosis (ALS), liver diseases including primary biliary cirrhosis, primary sclerosing cholangitis, non-alcoholic fatty liver disease/steatohepatitis, fibrosis, hepatitis C virus (HCV) and hepatitis B virus (HBV), diabetes and insulin resistance, cardiovascular disorders including atherosclerosis, cerebral hemorrhage, stroke and myocardial infarction, arthritis, rheumatoid arthritis, psoriatic arthritis and juvenile rheumatoid arthritis (JRA), osteoporosis, osteoarthritis, pancreatitis, fibrosis, encephalitis, psoriasis, Giant cell arteritis, ankylosing spondolytis, autoimmune hepatitis, human immunodeficiency virus (HIV), inflammatory skin conditions, transplant, cancer, allergies, endocrine diseases, wound repair, other autoimmune disorders, airway hyperresponsiveness and cell, virus, or prion-mediated infections or disorders.
Arthritis, including osteoarthritis, rheumatoid arthritis, arthritic joints as a result of injury, and the like, are common inflammatory conditions which would benefit from the therapeutic use of anti-inflammatory proteins, such as the antagonists of the present invention. For example, rheumatoid arthritis (RA) is a systemic disease that affects the entire body and is one of the most common forms of arthritis. Since rheumatoid arthritis results in tissue damage, TLR3 ligands could be present at the site of the inflammation. Activation of TLR3 signaling may perpetuate inflammation and further tissue damage in the inflamed joint. Several animal models for rheumatoid arthritis are known in the art. For example, in the collagen-induced arthritis (CIA) model, mice develop chronic inflammatory arthritis that closely resembles human rheumatoid arthritis. Administration of the TLR3 antagonists of the present invention to the CIA model mice can be used to evaluate the use of these antagonists to ameliorate symptoms and alter the course of diseases.
Diabetes mellitus, diabetes, refers to a disease process derived from multiple causative factors and characterized by hyperglycemia (LeRoith et al., (eds.), Diabetes Mellitus, Lippincott-Raven Publishers, Philadelphia, Pa. U.S.A. 1996), and all references cited therein. Uncontrolled hyperglycemia is associated with increased and premature mortality due to an increased risk for microvascular and macrovascular diseases, including nephropathy, neuropathy, retinopathy, hypertension, cerebrovascular disease and coronary heart disease. Therefore, control of glucose homeostasis is a critically important approach for the treatment of diabetes.
Underlying defects lead to a classification of diabetes into two major groups: type I diabetes (insulin dependent diabetes mellitus, IDDM), which arises when patients lack insulin-producing beta-cells in their pancreatic glands, and type 2 diabetes (non-insulin dependent diabetes mellitus, NIDDM), which occurs in patients with an impaired beta-cell insulin secretion and/or resistance to insulin action.
Type 2 diabetes is characterized by insulin resistance accompanied by relative, rather than absolute, insulin deficiency. In insulin resistant individuals, the body secretes abnormally high amounts of insulin to compensate for this defect. When inadequate amounts of insulin are present to compensate for insulin resistance and adequately control glucose, a state of impaired glucose tolerance develops. In a significant number of individuals, insulin secretion declines further and the plasma glucose level rises, resulting in the clinical state of diabetes. Adipocity-associated inflammation has been strongly implicated in the development of insulin resistance, type 2 diabetes, dyslipidemia and cardiovascular disease. Obese adipose recruits and retains macrophages and can produce excessive pro-inflammatory cytokines including TNF-α and IL-6, free fatty acids and adipokines, which can interfere with insulin signaling and induce insulin resistance. TLR3 activation on macrophages may contribute to the pro-inflammatory status of the adipose. Several animal modes of insulin resistance are known. For example, in a diet-induced obesity model (DIO) animals develop hyperglycemia and insulin resistance accompanied by weight gain. Administration of TLR3 antagonists of the present invention to the DIO model can be used to evaluate the use of the antagonists to ameliorate complications associated with type 2 diabetes and alter the course of the disease.
Exemplary cancers may include at least one malignant disease in a cell, tissue, organ, animal or patient, including, but not limited to leukemia, acute leukemia, acute lymphoblastic leukemia (ALL), B-cell or T-cell ALL, acute myeloid leukemia (AML), chronic myelocytic leukemia (CML), chronic lymphocytic leukemia (CLL), hairy cell leukemia, myelodyplastic syndrome (MDS), a lymphoma, Hodgkin's disease, a malignant lymphoma, non-Hodgkin's lymphoma, Burkitt's lymphoma, multiple myeloma, Kaposi's sarcoma, colorectal carcinoma, pancreatic carcinoma, renal cell carcinoma, breast cancer, nasopharyngeal carcinoma, malignant histiocytosis, paraneoplastic syndrome/hypercalcemia of malignancy, solid tumors, adenocarcinomas, squamous cell carcinomas, sarcomas, malignant melanoma, particularly metastatic melanoma, hemangioma, metastatic disease, cancer related bone resorption and cancer related bone pain.
Exemplary cardiovascular diseases may include cardiovascular disease in a cell, tissue, organ, animal, or patient, including, but not limited to, cardiac stun syndrome, myocardial infarction, congestive heart failure, stroke, ischemic stroke, hemorrhage, arteriosclerosis, atherosclerosis, restenosis, diabetic atherosclerotic disease, hypertension, arterial hypertension, renovascular hypertension, syncope, shock, syphilis of the cardiovascular system, heart failure, cor pulmonale, primary pulmonary hypertension, cardiac arrhythmias, atrial ectopic beats, atrial flutter, atrial fibrillation (sustained or paroxysmal), post perfusion syndrome, cardiopulmonary bypass inflammation response, chaotic or multifocal atrial tachycardia, regular narrow QRS tachycardia, specific arrhythmias, ventricular fibrillation, His bundle arrhythmias, atrioventricular block, bundle branch block, myocardial ischemic disorders, coronary artery disease, angina pectoris, myocardial infarction, cardiomyopathy, dilated congestive cardiomyopathy, restrictive cardiomyopathy, valvular heart diseases, endocarditis, pericardial disease, cardiac tumors, aortic and peripheral aneurysms, aortic dissection, inflammation of the aorta, occlusion of the abdominal aorta and its branches, peripheral vascular disorders, occlusive arterial disorders, peripheral atherosclerotic disease, thromboangiitis obliterans, functional peripheral arterial disorders, Raynaud's phenomenon and disease, acrocyanosis, erythromelalgia, venous diseases, venous thrombosis, varicose veins, arteriovenous fistula, lymphederma, lipedema, unstable angina, reperfusion injury, post pump syndrome and ischemia-reperfusion injury.
Exemplary neurological diseases may include neurologic disease in a cell, tissue, organ, animal or patient, including, but not limited to neurodegenerative diseases, multiple sclerosis, migraine headache, AIDS dementia complex, demyelinating diseases, such as multiple sclerosis and acute transverse myelitis; extrapyramidal and cerebellar disorders such as lesions of the corticospinal system; disorders of the basal ganglia or cerebellar disorders; hyperkinetic movement disorders such as Huntington's Chorea and senile chorea; drug-induced movement disorders, such as those induced by drugs which block CNS dopamine receptors; hypokinetic movement disorders, such as Parkinson's disease; Progressive supranucleo Palsy; structural lesions of the cerebellum; spinocerebellar degenerations, such as spinal ataxia, Friedreich's ataxia, cerebellar cortical degenerations, multiple systems degenerations (Mencel, Dejerine-Thomas, Shi-Drager, and Machado-Joseph); systemic disorders (Refsum's disease, abetalipoprotemia, ataxia, telangiectasia, and mitochondrial multisystem disorder); demyelinating core disorders, such as multiple sclerosis, acute transverse myelitis; and disorders of the motor unit such as neurogenic muscular atrophies (anterior horn cell degeneration, such as amyotrophic lateral sclerosis, infantile spinal muscular atrophy and juvenile spinal muscular atrophy); Alzheimer's disease; Down's Syndrome in middle age; Diffuse Lewy body disease; Senile Dementia of Lewy body type; Wernicke-Korsakoff syndrome; chronic alcoholism; Creutzfeldt-Jakob disease; Subacute sclerosing panencephalitis, Hallerrorden-Spatz disease and Dementia pugilistica.
Exemplary fibrotic conditions may include liver fibrosis (including but not limited to alcohol-induced cirrhosis, viral-induced cirrhosis, autoimmune-induced hepatitis); lung fibrosis (including but not limited to scleroderma, idiopathic pulmonary fibrosis); kidney fibrosis (including but not limited to scleroderma, diabetic nephritis, glomerular nehpritis, lupus nephritis); dermal fibrosis (including but not limited to scleroderma, hypertrophic and keloid scarring, burns); myelofibrosis; neurofibromatosis; fibroma; intestinal fibrosis; and fibrotic adhesions resulting from surgical procedures. In such a method, the fibrosis can be organ specific fibrosis or systemic fibrosis. The organ specific fibrosis can be associated with at least one of lung fibrosis, liver fibrosis, kidney fibrosis, heart fibrosis, vascular fibrosis, skin fibrosis, eye fibrosis, bone marrow fibrosis or other fibrosis. The lung fibrosis can be associated with at least one of idiopathic pulmonary fibrosis, drug induced pulmonary fibrosis, asthma, sarcoidosis or chronic obstructive pulmonary disease. The liver fibrosis can be associated with at least one of cirrhosis, schistomasomiasis or cholangitis. The cirrhosis can be selected from alcoholic cirrhosis, post-hepatitis C cirrhosis, primary biliary cirrhosis. The cholangitis is sclerosing cholangitis. The kidney fibrosis can be associated with diabetic nephropathy or lupus glomeruloschelerosis. The heart fibrosis can be associated with myocardial infarction. The vascular fibrosis can be associated with postangioplasty arterial restenosis or atherosclerosis. The skin fibrosis can be associated with burn scarring, hypertrophic scarring, keloid, or nephrogenic fibrosing dermatopathy. The eye fibrosis can be associated with retro-orbital fibrosis, postcataract surgery or proliferative vitreoretinopathy. The bone marrow fibrosis can be associated with idiopathic myelofibrosis or drug induced myelofibrosis. The other fibrosis can be selected from Peyronie's disease, Dupuytren's contracture or dermatomyositis. The systemic fibrosis can be systemic sclerosis or graft versus host disease.
Administration/Pharmaceutical Compositions
The “therapeutically effective amount” of the agent effective in the treatment or prevention of conditions where suppression of TLR3 activity is desirable can be determined by standard research techniques. For example, the dosage of the agent that will be effective in the treatment or prevention of inflammatory condition such as asthma, Crohn's Disease, ulcerative colitis or rheumatoid arthritis can be determined by administering the agent to relevant animal models, such as the models described herein.
In addition, in vitro assays can optionally be employed to help identify optimal dosage ranges. Selection of a particular effective dose can be determined (e.g., via clinical trials) by those skilled in the art based upon the consideration of several factors. Such factors include the disease to be treated or prevented, the symptoms involved, the patient's body mass, the patient's immune status and other factors known by the skilled artisan. The precise dose to be employed in the formulation will also depend on the route of administration, and the severity of disease, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.
In the methods of the invention, the TLR3 antagonist may be administered singly or in combination with at least one other molecule. Such additional molecules may be other TLR3 antagonist molecules or molecules with a therapeutic benefit not mediated by TLR3 receptor signaling. Antibiotics, antivirals, palliatives and other compounds that reduce cytokine levels or activity are examples of such additional molecules.
The mode of administration for therapeutic use of the agent of the invention may be any suitable route that delivers the agent to the host. Pharmaceutical compositions of these agents are particularly useful for parenteral administration, e.g., intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous or intranasal.
The agent of the invention may be prepared as pharmaceutical compositions containing an effective amount of the agent as an active ingredient in a pharmaceutically acceptable carrier. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the active compound is administered. Such pharmaceutical vehicles can be liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. For example, 0.4% saline and 0.3% glycine can be used. These solutions are sterile and generally free of particulate matter. They may be sterilized by conventional, well-known sterilization techniques (e.g., filtration). The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, stabilizing, thickening, lubricating and coloring agents, etc. The concentration of the agent of the invention in such pharmaceutical formulation can vary widely, i.e., from less than about 0.5%, usually at or at least about 1% to as much as 15 or 20% by weight and will be selected primarily based on required dose, fluid volumes, viscosities, etc., according to the particular mode of administration selected.
Thus, a pharmaceutical composition of the invention for intramuscular injection could be prepared to contain 1 ml sterile buffered water, and between about 1 ng to about 100 mg, e.g. about 50 ng to about 30 mg or more preferably, about 5 mg to about 25 mg, of a TLR3 antibody antagonist of the invention. Similarly, a pharmaceutical composition of the invention for intravenous infusion could be made up to contain about 250 ml of sterile Ringer's solution, and about 1 mg to about 30 mg and preferably 5 mg to about 25 mg of an antagonist of the invention. Actual methods for preparing parenterally administrable compositions are well known and are described in more detail in, for example, “Remington's Pharmaceutical Science”, 15th ed., Mack Publishing Company, Easton, Pa.
The antibody antagonists of the invention can be lyophilized for storage and reconstituted in a suitable carrier prior to use. This technique has been shown to be effective with conventional immunoglobulins and protein preparations and art-known lyophilization and reconstitution techniques can be employed.
The present invention will now be described with reference to the following specific, non-limiting examples.
Example 1
Identification and Derivation of Anti-huTLR3 Antagonist mAbs
The MorphoSys Human Combinatorial Antibody Library (HuCAL®) Gold phage display library (Morphosys AG, Martinsried, Germany) was used as a source of human antibody fragments and was panned against a purified TLR3 antigen generated from the expression of amino acids 1-703 of human TLR3 (huTLR3) (SEQ ID NO: 4) with a C-terminal poly-histidine tag and purified by immobilized metal affinity chromatography. Amino acids 1-703 correspond to the predicted extracellular domain (ECD) of huTLR3. Fab fragments (Fabs) that bound specifically to huTRL3 ECD were selected by presenting the TLR3 protein in a variety of ways so that a diverse set of antibody fragments could be identified, sequenced and confirmed as unique. From different panning strategies, 62 candidates (different V-region sequences) were identified as unique hTLR3 ECD binders.
The 62 candidates identified as huTLR3 ECD binders were screened for neutralizing activity in a range of cell-based assays relevant to identifying anti-inflammatory activity. Using preliminary activity data (see Example 2 below), four candidates (Fabs 16-19) defining families 16-19 were selected from the 62 as parents for CDR maturation of heavy chain CDR2 (HCDR2) and light chain CDR3 (LCDR3). One of the parental candidates (candidate 19) exhibited an N-linked glycosylation site in HCDR2; a Ser to Ala (S to A) mutation was made in this candidate to delete the site. Following CDR maturation of the four parental candidates, a total of 15 progeny candidates (candidates 1-15) were identified for further characterization as described in Example 2 below. A listing of the light and heavy chain variable regions present in each of the 19 candidates is shown in Table 3 above. The candidates are herein referred to as mAbs 1-19 or Fabs 1-19, depending whether they were Fabs or cloned as full length antibody chains (Example 3). Due to expression vector design, the mature amino termini of the variable regions for all candidates were QVE for heavy chain and DI for the light chain. The preferred sequences at these termini are those in the respective germline genes with high identity to the candidate sequences. For families 17 and 18 the germline sequences are QVQ for VH and SY for VL. For family 19, the sequences are EVQ for VH and DI for VL. The SY sequence is unique to the lambda subgroup 3 and there are reports of heterogeneity with either S or Y as the amino terminal residue. Thus, the QSV consensus terminus from the prominent lambda subgroup 1 was considered a more suitable replacement for DIE for VL of families 17 and 18. These changes were introduced into candidates 9, 10 and 12 from family 18 and candidates 14 and 15 from family 19. In this process, both the VH and VL regions of these antibodies were codon optimized. The amino acid sequences of the light chain variable region N-terminal germline variants of candidates 9, 10 and 11 are shown in SEQ ID NO:s 209-211, and the amino acid sequences of the heavy chain variable region N-terminal germline variants for candidates 9, 10, 12, 14, and 15 are shown in SEQ ID NO:s 212-216, respectively. The N-terminal variants of the candidates are herein referred to as candidate/mAb/Fab 9QVQ/QSV, 10QVQ/QSV, 12QVQ/QSV, 14EVQ or 15EVQ. The N-terminal germline variants were expressed as mAbs and showed no effect on binding to TLR3 or in their ability to inhibit TLR3 biological activity when compared to their parent counterparts (data not shown).
Example 2
Determination of TLR3 Antagonist Activity In Vitro
The 15 CDR-matured candidates described above were selected as potential human therapeutics and a range of binding and neutralizing activities were determined. The activity assays and results for the four parental Fabs, Fabs 16-19 and 15 CDR-matured Fabs, Fabs 1-15 or their non-germline V-region variants are described below.
Inhibition of NF-κB and ISRE Signaling Cascasde
293T cells were grown in DMEM and GlutaMax media (Invitrogen, Carlsbad, Calif.) supplemented with heat-inactivated FBS and transfected with 30 ng pNF-κB or ISRE firefly luciferase reporter plasmids, 13.5 ng pcDNA3.1 vector, 5 ng phRL-TK, and 1.5 ng pcDNA encoding FL TLR3 (SEQ ID NO: 2). The phRL-TK plasmid contains the Renilla luciferase gene driven by the HSV-1 thymidine kinase promoter (Promega, Madion, Wis.). TLR3 antibodies were incubated 30-60 min. before addition of poly(I:C) (GE Healthcare, Piscataway, N.J.). The plates were incubated 6 h or 24 h at 37° C. before the addition of the Dual-Glo luciferase reagent, and the plates were read on a FLUOstar plate reader. Normalized values (luciferase ratios) were obtained by dividing the firefly RLUs by the Renilla RLUs. Upon stimulation with the TLR3 agonist poly (I:C) (1 μg/ml), the NF-κB or ISRE signaling cascade stimulated firefly luciferase production was specifically inhibited by incubation of the cells with anti-TLR3 antibodies (0.4, 2.0 and 10 μg/ml) prior to stimulation. The results for the NF-κB assays are shown in FIG. 1 and are expressed as % inhibition of the Firefly/Renilla ratio with 5465 as the positive control (neutralizing anti-human TLR3 Mab) and an anti-human tissue factor mAb (859) as the human IgG4 isotype control. >50% inhibition was achieved with mAb concentrations 0.4-10 μg/ml. c1068 and TLR3.7 inhibited about 38% and 8% of TLR3 biological activity at 10 μg/ml. Similar results were obtained with the ISRE reporter gene assay (data not shown).
Cytokine Release in BEAS-2B Cells
BEAS-2B cells (SV-40 transformed normal human bronchial epithelial cell line) were seeded in a collagen type I coated dishes and incubated with or without anti-human TLR3 antibodies prior to addition of poly (I:C). Twenty-four hours after treatments, supernatants were collected and assayed for cytokine and chemokine levels using a custom multi-plex bead assay for detection of IL-6, IL-8, CCL-2/MCP-1, CCL5/RANTES, and CXCL10/IP-10. Results are shown in FIG. 2 as % inhibition of the individual cytokine/chemokine following mAb treatment at 0.4, 2.0 and 10 μg/ml. 5465 is a positive control; 859 is an isotype control.
Cytokine Release in NHBE Cells
Cytokine release was also assayed in normal human bronchial epithelial (NHBE) cells (Lonza, Walkersville, Md.). NHBE cells were expanded and transferred to collagen-coated dishes and incubated for 48 hours after which the media was removed and replenished with 0.2 ml of fresh media. The cells were then incubated with or without anti-human TLR3 mAbs 60 minutes prior to the addition of poly (I:C). Supernatants were collected after 24 hours and stored at −20° C. or assayed immediately for IL-6 levels. Results are graphed in FIG. 3 as % inhibition of IL-6 secretion following mAb treatment using doses between 0.001 and 50 μg/ml. 5465 is a positive control, 859 is an isotype control. Most mAbs inhibited at least 50% of IL-6 production at <1 μg/ml, and achieved 75% inhibition at <5 μg/ml.
Cytokine Release in PBMC Cells
Cytokine release was also assayed in human peripheral blood mononuclear cells (PBMC). Whole blood was collected from human donors into heparin collection tubes to which a Ficoll-Paque Plus solution was slowly layered underneath. The tubes were centrifuged and the PBMCs, that formed a white layer just above the Ficoll, were recovered and plated. The PBMCs were then incubated with or without anti-human TLR3 mAbs prior to the addition of 25 μg/ml poly(I:C). After 24 hrs, supernatants were collected and cytokine levels were determined using Luminex technology. Results are graphed in FIG. 4 as cumulative percentage inhibition of IFN-γ, IL-12 and IL-6 using a single dose of mAb (0.4 μg/ml) with 5465 is a positive control; hIgG4 is an isotype control.
Cytokine Release in HASM Cells
Briefly, human airway smooth muscle (HASM) cells were incubated with or without anti-human TLR3 mAbs prior to the addition of a synergistic combination of 500 ng/ml poly(I:C) and 10 ng/ml TNF-α. After 24 hrs, supernatants were collected and cytokine levels were determined using Luminex technology. Results are graphed in FIG. 5 as levels of the chemokine CCL5/RANTES using three doses of mAb (0.4, 2 and 10 μg/ml). 5465 is a positive control; hIgG4 is an isotype control.
The results from the in vitro assays in human cells confirm the ability of the antibodies of the invention to reduce cytokine and chemokines release as a result of binding to huTLR3.
Example 3
Full-length Antibody Constructs
The four parental Fabs (candidate nos. 16-19) and 15 progeny Fabs (candidate nos. 1-15) heavy chains were cloned onto a human IgG4 background with a S229P Fc mutation. Candidates 9QVQ/QSV, 10QVQ/QSV, 12QVQ/QSV, 14EVQ or 15EVQ were cloned onto a human IgG4 background with F235A/L236A and S229P Fc mutations.
The mature full-length heavy chain amino acid sequences are shown in SEQ ID NOs: 90-102 and 218-220 as follows:













