ZA200602754B - Effectors of innate immunity determination - Google Patents

Description

Methods of stimulating innate immunity using cationic peptides.

RELATED APPLICATION DATA

[0001] This application claims priority under 35 USC 120 to US Patent "Application Serial No. 10/308,905, filed December 2, 2002, and under 35 USC 119(e) to US Patent Application Serial No. 60/336,632, filed December 3, 2001, herein incorporated by reference in their entirety.

FIELD OF THE INVENTION

[0002] The present invention relates generally to peptides and specifically to peptides effective as therapeutics and for drug discovery related to pathologies resulting from microbial infections and for modulating innate immunity or anti- inflammatory activity. }

BACKGROUND OF THE INVENTION

[0003) Infectious diseases are the leading cause of death worldwide. According to a 1999 World Health Organization study, over 13 million people die from infectious diseases each year. Infectious diseases are the third leading cause of death in North

America, accounting for 20% of deaths annually and increasing by 50% since 1980.

The success of many medical and surgical treatments also hinges on the control of infectious diseases. The discovery and use of antibiotics has been one of the great achievements of modern medicine. Without antibiotics, physicians would be unable to perform complex surgery, chemotherapy or most medical interventions such as catheterization.

[0004] Current sales of antibiotics are US$26 billion worldwide. However, the overuse and sometimes unwarranted use of antibiotics have resulted in the evolution of new antibiotic-resistant strains of bacteria. Antibiotic resistance has become part of the medical landscape. Bacteria such as vancomycin-resistant Enterococcus, VRE, and methicillin-resistant Staphylococcus aureus and MRSA, strains cannot be treated 1

SUBSTITUTE SHEET (RULE 26)

with antibiotics and often, patients suffering from infections with such bacteria die.

Antibiotic discovery has proven to be one of the most difficult areas for new drug development and many large pharmaceutical companies have cut back or completely halted their antibiotic development programs. However, with the dramatic rise of antibiotic resistance, including the emergence of untreatable infections, there is a clear unmet medical need for novel types of anti-microbial therapies, and agents that impact on innate immunity would be one such class of agents.

[0005] The innate immune system is a highly effective and evolved general defense system. Elements of innate immunity are always present at low levels and are activated very rapidly when stimulated. Stimulation can include interaction of bacterial signaling molecules with pattern recognition receptors on the surface of the body’s cells or other mechanisms of disease. Every day, humans are exposed to tens of thousands of potential pathogenic microorganisms through the food and water we ingest, the air we breathe and the surfaces, pets and people that we touch. The innate immune system acts to prevent these pathogens from causing disease. The innate immune system differs from so-called adaptive immunity (which includes antibodies and antigen-specific B- and T-lymphocytes) because it is always present, effective immediately, and relatively non-specific for any given pathogen. The adaptive immune system requires amplification of specific recognition elements and thus takes days to weeks to respond. Even when adaptive immunity is pre-stimulated by vaccination, it may take three days or more to respond to a pathogen whereas innate immunity is immediately or rapidly (hours) available. Innate immunity involves a variety of effector functions including phagocytic cells, complement, etc, but is generally incompletely understood. Generally speaking many innate immune responses are “triggered” by the binding of microbial signaling molecules with pattern recognition receptors termed Toll-like receptors on the surface of host cells. Many of these effector functions are grouped together in the inflammatory response. However too severe an inflammatory response can result in responses that are harmful to the body, and in an extreme case sepsis and potentially death can occur.

[0006] The release of structural components from infectious agents during infection causes an inflammatory response, which when unchecked can lead to the potentially lethal condition, sepsis. Sepsis occurs in approximately 780,000 patients in North America annually. Sepsis may develop as a result of infections acquired in the community such as pneumonia, or it may be a complication of the treatment of trauma, cancer Or major surgery. Severe sepsis Occurs when the body is overwhelmed by the inflammatory response and body organs begin to fail. Up to 120,000 deaths occur annually in the United Stated due to sepsis. Sepsis may also involve pathogenic microorganisms or toxins in the blood (e.g., septicemia), which is a leading cause of death among humans. Gram-negative bacteria are the organisms most commonly associated with such diseases. However, gram-positive bacteria are an increasing cause of infections. Gram-negative and Gram-positive bacteria and their components can all cause sepsis.

[0007] The presence of microbial components induce the release of pro- inflammatory cytokines of which tumor necrosis factor-a. (TNF-a) is of extreme "importance. TNF-a and other pro-inflammatory cytokines can then cause the release of other pro-inflammatory mediators and lead to an inflammatory cascade. Gram- negative sepsis is usually caused by the release of the bacterial outer membrane component, lipopolysaccharide (LPS; also referred to as endotoxin). Endotoxin in the blood, called endotoxemia comes primarily from a bacterial infection, and may be released during treatment with antibiotics. Gram-positive sepsis can be caused by the release of bacterial cell wall components such as lipoteichoic acid (LTA), peptidoglycan (PG), thamnose-glucose polymers made by Streptococci, or capsular polysaccharides made by Staphylococci. Bacterial or other non-mammalian DNA that, unlike mammalian DNA, frequently contains unmethylated cytosine-guanosine dimers (CpG DNA) has also been shown to induce septic conditions including the production of TNF-a. Mammalian DNA contains CpG dinucleotides at a much lower frequency, often in a methylated form. In addition to their natural release during bacterial infections, antibiotic treatment can also cause release of the bacterial cell wall components LPS and LTA and probably also bacterial DNA. This can then hinder recovery from infection or even cause sepsis.

[0008] Cationic peptides are being increasingly recognized as a form of defense against infection, although the major effects recognized in the scientific and patent literature are the antimicrobial effects (Hancock, R.E.-W., and R. Lehrer. 1998.

Cationic peptides: a new source of antibiotics. Trends in Biotechnolo gy 16: 82-88.).

Cationic peptides having antimicrobial activity have been isolated from a wide variety of organisms. In nature, such peptides provide a defense mechanism against microorganisms such as bacteria and yeast. Generally, these cationic peptides are thought to exert their antimicrobial activity on bacteria by interacting with the cytoplasmic membrane, and in most cases, forming channels or lesions. In gram- negative bacteria, they interact with LPS to permeabilize the outer membrane, leading : to self promoted uptake across the outer membrane and access to the cytoplasmic ) membrane. Examples of cationic antimicrobial peptides include indolicidin, defensins, cecropins, and magainins. .

[0009] Recently it has been increasingly recognized that such peptides are . effectors in other aspects of innate immunity (Hancock, R.E.W. and G. Diamond. © 2000. The role of cationic peptides in innate host defenses. Trends in Microbiology - 8:402-410.; Hancock, R. EW. 2001. Cationic peptides: effectors in innate immunity and novel antimicrobials. Lancet Infectious Diseases 1:156-164) although it was not known if the antimicrobial and effector functions are independent.

[0010] Some cationic peptides have an affinity for binding bacterial products such as LPS and LTA. Such cationic peptides can suppress cytokine production in response to LPS, and to varying extents can prevent lethal shock. However it has not been proven as to whether such effects are due to binding of the peptides to LPS and

LTA, or due to a direct interaction of the peptides with host cells. Cationic peptides are induced, in response to challenge by microbes or microbial signaling molecules like LPS, by a regulatory pathway similar to that used by the mammalian immune system (involving Toll receptors and the transcription factor; NFB). Cationic peptides therefore appear to have a key role in innate immunity. Mutations that affect the induction of antibacterial peptides can reduce survival in response to bacterial challenge. As well, mutations of the Toll pathway of Drosophila that lead to decreased antifungal peptide expression result in increased susceptibility to lethal fungal infections. In humans, patients with specific granule deficiency syndrome, completely lacking in a-defensins, suffer from frequent and severe bacterial infections. Other evidence includes the inducibility of some peptides by infectious agents, and the very high concentrations that have been recorded at sites of inflammation. Cationic peptides may also regulate cell migration, to promote the ability of leukocytes to combat bacterial infections. For example, two human a- defensin peptides, HNP-1 and HNP-2, have been indicated to have direct chemotactic activity for murine and human T cells and monocytes, and human B-defensins appear to act as chemoattractants for immature dendritic cells and memory T cells through interaction with CCR6. Similarly, the porcine cationic peptide, PR-39 was found to be chemotactic for neutrophils. It is unclear however as to whether peptides of different structures and compositions share these properties.

[0011] The single known cathelicidin from humans, LL-37, is produced by myeloid precursors, testis, human keratinocytes during inflammatory disorders and airway epithelium. The characteristic feature of cathelicidin peptides is a high level of sequence identity at the N-terminus prepro regions termed the cathelin domain.

Cathelicidin peptides are stored as inactive propeptide precursors that, upon stimulation, are processed into active peptides.

SUMMARY OF THE INVENTION

[0012] The present invention is based on the seminal discovery that based on patterns of polynucleotide expression regulated by endotoxic lipopolysaccharide, lipoteichoic acid, CpG DNA, or other cellular components (e.g., microbe or their cellular components), and affected by cationic peptides, one can screen for novel compounds that block or reduce sepsis and/or inflammation in a subject. Further, based on the use of cationic peptides as a tool, one can identify selective enhancers of innate immunity that do not trigger the sepsis reaction and that can block/dampen inflammatory and/or septic responses.

[0013] Thus, in one embodiment, a method of identifying a polynucleotide or pattern of polynucleotides regulated by one or more sepsis or inflammatory inducing agents and inhibited by a cationic peptide, is provided. The method of the invention includes contacting the polynucleotide or polynucleotides with one or more sepsis or

EE y inflammatory inducing agents and contacting the polynucleotide or polynucleotides with a cationic peptide either simultaneously or immediately thereafter. Differences no in expression are detected in the presence and absence of the cationic peptide, and a change in expression, either up- or down-regulation, is indicative of a polynucleotide or pattern of polynucleotides that is regulated by a sepsis or inflammatory inducing agent and inhibited by a cationic peptide. In another aspect the invention provides a polynucleotide or polynucleotides identified by the above method. Examples of - sepsis or inflammatory regulatory agents include LPS, LTA or CpG DNA or microbial components (or any combination thereof), or related agents.

[0014] In another embodiment, the invention provides a method of identifying an agent that blocks sepsis or inflammation including combining a polynucleotide identified by the method set forth above with an agent wherein expression of the polynucleotide in the presence of the agent is modulated as compared with expression in the absence of the agent and wherein the modulation in expression affects an inflammatory or septic response.

[0015] In another embodiment, the invention provides a method of identifying a pattern of polynucleotide expression for inhibition of an inflammatory or septic response by 1) contacting cells with LPS, LTA and/or CpG DNA in the presence or absence of a cationic peptide and 2) detecting a pattern of polynucleotide expression for the cells in the presence and absence of the peptide. The pattern obtained in the presence of the peptide represents inhibition of an inflammatory or septic response.

In another aspect the pattern obtained in the presence of the peptide is compared to the pattern of a test compound to identify a compound that provides a similar pattern.

In another aspect the invention provides a compound identified by the foregoing method.

[0016] In another embodiment, the invention provides a method of identifying an agent that enhances innate immunity by contacting a polynucleotide or ’ polynucleotides that encode a polypeptide involved in innate immunity, with an agent of interest, wherein expression of the polynucleotide in the presence of the agent is . modulated as compared with expression of the polynucleotide in the absence of the agent and wherein the modulated expression results in enhancement of innate immunity. Preferably, the agent does not stimulate a sepsis reaction in a subject. In one aspect, the agent increases the expression of an anti-inflammatory polynucleotide.

Exemplary, but non-limiting anti-inflammatory polynucleotides encode proteins such as IL-1 R antagonist homolog 1 (A1167887), IL-10R beta (AA486393), IL-10R alpha (U00672) TNF Receptor member 1B (AA15041 6), TNF receptor member 5 (H98636), TNF receptor member 11b (AA194983), IK cytokine down-regulator of

HLA II (R39227), TGF-B inducible early growth response 2 (AI473938), CD2 (AA927710), IL-19 (NM_013371) or IL-10 (M57627). In one aspect, the agent decreases the expression of polynucleotides encoding proteasome subunits involved in NF-«B activation such as proteasome subunit 26S (NM_013371). In one aspect, the agent may act as an antagonist of protein kinases. In one aspect, the agent is a peptide . selected from SEQ ID NO:4-54.

[0017] In another embodiment, the invention provides a method of identifying a pattern of polynucleotide expression for identification of a compound that selectively enhances innate immunity. The invention includes detecting a pattern of polynucleotide expression for cells contacted in the presence and absence of a cationic peptide, wherein the pattern in the presence of the peptide represents stimulation of innate immunity; detecting a pattern of polynucleotide expression for cells contacted in the presence of a test compound, wherein a pattern with the test compound thatis similar to the pattern observed in the presence of the cationic peptide, is indicative of a compound that enhances innate immunity. It is preferred that the compound does not stimulate a septic reaction in a subject.

[0018] In another embodiment, the invention provides a method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject by identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by an increase in polynucleotide expression of at least 2 polynucleotides in Table 50, 51 and or 52, as compared to a non-infected subject. Also included is a polynucleotide expression pattern obtained by any of the methods described above. 7 _ i

[0019] In another aspect a cationic peptide that is an antagonist of CXCR-4 is provided. In still another aspect, a method of identifying a cationic peptide that is an antagonist of CXCR-4 by contacting T cells with SDF-1 in the presence of absence of a test peptide and measuring chemotaxis is provided. A decrease in chemotaxis in the presence of the test peptide is indicative of a peptide that is an antagonist of CXCR-4.

Cationic peptide also acts to reduce the expression of the SDF-1 receptor polynucleotide (NM_013371).

[0020] In all of the above described methods, the compounds or agents of the invention include but are not limited to peptides, cationic peptides, peptidomimetics, chemical compounds, polypeptides, nucleic acid molecules and the like.

[0021] In still another aspect the invention provides an isolated cationic peptide.

An isolated cationic peptide of the invention is represented by one of the following general formulas and the single letter amino acid code:

XX: X3IX PX IP Xs Xo X) (SEQ ID NO: 4), where X, is one or two of R, L or

K, X,isone of C, Sor A, Xs isonec of R or P, X4 is one of A or V and Xs is one of V or W;

X, LX XK XX, XsX3PX3X, (SEQ ID NO: 11), where X, is one or two of D,

E,S, TorN, X2 is one or two of P, Gor D, Xz is one of G, A, V,L,IorY, X,isone of R, Kor Hand Xsisone of S, T, C, Mor R;

Xi Xo X3XaWX4 WX, XsK (SEQ ID NO: 18), where X| is one to four chosen from A, P or R, X; is one or two aromatic amino acids (F, Y and W), X; is one of P or

K, X, is one, two or none chosen from A, P, Y or W and Xj is one to three chosen from Ror P;

XX X3XaX1 VX3XRGXeX3XeX 1 X3X) (SEQ ID NO: 25) where X| is one or two of R or K, X; is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H),

X;isC,S,M,DorAand XsisF,L, V,MorR;

XXX XeX 1 VXsXRGXe XXX: X3X (SEQ ID NO: 32), where X, is one or two of R or K, X; is a polar or charged amino acid (S, T, M,N, Q, D, E, K, R and H),

X; is one of C, S, M, D or A, Xs is one of F, I, V, Mor R and Xsisoneof A, I, S, M,

D or R; and

KX KX, FX, KMLMX,ALKKX; (SEQ ID NO: 39), where X; is a polar amino acid (C, S, T,M, Nand Q); X; isone of A, L, S or K and Xs is 1-17 amino acids chosen from G, A, V,L,L,P,F, S, T,K and H;

KWEKX>X 1X1 Xa XX 1 XXX Xi Xo Xo IFHTALKPISS (SEQ ID NO: 46), where

X is a hydrophobic amino acid and Xz is a hydrophilic amino acid.

[0022] Additionally, in another aspect the invention provides isolated cationic peptides KWKSFLRTFKSPVRTVFHTALKPISS (SEQ ID NO: 53) and

KWKSYAHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

[0023] Also provided are nucleic acid sequences encoding the cationic peptides of the invention, vectors including such polynucleotides and host cells containing the vectors.

[0024] In another embodiment, the invention provides methods for stimulating or enhancing innate immunity in a subject comprising administering to the subject a peptide of the invention, for example, peptides set forth in SEQ ID NO:1-4, 11, 18, 25, 32, 39, 46, 53 or 54. As shown in the Examples herein, innate immunity can be evidenced by monocyte activation, proliferation, differentiation or MAP kinase pathway activation just by way of example. In one aspect, the method includes further administering a serum factor such as GM-CSF to the subject. The subject is preferably any mammal and more particularly a human subject. . [0025] In another embodiment, the invention provides a method of stimulating innate immunity in a subject having or at risk of having an infection including administering to the subject a sub-optimal concentration of an antibiotic in : : combination with a peptide of the invention. In one aspect, the peptide is SEQ ID

NO:1 or SEQ ID NO:7.

BRIEF DESCRIPTION OF THE FIGURES

[0026] FIGURE 1 demonstrates the synergy of Seq ID No: 7 with cefepime in curing S.aureus infections. CD-1 mice (8/group) were given 1 x 10’ S. aureus in 5%

porcine mucin via IP injection. Test compound (50 pg —2.5 mg/kg) was given viaa separate IP injection 6 hours after S. aureus. At this time Cefepime was also given at a dose of 0.1 mg/kg. Mice were euthanized 24 hr later, blood removed and plated for viable counts. The average + standard error is shown. This experiment was repeated twice.

[0027] FIGURE 2 shows exposure to SEQ ID NO: | induces phosphorylation of

ERK 1/2 and p38. Lysates from human peripheral blood derived monocytes were exposed to 50 pg/ml of SEQ ID NO: 1 for 15 minutes. A) Antibodies specific for the phosphorylated forms of ERK and p38 were used to detect activation of ERK 1/2 and p38. All donors tested showed increased phosphorylation of ERK1/2 and p38 in response to SEQ ID NO: 1 treatment . One representative donor of eight. Relative amounts of phosphorylation of ERK (B) and p38(C) were determined by dividing the intensities of the phosphorylated bands by the intensity of the corresponding control band as described in the Materials and Methods.

[0028] FIGURE 3 shows LL-37 induced phosphorylation of ERK 1/2 does not occur in the absence of serum and the magnitude of phosphorylation is dependent upon the type of serum present. Human blood derived monocytes were treated with 50 pg/ml of LL-37 for 15 minutes. Lysates were run on a 12% acrylamide gel then transferred to nitrocellulose membrane and probed with antibodies specific for the phosphorylated (active) form of the kinase. To normalize for protein loading, the blots were reprobed with -actin. Quantification was done with ImageJ software. The

FIGURE 3 inset demonstrates that LL-37 is unable to induce MAPK activation in human monocytes under serum free conditions. Cells were exposed to 50 mg/ml of

LL-37 (+), or endotoxin free water (-) as a vehicle control, for 15 minutes. (A) After exposure to LL-37 in media containing 10% fetal calf serum, phosphorylated ERK 1/2 was detectable, however, no phosphorylation of ERK 1/2 was detected in the absence of serum (n=3). (B) Elk-1, a transcription factor downstream of ERK 1/2, was activated (phosphorylated) upon exposure to 50 pg/ml of LL-37 in media containing 10% fetal calf serum, but not in the absence of serum (n=2).

[0029] FIGURE 4 shows LL-37 induced activation of ERK 1/2 occurs at lower concentrations and is amplified in the presence of certain cytokines. When freshly isolated monocytes were stimulated in media containing both GM-CSF (100ng/ml) and IL-4 (100ng/m1) LL-37 induced phosphorylation of ERK 1/2 was apparent at concentrations as low as 5 pg/ml. This synergistic activation of ERK 1/2 seems to be due primarily to GM-CSF.

[0030] Figure 5 shows peptide affects both transcription of various cytokine genes and release of IL-8 in the 16HBE4o- human bronchial epithelial cell line. Cells were grown to confluency on a semi-permeable membrane and stimulated on the apical surface with 50 pg/ml of SEQ ID NO: 1 for four hours. A) SEQ ID NO: 1 treated cells produced significantly more IL-8 than controls, as detected by ELISA in the supernatant collected from the apical surface, but not from the basolateral surface.

Mean + SE of three independent experiments shown, asterisk indicates p=0.002. B)

RNA was collected from the above experiments and RT-PCR was performed. A number of cytokine genes known to be regulated by either ERK 1/2 or p38 were up- : regulated upon stimulation with peptide. The average of two independent experiments is shown. .

DETAILED DESCRIPTION OF THE INVENTION

[0031) The present invention provides novel cationic peptides, characterized by a group of generic formulas, which have ability to modulate (e.g., up- and/or down regulate) polynucleotide expression, thereby regulating sepsis and inflammatory "responses and/or innate immunity. (0032] “Innate immunity” as used herein refers to the natural ability of an organism to defend itself against invasions by pathogens. Pathogens or microbes as used herein, may include, but are not limited to bacteria, fungi, parasite, and viruses.

Innate immunity is contrasted with acquired/adaptive immunity in which the organism develops a defensive mechanism based substantially on antibodies and/or immune lymphocytes that is characterized by specificity, amplifiability and self vs. non-self dsicrimination. With innate immunity, broad, nonspecific immunity is provided and there is no immunologic memory of prior exposure. The hallmarks of innate immunity are effectiveness against a broad variety of potential pathogens, independence of prior exposure to a pathogen, and immediate effectiveness (in contrast to the specific immune response which takes days to weeks to be elicited). In addition, innate immunity includes immune responses that affect other diseases, such as cancer, inflammatory diseases, multiple sclerosis, various viral infections, and the like.

[0033] As used herein, the term “cationic peptide” refers to a sequence of amino acids from about § to about 50 amino acids in length. In one aspect, the cationic peptide of the invention is from about 10 to about 35 amino acids in length. A peptide is “cationic” if it possesses sufficient positively charged amino acids to have a pKa greater than 9.0. Typically, at least two of the amino acid residues of the cationic peptide will be positively charged, for example, lysine or arginine. “Positively charged” refers to the side chains of the amino acid residues which have a net positive charge at pH 7.0. Examples of naturally occurring cationic antimicrobial peptides which can be recombinantly produced according to the invention include defensins, " cathelicidins, magainins, melittin, and cecropins, bactenecins, indolicidins, polyphemusins, tachyplesins, and analogs thereof. A variety of organisms make cationic peptides, molecules used as part of a non-specific defense mechanism against microorganisms. When isolated, these peptides are toxic to a wide variety of microorganisms, including bacteria, fungi, and certain enveloped viruses. While cationic peptides act against many pathogens, notable exceptions and varying degrees of toxicity exist. However this patent reveals additional cationic peptides with no toxicity towards microorganisms but an ability to protect against infections through stimulation of innate immunity, and this invention is not limited to cationic peptides : with antimicrobial activity. In fact, many peptides useful in the present invention do not have antimicrobial activity.

[0034] Cationic peptides known in the art include for example, the human cathelicidin LL-37, and the bovine neutrophil peptide indolicidin and the bovine variant of bactenecin, Bac2A.

LL-37 LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES (SEQ

DN olicidin. ILPWKWPWWPWRR:NH (SEQ ID NO: 2)

Bac2A RLARIVVIRVAR-NH, (SEQ ID NO: 3)

[0035] In innate immunity, the immune response is not dependent upon antigens.

The innate immunity process may include the production of secretory molecules and cellular components as set forth above. In innate immunity, the pathogens are recognized by receptors encoded in the germline. These Toll-like receptors have broad specificity and are capable of recognizing many pathogens. When cationic peptides are present in the immune response, they aid in the host response to pathogens. This change in the immune response induces the release of chemokines, which promote the recruitment of immune cells to the site of infection.

[0036] Chemokines, or chemoattractant cytokines, are a subgroup of immune factors that mediate chemotactic and other pro-inflammatory phenomena (See, Schall, 1991, Cytokine 3:165-1 83). Chemokines are small molecules of approximately 70-80 residues in length and can generally be divided into two subgroups, @ which have two

N-terminal cysteines separated by a single amino acid (CxC) and 8 which have two adjacent cysteines at the N terminus (CC). RANTES, MIP-1a and MIP-18 are members of the 8 subgroup (reviewed by Horuk, R., 1994, Trends Pharmacol. Sci, 15:159-165; Murphy, P. M.,, 1994, Annu. Rev. Immunol., 12:593-633). The amino terminus of the chemokines RANTES, MCP-1, and MCP-3 have been implicated in the mediation of cell migration and inflammation induced by these chemokines. This involvement is suggested by the observation that the deletion of the amino terminal 8 residues of MCP-1, amino terminal 9 residues of MCP-3, and amino terminal 8 residues of RANTES and the addition of 2 methionine to the amino terminus of

RANTES, antagonize the chemotaxis, calcium mobilization and/or enzyme release stimulated by their native counterparts (Gong et al., 1996 J. Biol. Chem. 271:10521- 10527; Proudfoot et al., 1996 J. Biol. Chem. 271:2599-2603). Additionally, a chemokine-like chemotactic activity has been introduced into MCP-1 via a double mutation of Tyr 28 and Arg 30 to leucine and valine, respectively, indicating that internal regions of this protein also play a role in regulating chemotactic activity (Beall et al, 1992, J. Biol. Chem. 267:3455-3459).

[0037] The monomeric forms of all chemokines characterized thus far share significant structural homology, although the quaternary structures of a and B groups are distinct. While the monomeric structures of the 8 and oe chemokines are very similar, the dimeric structures of the two groups are completely different. An additional chemokine, lymphotactin, which has only one N terminal cysteine has also been identified and may represent an additional subgroup (v) of chemokines (Yoshida et al., 1995, FEBS Lett. 360:155-159; and Kelner et al., 1994, Science 266:1395- 1399).

[0038] Receptors for chemokines belong to the large family of G-protein coupled, 7 transmembrane domain receptors (GCR’s) (See, reviews by Horuk, R., 1994,

Trends Pharmacol. Sci. 15:159-165; and Murphy, P. M., 1994, Annu. Rev. Immunol. 12:593-633). Competition binding and cross-desensitization studies have shown that chemokine receptors exhibit considerable promiscuity in ligand binding. Examples "demonstrating the promiscuity among £8 chemokine receptors include: CC CKR-1, which binds RANTES and MIP-1a (Neote et al., 1993, Cell 72: 415-425), CC CKR-4, which binds RANTES, MIP-1¢, and MCP-1 (Power et al., 1995, J. Biol. Chem. 270:19495-19500), and CC CKR-5, which binds RANTES, MIP-1¢, and MIP-18 (Alkhatib et al., 1996, Science, in press and Dragic et al., 1996, Nature 381:667-674).

Erythrocytes possess a receptor (known as the Duffy antigen) which binds both cand £8 chemokines (Horuk et al., 1994, J. Biol. Chem. 269:17730-17733; Neote et al., 1994, Blood 84:44-52; and Neote et al., 1993, J. Biol. Chem. 268:12247-12249). Thus the sequence and structural homologies evident among chemokines and their receptors allows some overlap in receptor-ligand interactions.

[0039] In one aspect, the present invention provides the use of compounds including peptides of the invention to reduce sepsis and inflammatory responses by acting directly on host cells. In this aspect, a method of identification of a polynucleotide or polynucleotides that are regulated by one or more sepsis or inflammatory inducing agents is provided, where the regulation is altered by a cationic peptide. Such sepsis or inflammatory inducing agents include, but are not limited to endotoxic lipopolysaccharide (LPS), lipoteichoic acid (LTA) and/or CpG

DNA or intact bacteria or other bacterial components. The identification is performed by contacting the polynucleotide or polynucleotides with the sepsis or inflammatory inducing agents and further contacting with a cationic peptide either simultaneously or immediately after. The expression of the polynucleotide in the presence and absence of the cationic peptide is observed and a change in expression is indicative of a polynucleotide or pattern of polynucleotides that is regulated by a sepsis or inflammatory inducing agent and inhibited by a cationic peptide. In another aspect, the invention provides a polynucleotide identified by the method.

[0040] Once identified, such polynucleotides will be useful in methods of screening for compounds that can block sepsis or inflammation by affecting the expression of the polynucleotide. Such an effect on expression may be either up regulation or down regulation of expression. By identifying compounds that do not trigger the sepsis reaction and that can block or dampen inflammatory or septic responses, the present invention also presents a method of identifying enhancers of innate immunity. Additionally, the present invention provides compounds that are used or identified in the above methods.

[0041] Candidate compounds are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced.

Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, and the like to produce structural analogs. Candidate agents are also found among biomolecules including, but not limited to: peptides, peptidiomimetics, saccharides, fatty acids, steroids, purines, pyrimidines, polypeptides, polynucleotides, chemical compounds, derivatives, structural analogs or combinations thereof.

[0042] Incubating components of a screening assay includes conditions which allow contact between the test compound and the polynucleotides of interest. : Contacting includes in solution and in solid phase, or in a cell. The test compound may optionally be a combinatorial library for screening a plurality of compounds.

Compounds identified in the method of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a compound.

[0043] Generally, in the methods of the invention, a cationic peptide is utilized to detect and locate a polynucleotide that is essential in the process of sepsis or inflammation. Once identified, a pattern of polynucleotide expression may be obtained by observing the expression in the presence and absence of the cationic peptide. The pattern obtained in the presence of the cationic peptide is then useful in identifying additional compounds that can inhibit expression of the polynucleotide and therefore block sepsis or inflammation. It is well known to one of skill in the art that non-peptidic chemicals and peptidomimetics can mimic the ability of peptides to bind to receptors and enzyme binding sites and thus can be used to block or stimulate biological reactions. Where an additional compound of interest provides a pattern of polynucleotide expression similar to that of the expression in the presence of a cationic peptide, that compound is also useful in the modulation of sepsis or an innate "immune response. In this manner, the cationic peptides of the invention, which are known inhibitors of sepsis and inflammation and enhancers of innate immunity are useful as tools in the identification of additional compounds that inhibit sepsis and inflammation and enhance innate immunity.

[0044] As canbeseen inthe Examples below, peptides of the invention have a widespread ability to reduce the expression of polynucleotides regulated by LPS.

High levels of endotoxin in the blood are responsible for many of the symptoms seen during a serious infection or inflammation such as fever and an elevated white blood cell count. Endotoxin is a component of the cell wall of Gram-negative bacteria and is a potent trigger of the pathophysiology of sepsis. The basic mechanisms of inflammation and sepsis are related. In Example 1, polynucleotide arrays were utilized to determine the effect of cationic peptides on the transcriptional response of epithelial cells. Specifically, the effects on over 14,000 different specific polynucleotide probes induced by LPS were observed. The tables show the changes seen with cells treated with peptide compared to control cells. The resulting data indicated that the peptides have the ability to reduce the expression of polynucleotides induced by LPS.

[0045] Example 2, similarly, shows that peptides of the invention are capable of neutralizing the stimulation of immune cells by Gram positive and Gram negative bacterial products. Additionally, it is noted that certain pro-inflammatory : polynucleotides are down-regulated by cationic peptides, as set forth in table 24 such : as TLR1 (AI339155), TLR2 (T57791), TLRS (N41021), TNF receptor-associated factor 2 (T55353), TNF receptor-associated factor 3 (AA504259), TNF receptor superfamily, member 12 (W71984), TNF receptor superfamily, member 17 (AA987627), small inducible cytokine subfamily B, member 6 (AI889554), IL-12R beta 2 (AA977194), IL-18 receptor 1 (AA482489), while anti-inflammatory polynucleotides are up-regulated by cationic peptides, as seen in table 25 such as IL-1

R antagonist homolog 1 (AI167887), IL-10 R beta (AA486393), TNF Receptor member 1B (AA150416), TNF receptor member 5 (H98636), TNF receptor member 11b (AA194983), IK cytokine down-regulator of HLA II (R39227), TGF-B inducible early growth response 2 (A1473938), or CD2 (AA927710). The relevance and application of these results are confirmed by an in vivo application to mice.

[0046] In another aspect, the invention provides a method of identifying an agent that enhances innate immunity. In the method, a polynucleotide or polynucleotides that encode a polypeptide involved in innate immunity is contacted with an agent of interest. Expression of the polynucleotide is determined, both in the presence and absence of the agent. The expression is compared and of the specific modulation of expression was indicative of an enhancement of innate immunity. In another aspect, the agent does not stimulate a septic reaction as revealed by the lack of upregulation of the pro-inflammatory cytokine TNF-a. In still another aspect the agent reduces or blocks the inflammatory or septic response. In yet another aspect, the agent reduces the expression of TNF-a and/or interleukins including, but not limited to, IL-18, IL-6,

IL-12 p40, IL-12 p70, and IL-8. 17 id

[0047] In another aspect, the invention provides methods of direct polynucleotide regulation by cationic peptides and the use of compounds including cationic peptides to stimulate elements of innate immunity. In this aspect, the invention provides a method of identification of a pattern of polynucleotide expression for identification of a compound that enhances innate immunity. In the method of the invention, an initial detection of a pattern of polynucleotide expression for cells contacted in the presence and absence of a cationic peptide is made. The pattern resulting from polynucleotide expression in the presence of the peptide represents stimulation of innate immunity.

A pattern of polynucleotide expression is then detected in the presence of a test compound, where a resulting pattern with the test compound that is similar to the pattern observed in the presence of the cationic peptide is indicative of 2 compound that enhances innate immunity. In another aspect, the invention provides compounds that are identified in the above methods. In another aspect, the compound of the invention stimulates chemokine or chemokine receptor expression. Chemokine or chemokine receptors may include, but are not limited to CXCR4, CXCR1, CXCR2,

CCR2, CCR4, CCRS, CCR6, MIP-1 alpha, MDC, MIP-3 alpha, MCP-1, MCP-2,

MCP-3, MCP-4, MCP-5, and RANTES. In still another aspect, the compound is a peptide, peptidomimetic, chemical compound, or a nucleic acid molecule.

[0048] In still another aspect the polynucleotide expression pattern includes expression of pro-inflammatory polynucleotides. Such pro-inflammatory : polynucleotides may include, but are not limited to, ring finger protein 10 (D87451), serine/threonine protein kinase MASK (AB040057), KIAA0912 protein (AB020719),

KIAAO0239 protein (D87076), RAP1, GTPase activating protein 1 (M64788), FEM-1- like death receptor binding protein (AB007856), cathepsin S (M90696), hypothetical protein FLJ20308 (AK000315), pim-1 oncogene (M54915), proteasome subunit beta type 5 (D29011), KIAA0239 protein (D87076), mucin 5 subtype B tracheobronchial (AJ001403), cAMP response element-binding protein CREBPa, integrin alpha M (703925), Rho-associated kinase 2 (NM_004850), PTDO017 protein (AL050361) unknown genes (AK001143, AK034348, AL049250, AL16199, AL031983) and any combination thereof. In still another aspect the polynucleotide expression pattern includes expression of cell surface receptors that may include but is not limited to retinoic acid receptor (X06614), G protein-coupled receptors (294155, X81892,

U52219, U22491, AF015257, U66579) chemokine (C-C motif) receptor 7 (L31584), tumor necrosis factor receptor superfamily member 17 (229575), interferon gamma receptor 2 (U05875), cytokine receptor-like factor 1 (AF059293), class | cytokine receptor (AF053004), coagulation factor II (thrombin) receptor-like 2 (U92971), leukemia inhibitory factor receptor (NM_002310), interferon gamma receptor 1 (AL050337). )

[0049] In Example 4 it can be seen that the cationic peptides of the invention alter polynucleotide expression in macrophage and epithelial cells. The results of this example show that pro-inflammatory polynucleotides are down-regulated by cationic peptides (Table 24) whereas anti-inflammatory polynucleotides are up-regulated by cationic peptides (Table 25).

[0050] It is shown below, for example, in tables 1-15, that cationic peptides can neutralize the host response to the signaling molecules of infectious agents as well as modify the transcriptional responses of host cells, mainly by down-regulating the pro- inflammatory response and/or up-regulating the anti-inflammatory response. :

Example S shows that the cationic peptides can aid in the host response to pathogens by inducing the release of chemokines, which promote the recruitment of immune cells to the site of infection. The results are confirmed by an in vivo application to mice.

[0051] It is seen from the examples below that cationic peptides have a substantial influence on the host response to pathogens in that they assist in regulation of the host immune response by inducing selective pro-inflammatory responses that for example promote the recruitment of immune cells to the site of infection but not inducing potentially harmful pro-inflammatory cytokines. Sepsis appears to be caused in part by an overwhelming pro-inflammatory response to infectious agents. Cationic peptides aid the host in a “balanced” response to pathogens by inducing an anti- inflammatory response and suppressing certain potentially harmful pro-inflammatory responses.

[0052] In Example 7, the activation of selected MAP kinases was examined, to study the basic mechanisms behind the effects of interaction of cationic peptides with cells. Macrophages activate MEK/ERK kinases in response to bacterial infection.

MEK is a MAP kinase kinase that when activated, phosphorylates the downstream kinase ERK (extracellular regulated kinase), which then dimerizes and translocates to the nucleus where it activates transcription factors such as Elk-1 to modify polynucleotide expression. MEK/ERK kinases have ‘been shown to impair replication of Salmonella within macrophages. Signal transduction by MEK kinase and NADPH oxidase may play an important role in innate host defense against intracellular pathogens. By affecting the MAP kinases as shown below the cationic peptides have an effect on bacterial infection. The cationic peptides can directly affect kinases.

Table 21 demonstrates but is not limited to MAP kinase polynucleotide expression changes in response to peptide. The kinases include MAP kinase kinase 6 (H070920),

MAP kinase kinase 5 (W69649), MAP kinase 7 (H39192), MAP kinase 12 (AI936909) and MAP kinase-activated protein kinase 3 (W68281).

[0053] In another method, the methods of the invention may be used in } combination, to identify an agent with multiple characteristics, i.e. a peptide with anti- inflammatory/anti-sepsis activity, and the ability to enhance innate immunity, in part by inducing chemokines in vivo.