Candidate
SEQ ID NO:


















16
90



17
91



18
92



19
93



 1
94



 2
95



 3
96



 4
97



5, 6, 7
98



 8
99



 9
100



10, 11, 12
101



13, 14, 15
102



9EVQ
218



10EVQ, 12EVQ
219



14EVQ, 15EVQ
220









For expression, these heavy chain sequences can include an N-terminal leader sequence such as MAWVWTLLFLMAAAQSIQA (SEQ ID NO: 103). Exemplary nucleotide sequences encoding the heavy chain of candidates 14EVQ and 15EVQ with a leader sequence and the mature form (without a leader sequence) are shown in SEQ ID NOs: 104 and 105, respectively. Likewise, for expression, the light chain sequences of the antibodies of the invention can include an N-terminal leader sequence such as MGVPTQVLGLLLLWLTDARC (SEQ ID NO: 106). Exemplary nucleotide sequences encoding the light chain of codon optimized candidate 15 with a leader sequence and the mature form (without a leader sequence) are shown in SEQ ID NOs: 107 and 108, respectively.
Example 4
Characterization of Anti-TLR3 mAb binding
EC50 values for the binding of the mAbs to human TLR3 extracellular domain (ECD) were determined by ELISA. Human TLR3 ECD protein was diluted to 2 μg/ml in PBS and 100 μl aliquots were dispensed to each well of a 96-well plate (Corning Inc., Acton, Mass.). After overnight incubation at 4° C., the plate was washed 3 times in wash buffer consisting of 0.05% Tween-20 (Sigma-Aldrich) in PBS. The wells were blocked with 200 μl blocking solution consisting of 2% I-Block (Applied Biosystems, Foster City, Calif.) and 0.05% Tween-20 in PBS. After blocking for 2 hours at room temperature the plate was washed 3 times followed by addition of serial dilutions of the anti-TLR3 mAb candidates 1 to 19 in blocking buffer. The anti-TLR3 mAbs were incubated for 2 hours at room temperature and washed 3 times. This was followed by addition of a peroxidase-conjugated sheep anti-human IgG (GE Healthcare, Piscataway, N.J.) diluted 1:4000 in blocking buffer, incubated for 1 hour at room temperature followed by 3 washes in wash buffer. Binding was detected by 10-15 minute incubation in TMB-S (Fitzgerald Industries International, Inc., Concord, Mass.). The reaction was stopped with 25 μl 2N H2SO4 and absorbance read at 450 nm with subtraction at 650 nm using a SPECTRA Max spectrophotometer (Molecular Devices Corp., Sunnyvale, Calif.). EC50 values were determined by non-linear regression using GraphPad Prism software (GraphPad Software, Inc., San Diego, Calif.).
EC50 values were determined for binding to huTLR3 (Table 4) by incubating with 100 μl of 4-fold serial dilutions of mAbs from 2.5 μg/ml to 0.6 pg/ml. An anti-human tissue factor mAb 859 and hu IgG4κ were included as negative controls.









TABLE 4






Candidate no.
EC50 (ng/ml)


