[0054] In another aspect, the invention provides a method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject by identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by an increase in polynucleotide expression of at least 2 polynucleotides in Table 55 as compared to a non-infected subject. In another aspect the invention provides a method for inferring a state of infection in a mammalian subject from 2 nucleic acid sample of the subject by identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by a polynucleotide expression of at least 2 polynucleotides in Table 56 or Table 57 as compared to a non-infected subject. In one aspect of the invention, the state of infection is due to infectious agents or signaling molecules derived therefrom, such as, but not limited to, Gram negative bacteria and Gram positive bacteria, viral, fungal or parasitic agents.- In still another aspect the invention provides a polynucleotide expression pattern of a subject having a state of infection identified by the above method. Once identified, such -

polynucleotides will be useful in methods of diagnosis of a condition associated with the activity or presence of such infectious agents or signaling molecules. :

[0055] Example 10 below demonstrates this aspect of the invention. Specifically, table 61 demonstrates that both MEK and the NADPH oxidase inhibitors can limit bacterial replication (infection of IFN-y-primed macrophages by S. typhimurium triggers a MEK kinase). This is an example of how bacterial survival can be impacted by changing host cell signaling molecules.

[0056] In still another aspect of the invention, compounds are presented that inhibit stromal derived factor-1 (SDF-1) induced chemotaxis of T cells. . Compounds are also presented which decrease expression of SDF-1 receptor. Such compounds also may act as an antagonist or inhibitor of CXCR-4. In one aspect the invention provides a cationic peptide that is an antagonist of CXCR-4. In another aspect the invention provides a method of identifying a cationic peptide that is an antagonist of

CXCR-4. The method includes contacting T cells with SDF-1 in the presence of absence of a test peptide and measuring chemotaxis. A decrease in chemotaxis in the presence of the test peptide is then indicative of a peptide that is an antagonist of

CXCR-4. Such compounds and methods are useful in therapeutic applications in HIV patients. These types of compounds and the utility thereof is demonstrated, for example, in Example 11 (see also Tables 62, 63). In that example, cationic peptides are shown to inhibit cell migration and therefore antiviral activity.

[0057] In one embodiment, the invention provides an isolated cationic peptides having an amino acid sequence of the general formula (Formula A):

X; Xo X3DXPXIPX Xa X; (SEQ ID NO: 4), wherein X, is one or two of R, L or K, X; is one of C, S or A, X; isone of R or P, X; is one of A or V and Xsis one of Vor W.

Examples of the peptides of the invention include, but are not limited to:

LLCRIVPVIPWCK (SEQ ID NO: 5), LRCPIAPVIPVCKK (SEQ ID NO: 6),

KSRIVPAIPVSLL (SEQ ID NO: 7), KKSPIAPAIPWSR (SEQ ID NO: 8),

RRARIVPAIPVARR (SEQ ID NO: 9) and LSRIAPAIPWAKL (SEQ ID NO: 10).

[0058] In another embodiment, the invention provides an isolated linear cationic peptide having an amino acid sequence of the general formula (Formula B):

X; LX; XK XXX sX:PX3X (SEQ ID NO: 1 1), wherein X; is one or two of D,E,S, T or N, X2 is one or two of P, Gor D, Xsisone of G, A, V,L, Tor Y, Xs isone of R, K or H and X; is one of S, T,C,M or R. Examples of the peptides of the invention include, but are not limited to: DLPAKRGSAPGST (SEQ ID NO: 12),

SELPGLKHPCVPGS (SEQ ID NO: 13), TTLGPVKRDSIPGE (SEQ ID NO: 14),

SLPIKHDRLPATS (SEQ ID NO: 15), ELPLKRGRVPVE (SEQ ID NO: 16) and

NLPDLKKPRVPATS (SEQ ID NO: 17).

[0059] In another embodiment, the invention provides an isolated linear cationic peptide having an amino acid sequence of the general formula (Formula C):

XX Xs Xa WX WX XK (SEQ ID NO: 18) (this formula includes CP12a and CP12d) , wherein X is one to four chosen from A, P or R, X; is one or two aromatic amino acids (F, Y and W), X3 is one of Por K, X, is one, two or none chosen from A, P, Y or W and Xs is one to three chosen from R or P. Examples of the peptides of the invention include, but are not limited to: RPRYPWWPWWPYRPRK (SEQ ID NO: 19), RRAWWKAWWARRK (SEQ ID NO: 20), RAPYWPWAWARPRK (SEQ ID

NO: 21), RPAWKYWWPWPWPRRK (SEQ ID NO: 22), RAAFKWAWAWWRRK (SEQ ID NO: 23) and RRRWKWAWPRRK (SEQ ID NO: 24).

[0060] In another embodiment, the invention provides an isolated hexadecameric cationic peptide having an amino acid sequence of the general formula (Formula D):

KX; X2X3XaX) VX3XRGXaX3 XX X5X, (SEQ ID NO: 25) wherein X; is one or two of

R or K, X; is a polar or charged amino acid (S, T, M, N, Q,D,E,K, R and H), X3 is

C,S,M,DorAandXsisF,I,V,MorR. Examples of the peptides of the invention include, but are not limited to: RRMCIKVCVRGVCRRKCRK (SEQ ID NO: 26), ~ KRSCFKVSMRGVSRRRCK (SEQ ID NO: 27), KKDAIKKVDIRGMDMRRAR (SEQ ID NO: 28), RKMVKVDVRGIMIRKDRR (SEQ ID NO: 29),

KQCVKVAMRGMALRRCK (SEQ ID NO: 30) and

RREAIRRVAMRGRDMKRMRR (SEQ ID NO: 31).

[0061] In still another embodiment, the invention provides an isolated hexadecameric cationic peptide having an amino acid sequence of the general formula (Formula E): XXX XX VX sX4RGXa Xs Xa Xi XX; (SEQ ID NO: 32), wherein X is one or two of R or K, X; is a polar or charged amino acid (S, T,M, N,Q, D, E, K, R and H), Xs is one of C, S, M, Dor A, X4 is one of F, I, V, M or R and Xs is one of A,

LS, M, D or R. Examples of the peptides of the invention include, but are not limited to: RTCVKRVAMRGIIRKRCR (SEQ ID NO: 33), KKQMMKRVDVRGISVKRKR (SEQ ID NO: 34), KESIKVIIRGMMVRMKK (SEQ ID NO: 35),

RRDCRRVMVRGIDIKAK (SEQ ID NO: 36), KRTAIKKVSRRGMSVKARR (SEQ

ID NO: 37) and RHCIRRVSMRGIIMRRCK (SEQ ID NO: 38). [0062) In another embodiment, the invention provides an isolated longer cationic peptide having an amino acid sequence of the general formula (Formula F):

KX, KX,FX,KMLMX,ALKK X; (SEQ ID NO: 39), wherein X; is a polar amino acid (C,S, T,M, Nand Q); X;isoneof A,L,SorK and Xj; is 1-17 amino acids chosen from G, A, V,L,I,P,F, S, T,K and H. Examples of the peptides of the invention include, but are not limited to: KCKLFKKMLMLALKKVLTTGLPALKLTK (SEQ

ID NO: 40), KSKSFLKMLMKALKKVLTTGLPALIS (SEQ ID NO: 41),

KTKKFAKMLMMALKKVVSTAKPLAILS (SEQ ID NO: 42),

KMKSFAKMLMLALKKVLKVLTTALTLKAGLPS (SEQ ID NO: 43),

KNKAFAKMLMKALKKVTTAAKPLTG (SEQ ID NO: 44) and

KQKLFAKMLMSALKKKTLVTTPLAGK (SEQ ID NO: 45).

[0063] In yet another embodiment, the invention provides an isolated longer cationic peptide having an amino acid sequence of the general formula (Formula G):

KWKX,X; X31 XXX Xa Xa Xi Xi Xo Xo [FHTALKPISS (SEQ ID NO: 46), wherein X| is a hydrophobic amino acid and X; is a hydrophilic amino acid. Examples of the peptides of the invention include, but are not limited to:

KWKSFLRTFKSPVRTIFHTALKPISS (SEQ ID NO: 47),

KWKSYAHTIMSPVRLIFHTALKPISS (SEQ ID NO: 48),

KWKRGAHRFMKFLSTIFHTALKPISS (SEQ ID NO: 49),

KWKKWAHSPRKVLTRIFHTALKPISS (SEQ ID NO: 50),

KWKSLVMMFKKPARRIFHTALKPISS (SEQ ID NO: 51) and

KWKHALMKAHMLWHMIFHTALKPISS (SEQ ID NO: 52).

[0064] In still another embodiment, the invention provides an isolated cationic peptide having an amino acid sequence of the formula:

KWKSFLRTFKSPVRTVFHTALKPISS (SEQ ID NO: 53) or

KWKSY AHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

[0065] The term «jsolated” as used herein refers to a peptide that is substantially free of other proteins, lipids, and nucleic acids (e.g., cellular components with which an in vivo-produced peptide would naturally be associated). Preferably, the peptide is at least 70%, 80%, or most preferably 90% pure by weight. {0066] The invention also includes analogs, derivatives, conservative variations, and cationic peptide variants of the enumerated polypeptides, provided that the analog, derivative, conservative variation, or variant has a detectable activity in which it enhances innate immunity or has anti-inflammatory activity. It is not necessary that the analog, derivative, variation, or variant have activity identical to the activity of the peptide from which the analog, derivative, conservative variation, or variant is derived.

[0067] A cationic peptide “variant” is an peptide that is an altered form ofa referenced cationic peptide. For example, the term “variant” includes a cationic peptide in which at least one amino acid of a reference peptide is substituted in an expression library. The term “reference” peptide means any of the cationic peptides of the invention (e.g., as defined in the above formulas), from which a variant, derivative, analog, or conservative variation is derived. Included within the term “derivative” is a hybrid peptide that includes at least a portion of each of two cationic peptides (e.g., 30-80% of each of two cationic peptides). Also included are peptides in which one or more amino acids are deleted from the sequence of a peptide enumerated herein, provided that the derivative has activity in which it enhances innate immunity or has anti-inflammatory activity. This can lead to the development of a smaller active molecule which would also have utility. For example, amino or carboxy terminal amino acids which may not be required for enhancing innate immunity or anti-inflammatory activity of a peptide can be removed. Likewise, additional derivatives can be produced by adding one or a few (e.g., less than 5)

amino acids to a cationic peptide without completely inhibiting the activity of the peptide. In addition, C-terminal derivatives, e.g., C-terminal methyl esters, and N- terminal derivatives can be produced and are encompassed by the invention. Peptides of the invention include any analog, homolog, mutant, isomer or derivative of the peptides disclosed in the present invention, so long as the bioactivity as described herein remains. Also included is the reverse sequence of a peptide encompassed by the general formulas set forth above. Additionally, an amino acid of “D” configuration may be substituted with an amino acid of “L” configuration and vice . versa. Alternatively the peptide may be cyclized chemically or by the addition of two or more cysteine residues within the sequence and oxidation to form disulphide bonds.

[0068] The invention also includes peptides that are conservative variations of those peptides exemplified herein. The term “conservative variation” as used herein denotes a polypeptide in which at least one amino acid is replaced by another, biologically similar residue. Examples of conservative variations include the substitution of one hydrophobic residue, such as isoleucine, valine, leucine, alanine, cysteine, glycine, phenylalanine, proline, tryptophan, tyrosine, norleucine or methionine for another, or the substitution of one polar residue for another, such as the substitution of arginine for lysine, glutamic for aspartic acid, or glutamine for asparagine, and the like. Neutral hydrophilic amino acids that can be substituted for one another include asparagine, glutamine, serine and threonine. The term “conservative variation” also encompasses a peptide having a substituted amino acid in place of an unsubstituted parent amino acid. Such substituted amino acids may include amino acids that have been methylated or amidated. Other substitutions will be known to those of skill in the art. In one aspect, antibodies raised to a substituted polypeptide will also specifically bind the unsubstituted polypeptide.

[0069] Peptides of the invention can be synthesized by commonly used methods such as those that include t-BOC or FMOC protection of alpha-amino groups. Both methods involve stepwise synthesis in which a single amino acid is added at each step starting from the C-terminus of the peptide (See, Coligan, et al., Current Protocols in

Immunology, Wiley Interscience, 1991, Unit 9). Peptides of the invention can also be synthesized by the well known solid phase peptide synthesis methods such as those "described by Merrifield, J. Am. Chem. Soc., 85:2149, 1962) and Stewart and Young,

Solid Phase Peptides Synthesis, Freeman, San Francisco, 1969, pp.27-62) using a copoly(styrene-divinylbenzene) containing 0.1-1.0 mMol amines/g polymer. On completion of chemical synthesis, the peptides can be deprotected and cleaved from the polymer by treatment with liquid HF-10% anisole for about 1/4-1 hours at 0°C.

After evaporation of the reagents, the peptides are extracted from the polymer witha 1% acetic acid solution, which is then lyophilized to yield the crude material. The peptides can be purified by such techniques as gel filtration on Sephadex G-15 using 5% acetic acid as a solvent. Lyophilization of appropriate fractions of the column eluate yield homogeneous peptide, which can then be characterized by standard techniques such as amino acid analysis, thin layer chromatography, high performance liquid chromatography, ultraviolet absorption spectroscopy, molar rotation, or measuring solubility. If desired, the peptides can be quantitated by the solid phase

Edman degradation.

[0070] The invention also includes isolated nucleic acids (e.g., DNA, cDNA, or

RNA) encoding the peptides of the invention. Included are nucleic acids that encode analogs, mutants, conservative variations, and variants of the peptides described herein. The term “isolated” as used herein refers to a nucleic acid that is substantially free of proteins, lipids, and other nucleic acids with which an in vivo-produced nucleic acids naturally associated. Preferably, the nucleic acid is at least 70%, 80%, or preferably 90% pure by weight, and conventional methods for synthesizing nucleic acids in vitro can be used in lieu of in vivo methods. As used herein, “nucleic acid” refers to a polymer of deoxyribo-nucleotides or ribonucleotides, in the form of a separate fragment or as a component of a larger genetic construct (e.g., by operably linking a promoter to a nucleic acid encoding a peptide of the invention). Numerous genetic constructs (e.g., plasmids and other expression vectors) are known in the art and can be used to produce the peptides of the invention in cell-free systems or prokaryotic or eukaryotic (e.g., yeast, insect, or mammalian) cells. By taking into account the degeneracy of the genetic code, one of ordinary skill in the art can readily synthesize nucleic acids encoding the polypeptides of the invention. The nucleic acids of the invention can readily be used in conventional molecular biology methods to produce the peptides of the invention.

[0071] DNA encoding the cationic peptides of the invention can be inserted into an “expression vector.” The term “expression vector” refers to a genetic construct such as a plasmid, virus or other vehicle known in the art that can be engineered to contain a nucleic acid encoding a polypeptide of the invention. Such expression vectors are preferably plasmids that contain a promoter sequence that facilitates transcription of the inserted genetic sequence in a host cell. The expression vector typically contains an origin of replication, and a promoter, as well as polynucleotides that allow phenotypic selection of the transformed cells (e.g., an antibiotic resistance polynucleotide). Various promoters, including inducible and constitutive promoters, can be utilized in the invention. Typically, the expression vector contains a replicon site and control sequences that are derived from a species compatible with the host cell.

[0072] Transformation or transfection of a recipient with a nucleic acid of the invention can be carried out using conventional techniques well known to those skilled in the art. For example, where the host cell is E. coli, competent cells that are "capable of DNA uptake can be prepared using the CaCl, MgCl; or RbCl methods known in the art. Alternatively, physical means, such as electroporation or microinjection can be used. Electroporation allows transfer of a nucleic acid into a cell by high voltage electric impulse. Additionally, nucleic acids can be introduced into host cells by protoplast fusion, using methods well known in the art. Suitable . methods for transforming eukaryotic cells, such as electroporation and lipofection, also are known. (0073) “Host cells” or “Recipient cells” encompassed by of the invention are any cells in which the nucleic acids of the invention can be used to express the polypeptides of the invention. The term also includes any progeny of a recipient or host cell. Preferred recipient or host cells of the invention include E. coli, S. aureus and P. aeruginosa, although other Gram-negative and Gram-positive bacterial, fungal and mammalian cells and organisms known in the art can be utilized as long as the expression vectors contain an origin of replication to permit expression in the host.

[0074] The cationic peptide polynucleotide sequence used according to the method of the invention can be isolated from an organism or synthesized in the laboratory.

Specific DNA sequences encoding the cationic peptide of interest can be obtained by: 1) isolation of a double-stranded DNA sequence from the genomic DNA; 2) chemical manufacture of a DNA sequence to provide the necessary codons for the cationic peptide of interest; and 3) in vitro synthesis of a double-stranded DNA sequence by reverse transcription of mRNA isolated from a donor cell. In the latter case, a double- stranded DNA complement of mRNA is eventually formed which is generally referred to as cDNA.

[0075] The synthesis of DNA sequences is frequently the method of choice when the entire sequence of amino acid residues of the desired peptide product is known. In the present invention, the synthesis of a DNA sequence has the advantage of allowing the incorporation of codons which are more likely to be recognized by a bacterial host, thereby permitting high level expression without difficulties in translation. In addition, virtually any peptide can be synthesized, including those encoding natural cationic peptides, variants of the same, or synthetic peptides.

[0076] When the entire sequence of the desired peptide is not known, the direct synthesis of DNA sequences is not possible and the method of choice is the formation of cDNA sequences. Among the standard procedures for isolating cDNA sequences of interest is the formation of plasmid or phage containing cDNA libraries which are derived from reverse transcription of mRNA which is abundant in donor cells that have a high level of genetic expression. When used in combination with polymerase chain reaction technology, even rare expression products can be cloned. In those cases where significant portions of the amino acid sequence of the cationic peptide are known, the production of labeled single or double-stranded DNA or RNA probe sequences duplicating a sequence putatively present in the target cDNA may be employed in DNA/DNA hybridization procedures which are carried out on cloned copies of the cDNA which have been denatured into a single stranded form (Jay, et al., Nuc. Acid Res., 11:2325, 1983).

[0077] The peptide of the invention can be administered parenterally by injection or by gradual infusion over time. Preferably the peptide is administered ina therapeutically effective amount to enhance or to stimulate an innate immune response. Innate immunity has been described herein, however examples of indicators of stimulation of innate immunity include but are not limited to monocyte activation, proliferation, differentiation or MAP kinase pathway activation.

[0078] The peptide can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally. Preferred methods for delivery of the peptide include orally, by encapsulation in microspheres or proteinoids, by aerosol delivery to the lungs, or transdermally by iontophoresis or transdermal electroporation. Other methods of administration will be known to those skilled in the art.

[0079] Preparations for parenteral administration of a peptide of the invention include sterile aqueous or non-aqueous solutions, suspensions, and emulsions.

Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.

Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media Parenteral vehicles include sodium chloride solution, Ringer’s dextrose, dextrose and sodium chloride, lactated Ringer’s, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer’s dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti- oxidants, chelating agents, and inert gases and the like.

[0080] In one embodiment, the invention provides a method for synergistic therapy. For example, peptides as described herein can be used in synergistic combination with sub-inhibitory concentrations of antibiotics. Examples of particular classes of antibiotics useful for synergistic therapy with the peptides of the invention include aminoglycosides (e.g., tobramycin), penicillins (e.g., piperacillin),

cephalosporins (e.g., ceftazidime), fluoroquinolones (e.g., ciprofloxacin), carbapenems (e.g., imipenem), tetracyclines and macrolides (e.g., erythromycin and clarithromycin). Further to the antibiotics listed above, typical antibiotics include aminoglycosides (amikacin, gentamicin, kanamycin, netilmicin, tobramycin, s- treptomycin, azithromycin, clarithromycin, erythromycin, erythromycin e- stolate/ethylsuccinate/gluceptate/lactobionate/stearate), beta-lactams such as - penicillins (e.g., penicillin G, penicillin V, methicillin, nafcillin, oxacillin, cloxacillin, dicloxacillin, ampicillin, amoxicillin, ticarcillin, carbenicillin, mezlocillin, azlocillin and piperacillin), or cephalosporins (e.g. cephalothin, cefazolin, cefaclor, ¢- efamandole, cefoxitin, cefuroxime, cefonicid, cefmetazole, cefotetan, cefprozil, loracarbef, cefetamet, cefoperazone, cefotaxime, ceftizoxime, ceftriaxone, ceftazidime, cefepime, cefixime, cefpodoxime, and cefsulodin). Other classes of antibiotics include carbapenems (e.g, imipenem), monobactams (e. g.,aztreonam), quinolones (e.g., fleroxacin, nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, enoxacin, lomefloxacin and cinoxacin), tetracyclines (e.g., doxycycline, minocycline, tetracycline), and glycopeptides (e.g., vancomycin, teicoplanin), for example. Other antibiotics include chloramphenicol, clindamycin, trimethoprim, sulfamethoxazole, nitrofurantoin, rifampin, mupirocin and the cationic peptides.

[0081] The efficacy of peptides was evaluated therapeutically alone and in combination with sub-optimal concentrations of antibiotics in models of infection. S. aureus is an important Gram positive pathogen and a leading cause of antibiotic resistant infections. Briefly, peptides were tested for therapeutic efficacy inthe §. aureus infection model by injecting them alone and in combination with sub-optimal doses of antibiotics 6 hours after the onset of infection. This would simulate the circumstances of antibiotic resistance developing during an infection, such that the

MIC of the resistant bacterium was too high to permit successful therapy (i.e the antibiotic dose applied was sub-optimal). It was demonstrated that the combination of antibiotic and peptide resulted in improved efficacy and suggests the potential for combination therapy (see Example 12).

[0082] The invention will now be described in greater detail by reference to the following non-limiting examples. While the invention has been described in detail with reference to certain preferred embodiments thereof, it will be understood that modifications and variations are within the spirit and scope of that which is described and claimed.

EXAMPLE 1

ANTISEPSIS/ANTIINFLAMMATORY ACTIVITY

[0083] Polynucleotide arrays were utilized to determine the effect of cationic peptides on the transcriptional response of epithelial cells. The A549 human : epithelial cell line was maintained in DMEM (Gibco) supplemented with 10 % fetal bovine serum (FBS, Medicorp). The A549 cells were plated in 100 mm tissue culture dishes at 2.5 x 10° cells/dish, cultured overnight and then incubated with 100 ng/ml E. coli O111:B4 LPS (Sigma), without (control) or with 50 pg/ml peptide or medium alone for 4 h. After stimulation, the cells were washed once with diethyl pyrocarbonate-treated phosphate buffered saline (PBS), and detached from the dish using a cell scraper. Total RNA was isolated using RNAqueous (Ambion, Austin,

TX). The RNA pellet was resuspended in RNase-free water containing Superase-In (RNase inhibitor; Ambion). DNA contamination was removed with DNA-free kit,

Ambion). The quality of the RNA was assessed by gel electrophoresis on a 1% agarose gel.

[0084] The polynucleotide arrays used were the Human Operon arrays (identification number for the genome is PRHU04-S1), which consist of about 14,000 . human oligos spotted in duplicate. Probes were prepared from 10 ug of total RNA and labeled with Cy3 or CyS labeled dUTP. The probes were purified and hybridized to printed glass slides overnight at 42°C and washed. After washing, the image was captured using a Perkin Elmer array scanner. The image processing software (Imapolynucleotide 5.0, Marina Del Rey, CA) determines the spot mean intensity, median intensities, and background intensities. A “homemade” program was used to remove background. The program calculates the bottom 10 % intensity for each subgrid and subtracts this for each grid. Analysis was performed with Genespring software (Redwood City, CA). The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with peptide compared to control cells can be found in Tables 1 and 2. These tables 2 reflect only those polynucleotides that demonstrated significant changes in expression of the 14,000 polynucleotides that were tested for altered expression. The data indicate that the peptides have a widespread ability to reduce the expression of polynucleotides that were induced by

LPS.

[0085] In Table 1,the peptide, SEQ ID NO: 27 is shown to potently reduce the expression of many of the polynucleotides up-regulated by E. coli O111:B4 LPS as studied by polynucleotide microarrays. Peptide (50 pg/ml) and LPS (0.1 pg/ml) or

LPS alone was incubated with the A549 cells for 4 h and the RNA was isolated. Five ug total RNA was used to make Cy3/Cy5 labeled cDNA probes and hybridized onto

Human Operon arrays (PRHUO04). The intensity of unstimulated cells is shown in the third column of Table 1. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS simulated cells divided by in the intensity of unstimulated cells. The “Ratio: LPS+ ID 27/control” column refers to the intensity of polynucleotide expression in cells stimulated with LPS and peptide divided by unstimulated cells. :

Table 1: Reduction, by peptide SEQ ID 27, of A549 human epithelial cell polynucleotide expression up-regulated by E.coli O111:B4 LPS

Accession Polynucleotide Control: Ratio: Ratio: LPS+ 1D

Number” Gene Function Media only LPS/control 27/control

ADP- ribosylation 104510 factor 0.655 213.6 14 ring finger

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number® Gene Function Media only LPS/control 27/control = [] [ oe

I I A A

Ric -like ’ expressed in mucin subtype B tracheobronchi = LLL serine/threonin e protein er | or interferon

RNA lariat debranching

NM_016216 enzyme 6.151 223 109 hypothetical :

ATS | Ue | tw | vs | 06

FEM-1-like death receptor

AB007856 | binding protein 2.627 15.7 growth arrest- cytosolic ovarian

EI

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number® Gene Function Media only LPS/control 27/control = oe E [ weer [ : myeloid/lympho id or mixed- lineage leukemia translocated to

D14539 1 2.033 11.6 3.1. integration site for Epstein-Barr

X76785 virus 0.728 11.6 pim-1

Cos | omen | on | we | ow caspase recruitment :

MEI integrin_alpha

Cs |i | om |e |e

CT ADP- ribosylation

NM_001663 factor 6 0.439 9.7 1.7

RAS p21 protein

M23379 activator 0.567 9.3 2.8 thymidine kinase 1

K02581 soluble 3.099 3.5 transmembrane 9 superfamily

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number” | Gene Function Media only LPS/control 27/control

Intensity zinc finger on | mre | ww | 0 | ow hypothetical | . wen | ow | wo | ow guanine nucleotide :

MEI

DKF Zpd34J181

Ee I

ATP-binding cassette sub- family C (CFTR/MRP)

AF085692 | member 3 3.175 6.5 24 hypothetical protein

AK001239 FLJ10377 2.204 6.4 1.3

ATPase

Na+/K+ transporting beta 3

NM_001679 polypeptide 2.402 6.3 unactive progesterone £24804 receptor 3.403 dual specificity

I ed I EP ligase | DNA_

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number® Gene Function Media only LPS/control 27/control

S] a [ colony stimulating factor 3

M59820 receptor 0.38 5.7 2.0 spermidine/ spermine N1- : acetyltransfera

AL050290 se 2.724 1.4 a oo) I EL RC retinoic acid

I A EE putative L-type neutral amino

AB007896 | acid transporter 0.94 5.3 1.8

DKFZP564B11 ws [moon | um | os | ow hypothetical hypothetical pre-B-cell | 1. : leukemia trans- }

MB86546 cription factor 1 1.113 5.2 22 zona pellucida

I eee ER replication

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number® Gene Function Media only LPS/control 27/control

Intensity . [een leukemia dentatorubral- pallidoluysian cytosolic acyl : coenzyme A thioester

U91316 hydrolase 2.043 4.7 1.4 death- associated protein kinase

X76104 1 1.118 4.6 1.8

TAs | Oven | wm | es | 17

KIAA0095 gene oon [| om | ow | uw

I a IE I BRC monocyte to

N : macrophage differentiation-

X85750 associated 43 1.1

CD164 antigen_

D14043 sialomucin 1.683 4.2 1.0

I NL CL LJ

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number® | Gene Function Media only LPS/control 27/control [a [

I cs I NE melanoma- associated

U19796 antigen 1.618 hypothetical hypothetical so | ro | vw | ow | uw

Aww | wane | en | ss | 0 sterol-C4- methyl oxidase- [ow | 0 hypothetical mse | pe | ve |v | ow

Re | wow | s& | 37 | 0s hypothetical

RAN member

RAS oncogene aldehyde dehydrogenase

FH1/FH2 domain- containing

NM_013241 protein 1.264 33

Accession Polynucleotide Control: Ratio: Ratio: LPS+ ID

Number” Gene Function Media only LPS/control 27/control

Intensity esterase

D/formylglutathi anaphase- promoting complex

NM_016237 subunit 5 2.71 32

KIAAQ669 gene : hypothetical

Ee protein phosphatase 6 : catalytic

X92972 subunit 2.615 3.1 1.1

TT proteasome 26S subunit

Usa |STholg| Tw 31 | ov electron- transfer- flavoprotein alpha

J04058 polypeptide 3.265 3.1 1.2 interleukin 6 signal galactosidase__

Accession Polynucleotide Coatrol: Ratio: Ratio: LPS+ ID

Number® Gene Function Media only LPS/control 27/control

Intensity wo | Uw |e | 0 | 06 mitogen- activated : protein kinase 13 lamin B . :

I a IC J IN LS tumor necrosis factor receptor superfamily

M32315 member 1B 0.639 2.4 04

LPS-induced

TNF-alpha interferon gamma : AI] Accession Numbers in Table 1 through Table 64 refer to GenBank’ Accession

Numbers.

[0086] In Table 2, the cationic peptides at a concentration of 50 pg/ml were shown to potently reduce the expression of many of the polynucleotides up-regulated by 100 : ng/ml E. coli O111:B4 LPS as studied by polynucleotide microarrays. Peptide and

LPS or LPS alone was incubated with the A549 cells for 4 h and the RNA was isolated. 5 pug total RNA was used to make Cy3/Cy5 labeled cDNA probes and hybridized onto Human Operon arrays (PRHU04). The intensity of unstimulated cells is shown in the third column of Table 2. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS-simulated cells divided by in the intensity of unstimulated cells. The other columns refer to the intensity of polynucleotide expression in cells stimulated with LPS and peptide divided by unstimulated cells. : :

[0087] Table 2: Human A549 Epithelial Cell Polynucleotide Expression up- regulated by E.coli O111:B4 LPS and reduced by Cationic Peptides :

Accession Control: | Ratio: Ratio: Ratio: Ratio:

Number Media LPS/ | LPS+ID 27 LPS+ID 16/ LPS+ID 22/ only control control control . control

Intensi ;

ADP- ribosylation oon 2 Lae foe] an | mo

Ring finger . ovis [one | om [wr] a | sa | an

Hypothetical : [al PY PY ER I

OC I J NL FREE

MHC class II ) wows [pores | was [ses | un | mn | om

Hypothetical sono [peer | ow | ma | sm | wn | on

Hypothetical ons sous | 0s | 5a | un | om | on

EE NE NL NJ EI a 41

SUBSTITUTE SHEET (RULE 26)

Accession Control: | Ratio: Ratio: “Ratio: . Ratio:

Number Media | LPS/ | LPS+ID27/ | LPS+ID 16/ | LPS+ID 22/

EERE EE

Intensi .

Thioredoxin- peroxide

L19185 reductase 1 16.3 © 0.18

OH eeomianaT| 00 155 | tm | aw | 0B

FEM-1-like : death receptor : on [222 Lr] en |e |e cytosolic , ovarian carcinoma | .

AK000353 |agl 0.45 1.02 1.73 233 smooth muscle iow |e | on | na | sn | oo | on

Ce LC ve hypothetical wan fron | or Joo | on | as | ow phospholipase C won_Jtar | om | 2 | aw | om | ow hypothetical cms wo | ao | os | iw | ou | a retinoic acid

EE EE putative L-type ; : neutral amino Co

AB007896 | acid transporter 53 2.15 C241 42

SUBSTITUTE SHEET (RULE 26)

Accession Gene Control: | Ratio: Ratio: Ratio: | Ratio:

Number Media LPS/ | LPS+HID 27/ | LPSHID 16/ | LPS+ID 22/ only control control control © control

Intensi

BAI -associated

AB010894 | protein 1.38 1.03 hypothetical :

El I I I EE ankyrin 7_

I el I I EE inter-alpha a rt I I PV I " { brain and } nasopharyngeal : susceptibility : :

AF095687 | protein 2:1 0.48 © 0.98

NK cell : . activation inducing ligand ;

NM_016382 | NAIL 027 | 21 0.81 © 0.04

KIAA0981 nn [mer | [a0 | oo | on | en

EXAMPLE 2 :

NEUTRALIZATION OF THE STIMULATION OF IMMUNE CELLS

[0088] The ability of compounds to neutralize the stimulation of immune cells by both Gram-negative and Gram-positive bacterial products was tested. Bacterial 43

SUBSTITUTE SHEET (RULE 26)

products stimulate cells of the immune system to produce inflammatory cytokines and when unchecked this can lead to sepsis. Initial experiments utilized the murine macrophage cell line RAW 264.7, which was obtained from the American Type

Culture Collection, (Manassas, VA), the human epithelial cell line, A549, and primary macrophages derived from the bone marrow of BALB/c mice (Charles River : Laboratories, Wilmington, MA). The cells from mouse bone marrow were:cultured in

Aa 44

SUBSTITUTE SHEET (RULE 26)

150-mm plates in Dulbecco’s modified Eagle medium (DMEM,; Life Technologies,

Burlington, ON) supplemented with 20 % FBS (Sigma Chemical Co,St. Louis, MO) © and 20 % L cell-conditioned medium as a source of M-CSF. Once macrophages were 60-80 % confluent, they were deprived of L cell-conditioned medium for 14-16 h to render the cells quiescent and then were subjected to treatments with 100 ng/ml LPS or 100 ng/ml LPS + 20 pg/ml peptide for 24 hours. The release of cytokines into the culture supernatant was determined by ELISA (R&D Systems, Minneapolis, MN).

The cell lines, RAW 264.7 and A549, were maintained in DMEM supplemented with % fetal calf serum. RAW 264.7 cells were seeded in 24 well plates at a density of 10° cells per well in DMEM and A549 cells were seeded in 24 well plates at a density of 10° cells per well in DMEM and both were incubated at 37°C in 5 % CO; overnight. DMEM was aspirated from cells grown overnight and replaced with fresh medium. In some experiments, blood from volunteer human donors was collected (according to procedures accepted by UBC Clinical Research Ethics Board, certificate

C00-0537) by venipuncture into tubes (Becton Dickinson, Franklin Lakes, NJ) containing 14.3 USP units heparin/ml blood. The blood was mixed with LPS with or without peptide in polypropylene tubes at 37°C for 6 h. The samples were centrifuged for 5 min at 2000 x g, the plasma was collected and then stored at —20°C until being analyzed for [IL-8 by ELISA (R&D Systems). In the experiments with cells, LPS or other bacterial products were incubated with the cells for 6-24 hr at 37°C in § % COs. : S. typhimurium LPS and E. coli 0111:B4 LPS were purchased from Sigma. ‘Lipoteichoic acid (LTA) from S. aureus (Sigma) was resuspended in endotoxin free water (Sigma). The Limulus amoebocyte lysate assay (Sigma) was performed on ] LTA preparations to confirm that lots were not significantly contaminated by endotoxin. Endotoxin contamination was less than 1 ng/ml, a concentration that did not cause significant cytokine production in the RAW 264.7 cells. Non-capped lipoarabinomannan (AralLAM ) was a gift from Dr. John T. Belisle of Colorado State

University. The AraLAM from Mycobacterium was filter sterilized and the endotoxin contamination was found to be 3.75 ng per 1.0 mg of LAM as determined by Limulus

Amebocyte assay. At the same time as LPS addition (or later where specifically described), cationic peptides were added at a range of concentrations. The supernatants were removed and tested for cytokine production by ELISA (R&D

Systems). All assays were performed at least three times with similar results. To confirm the anti-sepsis activity in vivo, sepsis was induced by intraperitoneal injection of 2 or 3 pg of E. coli O111:B4 LPS in phosphate-buffered saline (PBS; pH 7.2) into galactosamine-sensitized 8- to 10- week-old female CD-1 or BALB/c mice. In experiments involving peptides, 200 pg in 100p! of sterile water was injected at separate intraperitoneal sites within 10 min of LPS injection. In other experiments,

CD-1 mice were injected with 400 pg E. coli O111 :B4 LPS and 10 min later peptide (200 pg) was introduced by intraperitoneal injection. Survival was monitored for 48 hours post injection. :

[0089] Hyperproduction of TNF-a has been classically linked to development of sepsis. The three types of LPS, LTA or AralLAM used in this example represented products released by both Gram-negative and Gram-positive bacteria. Peptide, SEQ

ID NO: 1, was able to significantly reduce TNF-a production stimulated by S. typhimurium, B. cepacia, and E. coli Ol 11:B4 LPS, with the former being affected to a somewhat lesser extent (Table 3). At concentrations as low as 1 pg/ml of peptide (0.25 nM) substantial reduction of TNF-a production was observed in the latter two cases. A different peptide, SEQ ID NO: 3 did not reduce LPS-induced production of : TNF-a in RAW macrophage cells, demonstrating that this is not a uniform and predictable property of cationic peptides. Representative peptides from each Formula were also tested for their ability to affect TNF-a production stimulated by E. coli

O111:B4 LPS (Table 4). The peptides had a varied ability to reduce TNF-a production although many of them lowered TNF-a by at least 60%.

[0090] At certain concentrations peptides SEQ ID NO: 1 and SEQ ID NO: 2, could also reduce the ability of bacterial products to stimulate the production of IL-8 by an epithelial cell line. LPS is a known potent stimulus of IL-8 production by epithelial cells. Peptides, at low concentrations (1-20 pg/ml), neutralized the IL-8 induction responses of epithelial cells to LPS (Table 5-7). Peptide SEQ ID 2 also inhibited

LPS-induced production of IL-8 in whole human blood (Table 4). Conversely, high concentrations of peptide SEQ ID NO: 1 (50 to 100 pg/ml) actually resulted in increased levels of IL-8 (Table 5). This suggests that the peptides have different effects at different concentrations.

[0091] The effect of peptides on inflammatory stimuli was also demonstrated in primary murine cells, in that peptide SEQ ID NO: 1 significantly reduced TNF-a production (>90 %) by bone marrow-derived macrophages from BALB/c mice that had been stimulated with 100 ng/ml E. coli 0111:B4 LPS (Table 8). These experiments were performed in the presence of serum, which contains LPS-binding protein (LBP), a protein that can mediate the rapid binding of LPS to CD14. Delayed addition of SEQ ID NO: 1 to the supernatants of macrophages one hour after stimulation with 100 ng/ml E. coli LPS still resulted in substantial reduction (70 %) of

TNF-a production (Table 9).