1
17.18



2
53.12



3
23.42



4
12.77



5
19.94



6
19



7
16.13



8
18.58



9
22.61



10
15.84



11
26.33



12
25.59



13
23.51



14
33.59



15
32.64



16
43.66



17
13.8



18
9.68



19
66.54









Binding affinity for huTLR3 ECD was also determined by Biacore analysis. The data (not shown) indicated that the mAbs 1-19 had a Kd for huTLR3 ECD of less than 10−8 M.
Example 5
Competitive Epitope Binding
Epitope binding experiments were performed to determine the anti-TLR3 antibody competition groups or “epitope bins”.
For competitive ELISA, 5 μl (20 μg/ml) of purified human TLR3 ECD protein generated as described in Example 1 was coated on MSD HighBind plate (Meso Scale Discovery, Gaithersburg, Md.) per well for 2 hr at room temperature. 150 μl of 5% MSD Blocker A buffer (Meso Scale Discovery) was added to each well and incubated for 2 hr at room temperature. Plates were washed three times with 0.1 M HEPES buffer, pH 7.4, followed by the addition of the mixture of labeled anti-TLR3 mAb with different competitors. Labeled antibodies (10 nM) were incubated with increasing concentrations (1 nM to 2 μM) of unlabeled anti-TLR3 antibodies, and then added to the designated wells in a volume of 25 μl mixture. After 2-hour incubation with gentle shaking at room temperature, plates were washed 3 times with 0.1 M HEPES buffer (pH 7.4). MSD Read Buffer T was diluted with distilled water (4-fold) and dispensed at a volume of 150 μl/well and analyzed with a SECTOR Imager 6000. Antibodies were labeled with MSD Sulfo-TagTM NHS-ester according to manufacturer's instructions (Meso Scale Discovery).
The following anti-TLR3 antibodies were evaluated: mAbs 1-19 obtained from MorphoSys Human Combinatorial Antibody Library (shown in Table 3a); c1068 (described in WO06/060513A2), c1811 (rat anti-mouse TLR3 mAb produced by a hybridoma generated from rats immunized with mouse TLR3 protein), TLR3.7 (eBiosciences, San Diego, Calif., cat no 14-9039) and IMG-315A (generated against human TLR3 amino acids amino acids 55-70 (VLNLTHNQLRRLPAAN) (residues 55-70 of SEQ ID NO: 2) from Imgenex, San Diego, Calif.). For mAbs 9, 10, 12, 14 and 15, variants 9QVQ/QSV, 10QVQ/QSV, 12QVQ/QSV, 14EVQ or 15EVQ were used in this study.
Based on competiton assays, anti-TLR3 antibodies were assigned to five distinct bins. Bin A: mAbs 1, 2, 13, 14EVQ, 15EVQ, 16, 19; Bin B: mAbs 3, 4, 5, 6, 7, 8, 9QVQ/QSV, 10QVQ/QSV, 11, 12QVQ/QSV, 17, 18; Bin C: antibody Imgenex IMG-315A; Bin D: antibodies TLR3.7, c1068; and Bin E: antibody c1811.
Example 6
Epitope Mapping
Representative antibodies from distinct epitope bins as described in Example 5 were selected for further epitope mapping. Epitope mapping was performed using various approaches, including TLR3 segment swapping experiments, mutagenesis, H/D exchange and in silico protein-protein docking (The Epitope Mapping Protocols, Methods in Molecular Biology, Volume 6, Glen E. Morris ed., 1996).
TLR3 Segment Swapping.
TLR3 human-mouse chimeric proteins were used to locate gross antibody binding domains on TLR3. The human TLR3 protein extracellular domain was divided into three segments (aa 1-209, aa 210-436, aa 437-708 according to amino acid numbering based on human TLR3 amino acid sequence, GenBank Acc. No. NP—003256). MT5420 chimeric protein was generated by replacing human TLR3 amino acids 210-436 and 437-708 by corresponding mouse amino acids (mouse TLR3, GenBank Acc. No. NP—569054, amino acids 211-437 and 438-709). The MT6251 chimera was generated by replacing human amino acids at positions 437-708 by mouse TLR3 amino acids (mouse TLR3, GenBank Acc. No. NP—569054, amino acids 438-709). All constructs were generated in the pCEP4 vector (Life Technologies, Carslbad, Calif.) using standard cloning procedures. The proteins were transiently expressed in HEK293 cells as V5-His6 C-terminal fusion proteins, and purified as described in Example 1.
mAb c1068.
mAb c1068 bound human TLR3 ECD with high affinity but did not bind well to murine TLR3. c1068 lost its ability to bind to both MT5420 and MT6251, demonstrating that the binding site was located within the amino acids 437-708 of the WT human TLR3 protein.
mAb 12QVQ/QSV.
mAb 12QVQ/QSV bound both chimeras, indicating that the binding site for mAb 12QVQ/QSV was located within the amino acids 1-209 of the human TLR3 protein having a sequence shown in SEQ ID NO:2.
In Silico Protein-Protein Docking.
The crystal structure of mAb 15EVQ (see below) and the published human TLR3 structure (Bell et al., J. Endotoxin Res. 12:375-378, 2006) were energy minimized in CHARMm (Brooks et al., J. Computat. Chem. 4:187-217, 1983) for use as the starting models for docking. Protein docking was carried out with ZDOCKpro 1.0 (Accelrys, San Diego, Calif.), which is equivalent to ZDOCK 2.1 (Chen and Weng, Proteins 51: 397-408, 2003) with an angular grid of 6 degrees. Known N-linked glycosylation site Asn residues in human TLR3 (Asn 52, 70, 196, 252, 265, 275, 291, 398, 413, 507 and 636) (Sun et al., J. Biol. Chem. 281:11144-11151, 2006) were blocked from participating in the antibody-antigen complex interface by an energy term in the ZDOCK algorithm. 2000 initial poses were output and clustered and the docking poses were refined and rescored in RDOCK (Li et al., Proteins 53:693-707, 2003). The 200 poses with the highest initial ZDOCK scores and 200 top RDOCK poses were visually inspected.
Crystallization of mAb 15EVQ was carried out by the vapor-diffusion method at 20° C. (Benvenuti and Mangani, Nature Protocols 2:1633-51, 2007). The initial screening was set up using a Hydra robot in 96-well plates. The experiments were composed of droplets of 0.5 μl of protein solution mixed with 0.5 μl of reservoir solution. The droplets were equilibrated against 90 μl of reservoir solution. The Fab solution in 20 mM Tris buffer, pH 7.4, containing 50 mM NaCl was concentrated to 14.3 mg/ml using Amicon Ultra-5 kDa cells. The screening was performed with the Wizard I & II (Emerald BioSystems, Bainbridge Island, Wash.) and in-house crystallization screens.
X-ray diffraction data were collected and processed using the Rigaku MicroMaxTM-007HF microfocus X-ray generator equipped with an OsmicTM VariMaxTM confocal optics, Saturn 944 CCD detector, and an X-streamTM 2000 cryocooling system (Rigaku, Woodlands, Tex.). Diffraction intensities were detected over a 270° crystal rotation with the exposure time of 120 s per half-degree image. The X-ray data were processed with the program D*TREK (Rigaku). The structure was determined by the molecular replacement method using the program Phaser or CNX (Accelrys, San Diego, Calif.). Atomic positions and temperature factors were refined with REFMAC using all data in the resolution range 15-2.2 Å for mAb 15 and 50-1.9 Å for mAb 12. Water molecules were added at the (Fo-Fc) electron density peaks using the cut-off level of 3σ. All crystallographic calculations were performed with the CCP4 suite of programs (Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50:760-763). Model adjustments were carried out using the program COOT (Emsley et al., Acta Crystallogr. D60:2126-2132, 2004).
The resolved crystal structure of mAb 15EVQ showed that the antibody combining site was characterized by a number of negatively charged residues in the heavy chain (D52, D55, E99, D106 and D109). Thus, recognition between mAb 15EVQ and TLR3 most likely involved positively charged residues. The protein-protein docking simulations performed suggested that two large patches on TLR3 involving multiple positive charge residues showed good complementarity to the antibody. The residues on TLR3 in the interface of the TLR3—anti-TLR3 antibody simulated complexes were R64, K182, K416, K467, Y468, R488, R489 and K493.
Mutagenesis Studies.
Single and combination point mutations were introduced into surface residues of TLR3 ECD in the regions identified above to contain the epitopes of mAb 12 and mAb 15EVQ and the mutant proteins were tested for antibody binding.
The nucleotide sequence encoding human TLR3 amino acids 1-703 (the ECD), (SEQ ID NO: 4; GenBank accession number NP—003256), was cloned using standard protocols. All mutants were generated by site directed mutagenesis using the Strategene Quickchange II XL kit (Stratagene, San Diego, Calif.) according to the manufacturer's protocol, using the oligonucleotides shown in Table 5a. Mutations were verified by DNA sequencing. The proteins were expressed under a CMV promoter as C-terminal His-tag fusions in HEK293 cells, and purified as described in Example 1.
Table 5a. Oligonucleotides Used for Site-Directed Mutagenesis.
Sequences of the sense oligonucleiotides are shown. The anti-sense oligonucleotides with complementary sequences were used in the mutagenesis reaction.














SeqID


Variant
Oligo
NO:







R64E
5′ CCTTACCCATAATCAACTCGAGAGATTACCAGCCGCCAAC 3′
136


 


K182E
5′CAAGAGCTTCTATTATCAAACAATGAGATTCAAGCGCTAAAAAGTGAAG 3′
137


 


K416E
5′ CCTTACACATACTCAACCTAACCGAGAATAAAATCTCAAAAATAG 3′
138


 


K467E/Y468A
5′ GAAATCTATCTTTCCTACAACGAGGCCCTGCAGCTGACTAGGAACTC 3′
139


 


R488/R489/K493E
5′ GCCTTCAACGACTGATGCTCGAGGAGGTGGCCCTTGAGAATGTGGATAGCTCTCCTTC 3′
140


 


T472S/R473T/N474S
5′ GTACCTGCAGCTGTCTACGAGCTCCTTTGCCTTGGTCCC 3′
141


 


N196A
5′ GAAGAACTGGATATCTTTGCCGCTTCATCTTTAAAAAAATTAGAGTTG 3′
169


 


Q167A
5′ GTCATCTACAAAATTAGGAACTGCGGTTCAGCTGGAAAATCTCC 3′
170


 


K163E
5′ CTCATAATGGCTTGTCATCTACAGAATTAGGAACTCAGGTTCAGC 3′
171


 


K147E
5′ GAAAATTAAAAATAATCCCTTTGTCAAGCAGGAGAATTTAATCACATTAGATCTGTC 3′
172


 


K145E
5′ GAAAATTAAAAATAATCCCTTTGTCGAGCAGAAGAATTTAATCACATTAG 3′
173


 


V144A
5′ CAGAAAATTAAAAATAATCCCTTTGCAAAGCAGAAGAATTTAATCACATTAG 3′
174


 


N140A
5′ CCAACTCAATCCAGAAAATTAAAGCTAATCCCTTTGTCAAGCAGAAG 3′
175


 


D116R
5′ CAATGAGCTATCTCAACTTTCTCGTAAAACCTTTGCCTTCTGCAC 3′
176


 


D536K
5′ GTCTTGAGAAACTAGAAATTCTCAAGTTGCAGCATAACAACTTAGCAC 3′
177


 


D536A
5′ CTTGAGAAACTAGAAATTCTCGCATTGCAGCATAACAACTTAGCAC 3′
178


 


K619E
5′ CTAAAGTCATTGAACCTTCAGGAGAATCTCATAACATCCGTTG 3′
179


 


K619A
5′ CTCTAAAGTCATTGAACCTTCAGGCGAATCTCATAACATCCGTTGAG 3′
180


 


E570R
5′ CCACATCCTTAACTTGAGGTCCAACGGCTTTGACGAG 3′
181


 


N541A
5′ GAAATTCTCGATTTGCAGCATAACGCCTTAGCACGGCTCTGGAAAC 3′
182


 


Q538A
5′ GAGAAACTAGAAATTCTCGATTTGGCGCATAACAACTTAGCACGGC 3′
183


 


H539E
5′ CTAGAAATTCTCGATTTGCAGGAAAACAACTTAGCACGGCTCTG 3′
184


 


H539A
5′ CTAGAAATTCTCGATTTGCAGGCTAACAACTTAGCACGGCTCTG 3′
185


 


N517A
5′ CATTCTGGATCTAAGCAACAACGCCATAGCCAACATAAATGATGAC 3′
186


 


Y465A
5′ GAAAATATTTTCGAAATCTATCTTTCCGCCAACAAGTACCTGCAGCTGAC 3′
187


 


R488E
5′ GCCTTCAACGACTGATGCTCGAAAGGGTGGCCCTTAAAAATG 3′
188


 


R489E
5′ CTTCAACGACTGATGCTCCGAGAGGTGGCCCTTAAAAATGTGG 3′
189


 


K467E
5′ CGAAATCTATCTTTCCTACAACGAGTACCTGCAGCTGACTAG 3′
190









Binding Assays.
The binding activity of mAb 12QVQ/QSV and mAb 15EVQ to human TLR3 and generated variants was evaluated by ELISA. To expedite the process, mutants in the predicted mAb 15EVQ binding site were co-expressed in HEK cells by co-transfection of TLR3 ECD mutant containing a C-terminal His tag with mAb 12QVQ/QSV, followed by purification by metal affinity chromatography. The recovered sample was a complex of the TLR3 mutant with mAb 12. This approach was feasible because the mAb 12QVQ/QSV and mAb 15EVQ binding sites are distant from one another; and thus, point mutations at one site are unlikely to affect the epitope at the other site. These complexes were used in the ELISA binding assays. 5 μl per well of 20 μg/ml wild type TLR3 ECD or mutant proteins in PBS were coated on an MSD HighBind plate (Meso Scale Discovery, Gaithersburg, Md.). The plates were incubated at room temperature for 60 min and blocked overnight in MSD Blocker A buffer (Meso Scale Discovery, Gaithersburg, Md.) at 4° C. The following day the plates were washed and the MSD Sulfo-tag labeled mAb 15EVQ added at concentrations from 500 pM to 1 pM for 1.5 hours. After washes the labeled antibody was detected using MSD Read Buffer T and the plates were read using a SECTOR Imager 6000. To evaluate the binding activity of mAb 12QVQ/QSV to human TLR3 and variants, co-expression was carried out with mAb 15EVQ and binding ELISAs were performed as described for mAb 15EVQ, except that the detecting antibody was labeled mAb 12QVQ/QSV.
mAb 12QVQ/QSV:
The binding site for mAb 12QVQ/QSV was located within the amino acids 1-209 of the human TLR3 protein as determined in the segment swap studies. The following TLR3 mutants were evaluated: D116R, N196A, N140A, V144A, K145E, K147E, K163E, and Q167A. The wild type TLR3 and V144A mutant showed comparable binding to mAb 12QVQ/QSV (FIG. 6A). The antibody did not bind to TLR3D116R mutant and had significantly reduced binding affinity to the K145E mutant. Thus, residues D116 and K145 which are closely apposed on the surface of TLR3 were identified as key epitope sites for mAb 12QVQ/QSV (FIG. 7A).
The two critical residues of the mAb 12QVQ/QSV binding epitope were located near the face of the dsRNA binding site at the N-terminal segment of the TLR3 ectodomain (Pirher, et al., Nature Struct. & Mol. Biol., 15:761-763, 2008). The complete epitope will contain other residues in the neighboring regions, which were not revealed by mutational analyses performed. Not wishing to be bound to any particular theory, it is believed that binding of mAb 12QVQ/QSV on its TLR3 epitope may directly or indirectly interfere with dsRNA binding on TLR3 ectodomain, thereby disrupting receptor dimerization and activation of downstream signaling pathways.
mAb 15EVQ:
The following TLR3 mutants were evaluated: R64E, K182E, K416E, Y465A, K467E, R488E, R489E, N517A, D536A, D536K, Q538A, H539A, H539E, N541A, E570R, K619A, K619E, a double mutant K467E/Y468A, a triple mutant T472S/R473T/N474S, and a triple mutant R488E/R489E/K493E. The wild type TLR3, the R64E, K182E, K416E mutants and the triple mutant T472S/R473T/N474S showed comparable binding to mAb 15EVQ (FIG. 6B and Table 5b). The antibody did not bind to TLR3 mutants K467E, R489E, K467E/Y468A and R488E/R489E/K493E (FIGS. 6B and 6C). The remaining variants showed intermediate binding with the R488E having the greatest effect. All of these mutants bound to mAb 12QVQ/QSV. These results showed that resides K467 and R489 were critical determinants of the mAb 15EVQ epitope. Residue R488 also contributed to the epitope. These residues were closely apposed on the same surface of TLR3 (FIG. 7A). The results also showed that residues Y465, Y468, N517, D536, Q538, H539, N541, E570, and K619, all on the same surface as K467, R488 and R489, contributed to the epitope. This conclusion was further supported by the H/D exchange studies with mAb 15EVQ. FIG. 7A shows binding epitope sites for mAbs 12QVQ/QSV and 15EVQ (black) and C1068 mAb (grey) superimposed on the structure of human TLR3. The epitope for mAb 15EVQ covers residues Y465, K467, Y468, R488, R489, N517, D536, Q538, H539, N541, E570, and K619.
H/D Exchange Studies.
For H/D exchange, the procedures used to analyze the antibody perturbation were similar to that described previously (Hamuro et al., J. Biomol. Techniques 14:171-182, 2003; Horn et al., Biochemistry 45:8488-8498, 2006) with some modifications. Recombinant TLR3 ECD (expressed from Sf9 cells with C-terminal His-tag and purified) was incubated in a deuterated water solution for predetermined times resulting in deuterium incorporation at exchangeable hydrogen atoms. The deuterated TLR3 ECD was captured on a column containing immobilized mAb 15EVQ and then washed with aqueous buffer. The back-exchanged TLR3 ECD protein was eluted from the column and localization of deuterium containing fragments was determined by protease digestion and mass spec analysis. As a reference control, TLR3 ECD sample was processed similarly except it was exposed to deuterated water only after capture on the antibody column and then washed and eluted in the same manner as the experimental sample. Regions bound to the antibody were inferred to be those sites relatively protected from exchange and thus contain a higher fraction of deuterium than the reference TLR3 ECD sample. About 80% of the protein could be mapped to specific peptides. Maps of H/D exchange perturbation of TLR3 ECD by mAb 15EVQ are shown in FIG. 7B. Only the segment of TLR3 around the portion affected by mAb 15EVQ is shown for clarity. The remainder of the protein extending to the amino and carboxyl termini of TLR3 ECD was not affected appreciably.
The H/D exchange studies identified peptide segments 465YNKYLQL471, 514SNNNIANINDDML526 and 529LEKL532 of SEQ ID NO: 2 as regions where exchange on TLR3 was particularly altered by binding to mAb 15EVQ. By its nature, H/D exchange is a linear mapping method and usually cannot define which residues within the peptide segment are most affected by antibody binding. However, the extensive overlap between the H/D exchange and mutational results gives added confidence that the surface shown in FIG. 7A is the binding site for mAb 15. This binding site was in same linear amino acid sequence region as previously described for mAb c1068 (PCT Publ. no. WO06/060513A2) but it was found to be located on a completely non-overlapping surface (FIG. 7A) in agreement with the lack of cross-competition between these antibodies.
The mAb 15EVQ binding epitope was spatially proximal to the dsRNA binding site at the C-terminal segment on TLR3 (Bell et al., Proc. Natl. Acad. Sci. (USA) 103: 8792-8797, 2006; Ranjith-Kumar et al., J Biol Chem, 282: 7668-7678, 2007; Liu et al., Science, 320: 379-381, 2008). Not wishing to be bound to any particular theory, it is believed that binding of mAb 15EVQ on its TLR3 epitope causes steric clashes with a ligand dsRNA molecule and/or the dimer partner, preventing ligand binding and ligand-induced receptor dimerization.











TABLE 5b






Variant
mAb 15
Variant
mAb 12








wt TLR3 ECD
+++
wt TLR3 ECD
+++



R64E
+++
D116R
−



K182E
+++
N140A
++



K416E
+++
V144A
+++



Y465A
++
K145E
+



K467E
−
K147E
++



R488E
+
K163E
++



R489E
−
Q167A
++



N517A
++
N196A
++



D536K
++





D536A
++





Q538A
++





H539E
++





H539A
++





N541A
++





E570R
++





K619E
++





K619A
++





K467E/Y468A
−





R488/R489/K493E
−





T472S/R473T/N474S
+++









Example 7
Generation of Variants with Enhanced Thermal Stability
Structure-based engineering was conducted to generate antibody variants with increased thermal stability, with simultaneous efforts to maintain the biological activity and minimize immunogenicity.
mAb 15EVQ was selected for engineering. To minimize immunogenicity, only germline mutations predicted to be beneficial based upon structural considerations were pursued. The VL and VH sequences of mAb 15EVQ (SEQ ID NO: 41 and SEQ ID NO: 216, respectively) were aligned with the human germline genes using BLAST searches. The closest germline sequences identified were GenBank Acc. No. AAC09093 and X59318 for VH and VL, respectively. The following differences were identified between the germline VH, VL and those of the mAb 15EVQ VH and VL sequences: (VH) V34I, G35S, F50R, A61S, and Q67H; (VL) G30S, L31S, and A34N. The identified sequence differences were mapped onto the crystal structure of the mAb 15EVQ, and residues predicted to alter packing and interface interactions were selected for engineering. Based upon the crystal structure of the antibody (see Example 6), potential structure destabilizing residues were identified. (1) A small enclosed cavity was identified in the core of VH near V34. This cavity was large enough to accommodate a slightly larger sidechain such as Ile. (2) E99 of VH CDR3 was buried at the VH/VL interface without a H-bonding network. The negatively charged carboxylate group of E99 was in a generally hydrophobic environment with mostly van der Waals (vdw) contacts to neighboring residues. Burying a charge group is usually energetically unfavorable and thus has destabilizing effect. (3) F50 of VH is a VH/VL interface residue. Its aromatic sidechain is bulky and thus may have negative impact upon the pairing. H-bonding and vdw packing networks for the Fv were calculated and visually inspected in Pymol (www://_pymol_org). Buried cavities in the VH and VL domains were computed by Caver (Petrek et al., BMC Bioinformatics, 7:316, 2006). All molecular graphics figures were prepared in Pymol. Mutations were made to the expression vectors encoding Fab fragments or IgG4 full human antibodies generated as described in Example 3 using standard cloning techniques using Quick Change II XL Site Directed Mutagenesis Kit (Stratagene, San Diego, Calif.), Change-IT Multiple Mutation Site Directed Mutagenesis Kit (USB Corporation, Cleveland, Ohio) or Quick Change II Site Directed Mutagenesis Kit (Stratagene, San Diego, Calif.). The reactions were performed according to each manufacturer's recommendations. The obtained clones were sequenced for verification, and the resulting engineered variants were named mAbs 15-1-15-9. A listing of the SEQ ID NOs: for the CDRs, variable regions of light and heavy chains and full length heavy and light chains for mAb 15EVQ and its engineered variants is shown in Table 6. Table 7 shows primers for generation of each variant.








TABLE 6








SEQ ID NO:

















Candidate








Heavy
Light


no:
HCDR1
HCDR2
HCDR3
LCDR1
LCDR2
LCDR3
LV
HV
IgG4
chain




















15  
111
112
84
109
110
113
41
216
220
156


15-1
111
114
84
109
110
113
41
124
130
156


15-2
115
112
84
109
110
113
41
125
131
156


15-3
116
112
84
109
110
113
41
126
132
156


15-4
111
117
84
109
110
113
41
127
133
156


15-5
116
118
84
109
110
113
41
128
134
156


15-6
116
112
119
109
110
113
41
129
135
156


15-7
111
112
84
120
110
113
122
42
102
157


15-8
111
112
84
121
110
113
123
42
102
158


15-9
116
118
119
109
110
113
41
159
160
156









Binding of mAbs 15-1-15-9 to TLR3 was evaluated by ELISA immunoassay. Human TLR3 ECD (100 μl of 2 μg/ml TLR3-ECD) was bound to a black Maxisorb plate (eBioscience) overnight at 4° C. The plates were washed and blocked, and diluted antibodies were aliquoted at 50 μl per well in duplicate onto the wells. The plate was incubated at RT for 2 hours shaking gently. Binding was detected using luminescence POD substrate (Roche Applied Science, Mannheim, Germany, Cat. No. 11 582 950 001) and goat anti-human Fc:HRP (Jackson ImmunoResearch, West Grove, Pa., Cat. No. 109-035-098) and the plate was read in a SpectraMax plate reader (Molecular Devices, Sunnyvale, Calif.).












TABLE 7










Mutagenesis


Candidate


Seq ID
Resulting
template


no:
Mutants
Primers
NO:
palsmid #
palsmid #







15-1
HC: F50R
GCCTGGAGTGGATGGGCCGGATCGACCCCAGCG
142
5042
p4595




CGCTGGGGTCGATCCGGCCCATCCACTCCAGGC
143




 


15-2
HC: V34I
AGAGGTAACTCCCGTTGCGG
144
5046
p4584




GCATCTGGCGCACCCAGCCGATCCAGTAGTTGGTGAAG
145




 


15-3
HC: V34I/G35S
AGAGGTAACTCCCGTTGCGG
146
5045
p4584




GCATCTGGCGCACCCAGCTGATCCAGTAGTTGGTGAAG
147




 


15-4
HC: A61S/Q67H
AGAGGTAACTCCCGTTGCGG
144
5048
p4584




CGCTGATGGTCACGTGGCCCTGGAAGCTAGGGCTGTAGTTGGTGTAG
148




 


15-5
HC:
CTTCACCAACTACTGGATCAGCTGGGTGCGCCAGATGC
149
5069
p5042



F50R/V34I/G35S/
CGCTGATGGTCACGTGGCCCTGGAAGCTAGGGCTGTAGTTGGTGTAG
148





A61S/Q67H






 


15-6
HC:
CGCCATGTACTACTGCGCCCGCCAGCTGTACCAGGGCTAC
150
5070
p5045



V34I/G35S/E99Q
GTAGCCCTGGTACAGCTGGCGGGCGCAGTAGTACATGGCG
151




 


15-7
LC: G30S/L31S
GCCAGCCAGAGCATCAGCAGCTACCTGGCCTGGTACCAGC
152
5043
p4595




GCTGGTACCAGGCCAGGTAGCTGCTGATGCTCTGGCTGGC
153




 


15-8
LC: A34N
AGAGGTAACTCCCGTTGCGG
144
5047
p4588




CGGGCTTCTGCTGGTACCAGTTCAGGTAGCTGCTGATGCTCTG
154




 


15-9
HC:
CGCCATGTACTACTGCGCCCGCCAGCTGTACCAGGGCTAC
150
5097
p5069*



F50R/V34I/G35S/
GTAGCCCTGGTACAGCTGGCGGGCGCAGTAGTACATGGCG
151





A61S/Q67H/E99Q





*p5069 as a single gene for heavy chain. Variable reagion of p5069 swaped to p5070 backbone






DSC experiments were performed on a MicroCal's Auto VP-capillary DSC system (MicroCal, LLC, Northampton, Mass.) in which temperature differences between the reference and sample cells were continuously measured, and calibrated to power units. Samples were heated from 10° C. to 95° C. at a heating rate of 60° C./hour. The pre-scan time was 15 minutes and the filtering period was 10 seconds. The concentration used in the DSC experiments was about 0.5 mg/ml. Analysis of the resulting thermograms was performed using MicroCal Origin 7 software (MicroCal, LLC).
The thermal stability (Tm) of the generated variants was measured by DSC (Table 8). Binding of the antibody variants to TLR3 was comparable to that of the parental antibody.







TABLE 8







Summary of melting temperatures (TM) of the variants and


rationale for making them.











Candidate no:
Mutations
Rationale
TM (° C.)
ΔTM (° C.)