[0092] Consistent with the ability of SEQ ID NO: 1 to prevent LPS-induced production of TNF-a in vitro, certain peptides also protected mice against lethal shock induced by high concentrations of LPS. In some experiments, CD-1 mice were sensitized to LPS with a prior injection of galactosamine. Galactosamine-sensitized mice that were injected with 3 pg of E. coli 0111:B4 LPS were all killed within 4-6 hours. When 200 pg of SEQ ID NO: 1 was injected 15 min after the LPS, 50 % of the mice survived (Table 10). In other experiments when a higher concentration of :

LPS was injected into BALB/c mice with no D-galactosamine, peptide protected 100 % compared to the control group in which there was no survival (Table 13). Selected other peptides were also found to be protective in these models (Tables 1 1,12).

[0093] Cationic peptides were also able to lower the stimulation of macrophages by Gram-positive bacterial products such as Mycobacterium non-capped lipoarabinomannan (AraLAM) and S. aureus LTA. For example, SEQ ID NO: 1 inhibited induction of TNF-a in RAW 264.7 cells by the Gram-positive bacterial products, LTA (Table 14) and to a lesser extent AraLAM (Table 15). Another peptide, SEQ ID NO: 2, was also found to reduce LT A-induced TNF-a production by

RAW 264.7 cells. At a concentration of 1 ug/ml SEQ ID NO: 1 was able to substantially reduce (>75 %) the induction of TNF-a production by 1 pg/ml S. aureus

LTA. At 20 pg/ml SEQ ID NO: 1, there was >60 % inhibition of AraLAM induced

TNF-a. Polymyxin B (PMB) was included as a control to demonstrate that contaminating endotoxin was not a significant factor in the inhibition by SEQ ID NO: 1 of AraLAM induced TNF-a. These results demonstrate that cationic peptides can reduce the pro-inflammatory cytokine response of the immune system to bacterial products.

[0094] Table 3: Reduction by SEQ ID 1 of LPS induced TNF-a production in

RAW 264.7 cells. RAW 264.7 mouse macrophage cells were stimulated with 100 ng/ml S. typhimurium LPS, 100 ng/ml B. cepacia LPS and 100 ng/ml E. coli 011 1:B4

LPS in the presence of the indicated concentrations of SEQ ID 1 for 6 hr. The concentrations of TNF-a released into the culture supernatants were determined by

ELISA. 100 % represents the amount of TNF-a resulting from RAW 264.7 cells incubated with LPS alone for 6 hours (S. typhimurium LPS = 34.5 + 3.2 ng/ml, B. cepacia LPS = 11.6 £ 2.9 ng/ml, and E. coli 0111:B4 LPS = 30.8 £ 2.4 ng/ml).

Background levels of TNF-a production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-a levels ranging from 0.037 — 0.192 ng/ml. The data is from duplicate samples and presented as the mean of three experiments + standard error.

Amount of SEQ ID | Inhibition of TNF-a (%)* 1 (ug/mb B. cepacia LPS E. coli LPS S. typhimurium LPS 23.0+11.4 36.6 +7.5 9.8 + 6.6 55.4 +8 65.0+3.6 31.1+7.0 71.7458 81.0+3.5 58.5 +10.5 86.7+4.3 92.6 +2.5 73.1 +9.1

[0095] Table 4: Reduction by Cationic Peptides of E. coli LPS induced TNF-a production in RAW 264.7 cells. RAW 264.7 mouse macrophage cells were stimulated with 100 ng/ml E. coli 0111:B4 LPS in the presence of the indicated : concentrations of cationic peptides for 6 h. The concentrations of TNF-a. released into : the culture supernatants were determined by ELISA. Background levels of TNF-a production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in

TNF-a levels ranging from 0.037 — 0.192 ng/ml. The data is from duplicate samples and presented as the mean of three experiments + standard deviation.

Peptide (20 pg/ml) | Inhibition of TNF-a (%)

SEQIDD 5 TT 656%16

SEQID6 59.8+1.2

SEQID 7 506+ 0.6

SEQID 8 39.3+1.9

SEQID9 58.7+£ 0.8 “SEQID 10 55.50.52

SEQID 12 52.1% 0.38

SEQID 13 62.4 + 0.85

SEQID 14 50.8 + 1.67

I EL

LL CE

— wpm | wen wpa | ason wom [wets wow [wma wom | wen

I LJ

Peptide (20 pg/ml) | Inhibition of TNF-a (%) sow | eon

[0096] Table 5: Reduction by SEQ ID 1 of LPS induced IL-8 production in

A549 cells. A549 cells were stimulated with increasing concentrations of SEQ ID 1 in the presence of LPS (100 ng/ml E. coli 0111:B4) for 24 hours. The concentration of

IL-8 in the culture supernatants was determined by ELISA. The background levels of

IL-8 from cells alone was 0.172 + 0.029 ng/ml. The data is presented as the mean of three experiments + standard error.

SEQ ID 1 (ug/ml) Inhibition of IL-8 (%)

[0097] Table 6: Reduction by SEQ ID 2 of E. coli LPS induced IL-8 production in A549 cells. Human A549 epithelial cells were stimulated with increasing concentrations of SEQ ID 2 in the presence of LPS (100 ng/ml E. coli

O111:B4) for 24 hours. The concentration of IL-8 in the culture supernatants was determined by ELISA. The data is presented as the mean of three experiments + standard error.

Concentration of SEQ ID 2 (ug/ml) Inhibition of IL-8 (%)

Concentration of SEQ ID 2 (pg/ml) Inhibition of JL-8 (%)

[0098] Table 7: Reduction by SEQ ID 2 of E. coli LPS induced IL-8 in human blood. Whole human blood was stimulated with increasing concentrations of peptide and E.coli O111:B4 LPS for 4 hr. The human blood samples were centrifuged and the serum was removed and tested for IL-8 by ELISA. The data is presented as the average of 2 donors.

SEQID 2 (pg/mb IL-8 (pg/ml) {0099] Table 8: Reduction by SEQ ID 1 of E. coli LPS induced TNF-a production in murine bone marrow macrophages. BALB/c Mouse bone marrow- derived macrophages were cultured for either 6 h or 24 h with 100 ng/ml E. coli 0111:B4 LPS in the presence or absence of 20 ug/ml of peptide. The supernatant was collected and tested for levels of TNF-a by ELISA. The data represents the amount of

TNF-a resulting from duplicate wells of bone marrow-derived macrophages incubated with LPS alone for 6 h (1.1 + 0.09 ng/ml) or 24h (1.7 £ 0.2 ng/ml).

Background levels of TNF-a were 0.038 + 0.008 ng/ml for 6 h and 0.06 + 0.012 ng/ml for 24h.

SEQ ID 1 (ug/ml) Production of TNF-a (ng/ml)

I LL NL

I NS ILA

EL CC NN

I TL LC

SE A EL. NLR

I EI IN

I Cc LCL

[00100] Table9: Inhibition of E. coli LPS-induced TNF-a production by delayed addition of SEQ ID 1 to A549 cells. Peptide (20 pg/ml) was added at increasing time points to wells already containing A549 human epithelial cells and 100 ng/ml E. coli 0111:B4 LPS. The supernatant was collected after 6 hours and tested for levels of TNF-a by ELISA. The data is presented as the mean of three experiments + standard error.

Time of addition of SEQ ID 1 Inhibition of TNF-a. (%) min ome ow wees wees

EE EE ow mes

[00101] Table 10: Protection against lethal endotoxaemia in galactosamine- sensitized CD-1 mice by SEQ ID 1. CD-1 mice (9 weeks-old) were sensitized to endotoxin by three intraperitoneal injections of galactosamine (20 mg in 0.1 ml sterile

PBS). Then endotoxic shock was induced by intraperitoneal injection of E. coli 0111:B4 LPS (3 pgin 0.1 ml PBS). Peptide, SEQ ID 1, (200 pg/mouse = 8mg/kg) was injected at a separate intraperitoneal site 15 min after injection of LPS. The mice were monitored for 48 hours and the results were recorded.

D-Galactosamine E. coli Peptide or Total mice | Survival post endotoxin treatment 0111:B4 LPS buffer shock 0 [ww ms [soem mm [ow | ms [mw | oon

Ll cE

[00102] Table 11: Protection against lethal endotoxaemia in galactosamine- sensitized CD-1 mice by Cationic Peptides. CD-1 mice (9 weeks-old) were sensitized to endotoxin by intraperitoneal injection of galactosamine (20 mg in 0.1 ml sterile PBS). Then endotoxic shock was induced by intraperitoneal injection of E. coli 0111:B4 LPS (2 pg in 0.1 ml PBS). Peptide (200 pg/mouse = 8mg/kg) was injected at a separate intraperitoneal site 15 min after injection of LPS. The mice were monitored for 48 hours and the results were recorded.

Peptide Treatment | E. coli 0111:B4 | Number | Survival (%)

LPS added ‘of Mice

Comoro | ois | 5 | 0 same | Tm | 5 | @

LL sp ow [5 | 0

Ca L NTS NL

SET

[00103] Table 12: Protection against lethal endotoxaemia in galactosamine- sensitized BALB/c mice by Cationic Peptides. BALB/c mice (8 weeks-old) were sensitized to endotoxin by intraperitoneal injection of galactosamine (20 mg in 0.1 ml sterile PBS). Then endotoxic shock was induced by intraperitoneal injection of E. coli 0111:B4 LPS (2 pg in 0.1 ml PBS). Peptide (200 pg/mouse = 8mg/kg) was injected at a separate intraperitoneal site 15 min after injection of LPS. The mice were monitored for 48 hours and the results were recorded.

Peptide Treatment E. coli Number of Mice | Survival (%) i PP

EL LI ITT ER RA

ELE BN I NC

EL NT INL NLA wpe m |e | 7

ELIE TT CI A won| ow | © |»

EL ETN I RCN aka I A ER aL TTS AI RA

Son [Tw | © [0 wow [mw | 6 |v aL CN I EL aL NN RN RL aL I A RL

Spy | tw [6 0

LE NO IN A EL

ECL LI NL IC BI

ELL I ECR

EEE IS ICR RL

[00104] Table 13: Protection against lethal endotoxaemia in BALB/c mice by

SEQ ID 1. BALB/c mice were injected intraperitoneal with 400 pg E. coli 0111:B4

LPS. Peptide (200 pg/mouse = 8mg/kg) was injected at a separate intraperitoneal site and the mice were monitored for 48 hours and the results were recorded.

Peptide Treatment E. coli Number of Mice Survival (%) el I Bl

Nowe [wow | 5 | 0

[00105] Table 14: Peptide inhibition of TNF-a. production induced by S. © aureus LTA. RAW 264.7 mouse macrophage cells were stimulated with 1 pg/ml S. aureus LTA in the absence and presence of increasing concentrations of peptide. The supernatant was collected and tested for levels of TNF-a. by ELISA. Background levels of TNF-a. production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-c levels ranging from 0.037 — 0.192 ng/ml. The data is presented as the mean of three or more experiments + standard error.

IN 1:

IE BO CN

[00106] Table 15: Peptide inhibition of TNF-a production induced by

Mycobacterium non-capped lipoarabinomannan. RAW 264.7 mouse macrophage cells were stimulated with 1 ug/ml AralLAM in the absence and presence of 20 pg/ml peptide or Polymyxin B. The supernatant was collected and tested for levels of TNF- o by ELISA. Background levels of TNF-a production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-a levels ranging from 0.037 — 0.192 ng/ml. The data is presented as the mean inhibition of three or more experiments + standard error.

Peptide (20 pg/ml) Inhibition of TNF-a (%)

EXAMPLE 3

ASSESSMENT OF TOXICITY OF THE CATIONIC PEPTIDES

{00107] The potential toxicity of the peptides was measured in two ways. First, the

Cytotoxicity Detection Kit (Roche) (Lactate dehydrogenase -LDH) Assay was used.

It is a colorimetric assay for the quantification of cell death and cell lysis, based on the measurement of LDH activity released from the cytosol of damaged cells into the supernatant. LDH is a stable cytoplasmic enzyme present in all cells and it is released into the cell culture supernatant upon damage of the plasma membrane. An increase in the amount of dead or plasma membrane-damaged cells results in an increase of the

LDH enzyme activity in the culture supernatant as measured with an ELISA plate reader, ODggonm (the amount of color formed in the assay is proportional to the number of lysed cells). In this assay, human bronchial epithelial cells (16HBEo14,

HBE) cells were incubated with 100 pg of peptide for 24 hours, the supernatant removed and tested for LDH. The other assay used to measure toxicity of the cationic . peptides was the WST-1 assay (Roche). This assay is a colorimetric assay for the : quantification of cell proliferation and cell viability, based on the cleavage of the tetrazolium salt WST-1 by mitochondrial dehydrogenases in viable cells (a non- radioactive alternative to the [*H]-thymidine incorporation assay). In this assay, HBE cells were incubated with 100 pg of peptide for 24 hours, and then 10 pliwell Cell

Proliferation Reagent WST-1 was added. The cells are incubated with the reagent and the plate is then measured with an ELISA plate reader, ODggonm.

[00108] The results shown below in Tables 16 and 17 demonstrate that most of the peptides are not toxic to the cells tested. However, four of the peptides from Formula

F (SEQ ID NOS: 40, 41, 42 and 43) did induce membrane damage as measured by both assays.

[00109] Table 16: Toxicity of the Cationic Peptides as Measured by the LDH

Release Assay. Human HBE bronchial epithelial cells were incubated with 100 pg/ml peptide or Polymyxin B for 24 hours. LDH activity was assayed in the supernatant of the cell cultures. As a control for 100% LDH release, Triton X-100 was added.

The data is presented as the mean + standard deviation.

Only peptides SEQ ID 40,41,42 and 43 showed any significant toxicity.

—sopw | wes sepa | me spe [seer

LC LL

LLL I LL A

I J

[0100] Table 17: Toxicity of the Cationic Peptides as Measured by the WST-1

Assay. HBE cells were incubated with 100 ug/ml peptide or Polymyxin B for 24 hours and cell viability was tested. The data is presented as the mean * standard deviation. As a control for 100% LDH release, Triton X-100 was added. Only peptides SEQ ID 40,41,42 and 43 showed any significant toxicity. wens | owen

— ween [mon wow [meow

EL NE LU ov [wow

I LL EO wow | eon

EE LL A

ELL BCI

LA CLL

—wowy | wewon oo

EXAMPLE 4

POLYNUCLEOTIDE REGULATION BY CATIONIC PEPTIDES

[0101] Polynucleotide arrays were utilized to determine the effect of cationic peptides by themselves on the transcriptional response of macrophages and epithelial cells. Mouse macrophage RAW 264.7, Human Bronchial cells (HBE), or A549 human epithelial cells were plated in 150 mm tissue culture dishes at 5.6 x 10° cells/dish, cultured overnight and then incubated with 50 pg/ml peptide or medium alone for 4 h. After stimulation, the cells were washed once with diethyl pyrocarbonate-treated PBS, and detached from the dish using a cell scraper. Total

RNA was isolated using Trizol (Gibco Life Technologies). The RNA pellet was resuspended in RNase-free water containing RNase inhibitor (Ambion, Austin, TX).

The RNA was treated with DNasel (Clontech, Palo Alto, CA) for 1 h at 37°C. After adding termination mix (0.1 M EDTA [pH 8.0], 1 mg/ml glycogen), the samples were extracted once with phenol: chloroform: isoamyl alcohol (25:24:1), and once with chloroform. The RNA was then precipitated by adding 2.5 volumes of 100% ethanol : and 1/10" volume sodium acetate, pH 5.2. The RNA was resuspended in RNase-free water with RNase inhibitor (Ambion) and stored at -70°C. The quality of the RNA was assessed by gel electrophoresis on a 1% agarose gel. Lack of genomic DNA contamination was assessed by using the isolated RNA as a template for PCR amplification with B-actin-specific primers (5’-GTCCCTGTATGCCTCTGGTC-3’ (SEQ ID NO: 55) and 5’-GATGTCACGCACGATTTCC-3’ (SEQ ID NO: 56)).

Agarose gel electrophoresis and ethidium bromide staining confirmed the absence of an amplicon after 35 cycles. [0102) Atlas cDNA Expression Arrays (Clontech, Palo Alto, CA), which consist of 588 selected mouse cDNAs spotted in duplicate on positively charged membranes were used for early polynucleotide array studies (Tables 18,19), *?P-radiolabeled cDNA probes prepared from 5 pg total RNA were incubated with the arrays overni ght at 71°C. The filters were washed extensively and then exposed to a phosphoimager screen (Molecular Dynamics, Sunnyvale, CA) for 3 days at 4°C. The image was captured using a Molecular Dynamics PSI phosphoimager. The hybridization signals were analyzed using AtlasImage 1.0 Image Analysis software (Clontech) and Excel (Microsoft, Redmond, WA). The intensities for each spot were corrected for background levels and normalized for differences in probe labeling using the average values for 5 polynucleotides observed to vary little between the stimulation conditions: B-actin, ubiquitin, ribosomal protein S29, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and Ca?" binding protein. When the normalized hybridization intensity for a given cDNA was less than 20, it was assigned a value of to calculate the ratios and relative expression.

[0103] The next polynucleotide arrays used (Tables 21-26) were the Resgen

Human cDNA amays (identification number for the genome is PRHUO03-83), which consist of 7,458 human cDNAs spotted in duplicate. Probes were prepared from 15-20 ug of total RNA and labeled with Cy3 labeled UTP. The probes were purified and hybridized to printed glass slides overnight at 42°C and washed. After washing, the "image was captured using a Virtek slide reader. The image processing software (Imagene 4.1, Marina Del Rey, CA) determines the spot mean intensity, median : intensities, and background intensities. Normalization and analysis was performed with Genespring software (Redwood City, CA). Intensity values were calculated by subtracting the mean background intensity from the mean intensity value determined by Imagene. The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with peptide compared to control cells can be found in the Tables below.

[0104] The other polynucleotide arrays used (Tables 27-35) were the Human

Operon arrays (identification number for the genome is PRHU04-S1), which consist of about 14,000 human oligos spotted in duplicate. Probes were prepared from 10 ug of total RNA and labeled with Cy3 or Cy5 labeled dUTP. In these experiments, A549 epithelial cells were plated in 100 mm tissue culture dishes at 2.5 x 10° cells/dish.

Total RNA was isolated using RNAqueous (Ambion). DNA contamination was removed with DNA-free kit (Ambion). The probes prepared from total RNA were purified and hybridized to printed glass slides overnight at 42°C and washed. After washing, the image was captured using a Perkin Elmer array scanner. The image processing software (Imagene 5.0, Marina Del Rey, CA) determines the spot mean intensity, median intensities, and background intensities. An “in house” program was used to remove background. The program calculates the bottom 10% intensity for each subgrid and subtracts this for each grid. Analysis was performed with

Genespring software (Redwood City, CA). The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with peptide compared to control cells can be found in the Tables below.