15EVQ

WT

64.7
0


15-1
HV
F50R
VH/VL interface
69.3
4.6


15-2
HV
V34I
VH core packing
66.9
2.2


15-3
HV
V34I/G35S
H-bonding, VH core packing
71.2
6.5


15-4
HV
A61S/Q67H
VH/VL packing, VH surface charge distribution
65.4
0.7


15-5
HV
F50R/V34I/G35S/
VH/VL interface, H-bonding, VH core packing, VH/VL
76.2
11.5




A61S/Q67H
packing, VH surface charge distribution




15-6
HV
V34I/G34S/E99Q
H-bonding, VH core packing, removal of buried charge
75
10.3


15-7
LV
G30S/L31S
L-CDR1 surface polar residues
63.1
−1.6


15-8
LV
A34N
VL/VH interface
64
−0.7


15-9
HV
F50R/V34I/G35S/
VH/VL interface, H-bonding, VH core packing, VH/VL
76
11.3




A61S/Q67H/E99Q
packing, VH surface charge distribution, removal of







buried charge









Example 8
Generation of a Surrogate Anti-TLR3 Antibody
A chimeric antagonistic rat/mouse anti-mouse TLR3 antibody, herein named mAb 5429 was generated to evaluate effects of inhibiting TLR3 signaling in various in vivo models, as the humanized antibodies generated in Example 1 did not have sufficient specificity or antagonist activity for mouse TLR3. The surrogate chimeric mAb 5429 as well as its parent rat anti-mouse TLR3 antibody c1811 inhibited mouse TLR3 signaling in vitro, and in vivo, and ameliorated pathogenic mechanisms in several disease models in the mouse.
Data discussed below suggests a role for TLR3 in the induction and perpetuation of detrimental inflammation, and contribute to the rationale for the therapeutic use of TLR3 antagonists and TLR3 antibody antagonists, for example acute and chronic inflammatory conditions including hypercytokinemia, asthma and airway inflammation, inflammatory bowel diseases and rheumatoid arthritis, viral infections, and type II diabetes.
Generation of the Surrogate mAb 5429
CD rats were immunized with recombinant murine TLR3 ectodomain (amino acids 1-703 of seq ID NO: 162, GenBank Acc. No. NP—569054) generated using routine methods. Lymphocytes from two rats demonstrating antibody titers specific to murine TLR3 were fused to FO myeloma cells. A panel of monoclonal antibodies reactive to murine TLR3 were identified and tested for in vitro antagonist activity in the murine luciferase reporter and murine embryonic fibroblast assays. The hybridoma line C1811A was selected for further work. Functional variable region genes were sequenced from mAb c1811 secreted by the hybridoma. Cloned heavy chain and light chain variable region genes were then respectively inserted into plasmid expression vectors that provided coding sequences for generating a chimeric Rat/Balb C muIgG1/κ mAb designated as mAb 5429 using routine methods. The antibodies were expressed as described in Example 3. The amino acid sequences of the mAb 5429 heavy and light chain variable regions are shown in SEQ ID NO:164 and SEQ ID NO: 163, respectively, and the heavy and light chain full length sequences are shown in SEQ ID NO:166 and SEQ ID NO: 165, respectively. The heavy and light chain full length sequences of mAb c1811 are shown in SEQ ID NO: 168 and SEQ ID NO: 167, respectively.
Characterization of mAb 5429
mAb 5429 was characterized in a panel of in vitro assays for its neutralizing ability on TLR3 signaling. The activity assays and results are described below.
Murine Luciferase Reporter Gene Assay
The murine TLR3 cDNA (SEQ ID NO: 161, GenBank Acc. No: NM—126166) was amplified by PCR from murine spleen cDNA (BD Biosciences, Bedford, Mass.), and cloned into the pCEP4 vector (Life Technologies, Carslbad, Calif.) using standard methods. 200 μl HEK293T cells were plated in 96 well white clear-bottom plates at a concentration of 4×104 cells/well in complete DMEM, and used the following day for transfections using Lipofectamine 2000 (Invitrogen Corp., Carslbad, Calif.) using 30 ng pNF-κB firefly luciferase (Stratagene, San Diego, Calif.) or 30 ng pISRE firefly luciferase (BD Biosciences, Bedford, Mass.), 5 ng phRL-TK control Renilla luciferase (Promega Corp., Madison, Wis.) reporter plasmids, 1.5 ng pCEP4 encoding the full-length murine TLR3, and 13.5 ng empty pcDNA3.1 vector (Life Technologies, Carslbad, Calif.) to bring the total DNA amount to 50 ng/well. 24 hours post-transfection, the cells were incubated for 30 minutes to 1 hour at 37° C. with the anti-murine TLR3 antibodies in fresh serum-free DMEM before the addition of 0.1 or 1 μg/μl poly(I:C). The plates were harvested after 24 hours using the Dual-Glo Luciferase Assay System (Promega, Madison, Wis.). The relative light units were measured using a FLUOstar OPTIMA multi-detection reader with OPTIMA software (BMG Labtech GmbH, Germany). Normalized values (luciferase ratios) were obtained by dividing the firefly relative light units (RLUs) by the Renilla RLUs. mAb 5429 as well as its parent mAb c1811 and mAb 15 (Table 3a) reduced poly(I:C)-induced NF-κB and ISRE activation in a dose-dependent fashion (FIGS. 8A and 8B), demonstrating their abilities to antagonize the activity of TLR3. IC50s measured in the ISRE assay were 0.5, 22, and 0.7 μg/ml for mAb 5249, mAB 15 and mAb c1811, respectively.
Murine Embryonic Fibroblast (MEF) Assay
C57BL/6 MEF cells were obtained from Artis Optimus (Opti-MEFTM C57BL/6-0001). The cells were plated in 96-well flat bottom plates (BD Falcon) at 20,000 cells/well in 200 μl MEF media (DMEM with glutamax, 10% heat inactivated-FBS, 1×NEAA, and 10 μg/ml gentamycin). All incubations were done at 37° C./5% CO2. 24 hours after plating, mAb 5429 or mAb c1811 were added into wells. The plates were incubated with the mAbs for 1 hr, after which Poly(I:C) was added at 1 μg/ml in each well. The supernatants were collected after a 24-hour incubation. Cytokine levels were determined using a bead kit (Invitrogen Corp., Carslbad, Calif.) to detect CXCL10/IP-10 following manufacturer's protocol. The results were graphed using GraphPad Prism Software. Both antibodies reduced poly(I:C)-induced CXCL10/IP-10 levels in a dose-dependent manner, demonstrating the abilities of these antibodies to antagonize endogenous TLR3 and inhibit TLR3 signaling (FIG. 9).
Flow Cytometry—Surface Staining
C57BL/6 and TLR3 knockout (TLR3KO) (C57BL/6 background; female, 8-12 weeks of age, Ace Animals, Inc.), 10 per group, were dosed intraperitoneally with 1 ml of 3% Thioglycollate medium (Sigma) and 96 hrs later, the mice were euthanized and the peritoneum from each mouse was lavaged with 10 ml sterile PBS. Thioglycollate-elicited peritoneal macrophages were resuspended in PBS and cell viability was assessed using Trypan Blue staining. Cells were pelleted by centrifugation and resuspended in 250 μl FACS Buffer (PBS —Ca2+—Mg2+, 1% heat-inactivated FBS, 0.09% Sodium Azide) and were kept on wet ice. The CD16/32 reagent (eBioscience) was used at 10 μg/106 cells for 10 minutes to block Fc Receptors on the macrophages. The cells were distributed at 106 cells in 100 μl/well for surface staining. Alexa-Fluor 647 (Molecular Probes)-conjugated mAb c1811 and mAb 1679 (rat anti-mouse TLR3 antibody that had no TLR3 specificity, and thus used as an isotype control) were added at 0.25 μg/106 cells and incubated on ice in the dark for 30 minutes. The cells were washed and resuspended in 250 μl of FACS Buffer. The viability stain, 7-AAD (BD Biosciences, Bedford, Mass.), was added at 5 μl/well no more than 30 minutes before acquisition of samples on FACS Calibur to detect a dead cell population. Samples were collected by the FACS Calibur using Cell Quest Pro Software. FCS Express was used to analyze the collected data by forming histograms.
The binding of mAb c1811 to murine thioglycollate-elicited peritoneal macrophages from C57BL/6 and TLR3KO mice were evaluated by flow cytometry to determine binding specificity. mAb 5429 was not used in this assay since the mouse Fc region of this chimeric antibody was expected to contribute to non-specific binding. mAb c1811 exhibited no binding to TLR3KO macrophages, and increased binding to the cell surfaces of C57BL/6 peritoneal macrophages, suggesting a specificity of the mAb for TLR3 (FIG. 10). mAb 5429, having the same binding regions as mAb c1811, is assumed to have the same binding specificity as mAb c1811.
Example 9
TLR3 Antibody Antagonists Protect from TLR3-Mediated Systemic Inflammation
Model
The Poly(I:C)-induced systemic cytokine/chemokine model was used as a model of TLR3-mediated systemic inflammation. In this model, poly(I:C) (PIC) delivered intraperitoneally induced a systemic cytokine and chemokine response that was partially TLR3-mediated.
Female C57BL/6 mice (8-10 weeks old) or female TLR3KO mice (C57BL/6 background; 8-10 weeks old, Ace Animals, Inc.) were given mAb 5429 at 10, 20 or 50 mg/kg in 0.5 ml PBS, mAb c1811 at 2, 10 or 20 mg/kg in 0.5 ml PBS or 0.5 ml PBS alone (vehicle control) subcutaneously. 24 hours after antibody dosing, mice were given 50 μg poly(I:C) (Amersham Cat. No. 26-4732 Lot no. IH0156) in 0.1 ml PBS intraperitoneally. Retro-orbital blood was collected 1 and 4 hours after the poly(I:C) challenge. Serum was prepared from whole blood and analyzed for cytokine and chemokine concentrations by Luminex.
Results
Poly(I:C) delivered intraperitoneally induced a systemic cytokine and chemokine response that was partially TLR3-mediated, as evidenced by the significantly reduced production of a panel of chemokines and cytokines in the TLR3KO animals (Table 9A). The TLR3-dependent poly(I:C)-induced mediators were IL-6, KC, CCL2/MCP-1 and TNF-α at 1 hr post-poly(I:C) challenge, and IL-1α, CCL5/RANTES and TNF-α at 4 hr post-poly(I:C) challenge. Both mAb c1811 and mAb 5429 significantly reduced levels of these TLR3-dependent mediators, demonstrating the ability of the antibodies to reduce TLR3 signaling in vivo (Table 9B). Values in Table 9 are shown as mean cytokine or chemokine concentrations in pg/ml of six animals/group ±SEM. These data suggest that TLR3 antagonism can be beneficial in reducing excess TLR3-mediated cytokine and chemokine levels in conditions such as cytokine storm or lethal shock.









TABLE 9A






C57BL/6
TLR3KO



















PIC
−
+
−
+


mAb 5429 (mg/kg)
−
−
−
−


mAb c1811 (mg/kg)
−
−
−
−







1 h PIC challenge











TNFα
6.005 ± 0.32 
319.4 ± 34.1* 
9.13 ± 4.41
43.80 ± 10.13**


KC
129.3 ± 9.83 
 2357 ± 491.5*
152.0 ± 21.34
432.3 ± 90.66**


IL-6
40.91 ± 5.66 
 5317 ± 856.7*
120.1 ± 99.99
 1214 ± 294.9**


MCP-1
84.67 ± 18.45
694.6 ± 127.8*
67.85 ± 34.16
249.9 ± 55.60**







4 h PIC challenge











IL-1α
28.21 ± 17.78
796.7 ± 45.0* 
13.94 ± 13.84
408.5 ± 29.91**


RANTES
20.87 ± 1.738
 4511 ± 783.4*
36.01 ± 4.484
706.3 ± 84.36**


TNFα
0.10 ± 0  
561.7 ± 81.84*
3.215 ± 3.115
305.8 ± 53.63**





*p < 0.001: One Way ANOVA to C57BL/6 PBS


**p < 0.001 One Way ANOVA to C57BL/6 PIC














TABLE 9B






C57BL/6





















PIC
+
+
+
+
+
+


mAb 5429 (mg/kg)
50
20
10
−
−
−


mAb c1811 (mg/kg)
−
−
−
20
10
2







1 h PIC challenge













TNF-α
29.33 ± 3.78*** 
31.05 ± 1.59*** 
59.55 ± 12.71***
32.54 ± 3.89*** 
42.22 ± 7.04*** 
42.61 ± 10.58***


KC
466.3 ± 92.35***
440.3 ± 10.01***
744.6 ± 103.1** 
637.3 ± 151.0***
944.2 ± 130.9** 
919.3 ± 231.2** 


IL-6
480.2 ± 62.88***
375.9 ± 46.14***
705.2 ± 149.8***
739.2 ± 113.3***
1047 ± 222*** 
 1229 ± 378.4***


MCP-1
168.5 ± 15.04** 
321.6 ± 206.7  
219.2 ± 70.58* 
184.0 ± 14.92** 
278.3 ± 53.57  
414.9 ± 97.17  







4 h PIC challenge













IL-1α
343.0 ± 33.01***
452.6 ± 94.86** 
481.1 ± 121.0* 
354.8 ± 45.43***
351.7 ± 68.85***
352.4 ± 39.60***


RANTES
 1381 ± 169.7***
 2439 ± 308.7** 
 1601 ± 398.9***
 1303 ± 168.0***
 1365 ± 474.1***
 2209 ± 402.5** 


TNF-α
100.1 ± 8.5*** 
205.1 ± 41.85***
226.1 ± 64.72***
138.9 ± 26.0*** 
121.6 ± 38.85***
223.8 ± 47.74***





***p < 0.001,


**p < 0.01,


*p < 0.05: One Way ANOVA statistics were compared to the C57BL/6 + PIC group






Example 10
TLR3 Antibody Antagonists Reduce Airway Hyperresponsiveness
Model
Airway hyperresponsiveness was induced by Poly(I:C).
Female C57BL/6 mice (12 weeks old) or female TLR3KO mice (C57BL/6 background; 12 weeks old, Ace Animals, Inc.) were anesthetized with isoflurane and several doses (10-100 μg) of poly(I:C) in 50 μl sterile PBS were administered intranasally. Mice received three administrations of poly(I:C) (or PBS) with a 24 hour rest period between each administration. 24 hours following the last poly(I:C) (or PBS) administration, lung function and airway hyperresponsiveness to methacholine were measured using whole body plethysmography (BUXCO system). The mice were placed into the whole body plethysmograph chamber and allowed to acclimate for at least 5 minutes. Following baseline readings, mice were exposed to increasing doses of nebulized methacholine (Sigma, St. Louis, Mo.). The nebulized methacholine was administered for 2 minutes, followed by a 5-minute data collection period, followed by a 10-minute rest period before subsequent increasing-dose methacholine challenges. The increased airflow resistance was measured as Enhanced Pause (Penh) and is represented as the average Penh value over the 5-minute recording period (BUXCO system). Following lung function measurements, mice were euthanized and the lungs were cannulated. Bronchoalveolar lavages (BAL) were performed by injecting 1 ml of PBS into the lungs and retrieving the effluent. The lung tissues were removed and frozen. BAL fluids were centrifuged (1200 rpm, 10 min.) and the cell-free supernatants were collected and stored at −80° C. until analysis. Cell pellets were resuspended in 200 μl PBS for total and differential cell counts. The multiplex assay was performed following the manufacturer's protocol and the Multiplex Immunoassay Kit (Millipore, Billercia, Mass.).
Results
Previous observations demonstrated that the intranasal administration of poly(I:C) induced a TLR3-mediated impairment in lung function in mice with increased enhanced pause (PenH) measurement in whole body plethysmography (Buxco) at baseline and an increased responsiveness to aerosolized methacholine (an indicator of airway hyperesponsiveness) (PCT Publ. No. WO06/060513A2). This impairment in the lung function was associated with neutrophil recruitment into the lung, and increased levels of pro-inflammatory cytokines/chemokines in the lung. In this study, the effect of mAb 1811 and mAb 5429 was evaluated in poly(I:C)-induced impairment in lung function by administering each antibody at 50 mg/kg subcutaneously prior to poly(I:C) challenge.
TLR3-mediated impairment of lung function was significantly reduced by treatment of animals with TLR3 antibody antagonists prior to the poly(I:C) challenge. TLR3-mediated increases in baseline PenH and airway sensitivity to methacholine were prevented in the anti-TLR3 antibody-treated animals (FIG. 11). Further, TLR3-mediated recruitment of neutrophils into the mouse lung and generation of chemokines in the airways were reduced in the anti-TLR3 antibody-treated animals. The neutrophil numbers (FIG. 12) and the CXCL10/IP-10 levels (FIG. 13) were measured from the collected bronchoalveolar lavage fluid (BALF). The studies were repeated at least three times with similar results. Data shown in FIGS. 11, 12 and 13 are from one representative study. Each symbol represents a data point from one mouse, and the horizontal bars show group means. The study demonstrated that systemically-administered TLR3 antibody antagonists reached the lung, reduced TLR3-mediated impairment of lung function, neutrophil infiltration into the airway, chemokine generation and respiratory tract inflammation in the used model. Thus, TLR3 antagonists may be beneficial in the treatment or prevention of respiratory diseases characterized by airway hyperresponsiveness, such as asthma, allergic rhinitis, chronic obstructive pulmonary disease (COPD), and cystic fibrosis.
Example 10
TLR3 Antibody Antagonists Protect from Inflammatory Bowel Disease
Model
The DSS colitis Model was used as a model of inflammatory bowel disease.
Female C57BL/6 mice (<8 weeks old) or female TLR3KO mice (C57BL/6 background; <8 weeks old weighing between 16.5 g and 18 g, Ace Animals, Inc.) were fed gamma-irradiated food starting on day −1. DSS (Dextran sulfate) (MP Biomedicals, Aurora, Ohio, Catalog no: 160110; 35-50 kDa; 18-20% Sulfur, Lot no. 8247J) was diluted in autoclaved acidified drinking water to a final concentration of 5%. The DSS-water was administered for 5 days, after which it was replaced with plain water. Mice were allowed to drink water ad libitum throughout the study. All water bottles were weighed every day to record water consumption. On days 0, 2, and 4 mice were dosed intraperitoneally with 5 mg/kg (0.1 mg in 0.1 ml PBS) mAb 5429, mouse anti-TNF-α antibody, or PBS as a control. Mice were monitored daily throughout the study and were weighed on days 0 through 4 and day 7. Mice were euthanized on days 2 and 7 of the study. Abdominal cavities were opened and the ascending colons cut where they join the cecum. Colons were collected and fixed in 10% neutral buffered formalin. Colons were paraffin-embedded, sectioned and H&E stained (Qualtek Molecular Labs, Santa Barbara, Calif.). Colonic histopathological assessments were done in a blinded fashion by a veterinary pathologist as described below (PathoMetrix, San Jose, Calif.).
Histopathologic Evaluation
Two segments of large intestine, colon and rectum were evaluated and scored for the following changes: (i) single cell necrosis; (ii) epithelial ulceration; (iii) epithelial sloughing; (iv) cryptal abscess; (v) cell proliferation; (vi) cryptal cell proliferation; (vii) granulation tissue formation in the lamina propria; (viii) granulation tissue in the submucosa; (ix) submucosal inflammatory cell infiltrate, neutrophil predominant; and (x) submucosal edema.
A single, overall score of severity was given based on the following standards:

    
    
        0—non-existent
        1—mild, focal or occasionally found
        2—mild, multifocal
        3—moderate, frequently found but in limited areas
        4—severe, frequently found in many areas or extensions of the tissue submitted
        5—very severe, extends to large portions of the tissue submitted

Results

    
    


Previous observations demonstrated that TLR3KO animals showed significantly reduced histopathology compared with wild type mice in a model of inflammatory bowel disease induced by DSS ingestion (PCT Publ. No. WO06/60513A2), thus suggesting that TLR3 signaling plays a role in the pathogenesis in this model. It has been reported that commensal bacterial RNA or mammalian RNA released from necrotic cells can act as endogenous ligands to stimulate TLR3 signaling (Kariko et al., Immunity 23165-231175 2005; Kariko et al., J. Biol. Chem. 279:12542-12550 2004), and therefore TLR3 stimulation by endogenous ligands in the gut may enhance and perpetuate inflammation in the DSS colitis model.
Disease severity was ameliorated in DSS-exposed animals upon treatment with anti-TLR3 antibodies, as assessed by compound histopathology scores (FIG. 14). FIG. 14 shows means, standard deviations and 95% confidence intervals for disease severity scores as horizontal bars. Significant reduction in the scores were observed in the wild type DSS-exposed animals treated with anti-TLR3 antibodies (p<0.05) when compared to untreated wild type animals. DSS-exposed TLR3KO animals were protected from DSS-induced changes. DSS-exposed animals receiving anti-mouse TNF-α mAb demonstrated no improvement in histopathology in the DSS model. Therefore, the DSS model may be useful in evaluating therapeutics that may target the human patient population that is non-responsive to anti-TNF-α therapies, and neutralizing anti-TLR3 antibodies may have the potential to provide benefit to patients with inflammatory bowel disease who do not respond to anti-TNF-α therapies.
Model
The T cell Transfer Model was used as a model of inflammatory bowel disease. In this model, gut inflammation was induced in SCID mice by the transfer of a population of regulatory T cell-devoid naïve T cells from immune-competent mice, which attack antigen-presenting cells in the gut mucosa.
Naïve T-cells (CD4+CD45RBhigh T cells) were injected intraperitoneally into SCID recipients to induce chronic colitis. Mice were given either PBS (500 μl/mouse intraperitoneally; vehicle control), mAb 5429 (0.1 mg/mouse intraperitoneally), or anti-TNF-α antibody (0.05 mg/mouse intraperitoneally; positive control) beginning 48 hours following transfer of T-cells and then twice weekly throughout the 8 week study. At 8 weeks following T-cell transfer (or when mice lost >15% of their original body weight) animals were euthanized and colons removed. Colons were fixed, paraffin-embedded and H&E stained. Histopathology (cell infiltration, crypt abscesses, epithelial erosion, goblet cell loss, and bowel wall thickening) was assessed quantitatively in a blinded fashion.
Results
Disease severity was ameliorated in animals that received T-cell transfer upon treatment with anti-TLR3 antibodies, as assessed by significant reduction in the histopathology sum of scores when compared to the control animals (p<0.05) (FIG. 15A). For the sum of scores, crypt abscesses, ulceration, neutrophil influx, goblet cell loss, abnormal crypts, lamina propria inflammation and transmural involvement was assessed. Significant reduction was observed with crypt abscesses, ulceration and neutrophil influx (for all p<0.05) (FIG. 15B). Anti-TNF-α antibody was used as a positive control at doses known to provide optimal benefit.
Studies using two well known models of inflammatory bowel diseases, the DSS and the T-cell transfer model, demonstrated that systemically delivered TLR3 antibody antagonists reached the gut mucosa and reduced gastrointestinal tract inflammation induced through two different pathogenic mechanisms. Thus, TLR3 antagonists may be beneficial for the treatment of inflammatory bowel diseases, including anti-TNF-α-refractory cases, and other immune-mediated pathologies in the gastrointestinal tract.
Example 11
TLR3 Antibody Antagonists Protect from Collagen-Induced Arthritis
Model
The collagen-induced arthritis (CIA) model was used as a model of rheumatoid arthritis.
Male B10RIII mice (6-8 weeks old, Jackson Labs) were divided into groups of 15 per group (arthritis groups) or 4 per group (control mice). Arthritis groups were anesthetized with Isoflurane and given injections of Type II collagen (Elastin Products) and Freund's complete adjuvant supplemented with M. tuberculosis (Difco) on days 0 and 15. On day 12, mice with developing type II collagen arthritis were randomized by body weight into treatment groups and were dosed subcutaneously (SC) on days 12, 17, and 22 (d12, d17, 2d2) with mAb 5429 (25 mg/kg), the negative control antibody CVAM (a recombinant mAb of no known specificity in the mouse) (5 mg/kg) or anti-TNF-α antibody (5 mg/kg, positive control). In addition, control groups of mice were treated with vehicle (PBS) or dexamethasone (0.5 mg/kg, Dex, reference compound) subcutaneously (SC) daily (QD) on days 12-25. Animals were observed daily from days 12 through 26. Fore and Hind paws were evaluated by a clinical scoring system (shown below). Animals were euthanized on study day 26 and histopathology was assessed in a blinded fashion (scoring system described below). Efficacy evaluation was based on animal body weights, and clinical arthritis scores. All animals survived to study termination.
Clinical Scoring Criteria for Fore and Hind Paws


    
    
        0—normal
        1—hind or fore paw joint affected or minimal diffuse erythema and swelling
        2—hind or fore paw joints affected or mild diffuse erythema and swelling
        3—hind or fore paw joints affected or moderate diffuse erythema and swelling
        4—marked diffuse erythema and swelling, or =4 digit joints affected)
        5—severe diffuse erythema and severe swelling entire paw, unable to flex digits)

Histopathologic Scoring Methods for Mouse Joints with Type II Collagen Arthritis

    
    


When scoring paws or ankles from mice with lesions of type II collagen arthritis, severity of changes as well as number of individual joints affected were considered. When only 1-3 joints of the paws or ankles out of a possibility of numerous metacarpal/metatarsal/digit or tarsal/tibiotarsal joints were affected, an arbitrary assignment of a maximum score of 1, 2 or 3 for parameters below was given depending on severity of changes. If more than 2 joints were involved, the criteria below were applied to the most severely affected/majority of joints.
Clinical data for paw scores were analyzed using AUC for days 1-15, and % inhibition from controls were calculated.
Inflammation


    
    
        0—normal
        1—minimal infiltration of inflammatory cells in synovium and periarticular tissue of affected joints
        2—mild infiltration, if paws, restricted to affected joints
        3—moderate infiltration with moderate edema, if paws, restricted to affected joints
        4—marked infiltration affecting most areas with marked edema
        5—severe diffuse infiltration with severe edema

Pannus

        0—normal
        1—minimal infiltration of pannus in cartilage and subchondral bone
        2—mild infiltration with marginal zone destruction of hard tissue in affected joints
        3—moderate infiltration with moderate hard tissue destruction in affected joints
        4—marked infiltration with marked destruction of joint architecture, most joints
        5—severe infiltration associated with total or near total destruction of joint architecture, affects all joints

Cartilage Damage

        0—normal
        1—minimal to mild loss of toluidine blue staining with no obvious chondrocyte loss or collagen disruption in affected joints
        2—mild loss of toluidine blue staining with focal mild (superficial) chondrocyte loss and/or collagen disruption in affected joints
        3—moderate loss of toluidine blue staining with multifocal moderate (depth to middle zone) chondrocyte loss and/or collagen disruption in affected joints
        4—marked loss of toluidine blue staining with multifocal marked (depth to deep zone) chondrocyte loss and/or collagen disruption in most joints
        5—severe diffuse loss of toluidine blue staining with multifocal severe (depth to tide mark) chondrocyte loss and/or collagen disruption in all joints

Bone Resorption

        0—normal
        1—minimal with small areas of resorption, not readily apparent on low magnification, rare osteoclasts in affected joints
        2—mild with more numerous areas of, not readily apparent on low magnification, osteoclasts more numerous in affected joints
        3—moderate with obvious resorption of medullary trabecular and cortical bone without full thickness defects in cortex, loss of some medullary trabeculae, lesion apparent on low magnification, osteoclasts more numerous in affected joints
        4—marked with full thickness defects in cortical bone, often with distortion of profile of remaining cortical surface, marked loss of medullary bone, numerous osteoclasts, affects most joints
        5—severe with full thickness defects in cortical bone and destruction of joint architecture of all joints

Results

    
    