[0105] Semi-quantitative RT-PCR was performed to confirm polynucleotide array results. 1 pg RNA samples were incubated with 1 ul oligodT (500 pg/ml) and 1 pl mixed dNTP stock at 1 mM, in a 12 pl volume with DEPC treated water at 65°C for 5 min in a thermocycler. 4 pl 5X First Strand buffer, 2 pl 0.1M DTT, and 1 pl

RNaseOUT recombinant ribonuclease inhibitor (40 units/pl) — added and incubated at 42 °C for 2 min, followed by the addition of 1 ul (200 units) of

Superscript IT (Invitrogen, Burlington, ON). Negative controls for each RNA source were generated using parallel reactions in the absence of Superscript II. cDNAs were amplified in the presence of 5’ and 3’ primers (1.0 uM), 0.2 mM dNTP mixture, 1.5 mM MgCl, 1 U of Tag DNA polymerase (New England Biolabs, Missisauga, ON), and 1X PCR buffer. Each PCR was performed with a thermal cycler by using 30-40 cycles consisting of 30s of denaturation at 94 °C, 30s of annealing at either 52°C or 55 °C and 40s of extension at 72 °C. The number of cycles of PCR was optimized to lie in the linear phase of the reaction for each primer and set of RNA samples. A housekeeping polynucleotide B-actin was amplified in each experiment to evaluate extraction procedure and to estimate the amount of RNA. The reaction product was visualized by electrophoresis and analyzed by densitometry, with relative starting

RNA concentrations calculated with reference to p-actin amplification.

[0106] Table 18 demonstrates that SEQ ID NO: 1 treatment of RAW 264.7 cells up-regulated the expression of more than 30 different polynucleotides on small Atlas . microarrays with selected known polynucleotides. The polynucleotides up-regulated by peptide, SEQ ID NO: 1, were mainly from two categories: one that includes receptors (growth, chemokine, interleukin, interferon, hormone, neurotransmitter), cell surface antigens and cell adhesion and another one that includes cell-cell communication (growth factors, cytokines, chemokines, interleukin, interferons, hormones), cytoskeleton, motility, and protein turnover. The specific polynucleotides up-regulated included those encoding chemokine MCP-3, the anti-inflammatory © cytokine IL-10, macrophage colony stimulating factor, and receptors such as IL-1R-2 (a putative antagonist of productive IL-1 binding to IL-1R1), PDGF receptor B,

NOTCH4, LIF receptor, LFA-1, TGF receptor 1, G-CSF receptor, and IFNy receptor. The peptide also up-regulated polynucleotides encoding several metalloproteinases, and inhibitors thereof, including the bone morphogenetic proteins

BMP-1, BMP-2, BMP-8a, TIMP2 and TIMP3. As well, the peptide up-regulated specific transcription factors, including JunD, and the YY and LIM-1 transcription factors, and kinases such as Etk] and Csk demonstrating its widespread effects. It was also discovered from the polynucleotide array studies that SEQ ID NO: 1 down- regulated at least 20 polynucleotides in RAW 264.7 macrophage cells (Table 19). The polynucleotides down-regulated by peptide included DNA repair proteins and several inflammatory mediators such as MIP-1a., oncostatin M and IL-12. A number of the effects of peptide on polynucleotide expression were confirmed by RT-PCR (Table 20). The peptides, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 19, and SEQ ID NO: 1, and representative peptides from each of the formulas also altered the transcriptional responses in a human epithelial cell line using mid-sized microarrays (7835 polynucleotides). The effect of SEQ ID NO: 1 on polynucleotide expression was compared in 2 human epithelial cell lines, A549 and HBE. Polynucleotides related to the host immune response that were up-regulated by 2 peptides or more by a ratio of 2-fold more than unstimulated cells are described in Table 21.

Polynucleotides that were down-regulated by 2 peptides or more by a ratio of 2-fold more than unstimulated cells are described in Table 22. In Table 23 and Table 24, the human epithelial pro-inflammatory polynucleotides that are up- and down-regulated

} respectively are shown.

In Table 25 and Table 26 the anti-inflammatory . polynucleotides affected by cationic peptides are shown.

The trend becomes clear that the cationic peptides up-regulate the anti-inflammatory response and down-regulate the pro-inflammatory response.

It was very difficult to find a polynucleotide related to the anti-inflammatory response that was down-regulated (Table 26). The pro- inflammatory polynucleotides upregulated by cationic peptides were mainly polynucleotides related to mi gration and adhesion.

Of the down-regulated pro- inflammatory polynucleotides, it should be noted that all the cationic peptides affected several toll-like receptor (TLR) polynucleotides, which are very important in signaling the host response to infectious agents.

An important anti-inflammatory polynucleotide that was up-regulated by all the peptides is the IL-10 receptor.

IL-10 is an important cytokine involved in regulating the pro-inflammatory cytokines.

These polynucleotide expression effects were also observed using primary human macrophages as observed for peptide SEQ ID NO: 6 in Tables 27 and 28. The effect of representative peptides from each of the formulas on human epithelial cell expression of selected polynucleotides (out of 14,000 examined) is shown in Tables 31-37 below.

At least 6 peptides from each formula were tested for their ability to alter human epithelial polynucleotide expression and indeed they had a wide range of stimulatory effects.

In each of the formulas there were at least 50 polynucleotides commonly up-regulated by each of the peptides in the group.

Table 18: Polynucleotides up-regulated by peptide, SEQ ID NO: 1, treatment of

RAW macrophage cells’.

[0107] The cationic peptides at a concentration of 50 pg/ml were shown to potently induce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of unstimulated cells is shown in the third column. The “Ratio Peptide: Unstimulated” column refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. 0108) The changes in the normalized intensities of the housekeeping polynucleotides ranged from 0.8-1.2 fold, validating the use of these polynucleotides for normalization. When the normalized hybridization intensity for a given cDNA was less than 20, it was assigned a value of 20 to calculate the ratios and relative expression. The array experiments were repeated 3 times with different RNA : preparations and the average fold change is shown above. Polynucleotides with a two fold or greater change in relative expression levels are presented.

Polynucleo | Polynucleotide Function Unstimulated Ratio Accession tide / Intensity peptide: Number

Ee

Etk1 Tyrosine-protein kinase 20 43 M68513 i al I I

Corticotropin releasing 20 23 X72305 == I a il

OTH pomepoiori |__| 18 | vas

BMP-1 Bone 20 14 L24755 il ee EE A

Polynucleo | Polynucleotide Function Unstimulated Ratio Accession tide / Intensity peptide: Number = em

I EE EE

Receptor 20 14 U32329

Fe I a Ml il c-ret Oncopolynucleotide 20 13 X67812 il i=l I I

BMP-8a Bone 20 12 M97017 morphopolynucleotidetic fm

MCSF Macrophage colony 85 11 X05010 il =r EE

GCSFR Granulocyte colony- 20 11 | M58288 jal eno I

EC Cc LC I Li

Ee ce NES NO

IL-1p Interleukin precursor Nn M15131 oe

ET | Semper | @ |v | wow

CAR | Gomer || [see

EE eC LL I RC admis ||| ooo

I Ci CR I EL Bl

EC IR A I

Polynucleo | Polynucleotide Function | Unstimulated Ratio Accession tide / Intensity peptide: Number

Ela

ORR | Cremer | 3% | 4 [ov

Cammy | ow | ow |v om]

GADDA45 DNA -damage-inducible 88 3 128177 i = I A

ForDT | Apres |__| 7 | mew

YY (NF- Transcription factor 593 2 13968 1 Wi HH Bd

MLC1A Myosin light subunit 453 2 M19436 il <I I id

I Co EC II Nicci

Polynucleo | Polynucleotide Function Unstimulated Ratio Accession tide / Intensity peptide: Number

Ei cat

IGF-1Ra Insulin-like growth factor 218 2 | 100182 hl i I A ik

BMP-2 Bone 2 1.25602 morphopolynucleotidetic

HES

Brn-3.2 "Transcription factor 174 2 S68377

Ei Ml il [KFA | Knengmiyproein | 160 | 2 | DISS

BKLF CACCC Box- binding 138 2 U36340 = I I Bi

Table 19: Polynucleotides down-regulated by SEQ ID NO: 1 treatment of RAW macrophage cells®, :

~ WO 2005/025607 PCT/CA2004/001602

[0109] The cationic peptides at a concentration of 50 pg/ml were shown to reduce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of unstimulated cells is shown in the third column. The “Ratio Peptide: Unstimulated” column refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. The array experiments were repeated 3 times with different cells and the average fold change is shown below. Polynucleotides with an approximately two fold or greater change in relative expression levels are presented.

Unstimulated Ratio Accession

Polynucleotide / | Polynucleotide Function Intensity peptide: Number

RET | Wamp | m7 | 00 | wo :

Fe | mews | Br | om [vee

KRT18 Intermediate filament 318 0.28 M11686

A = I Ml hi

CL cowed | @ | ow [xe

Gee | tw | 0» | ova

FSIDNA | DW | a0 | 0s | oe

Unstimulated Ratio Accession

Polynucleotide / | Polynucleotide Function Intensity peptide: Number

Eh

I sc CN I sil

Ec I NE I Rit

KRT19 Intermediate filament 622 0.52 M28698

I i=l I il

GIO | Gwen || 0s | we

CTLA4 immunoglobin 468 0.57 X05719

I =< I I

MTRP Lysosome-associated 498 0.58 U34259 vil a I id

Table 20: Polynucleotide Expression changes in response to peptide, SEQ ID

NO: 1, could be confirmed by RT-PCR. (0110) RAW 264.7 macrophage cells were incubated with 50 pg/ml of peptide or media only for 4 hours and total RNA isolated and subjected to semi-quantitative RT-

PCR. Specific primer pairs for each polynucleotide were used for amplification of

RNA. Amplification of B-actin was used as a positive control and for standardization.

Densitometric analysis of RT-PCR products was used. The results refer to the relative fold change in polynucleotide expression of peptide treated cells compared to cells incubated with media alone. The data is presented as the mean + standard error of three experiments.

Table 21: Polynucleotides up-regulated by peptide treatment of A549 epithelial cells”.

[0111] The cationic peptides at concentrations of SO ng/ml were shown to increase the expression of several polynucleotides. Peptide was incubated with the human

A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHUO3-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio

Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Unstimulated Accession possess | ty [B05 T0001) amr

CC ICC cl NL I Eid

EL NC IC I EN is

TRE | om | a4 | 0 | a | 18 jane

Unstimulated Accession corn | mn [BT Two

LS I IE NE A LC

R superfamily, member

A I IY I

: R superfamily, member eva | wn [se] on | | [wer

R superfamily, member

I PY

CN WA NN LE id interleukin enhancer binding rsd IT I [ES RP oe interleukin enhancer binding

Saal NE ro BP cytokine inducible SH2- asl EN I PI PO [K cytokine, down-regulator ytokine inducible SH2- [K cytokine, down-regulator small inducible cytokine ubfamily A (Cys-Cys), ern | Ll | fun

GFB inducible early growth i IN PP IP A

SASL IL NC CA Il Ne a

SI WL IC NC i Nal ial adored | 0% [40 | 5 | 39 [51] moan

Unstimulated Accession reson mn [575 [3 or ee cor | ow [er | 1 [0 [ ntegrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 em | uf ntegrin, alpha 3 (antigen

CD49C, alpha 3 subunit of

Em | Ll Ldn

EC WO NE Il i gio Tendo] 00 | 17 | 50 _| 66 [53 [novos alcium and integrin binding disintegrin and ovis |_| 31 || aa |o am disintegrin and emmy | oot 11] 15 | oe Jos] wom disintegrin and orem meres 15 | 1 | ss Jas oon disintegrin and omc | ou | 15 | os | os Lao] mon adherin 1, type 1, E-cadherin cadherin 12, type 2 (N- so VO IS I Pe

ER NC i BL I Ll si) poem | ow | 30 | 75 | &5 [95 ww

Unstimulated Accession

NI fe a Cae

I IR NN I I A I catenin (cadherin-associated spr I I I aminin R 1 (67kD, ribosomal wien TO IO) IP JOR A killer cell lectin-like receptor eee | [or | oo | a [udamer] killer cell lectin-like receptor ovcemer | to [52 | Joo [a] won killer cell lectin-like receptor sips JRF OG IRV UF pos el NC LR Rl

EL WO Be I Kl ec preg ng TR | T00 | 17 | 23 | 0% 07 [Rated

WO NE ICO Nl WO

ES WO FE NC ad ii

SC WL NC ME Na ad BN

CL WO NL Nd

Human proteinase activated

Sli NO IV prostaglandin E receptor 3 pel IP VY [DP fo

Foor Reape | 105 | 25 | 10 | 05 [08 | Roan

VE NC HC I NO El 0a orowth factor receptor-bound el NP 4% I Op

Mouse Mammary Turmor ysiogl I I I PR I

Unstimulated Accession sons | oy [577 5 To vat

TS I NE NL NN E21

LC I NC NL NO el prostaglandin E receptor 1 srl I I growth factor receptor-bound so ofa] ee]

Epstein-Barr virus induced wera IR I PR I fH PE omplement component ee I WL NR

WL LL BC osine kinase, non-receptor, i I EP IV IP receptor tyrosine kinase-like ’ nrotein tyrosine phosphatase, mgr 10 | ua | os Jo ase protein tyrosine phosphatase, mee | _|35 | so | 0 | ore protein tyrosine phosphatase, brotein tyrosine phosphatase, _| 3] a | on fos osm brotein tyrosine phosphatase, hrotein tyrosine phosphatase, sgl IP IPR IR PO PY

Unstimulated Accession rss | oy [557 5 mo] em protein tyrosine phosphatase, envi IPR 0) 0 1 protein tyrosine phosphatase, ansieiguns INR 9) I fy pe protein tyrosine phosphatase, © protein tyrosine phosphatase, soil INO J protein tyrosine phosphatase, receptor type, C-associated em | a] | Lee

MAP kinase-activated protein

CoE NC LN 2 ch al

Pees | Too | 30 | 52 | 08 [02 | we mend | 0@ | 37 | 0_| 24 | 25 [root]

St I WO A ll i) rem ers] 00 | | 15 | 1 | | Nw reno] G8 | $4 | © [50] Naw regulator of G-protein ooo | on | al w |u| fumes regulator of G-protein wri I BN I PP

BCL2-interacting killer pail NPR I) I FY I Ye

Unstimulated Accession sur | sa [57] 85 TOT aspase 6, apoptosis-related apoptosis-related protein or | vi [ 22] ve | 2 foo woe caspase 8, apoptosis-related rome |v [53] 10 | oe [s]oass

Table 22: Polynucleotides down-regulated by peptide treatment of A549 epithelial cells®. : (0112) The cationic peptides at concentrations of 50 pg/ml were shown to decrease the expression of several polynucleotides. Peptide was incubated with the human

A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio

Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Unstimulated Accession irs | ey [7 [53 [TD] awe

A I NC RC Cd ak NCC I I LN a LE CC WE a I a

IN pose rd | 313 | ats |_| om [03 [asus

IN ceptor pray meter 12 | 407 | 059 | 03 |__| aoa war

IF Rowerinly mabe 7] 76 || os | 0s [os [awn

Unstimulated Accession ame | i |e Tis TST

RAF and TNF receptor-associated

CN al Wa NO Cll

IL-2 receptor, gamma (severe combined ny] wn [on] oa] we eS CI WC al NO Cdl

Ee NN WL Mc a ld el

SW NC al a a Bi eukotriene b4 receptor (chemokine roms | on | Lin en one mall inducible cytokine subfamily A orm | x | on || ou [onl mall inducible cytokine subfamily A rebel IF pf small inducible cytokine subfamily A peer IRS [PR FY I small inducible cytokine subfamily B

EERE hemotactic protein 2) 3.57 0.11 0.28 | 0.38 | AI889554 small inducible cytokine subfamily B oon | 2a | wn || ou small inducible cytokine A3 emia | an | 10 | on fon | Jun

Ct WL NC Cc Cl za

Comper mpm Carr | 191_| 0% | 08 | 051 [0 [ATG adherin 11, type 2, OB-cadherin ems oe Paien | 20 | 0% | 0m | ow [oa [aan . 7Q

Unstimulated Accession rn | tn [5 [5 ao]

Glens) | | HR adherin, EGF LAG seven-pass G-type SE H receptor 2, flamingo (Drosophila) : lle lr 5 Froben Gew)_| 1% _| 037 | 0a | 056 [06 RATT selectin L (lymphocyte adhesion ry | a on La [oa | Jo

Fo seer es || 1 | ox | 07 | 077 [oto Ho a Nc CN cl HO i) on as | io | ww [00s [oor [2s se

NC I CEC IE I Da

CL A NC Nl Wa il Ra disintegrin and metalloproteinase disintegrin-like and metalloprotease disintegrin-like and metalloprotease

Ferg roe | 00 | OA | a4 | Ta [0% [Rss diphtheria toxin receptor (heparin- hinding epidermal growth factor-like

Em | lien

Fc fragment of IgG, low affinity IIIb,

LC i I a id Rl on

Unstimulated Accession

I ee a iN WR NN NN NA

Fc fragment of IgE, high affinity I, ene on | on | vo soe ar leukocyte immunoglobulin-like .

Enrerull I EP pe Ee leukocyte immunoglobulin-like receptor, subfamily B (with TM and ead 0 I leukocyte immunoglobulin-like receptor, subfamily B (with TM and

Sd I PM eukocyte immunoglobulin-like oss | | os | an | on fon wm peroxisome proliferative activated protein tyrosine phosphatase, receptor ype, f polypeptide (PTPRF), interacting protein (liprin), al 219 | 043 1.06 N49751 wrotein tyrosine phosphatase, receptor inn IPN I RS protein tyrosine phosphatase, receptor

Sl I PY PEI pet we protein tyrosine phosphatase, receptor mmr | aw | on [on | |osfussen protein tyrosine phosphatase, receptor brotein tyrosine phosphatase, receptor- immer | 19 | 0 | ox | on [ox jn pom bron ogra we | ToT | 09% | 0 | 03 | 113 | ov 1

. Unstimulated Accession cir | 3 Ts lm poten [|| | || ___

Ee WO a a al id al

A re Fe se 10 | 100 _| 034 _| 08 | 210 [197] Voie

FO ie § ing pon? | 29 | 016_| 00s | 0% [05 | noun

FA ie Fe Fe 17___| T9000 | 091 | 0% [088 [ROSE

EN CE I i

FAP irs Kee _|_1_|_03_| 009 | 0 | 20 [AAAI

FP Fi re re | 15 | 065 | 041 | 0 Jou] orn

AP Vie Frey | 0 | 150 | 1 | 080 [09] Wat

WA I a a) eid

A I NN Rl I pO es | 00 |r | al | __ pe] mon oro Goren galings | 37597 | 027 | 06 | 0a [01 ae eT I NR CC Rl

Sc WC TO IE al Ce i orphan seven-transmembrane receptor, apoptosis antagonizing transcription

Se NTR Fy a I a NN Li) 82 83

J

Unstimulated] Ratio Peptide: Unstimulated | Accession

Polynucleotide/Protein Intensity EREIEEIER Number protease (interleukin 1, beta, onvertase) programmed cell death 8 (apoptosis- inducing factor) 1.07 1.94 | 0.08 | AA496348

R1 84 i

Table 23: Pro-inflammatory polynucleotides up-regulated by peptide treatment of A549 cells.

[0113] The cationic peptides at concentrations of 50 pg/ml were shown to increase the expression of certain pro-inflammatory polynucleotides (data is a subset of Table 21). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHUO3-83. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. :

Unstim. Accession mesma ttc | co [53 55 TO TT

IL-11 Ra; Receptor for pro-

TL-17 R; Receptor for IL-17, an inducer small inducible cytokine subfamily A, serail NS IS I

D31; Leukocyte and cell to cell integrin, alpha 2 (CD49B, alpha 2 ubunit of VLA-2 receptor; Adhesion to eukocytes 1.00 0.89 2.44 3.62 0.88 |AA463257 integrin, alpha 3 (antigen CD49C, alpha 1 subunit of VLA-3 receptor);

Leukocyte Adhesion 0.79 2.51 1.88 1.07 | AA424695

Unstim. Accession ynucleotide/Protein and function J fod grin, beta 4; Leukocyte adhesion [065 | 079 | 217 [1454 | 155 |AA4SSG6E ype lectin-like receptor-2;Leukocyte

Table 24: Pro-inflammatory polynucleotides down-regulated by peptide treatment of A549 cells. : [0114] The cationic peptides at concentrations of 50 ug/ml were shown to decrease the expression of certain pro-inflammatory polynucleotides (data is a subset of Table 22). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA : was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHUO3-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Unstim Ratio Peptide: Unstimulated Accession /nucleotide/Protein; Function BE pov -like receptor (TLR) 1; Response to gram * 2; Response to gram positive bacteria and . 5; May augment other TLR responses, : yonsive to flagellin io oi fos | || aon 7: Putative host defence mechanism [5.03 ] 013] 0.11 [ 020 | 0.40 | N30597

Treceptor-associated factor 2; Inflammation

I receptor-associated factor 3; Inflammation 315 Jos | [072] 032 JAAS04259) ar spent member 7 417 [0% [war | | oar | ww

Unstim [Ratio Peptide: Unstimulated [Accession

TO li ic NF HN NO

TF R spn reer nama | 267 || 038 | 038 | 036 [RAOSTT

RAF and TNF receptor-associated protein; small inducible cytokine subfamily A, member id 7) 1 mall inducible cytokine subfamily A, member

Sl [0 Po FO pS pv small inducible cytokine subfamily A, member il I J pe mall inducible cytokine subfamily B, member ero ace soe 35 ot [oe [on | 0 | ss small inducible cytokine subfamily B, member ce | sa on oro |v small inducible cytokine A3 (homologous to oor | | ipo us| orn [1-12 receptor, beta 2; Interleukin and re | es Joo on] | fue

Cio Dae | [09 [00 [697 [05 [ane selectin L (lymphocyte adhesion molecule 1);

Sl Dv 1 PP I ascular cell adhesion molecule 1; Leukocyte ml PS 4 PP intercellular adhesion molecule 3; Leukocyte

FOr 7 FF FO eS WO Rd sal

Table 25: Anti-inflammatory polynucleotides up-regulated by peptide treatment of A549 cells.

[0115] The cationic peptides at concentrations of 50 pg/ml! were shown to increase the expression of certain anti-inflammatory polynucleotides (data is a subset of Table 21). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHUO3-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Unstim Accession

SR be Cf Cr

IL-1 R antagonist homolog 1; Inhibitor of septic a ET Eo

TL-10 R beta; Receptor for cytokine synthesis mee 5 Apps | 0m _| 170) | 901 [1a SORONS

NR ar Apr COM) | 5571 | on [ow [|| OH

NR en 15 pots | T0_| 58 | aw [0] aon

IK cytokine, down-regulator of HLA IF; Inhibits egg I vg PO FA

GFB inducible early growth response 2; anti- era | un | 32 | [on oo

C57 Adhwsion moles binds LEAP | 100_| 262 | 087 [115 [0B AAs77I0

Table 26: Anti-inflammatory polynucleotides down-regulated by peptide treatment of A549 cells. ’ (0116] The cationic peptides at concentrations of 50 pg/ml were shown to increase : the expression of certain anti-inflammatory polynucleotides (data is a subset of Table 21). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHUO03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Unstim Accession

I ee foes

Table 27: Polynucleotides up-regulated by SEQ ID NO: 6, in primary human macrophages.

[0117] The peptide SEQ ID NO: 6 at a concentration of 50 pg/ml was shown to increase the expression of many polynucleotides. Peptide was incubated with the human macrophages for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio peptide treated : Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Gene (Accession Number) Control: Ratio peptide

Unstimulated | treated:contr cells ol

I cc BO J RL

I RCC EC J

I ic Ce IC NE ee TAO | os Uwewgewn | oe | s0] romeo noon he GROG) | 065 | 48

CN LN EC women

Ra oR BR 1-acylglycerol-3-phosphate O-acyltransferase 1 ew | ow

Vacuolar proton-ATPase, subunit D; V- im | wn |e potassium voltage-gated channel KQT-like

I LI pancreatic zymogen granule membrane : E2F transcription factor 5, p130-binding eukaryotic translation initiation factor 4A, guanine nucleotide binding protein, gamma mucosal vascular addressin cell adhesion

[romeo | om [30 i Co IT NR [mene | ow [

CL RC NC

I ec IE NC protein kinase, cAMP-dependent, regulatory,

POU domain, class 4, transcription factor 2

POU domain, class 2, associating factor 1 a IC NC

NADH dehydrogenase 1 alpha subcomplex, 10 : bone morphogenetic protein receptor, type IB interferon regulatory factor 2 (NM 002199) pts, in 1 (ROS)

Table 28: Polynucleotides down-regulated by SEQ ID NO: 6, in primary human macrophages.

[0118] The peptide SEQIDNO: 6ata concentration of 50 pg/ml was shown to increase the expression of many polynucleotides. Peptide was incubated with the human macrophages for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO4). The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio of

Peptide: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Gene (Accession Number) Control: Ratio peptide . Unstimulated treated:contr cells ol

Unknown (AL049263 17 | 006 integrin-linked kinase (U40282

KIAA0842 protein (AB020649 11 [013 |]

Unknown (AB037838

Granulin (AF055008 86 [014 olutathione peroxidase 3 002084

KIAAO152 gene product (D63486 09 1017 - I TGFBI-induced anti-apoptotic factor 1(D86970) | ____ 09 | ~~ 0.19 disintegrin protease (Y13323 hroteasome subunit beta type 7 (D38048 cofactor required for Spl transcriptional activation subunit 3 (AB033042 0.23

TNF receptor superfamily, member 14 (U81232 08 | 020 proteasome 26S subunit non-ATPase 8 (D38047 proteasome subunit beta type, 4 (D26600

TNF receptor superfamily member 1B (M32315 cytochrome c oxidase subunit Vie (X13238

S100 calcium-binding protein A4 (M80563 proteasome subunit alpha type, 6 (X59417 proteasome 26S subunit non-ATPase, 10

AL031177 0.32

MAP kinase kinase kinase 2 006609) | 08 | 032 ribosomal protein L11 (X79234 mar molioproimase 14 (Z4sd8y | 10 [032 ——oteasome subunitbeta type, S (D201) | 1s | 033 “MAP Kinasc.activated protein kinase 2 (UI2779) |__ 15 | 034 pase UIDT) | 0s [035 nD proto-oncogene (X5668) | 30 | 035 ——ieasome 26S subunit, ATPase, 3(M34079) | 13 | 035

OE recepor ke 1 (ABOI270h | 07 | 035 —ierferon slpha-indusible protein (ABOTOS6S) | 13 | 035

DF receptor L(NM 012428) | 16 | 035 ——— CamepsnDME33® | 46 | 036

MAP kinasc kinase 3(D87116) | 74 | 037

GF betanduced, M77389) | 18 | 037

Bir dll RTI EPS

AF016266 1.1 0.37 —roteasome subunitbeta type, 6 (M34079) | 13 | 038 clear receptor binding protein (NM 013392) | 52 | 038 — Unnown(AL0S0370) | 13 | 038 ~rotease inhibitor 1 alpha-l-antitrypsin (X01683) | 0.7 | 040 oroteasome subunit alpha type, 7 (AF054185) | 56 | 040

LPS induced TNF-alpha factor (NM 004862) | 53 | 041 — ansfominreceptor(X01060) | 14 | 042

Mic iieill NR EVER

AB009398 1.8 0.44

MAP kinssckinase5(U25265) | 13 | 0.44 — CathepsmL(Xi2451) | 15 | 044 —T{ receptor-associated kinase L (L76191) | 17 | 045

MAP kinasc kinase kinase kinase 2 (U07349) | 11 | 046

Ei dain] IY VR

AL022721 22 0.46

TNF superfamily, member 15 (AF039390) | 16 | 046 defender against cell death I (D15057) | 39 | 046

TNF superfamily member 10(U37518) | 287 | 046 |] camepsmHE(Xi6832) | 14a 1 047 protease inhibitor 12. (281326) | 06 | 048 proteasome subunit alpha type, 4(D00763) | — 26 | 049 proteasome 26S subunit ATPase, 1 (102426) | 18 | 049 ~protcasome 265 subunit ATPase, 2 (D11094) | 21 1 049 ~~ capmsel(Uel319) | 24 [049 ~~ mamxmetalloproteinase 7 (211887) | 25 [049 [

Table 29: Polynucleotides up-regulated by SEQ ID NO: 1, in HBE cells. (0119] The peptide SEQ ID NO: 1 at a concentration of 50 pg/ml was shown to increase the expression of many polynucleotides. Peptide was incubated with the human HBE epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO04). The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio

Peptide: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Accession Gene Control: Ratio peptide

Number Unstimulated | treated:control

EIS

Tm | ewes | oo | mer protein tyrosine phosphatase recepter- olfactory receptor, family 1, subfamily =] I {I cc NE IL dolichyl-diphosphooligosaccharide-

EN eral IV tumor necrosis factor,alpha-induced

ROSS | ews | 0%

AI | SECs se fy en | 055 | BT]

Accession Gene Control: Ratio peptide

Number Unstimulated | treated:control = 7 me | Owen | os | Aw “aw | Wepewouwsew | ov | B3 amen | ween | 19 | 5 a NL Ce I RL

IC I NN RL

Tw | wen | os | wo] 5,10-methenyltetrahydrofolate wowel | weew | ov |W

I eR NC

WORT | memepnencll | 08 | 9%

Ee I I I my | ween | ow |e a iE LL Rc

ER I NC

I I RL

Accession Control: Ratio peptide

Number Unstimulated | treated:control

ER a I A I BL

RT | eevee inn | 03 | 76

RR I Lo NN CL RC i GS NA RL

ILC I cL co CA [Em | Cpe tpn | 0% |e

Te | weew | ok | or

EE wee | oe

Thom | weew | om owe | wewA | ow | sl]

I IR NA

REE | geanecotis | 08

CL NC LI

AE | ween | oy | aw

TRAF family member-associated NFKB

I ai I

I I ct I I em | roves | mw

Accession Gene Control: Ratio peptide

Number Unstimulated | treated:control

EI

I I NN

UDP-N-acetyl-alpha-D- galactosamine:polypeptide N- sw | eo | 0% | ©

A ee BC

E a disintegrin and metalloprotease

ICL I IN IL

Ro | weom | Ww | ar

CO | WhmebomhiA | ow | a

Table 30: Polynucleotides down-regulated by Peptide (50 pg/ml), SEQ ID NO: 1, in HBE cells.

[0120] The peptide SEQ ID NO: 1 at a concentration of 50 y.g/ml was shown to decrease the expression of any polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO4). The intensity of polynucleotides in unstimulated cells is shown in the third column. The “Ratio

Peptide: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Accession Gene Control: Ratio of SEQ

Number Unstimulated | ID NO: 1- = [EE

Ee I R EE II

IC a LL I

I Ec IL IL

I eT SO ILC IL

IE A NI LN a C—O EU

OT moan Tonorg 1 | T__| 016

I I RJ ICL

Human mRNA for ornithine decarboxylase a LL I ILI

ATP synthase, H+ transporting mitochondrial

Esa IT

Accession Control: Ratio of SEQ

Number Unstimulated | ID NO: 1- wl I = anti-oxidant protein 2 (non-selenium glutathione peroxidase, acidic calcium-independent

I NE BELEN RRA

6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte e

R077 |r pn vaoyeomatid | 53 | oar

RRO? | pe denen binges | 68 | om

Accession Gene Control: Ratio of SEQ -

Number Unstimulated | ID NO: 1- = EE a i FcR LLL RC

I i I a I RL

Rome Gwen | or | om

Rison | ep meme fo gms | 75 | on

A | wew | or | oa tyrosine 3-monooxygenase/tryptophan 5-

Ams | oweem | me | oar mem | mew | 7 | on mew | wr | om mE | wes | wd | os

Accession Gene Control: Ratio of SEQ

Number | Unstimulated | ID NO: 1- a I =

FEES wen | es | 0

Om | ovmmeen | To

I I LI NL

Uweow | ws | on

Wo] ween | | om me | owen | we oe | wen | ws | on]

El I J CC ww | To | om

HES | Owewm |» | om

A wwe | m1 | om

Co | wweanwmy® | 96 | 05

Accession Gene Control: Ratio of SEQ

Number Unstimulated | ID NO: 1- = Ee

I dc Lc NC RRA

Em | mensreden |e | 09

ODE | ewnecotie | 80 | 02

Table 31: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula A Peptides.

[0121] The peptides at a concentration of 50 ug/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cys5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells.

Ss 8 = nn N nos |e — a lan le g = 2 2 pa on og [eo 06 ~ |= |=

B 8

SB en — ~ = NE;

A § << [+] on - as] 5% 2 NG ~~ f= n “

B 8 ~ =~ or fen - NS & B Ug) — 00 Oo ©

J IEEE ERE

“ E - * 8 n a |v

E2l = | = la ls § 9 = = = oc S

Bo ~ oS = \n

B = = a n

[3] 8 mw , | § 8, E © E

Eo aie lel BIE oE[sle|d 4 2|E E

[6] . [" i -_ | Of [= JY : . £228 SE iz|E|EEIEE EEE 53)

SEs} SEZ Elgg 2k BER NRE 50 S no |8 &|R E & 3 22 8 (> |E [=] . 2B p>] a fey J 2 2 ~ on | on 00 |B | © S18 [~ $20 5 iB Bl BEE Bl SE — Ne) —

S| S| 2] SSBB 2 ZE18] mn" 104

SUBSTITUTE SHEET (RULE 26)

sg - |e - ~ S| ow fw wv wv

A 8 “" a al & 3 o |= o ©

B 8 on «en «~ ~t $s § | 5 |=

A § oN ~ a= o N & 8 =} — ~ . 3 . : : 6 EB on - < o > 2 a 8 «a © —- of hol IN

Q . ’ “ § a |»n “0 ~ [= N ~ [—~

A § ~ fen [en =~ IQ Q ~ |e . 8 d [==] [2 £ = [=] oo [=] oo lo . t= o 2 a la § Q s S aig

[3] 2 = 8 5 |= (5 £1 |g § lg g ? 2 & E , © = 8 2 y . Q ke 3 : oa I> 8 SEE lslE (aE [ES] ESE LS

HELTER ELS E101 EE

SEleElElEe|lie EEE 7 E|E EB a 7 2 > lo |Z |3 S g a 3 o IR 8 5 s2kER] 8 5 2] 215 i= SEEE| S SR E | $2

SIR@2| $1 lh] 4 2] R12] 1NA 105

SUBSTITUTE SHEET (RULE 26)

S Ew a le |= ss 18 8 " VS a a) < |e (3) . a gl<] = SRIFIR]I =F Ss ©

S : 6 Ble| =~ Toa |e je Is ~ |» °Q ot] ‘ey [oo

A § |« ~ a jn |e |e on |en - his NETS FY : o i -E << ~ aN

PRE - BL : oN — : ! 8B §|v 2 e~ [od + = 2 8 5 [= a © |e |< ~ & oy a § Ie wv ~ | [eN 0 wn ~~

[5] . B ; 8 wv) ~ a jn n N i ln o . 8 Qs = ole |e |e oS = 2 oo a 8 Q cs |e |e Ss i & 8 iE | 5)

Q £8 § B 8. 3 2 El : : =H | @ = a 5 3 = e CR gE |B _|E 3 5 2 EF aE RE

BE 515 § AIRE £18 212 5} = 2 2 8: ‘8

ES 5|8 8 : : eo [5 : § gE

HELENA EERE EE

- co [00 gt = wn [nn <t . (2 © : 8 gla| = ScleE| BB 2 2| EIR g =z 2 3 8 8 & b= = 181" Q I 2 = 2) 419152 <3 < g 25 108 106

SUBSTITUTE SHEET (RULE 26)

SB < < “ ~ oll EE a. < < + hl : ] 8 & B = - a NA ° © lo 2

Aa § hi A a) Q ~ od oF Lgl

Q

6 © on < x |o : a8 § p> ~ oe e~ & 8 oe a ~ < | (= Cm : 8 § o ~ ol ~ | jn : v 8 s ~ ~ Tr © : ~

Hi © e A < 9 :

ER - - 2 lw Cm 8 3 “ye SI Cl I

ES 8 = 8 & Ca 8 oo . @ [=] [=] : [= oS = o o (6 |e

Q o

FE a. g : 8 |.8 @ =) IS

J OO - - F - | 5 |B 5 E32

S lElfslEeB Elles lE gis 2

BERE 5 Ble - 818 3/8 & §& £15185 § 2 a &< 5 : 2

SiR EL EL ERE HER: = 2 ce < © :

R=] = o o “ ; 2 2 3 8 © < 3 18 |e © ee gg <e S [=3 N S 1g 3 = 82 | o = a BERS 8 g| £ 2) % 5] %13 13 3

TNL . 107

SUBSTITUTE SHEET (RULE 26)

e t ~~ <, < “0 “a © i) a) § oe) on a) on on = 2)

[3]

CC ® Eas - C= " © a] g a je on a) wv wi Joo . o N & 8 a ~ ~ 9 |e 3 § © on " — « 8 g- on on <t ~ °

S : wv f= =] a ~ =) ~ © a 5 o «i J ~N ~N ~ hd ;

BT wv Ld ‘~ =) . i= ~ ~N

[3] © a |e a ~ < + =] : had . ' Q . on | - on 5 : g . } : L — Oo 5 — Ir] : e J<| 15 lo 8 IE |€ 5 23 g 8 |B 8 “ = 5 <ls 7 8 t 8 |Z g 2 |2 gS ls 8 S 8 |H 2 8 8 e £18 52 2 ‘ale

ERE AAR A RY

SCE EERE R|FE|E 8 BIFE|EE ES [x vy oa =~ . 2 5 IN ~ g on XQ

E5182 21 2| &| E g| g 22

Q KR |e A] = on b= p= vn < Z |= No I] S o |Q

TE |< al 2 S| % S| 4% 2 = 107 108

SUBSTITUTE SHEET (RULE 26) f cg oy ~| =] ole| alo] al = a g on on on “ on (en on len a «~ 3 a S ~ SI Lo] wy a : a £ ~ sls| 4d K 3 I wy (3) a Ty a § “ = e “ ~ I ~~ = jen 00 «a § ei = ($ ~ phy .. 3 8 5 " N a ~~ x |2 a 8 < «~ 3) I) ~ |= 4) (3) a § «a ~ ~ ~~ oN ae} 31

T wu on <t on [=] ol a on — — =} Y 2 en V) — ol ~~ 1O

PA “ © ;m < ~ I" a _ = 8 ol if Wk FE [Els lz [EE © < 8 le Z 2 olf = E 8 5 g = 2 4 .