Dexamethasone (Dex) and anti-mouse TNF-α antibody was used as a positive control, PBS was used as vehicle control, and CVAM was used as a negative control antibody. All treatments were initiated on day 12 of the study, during the development of joint disease. Disease incidence for vehicle-treated disease control animals was 100% by study day 22. Negative control groups treated with vehicle or CVAM antibody had the highest clinical scores. Significantly reduced clinical scores were observed for the groups treated with Dex (p<0.05 for d18-d26), 5 mg/kg anti-TNF-α antibody (p<0.05 for d18-26), or 25 mg/kg mAb 5429 (p<0.05 for d18-d23 and d25-d26) (FIG. 16). Clinical arthritis scores expressed as area under the curve (AUC) were significantly reduced by treatment with 25 mg/kg mAb 5429 (43% reduction), 5 mg/kg anti-TNF-α antibody (52%), or Dex (69%) as compared to vehicle controls. FIG. 17 shows means and standard deviations for AUC for each group.
Histopathological effects of the treatments were also assessed. Paw bone resorption was significantly decreased by treatment with 25 mg/kg mAb 5429 (47% decrease) as compared to vehicle controls. Positive control mice treated with 5 mg/kg anti-TNF-α antibody had significantly decreased paw inflammation (33%), cartilage damage (38%), and summed paw scores (37%). Treatment with Dex significantly reduced all paw histopathology parameters (73% reduction of summed scores).
These data demonstrate that TLR3 antibody antagonists improve clinical and histopathological disease symptoms in the CIA model, and suggest the use of TLR3 antagonists for treatment of rheumatoid arthritis.
Example 12
TLR3 Antibody Antagonists Protect from Acute Lethal Viral Infections
Model
An influenza A virus challenge model was used as a model of acute lethal viral infection.
On Day −1, 4, 8, and 12, female C57BL/6 mice (12 weeks old) or female TLR3KO mice (C57BL/6 background; 12 weeks old, ACE Animals, inc., 15 mice per group) were dosed subcutaneously 20 mg/kg mAb 5429, or PBS alone. On day 0, the mice were anesthetized by isoflurane and were intranasally administered Influenza A/PR/8/34 virus (ATCC, Rockland, Md., Lot no. 218171), in 25 μl PBS (equivalent to 105.55 CEID50). Animals were observed two times a day for changes in body weight and survival over the period of 14 days. A clinical scoring system was used to evaluate the level of disease progression and subtle improvements in response to Influenza A virus treatment.
Clinical Scores


    
    
        0—normal, alert and reactive, no visible signs of illness
        1—ruffled coat, with or without slightly reduced ambulation
        2—ruffled coat, hunched posture when walking, reluctant ambulation, labored breathing
        3—ruffled coat, labored breathing, ataxia, tremor
        4—ruffled coat, inability to ambulate with gentle prodding, unconsciousness, feels cold to the touch
        5—found dead

Results

    
    


Survival, daily clinical scores, and changes in body weight were evaluated in the study. Both influenza A infected WT mice administered mAb 5429 (20 mg/kg) and influenza A infected TLR3KO not receiving mAb 5429 demonstrated a statistically significant increase in survival (p<0.001 and p<0.01, respectively) when compared to C57BL/6 mice inoculated with the Influenza virus, indicating that antagonism or deficiency of TLR3 can prevent influenza-induced mortality (FIG. 18). Clinical scores were significantly reduced in the group receiving 20 mg/kg mAb 5429, as well as in the TLR3KO group (FIG. 19). The body weight of the mice was observed over a period of 14 days after influenza virus administration. Body weight decreased steadily in C57BL/6 mice dosed with Influenza A virus. However, both the C57BL/6 mice dosed with 20 mg/kg mAb 5429 and the TLR3KO mice demonstrated significantly greater body weight relative to the WT C57BL/6 mice inoculated with Influenza virus (FIG. 20). These results demonstrated that TLR3 antibody antagonists reduced clinical symptoms and mortality in an acute lethal influenza viral infection model, and suggested that TLR3 antagonists may provide protection for humans in acute infectious states.
Example 13
TLR3 Antibody Antagonists Improve Hyperglycemia and Reduce Plasma Insulin
Model
The Diet-induced obesity (DIO) model was used as a model of hyperglycemia and insulin resistance, and obesity.
C57BL/6 WT animals (about 3 weeks old, Jackson Labs) and TLR3KO animals (C57BL/6 background; about 3 weeks old, Ace Animals, Inc.) were maintained on a high fat diet for 12 to 16 weeks. Both TLR3KO and WT C57BL/6 mice were fed either with normal chow or high-fat diet (Purina TestDiet cat. no. 58126) consisting of 60.9% kcal fat and 20.8% kcal carbohydrates. Mice were maintained on a 12:12-h light-dark cycle, with water and food ad libitum. The weight of each mouse within each group was measured weekly. mAb 5429 was given intraperitoneally twice a week for the first week followed by once a week dosing for total of 7 weeks. Fasting retro-orbital blood serum samples were used for insulin measurements at the time points indicated. Glucose tolerance tests were performed by i.p administration of glucose at 1.0 mg/g body weight after overnight fast at week 7. In addition, fasting insulin and glucose levels were measured.
HOMA-IR was determined from the equation based on the levels of fasting glucose and insulin levels (12) using following equation: HOMA-IR=((fasting glucose (mmol/l)×fasting insulin (mU/l))/22.5 (Wallace et al., Diabetes Care 27:1487-1495, 2004). Fasting blood glucose (BG) was determined using glucose oxidase assay. Fasting insulin levels were determined using the insulin rat/mouse ELISA kit (Crystal Chem, cat. No. 90060).
Results
After 12-16 weeks on high fat diet, the WT DIO animals were hyperglycemic and hyperinsulinemic. Glucose tolerance was improved in the WT DIO animals but not in the TLR3KO DIO animals upon treatment with mAb 5429. Significantly reduced blood glucose levels were observed in mAb 5429 treated animals post glucose challenge at 60, 90, 120, and 180 min when compared to control (PBS only) (FIG. 21A). About 21% reduction in AUC was observed in the mAb 5429 treated WT DIO animals when compared to the WT DIO mice not receiving the mAb. Fasting insulin levels were also reduced in the WT DIO animals treated with mAb 5429 (FIG. 22). TLR3KO DIO animals showed no improvement in fasting insulin upon mAb 5429 treatment. Homeostatic model assessment (HOMA) analysis indicated improved insulin sensitivity in the WT DIO animals treated with mAb 5429, but not in the TLR3KO DIO animals. The HOMA-IR values were 14.0+9.8, 8.7+4.9, 9.0+3.0 for WT DIO, 5 mg/kg of WT DIO mAb 5429, and 20 mg/kg of WT DIO mAb 5429 animals, respectively. No effect was observed in TLR3KO DIO animals.
The study demonstrated that TLR3 antibody antagonists improved insulin resistance and reduced fasting glucose in the DIO model without weight loss, suggesting that TLR3 antagonists may be beneficial for the treatment of hyperglycemia, insulin resistance, and type II diabetes.
Example 14
TLR3 Antibody Antagonists Protect from Bacteria and Virus-Induced Inflammatory Responses
Reagents
Nontypeable Haemophilus influenza (NTHi) strains 35, isolated from a COPD patient with bacterial exacerbations, was obtained from Dr. T. F. Murphy (Buffalo VA Medical Center, Buffalo, N.Y.). Human rhinovirus 16 was obtained from the American Type Culture Collection (ATCC) with TCID(50)=2.8×107/ml.
NTHi Stimulation Assays
NHBE cells (Lonza, Wakersville, Md.) were seeded in Microtest 96-well tissue culture plates (BD Biosciences, Bedford, Mass.) at 1×105/well. NTHi grown on agar plates for 16-20 hr were resuspended in growth medium at  ̃2×108 cfu/ml, treated with 100 μg/ml gentamycin for 30 min. and added at  ̃2×107/well to 96-well plates containing NHBEs. After 3 hours, supernatants were removed and replaced with fresh growth medium with or without antibodies (0.08 to 50 μg/ml final concentration). After additional 24 hr incubation, presence of cytokines and chemokines in cell supernatants was assayed in triplicate with a Cytokine 25-plex AB bead kit, Human (including IL-1β, IL-1RA, IL-2, IL-2R, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL12p40p70, IL-13, IL-15, IL-17, TNF-α, IFN-α, IFN-γ, GM-CSF, MIP-1a, MIP-1α, IP-1β, MIG, Eotaxin, RANTES and MCP-1) (Life Technologies, Carslbad, Calif.) in the Luminex 10015 multiplex fluorescence analyzer and reader system (Luminex Corporation, Austin, Tex.).
Rhinovirus Stimulation Assays
NHBE cells were seeded in Microtest 96-well tissue culture plates (BD Biosciences, Bedford, Mass.) at 1×105 cells/well. The next day, antibodies (0.08 to 50 μg/ml final concentration) were added to NHBE or BEAS-2B cells and incubated for 1 hr, followed by addition of 10 μl/well of rhinovirus. After additional 24 hr incubation, presence of cytokines and chemokines in cell supernatants was assayed by luminex assays as described above.
Results
mAb 15EVQ inhibited NTHi induced IP-10/CXCL10 and RANTES/CCL5 production in a dose-dependent manner, while the control antibody, human IgG4 (Sigma, St. Louis, Mo.), showed no inhibitory effect on NTHi stimulation (FIG. 23A). mAb 15EVQ also inhibited rhinovirus induced CXCL10/IP-10 and CCL5/RANTES production (FIG. 23B).
Example 15
TLR3 Antibody Antagonists Suppress Inflammatory Responses in Astroctyes
Methods
Normal human astrocytes from 2 donors (Lonza, Walkersville, Md.) were plated in a 24 well plate at 75,000 cells/well and allowed to attach overnight. The next day, the astrocytes were treated with 200 ng/ml poly(I:C) and/or 10 μg/ml mAb 18 for 24 hours. Cytokines were measured by Luminex.
Results
Poly(I:C)— induced production of IL-6, IL-8, IL-12, IFN-α, IFN-γ, CXCL9/MIG, CCL3/MIP-1α, CCL4, CCL5/RANTES and CXCL10/IP-10 were inhibited by mAb 18, as shown in Table 10.












TABLE 10








IL-6
IL-8
IL-12
IFN-α
IFN-γ





Donor 1







untreated
876.0 ± 36.8
539.7 ± 32.6
16.6 ± 0.5
28.8 ± 1.5
12.3 ± 0.3


mAb 18
1011.9 ± 57.4 
1401.9 ± 49.7 
17.1 ± 0.5
31.6 ± 0.7
10.4 ± 0.2


Poly(I:C)
ol*
ol
30.3 ± 1.5
47.1 ± 3.1
35.9 ± 1.0


Poly(I:C) + mAb 18
2225.0 ± 108.1
6104.4 ± 259.9
16.8 + 0.9
30.5 ± 1.6
11.7 ± 0.6


Donor 2







untreated
729.1 ± 7.1 
248.2 ± 4.7 
  14 ± 0.5
19.5 ± 1.8
10.5 ± 0.5


mAb 18
779.0 ± 9.8 
1132.6 ± 30.6 
14.3 ± 0.6
20.8 ± 1.9
10.5 ± 0.1


Poly(I:C)
ol
ol
25.5 ± 0.4
36.3 ± 1.9
30.8 ± 0.9


Poly(I:C) + mAb 18
3393.3 ± 107.5
8660.4 ± 354.3
16.2 ± 0.3
24.7 ± 1.2
12.6 ± 0.3
















CXCL9/MIG
CCL3/MIP-1a
CCL4
CCL5/RANTES
CXCL10/IP-10





Donor 1







untreated
12.6 ± 0.7
  21 ± 0.9
14.8 ± 0.7
bl**
bl


mAb 18
14.8 ± 1.7
19.5 ± 1.5
14.8 ± 1.1
bl
bl


Poly(I:C)
78.3 ± 4.8
1569.3 ± 36.9 
159.7 ± 12.7
788.2 ± 94.9
461.4 ± 10.3


Poly(I:C) + mAb 18
18.5 ± 1.6
31.2 ± 1.9
13.2 ± 0.9
bl
 6.9 ± 0.5


Donor 2







untreated
 9.9 ± 1.6
12.3 ± 1.7
11.3 ± 0.3
bl
bl


mAb 18
 8.9 ± 0.7
13.2 ± 1.5
11.1 ± 0.7
bl
bl


Poly(I:C)
  62 ± 3.8
1552.9 ± 41.1 
140.7 ± 4.8 
546.8 ± 21.7
533.2 ± 15  


Poly(I:C) + mAb 18
18.3 ± 2.7
66.6 ± 3.8
12.1 ± 0.8
bl
29.1 ± 6.2





*ol: over detection level


**bl: below detection level






Example 16
TLR3 Antibody Antagonists Suppress Inflammatory Responses in Endothelial Cells
Methods
HUVEC cells (Lonza, Walkersville, Md.) were cultured in serum-containing growth medium recommended by Lonza. Cells were resuspended in serum-free media (Lonza, Walkersville, Md.), plated in 96-well plates at 3×105 cells/ml, and incubated at 37° C., 5% CO2 for 24 hrs. Poly(I:C) (GE Healthcare, Piscataway, N.J.) was added at increasing concentrations (1.5 to 100 μg/ml) and incubated for another 24 hours at 37° C. For cytokine inhibition assays, mAb 15EVQ was added to the cells at various concentrations (0-50 μg/ml) and incubated for 30 min, after which 20 μg/ml poly(I:C) was added for 24 hours. Cell supernatants were collected and cytokine levels were measured using the human cytokine 30-plex kit and Luminex MAP technology (Invitrogen Corp., Carslbad, Calif.). To measure sICAM-1 expression, the HUVEC cells were treated with 20 μg/ml poly(I:C) and various concentrations of mAb 15EVQ (0.8-50 μg/ml). The cell supernatants were analyzed for sICAM-1 expression by ELISA (R&D systems). Cell viability was measured using the CellTiterGlo kit (Promega, Madison, Wis.).
Results
HUVEC cells produced the following cytokines in response to poly(I:C): IL-1RA, IL-2, IL-2R, IL-6, IL-7, CXCL8/IL-8, IL-12 (p40/p70), IL-15, IL-17, TNF-α, IFN-α, IFN-γ, GM-CSF, CCL3/MIP-1α, CCL4/MIP-1β, CXCL10/IP-10, CCL5/RANTES, CCL2/MCP-1, VEGF, G-CSF, FGF-basic, and HGF (Table 11). mAb 15EVQ dose-dependently reduced levels of all cytokines induced by poly(I:C) (Table 12). The ability of mAb 15EVQ to reduce poly(I:C)-induced production of TNF-α, CCL2/MCP-1, CCL5/RANTES, and CXCL10/IP-10 suggested that inhibition of TLR3-mediated activities may protect against leukocyte and T cell infiltration that can lead to atherosclerosis. Also, inhibition of VEGF by mAb 15EVQ suggested a potential benefit of TLR3 blockade in pathologies mediated by VEGF including angiogenesis in a variety of cancers and ocular diseases such as age-related macular degeneration.
TNF-α and IFN-γ function in leukocyte recruitment and increase the expression of adhesion molecules on the activated endothelium (Doukas et al., Am. J. Pathol. 145:137-47, 1994; Pober et al., Am. J. Pathol. 133:426-33, 1988). CCL2/MCP-1, CCL5/RANTES, and CXCL10/IP-10 have been implicated in monocyte and T cell recruitment and contribute to the development of atherosclerosis (Lundgerg et al., Clin. Immunol. 2009). The generation of VEGF by endothelial cells has been linked to abnormal tissue growth or tumors in a variety of cancers during angiogenesis (Livengood et al., Cell. Immunol. 249:55-62, 2007).
Soluble Intercellular Adhesion Molecule 1 (sICAM-1) is generated by proteolytic cleavage and is a marker for endothelial cell activation. ICAM-1 plays a key role in leukocyte migration and activation and is upregulated on endothelial cells and epithelial cells during inflammation where it mediates adhesion to leukocytes via integrin molecules LFA-1 and Mac-1. Poly(I:C) activated the endothelial cells to upregulate sICAM-1 expression and the uregulation was reduced by treatment with mAb 15EVQ (FIG. 24A).










TABLE 11







Poly(I:C)





μg/ml
IL-6
CXCL8/IL-8
CCL2/MCP-1





10   
848.8 + 50.9
12876.0 + 2314.0 
11813.4 + 1420.9 


5  
751.3 + 2.1 
11363.7 + 108.2 
11365.7 + 113.1 


2.5 
607.1 + 91.6
10961.5 + 2200.7 
11607.3 + 2155.7 


1.25
 419.2 + 178.4
9631.5 + 3675.8
11690.9 + 3189.9 


0.63
263.8 + 81.4
6231.9 + 1568.0
9075.6 + 1152.2


0.31
 183.5 + 168.3
5257.9 + 1855.0
8106.8 + 1193.1


0.16
111.9 + 72.5
4057.6 + 1127.4
6619.8 + 1728.2


no poly(I:C)
0.00
1286.6 + 300.8 
1360.1 + 245.4 















Poly(I:C) μg/ml
IL-2R
IL-15
IL-17






100   
784.4 + 45.4
61.3 + 12.5
43.8 + 5.3 



50  
718.6 + 56.8
61.3 + 12.5
47.6 + 0  



25  
735.7 + 23.4
56.7 + 18.9
58.3 + 4.9 



12.5 
650.5 + 29.8
38.8 + 6.5 
39.8 + 10.9



 6.25
643.4 + 39.9
34.2 + 0  
32.1 + 0  



 3.13
681.8 + 24.3
38.8 + 6.5 
43.8 + 5.3 



 1.56
578.6 + 10.5
29.4 + 6.7 
36.1 + 5.6 



no poly(I:C)
0.0
0.0
0.0













Poly(I:C) μg/ml
IFNα
CXCL10/IP-10
CCL4/MIP-1β





100   
50.7 + 0  
3803.1 + 185.5
234.5 + 19.7 


50  
44.9 + 1.7
2235.9 + 184.6
291.6 + 41.8 


25  
46.1 + 0  
2403.0 + 271.9
278.7 + 4.7 


12.5 
41.2 + 3.5
2185.4 + 64.9 
243.8 + 63.4 


 6.25
36.1 + 0  
2100.0 + 288.1
201.9 + 46.2 


 3.13
40.0 + 1.8
3553.2 + 197.1
191.5 + 20.8 


 1.56
42.5 + 1.7
2064.3 + 242.1
165.3 + 16.3 


no poly(I:C)
0.0
0.0
0.0













Poly(I:C) μg/ml
RANTES
TNFα
VEGF





100   
 6266.9 + 1708.7
12.8 + 3.2 
581.1 + 181.4


50  
2919.7 + 119.4
11.5 + 3.2 
637.9 + 47.7 


25  
2805.1 + 176.7
9.8 + 2.8
700.3 + 62.5 


12.5 
2598.6 + 68.6 
7.3 + 0.9
513.2 + 73.5 


 6.25
2449.2 + 830.6
6.9 + 1.4
440.4 + 29.5 


 3.13
3117.1 + 795.7
7.3 + 0.9
393.9 + 40.2 


 1.56
2481.0 + 719.3
6.0 + 1.8
358.4 + 74.8 


no poly(I:C)
 4.9 + 4.5
1.9 + 0.4
32.1 + 8.8 





concentrations shown as pg/ml





















TABLE 12





mAb 15










(μg/ml)
50.00
10.00
2.00
0.40
0.08
0.016
0.003
0







PIC
+
+
+
+
+
+
+
−


IL-6
177.8 ± 
214.6 + 
359.2 + 
727.2 + 
10000 + 
10000 + 
10000 + 
10000 + 



5.6 *
3.6 *
57.6 *
50.5 *
0
0
0
0


CXCL8/
1040.7 ± 
1765.9 + 
6460.3 + 
57349.5 + 
72422.8 + 
47047.5 + 
76066.5 + 
96478.0 + 


IL-8
185.9
97.1
3684.4
6293.4
88279.2
52393.1
11354.1
122298.4


CCL2/
1187.7 ± 
1955.4 + 
9054.4 + 
20000 + 
20000 + 
20000 + 
20000 + 
20000 + 


MCP-1
165.4 *
72.7 *
4110.9 *
0.0
0.0
0.0
0.0
0.0


IL-2R
25.0 ± 
0.0 + 
312.3 + 
521.5 + 
664.7 + 
661.2 + 
698.4 + 
654.2 + 



35.3 *
0.0 *
137.6 *
5.5
9.8
14.8
57.6
14.8


IL-15
0.0 ± 
0.0 + 
0.0 + 
4.1 + 
38.8 + 
43.4 + 
38.8 + 
43.4 + 



0.0 *
0.0 *
0.0 *
0.0 *
6.5
0.0
6.5
0.0


IL-17
1.3 ± 
11.8 + 
11.8 + 
27.9 + 
47.4 + 
54.3 + 
40.0 + 
51.2 + 



1.8 *
16.8
16.8
6.0
10.4
20.2
0.0
5.1


IFNα
0.9 ± 
0.9 + 
19.0 + 
36.1 + 
44.9 + 
41.2 + 
47.3 + 
40.0 + 



1.3 *
1.3 *
7.7 *
0.0
1.7
3.5
1.7
1.8


CXCL10/
0.0 ± 
58.1 + 
633.0 + 
1441.4 + 
3023.8 + 
2107.5 + 
2346.4 + 
2157.4 + 


IP-10
0.0 *
2.6 *
471.6 *
97.1
166.1
372.6
226.1
282.7


CCL4/
0.0 ± 
0.0 + 
2.9 + 
62.1 + 
176.6 + 
227.5 + 
248.3 + 
281.7 + 


MIP-1β
0.0 *
0.0 *
4.1 *
7.2 *
21.3 *
19.9
19.4
37.5


RANTES
3.0 ± 
15.4 + 
201.1 + 
952.4 + 
2454.4 + 
2698.1 + 
2624.4 + 
3459.7 + 



0.0 *
4.5 *
169.1 *
41.1 *
98.5 *
88.6 *
129.8 *
181.8


TNFα
1.9 ± 0.4 *
1.6 + 0.0 *
2.2 + 0.0 *
3.4 + 0.0
6.3 + 0.5
8.5 + 0.0
7.6 + 1.4
6.9 + 2.3


VEGF
87.2 ± 
28.6 + 
88.3 + 
156.1 + 
479.6 + 
544.6 + 
533.5 + 
607.3 + 



8.7 *
8.7 *
52.1 *
6.4 *
14.1
8.3
70.2
29.9





* Indicates significant p-values (less than 0.05) comparing mAb15 concentration vs. poly(I:C) alone


Values are mean (pg/ml) ± SEM






This suggested that TLR3 antibody antagonists can inhibit leukocyte trafficking and thus tissue damage caused by the influx of inflammatory cells.
For viability assays, HUVECs were cultured, plated and stimulated with poly(I:C) as described above. mAb 15EVQ dose-dependently restored poly(I:C)-induced reduction in HUVEC cell viability (FIG. 24B).
Down-modulation of endothelial cell activation can suppress excessive immune cell infiltration and reduce tissue damage caused by cytokines that are increased during inflammatory conditions. Inflammation and overexpression of cytokines and adhesion molecules on endothelial cells are key contributors to developing atherosclerosis and hypertension. These data provide rationale for exploring the potential benefit of TLR3 antagonists for use in diseases of the blood vessels including vasculitides, and those featuring endothelial dysfunction. Another disease that is affected by inflammation and overexpressed cytokines is Kaposi's sarcoma (KS) that is common in immunosuppressed and HIV infected individuals and is caused by Kaposi's sarcoma herpes virus (KSHV). VEGF and cytokine production contribute to the survival of KS cells (Livengood et al., Cell Immunol. 249:55-62, 2007). TLR3 antagonists could be beneficial at reducing angiogenic risks associated with KS and other tumors and at preventing cell viability loss and protecting endothelial barrier integrity to prevent vascular leakage, a potentially serious condition associated with organ failure and life-threatening inflammatory conditions such as sepsis. TLR3 antagonism may also be beneficial in viral infections involving endothelial cell pathology such as the viral hemorrhagic fevers caused by members of the families flaviviridae (e.g. Dengue, yellow fever), filoviridae (Ebola, Marburg), bunyaviridae (e.g. Hantavirus, Nairovirus, Phlebovirus), and arenaviridae (e.g. Lujo, Lassa, Argentine, Bolivian, Venezuelan hemorrhagic fevers (Sihibamiya et al., Blood 113:714-722, 2009).
Example 17
Cross-Reactivity of TLR3 Antibody Antagonists with Cynomolgus and Murine TLR3
Activity against cynomolgus or murine TLR3 were assessed using the ISRE reporter gene assay as described in Example 2. The cynomolgus (SEQ ID NO: 217) and murine TLR3 cDNAs (SEQ ID NO: 161) were amplified from whole blood and cloned into the pCEP4 vector (Clontech), and expressed as described above. mAb 15EVQ had IC50s of 4.18 μg/ml and 1.74 μg/ml in the cyno NF-κB and ISRE assays, respectively, compared to IC50s of 0.44 and 0.65 μg/ml in the human TLR3NF-kB and ISRE assays, respectively. Isotype control antibodies had no effect in these assays.

## Claims

1. An isolated polynucleotide encoding an antibody heavy chain variable region (VH) comprising the heavy chain complemetarity determining regions (HCDR) 1, 2 and 3 (HCDR1, HCDR2 and HCDR3) amino acid sequences as shown in SEQ ID NOs: 82, 196 and 84, wherein the HCDR2 of SEQ ID NO: 196 is further defined as shown in Formula (V):









(V)



Xaa24-I-D-P-S-D-S-Y-T-N-Y-Xaa25-P-S-F-Q-G,





wherein
Xaa24 may be Phe or Arg; and
Xaa25 may be Ala or Ser.

2. The isolated polynucleotide of claim 1, wherein the HCDR2 comprises the amino acid sequence as shown in SEQ ID NOs: 83, 86, 112, 114, 117 or 118.

3. The isolated polynucleotide of claim 1, wherein the VH comprises the amino acid sequence as shown in SEQ ID NOs: 38, 40, 42, 124-129 or 216.

4. An isolated polynucleotide encoding an antibody light chain variable region (VL) comprising the light chain complementarity determining regions (LCDR) 1, 2 and 3 (LCDR1, LCDR2 and LCDR3) amino acid sequences as shown in SEQ ID NOs: 79, 80 and 195, wherein the LCDR3 of SEQ ID NO: 193 is further defined as shown in Formula (VI):









(VI)



Q-Q-Xaa18-Xaa19-Xaa20-Xaa21-Xaa22-Xaa23-T,





wherein
Xaa18 may be Tyr, Gly or Ala;
Xaa19 may be Gly, Glu or Asn;
Xaa20 may be Ser or Thr;
Xaa21 may be Val, Ile or Leu;
Xaa22 may be Ser or Leu; and
Xaa23 may be Ile, Ser, Pro or Tyr.

5. The isolated polynucleotide of claim 4, wherein the LCDR3 comprises the amino acid sequence as shown in SEQ ID NOs: 81, 85, 87 or 113.

6. The isolated polynucleotide of claim 5, wherein the VL comprises the amino acid sequence as shown in SEQ ID NOs: 37, 39, 41, 122 or 123.

7. A vector comprising the isolated polynucleotide as in any one of claims 1-6.

8. An isolated host cell comprising the vector of claim 7.

9. A method of making an antibody that binds toll-like receptor 3 (TLR3) comprising culturing the host cell of claim 8 and recovering the antibody produced by the host cell.