Eg SIE BLE EQ EE BIE % |g |3 Z e|8iz sig £|8 » 8 gl B =] ©

S181 88 i= 3 BOISE BIER BE &

AER RICE SE TIER TIS E a |&L dlc Bila E |« a a |&F(2 8 a Sl & = 2 jb «Qa o (= = ln gg) 19] g| 8 #8 2l=l 2E! =| g

SZ br < a I 2 |e S (= I~ = a8 = Sle| 212 3] 3 108 109

SUBSTITUTE SHEET (RULE 26)

Table 32: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula B Peptides. :

[0122] The peptides at a concentration of 50 pg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO4). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and CyS5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. oo 109 110

SUBSTITUTE SHEET (RULE 26)

x . -

E aX - ~

S gE ~ “ ~ a E |Z a ¥ = [>] a BE r~ — je = E a al Glel=l= 8 8 ¥ En =) 0 ~ ~ |= =)

C2 BERNE @ | Pl ba DR PN =I @ |e vy eo la lo | ~ i JPA 3 PE A = IPS is a s | - & Plo lw |~ | -] << -

CS ERE lESle| | S al jel . 8 sg 3

Eelslcllzlz]| s| 5 alzlola] = sg Q S = c I= oc cs |e. = 8

E

Ealslzfsle 3 AE oS S oS Ss |e oS: =) hd : z 5 RI [Eg |§ sv] 18) |Bl2 & ex |g 5 ERE S BE © loo Sle 18 5 CI] < |B |§- — a BIE |L oo so oo |.80].8 —_

EEE |2IEIE 5 slg EES EE £13 2 |& 5 2 § Pr 2 |5 >| 2% 2 8 EFIZ_IElEFIEISE(EE © f8IElEISS 8 iat LRERIFRGH IR 2 le |v |= [2 wv o le la es - «~ ° [*] — © QQ oO — 7 21318 a Ie o o [8 SRE |= IS: ~ 22518 |3 N =v sSRIBIZIS bA <=33 RE S| S|¥| 2REKRE = 110 111 ’

SUBSTITUTE SHEET (RULE 26)

= £ vy he] «N << 040 3 N ~ = S o~ Yo) r~ oN a [en | «o~ 8 t 0 10 ©“ on wv [5 % T - 8 ho] ty joo | [oo Of] Oo. ~ : =) g o~ < | jen ie on [2g [3] :

[3]

Cs oo : —- - x rll Ly © jog |— 2) i] -— 8 g wv ol oy [2} on oN on oN [og] [¥) a t ~ oy (0 2 «+ |< — a El <| =| S [a | |= of o [*}

S & ~ © |e r =] S {'=] Oo | wv) ? wv ~ on [00 jen AN fe |e ge 7 o oo lo So |e ® =m — ] gs 7 =) = o o lo lo |e =] o . < . g 8 5 _ = . [TR -_— a [=] g 2 | 3 8 & |g & ga : 8 8 © Zl (8 0 8 (8

TE IEE IE SEER IE IE,

HHI ELLE

EE EEB IEE ES EERE a = g 3 2 8 |x 1g ® £ on I a l= 19 lo la [wv |v |v — N d9| 2| S12) SBREEERERE| | 8

Ql S12 32 a JRF S| % 11 112

SUBSTITUTE SHEET (RULE 26)

& El- |~ ~ ~ |= =) nw |= ‘en g EB |~ | a ~ |e nS {od en 8S 2 Elalelal 2 oN [0 al al2 [>] ng © | = 8 lala] <2 a & oo A a lea |v. oa g iE

I Ex o — o o0 ~ ~ oy a8 go a EN ~ a a “ a

S

4 F ~ - & N ed «a | og | in g E ~ on en |e LG =~ ~ o ) & © - 5 ot! —- ct 0 | IY rl hi] a 8 < | = oa jn [en a |e on [>] =

Er sle| sls] sl] 2p g 9° = Slo |e cS cS

CT ols lon |e © |» a ole le] = loo ~

E Fle i2 |e “4 |S a I |= |= allel = 8 Qie le |= oc |o = cS |e |e oc |o = 9 ° 2 a gl] 2 |Q § le g 8 w 18 IE

Els |g & 2 & £

O aie 5 a | fn SAE 2 Iga eg 212128 |g slel3f Blawlslf |sE|EilEf Bf

HAH ELE SEER TE

(1 o ESE 3 2 = S82 la fF ¢ Ee & S ~ 53 (FR L|2 2 sls ls sls] 2 2 lz A

TEER Eg] Elz] sR 8 23 g 212122 Sg gig 2818 = 5S ~ ~ ~ <Zz 33g ¥12| 2x] 522 9 RIE 112 113

SUBSTITUTE SHEET (RULE 26)

- © ~ ala jo |e - 5 NE Rel PR PO a (vu len (en 8 3 $ © © on < - £2 = |e - ~ 8B 8

Ww E — < = BR a |e 3 8 sg a « = BIS PR gs

Ela |v NE N 00 “ 8 |= |e b- ~ oA ~ oi 8 s 8S Elna] = a |m |e ~ — “

AH jen |en on on jen |en on [2a} ~ 8 8

Essa g | al 8 S gE YS S | s| so S

Esk 5 5 3igREBR 8 Qe = o c |o | cS [> gl |8 5 ° E, ° 8 s [2] |B Till ls 1B 3 ° . Q [33 . 108 Ble | es|ElslE (ELF eel [E

SEER gle eli §|8 2 < [B

EZ |E 2 BlElEIBEIE RIZE & 9 2 20 wn Pa S LIE BIS & O18 8 lov len ve) ~ a ©

FICE «| EER| =| E| cEleER

EBS p= g 18 |Z oN = CREE ERE <=R1H| 8 30 5] 2] RPREPRR < = I: Q tor 112 114

SUBSTITUTE SHEET (RULE 26)

£ E

CRI FR FO Pt =] S <¢ ~N | T 3 Elo le fo asgl®|” ¥Elale ln 8 s [=] on 2 Eo 8 sg

J PA PU

: a S oN

T wn = vy T3ikp: 3 nln on

E a

REI

5] |E £ 3 5 c 2 ]8 [8 & 2 g

El 8 |= [=3 eg 5 | 8 a || a 125g [¥] Zz ha <= 12134 114 115

SUBSTITUTE SHEET (RULE 26)

Table 33: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula C Peptides. : [0123] The peptides at a concentration of 50 pg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU(04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling - of cDNA with the dyes Cy3 and Cy5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. 115 116

SUBSTITUTE SHEET (RULE 26)

§ E OP o ps. n : a B| Sle =| See [3 [¥]

GE ~ =) ve) hoc =} ~ [>] eB : or — — — | on

S ag 3

ZB oe a | ~| wl ‘a a 2 ZFS] &] 2] 4 ll ERI I a 8 : :

Sg Ql] S| 9 a io 8 = : & £ ~ = ¥-) © |e oa .00 <1 od oo ~ ~ |e wn 0% a 3 ® — — gE 2 S18 s| 2 S 2 Q S |e = P= S |e

[7] ° on — <r — ol [-3 []

Ld . 8 g on

E 5) 4 8 si218|g8 & Ss 2

B12 gE slzlZlE gy 2 [8

SIE 28 ESE dE |§ [8 i: a g A 88 |8 & no gs g(ElB|E 55 ~|8 8 gc |2 2 8 & 5

Ld 8 [= > © 8 S |.8 = SO . eo TER AE EERE Dez EE & < ; EES EE|FlRE 58 «8 8 ge 5 n |v |e : wv o on es --) vw [S13 0 o a $ a @ S 2 |= IN] = - [+] g o |S x = PN =] o on 3 ~~ [> = nn |v |= Nd [= ~ |= — soma [> o |e | i= [a] a DIS <¢ S — <= 22] 8] 8 g | 2] 2 2 S| =| <8 b%) 11& . 117

SUBSTITUTE SHEET (RULE 26)

pi t NA od] n |<2 a) ~ ln

Ne) ~~ < |= 0 iv) gn a a < | N=) L-] =~ | . 8

S £ wy ° | «| <. oo on =) = ol en jen 0 |e «~ g | oa 38 . - °F : : a & wn | < IN <S © =) = < | ~N |en © ; ~

S : 8 I < © (oo ~~ ~ — eo | on 8 a pa on jen 3 ~ ~ Ind ER

Ss : .

I FA

- 8 © 0 | Sl hd ~ Lo Le : =] g wv) wv jn wv | T < |< [>]

S wn [a] o] [=a — (00 ; <r

E S| S S N = |S = 8 = = = Sie ©

[7] : ° : : 18 c |e oc |e =) clef © " 5 2 on : :

E = a ho = 8 8

S 2 a 6) 8 . E g 8 . 2 = E 3 g g 5 9) ST glg Q g g 2 |8 | 3 4 3 ; B E o < £ H 8 gs |g 2

SHEE EARL

2 PEEP 2g|FE|EE|S|< |B S|E|E 3 g 5 - ©° a lon o < la : g 2 o |2 g LIQ 8 |a gs 8 a S j= a is pat} S |e 0 Sel a

Ss z 3 = 18 28 - b= > Isl = < ~ g a = 3 J a

S12] 88] =| 2 2 ¥2| 8 117 118

SUBSTITUTE SHEET (RULE 26)

$s 3 ° > n o [Df || ew Is a Ee al S19] ARG IEIRG| wn] 2

S

4 Ea I) EL \-)

HIE: s 2 [|= |e |< |« < &§ E a g(@|” oN oN oo on |e on oN [>] 8 82 |= TR Corl OC WO CT - [2 a 55" ad je QF |» 0 le : [*4 & Ele |» o wllels] Z|e

Bg §|1°]° «i < [Q [= |» = |e [74 .

Ele loo oe ) ) N |= ™~ wn «a 1 a § <t |< < ~t |en en on |en «a jen v E

E> a S | — a 5 g & oc oc |e = oS =

L*} 3

EZIE 8 8 @ “a SSE g Vie |e = oS = o s ls : o . i g i=l a 5 RK 8g = |B 3 Fo BS g 12 2 vw BIE 3 g I g ~ g 8 2 lo SB ‘a — og J

ClE|5|8 252 s|S|E|B|E|S|e g|E |B 8

SEE EEE EEE eldlaelEm 18 2 [5 Elgg ldE | Ed)E 35 [EIsEE EEE S CREE HE hd R 1 - wv Jv =] [> t~ oN 2 len a [v 3 Els ly lz a |B z= 18 |g (28 ao |¥ 2 IS $s 31 IE IR] % |= Ie 18 |1R Ig |e 3 i= 2 ie $2868] E5| SRISIEREIS| BE] Ef 2IRIB| RZ 22d 812 2 118 : 119

SUBSTITUTE SHEET (RULE 26)

° — 0 |< |= ~ © | a ) a ~ = ~ < | : - |e 2 i ola ~ = |e « a fe

Sg ERR [>] .

EEE a 8 << |N joo cn on © [*] & E wl | we r~ - a § wv (e~ <t wv on on |< [*} 2 Ek oe - ~- |e a o oy a 8 on (en on on |n [] aN ’ [*} .

T wn 0 len ~ | N-E

EZ = |»n — =m [*] .

BT

Esl algle| al slgl| 3| gk| & 2 5 S = cS |e |e o = oc [¥] 8 1] z R © bo .o— D o = &

Py , 8 & £ 8 2 2 § © : : |e 8 g |5 & gE |3 23 a d |g 3 s _ 18 5 ELBE R |2

EilslsltalCellslialzslelg Sel 2 13 ERLE LR ERLE . = = a Fl

E SR ElEz|3 EE EE 83 g 38 |8

E- Iie 2 A i 2 SBE] E| SRE] 2 zle 2 |e s2| SRE| 28| EER] 8! £8 2 |3 «=| gl4j3| 8 ER|g| 8] SA] 2B

Do < oD = | = lw 119 120 :

SUBSTITUTE SHEET (RULE 26)

SE] =| |o |n lo =| 2 en en |e <r en

LX)

QE] alae] 9lela =} 8 nn | en ~ § £ < Ee TO 14 -< = -] on o~jN oy © 8 E os | «alae |= a a on {on «~ |N <t [¥] 8 £ ll hee 00 ] [221 [aa] ~~ . a 3 & g <I —- a 8 oN |e oN [>]

E23] 3] als

Q [= o QO CO [*] f- pd hd oo ~~ [on — oe 1 << o oe |e [= <9

Q Q

3 2 8] |e 3 ESE g 7 % B.

BOE lelsf [Ee

HIRE

.|@ °

Bb © 2 Bb = = 2 2 -

Fi Gls SELLE g 8 RID |S Si= IQ |=

[7] I= ~ (7a) wv S Po

SRE] 2EIR2 120 121

SUBSTITUTE SHEET (RULE 26)

Table 34: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula D Peptides.

[0124] The peptides at a concentration of 50 pg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO4). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of : cDNA with the dyes Cy3 and CyS5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity . of unstimulated cells. 17 122

SUBSTITUTE SHEET (RULE 26)

on) EE} . +s J Te -

A Ella] = ® |= S 8

S$ ln ~ |e © foo oy — CoN . . a 8° |” NN | ~~ iN ol [ve fen

S : & © — ~ ©

Sg ee a

QE ~ a - . « 8 «a pti —- on Cn a 8 «~ S |= A oi CN © : = ‘2

SE « Te l= |e © 2 C= a § La) ha] < |N jn ~ eS - 3g sg T° — o jo |o oS CN :

E32] 55] 25 = gee Ss | Ss | Cox : [}] IY : ol | PR FE FS 8, 9 o ATE 3) : 8 8 |= © > SN oot [TY ’ . Qo Q 13} ES — = g 0 « B=] »e «© § 2] g |B (E a EERE 9 E18 8%

BER IHIE SEE ss eSB 2 58 : ~ 18 Bie ® «Is 2% 3 (3 Liz FE

SETIER SIT iy gla 8

Oe 3 8 Qa Rg &l€ 0 eX & 8 € 5 = a $2.8 212] [B18] & 2 © 5

EEE EB] ERIE] 8 gl 8 <=8 3 2 18 = I= |= i Q . 8 3 21%] 222] 2 21 5

TAN

123

SUBSTITUTE SHEET (RULE 26)

2 EF ° o

SB _

BERN] pr - A pd 8 $B - o

[7]

BE

8 sg

A eo a EIS on ~ on 2 2 |] < ~ 0 at) § Eo |v ~ |= on ~ 8 |v | ~ |= on ~

Bs

Eels a 5 2 2

E72 I% S p Ss

Eales 5 8 3 8 Qiloc |e =~ oS =I

Ld . . y= Q E h4 . ’ 21 1B u31€ 2 § |» o

E| |18 52% 8 5) B [2 7

ARERR = gq |e 8

Sle Balm Bgl J lslE2. 124.) diz 2SEc 8c BS(el8ln Bley

AE RIE E EZR BlE Ed £ 5 E382 5 gq Z|8 afm E eo : 2 °

LS @ loo |r~ 2 a - | 0 “ g g12 8 3 2 = |3 | S 8 4 on |® S, S by QO FI 5 aN pa] <=133 a 51S 3 S

EB 2 SRE] 2 % 124

SUBSTITUTE SHEET (RULE 26)

- © © |< fm 8 8 [>] gE a |. Na] ow a Nm N [vn |o a § © «i ae on = Ne wn {ed je oo

H]

PO] a k i] N I oN (rs =| on ~ a fen ~ |S 8 s a © 8 & sl gl 3) al 2 wy wy 8 s

SE o 8 g ~ RS A LE I] oo 3 : & © :

S 5 ~ o 0 El bt < 8 g oN | a) on Xie « Ld)

Tw —

HIER EIERHEB

8 Y « wv |O on QO OO oO

TT en — ~ —_ La {s\} Lal $=

E> © n © < | a |S 8 La! << ~ o |e SS |e - wv ~N 8 R= g ‘Q —_ |? » = a = 2 ° te 2% | 3 _|E[E 3] sg 18 giv 218 ew iE 8 | Elm alg |B § 8 sleElR Salk 8]; 23 8123

Eo iliZlss Bree NE

SHURE HIRT EEL RL

“nw BB EE(d & 3 5 58 = (8 2 eB (2

I-Ie ) ol

L 9 [= [=a] © 00 00 -— - SS a) «© 1% )

ZF s| 8 28 2] 2BI2IR| sie z 3 S I | | = 188 Ix nw lo 18 < E 5 2 | & S x QQ

A p | SIRE|R]| X|5 [4 14 . 125

SUBSTITUTE SHEET (RULE 26)

po ® ON 00 [I~ [=] [¥} . 8 ; [*] a E a [7 bd Te) < |= |v a E |» |= pu R «|S |e |= [7%]

E a 3 | — x Rh N < a a [en ~ aN |e ~ oN 8 s g a x oN Nn jo . a E 3 < < GS [a |= © . $B <t = + 0 . . . — [*]

Tw i E — 0 wn

E o, Ce a | eo |e ~ © [r= = = SS! c [Ss © = |e

I) Q o = S| o o lo hd . < 8 = 5 8 s | EIR E.2| |B ea dg 3 ~ ° 3 Ic : || 122 BE IF Bl IEEE Iz ee] dg 5 g . a a = Q g g 8 2 5g 518 . 8 R= 3B k=) 8 g 21% |% Sid 8 |g 8 |S 8 § a 2 (8 £152 £12 £2 EEIEIE El 8 5|aR|8 a 8 S18 8 B|E © 8 2 Bo = € 5 - < “a x vy mn ts Jen |e . a len (O EU Ds =~ £552 2! 8 SER a El |S @ g z 18 |& =3 a o |8 [2 S 5 [2 [|e |o = (=A) oo f=4 = — 2 (<4 > SE 2314] 5 2d < 126

SUBSTITUTE SHEET (RULE 26)

I: sos is © mla| wl] o|=|= a E - ed A «|e le «jen jen [*]

S © ~ Ca : ~ wn co [YN wo ) =) a FE on ’ . a g wo ~ on A a ~

Ad .

RE a| wie ala | =jaje]| win] neo = 8 o~ ea ln a on jn an Lalla en wn |r 1 >] a 2 ~ =| S| <a | © 8 8 ~ pT bo en en Vol aA | oN ~ © $ T ~ a & — ~ | 00. © ~ [® a |e = 8 on < IK on I EVAR Fad wo hd . ® wv »

E51 © 8s a = IR g| 38 8 h dl Al I id © |e = oc |o t pd < 7s) «2 |en ~

Ed a — a | 5 , N gE kl LE OIE | Is « (8 |% [Bl 3%] |F |E|3)3 ° =] bE] & g Q a. wv) a. 3 [8 |& (5%: Pla |2 (ES Ig © a 8 le gE 8 Lig |8 |= RE E |g a 8 § & ‘u 2 gle aT g 5 g 3 g: yd 8 gle g —- 18 88 |= SE)

NAH I HARA

2, i. 2 2 a — wv WV | 0 oo -] 4 oo 28] o| 98 cB 8a] SE] ERIE g 2 3 S jm haf bo NS =gb > |% SS IS é Z 2 99 & |S ale 18 Ss [= a bat 2| SRE| S]E| S|3R| %]2| 2]R|3 127 :

SUBSTITUTE SHEET (RULE 26)

E rll hd 2 < : =) g on |on on on [>]

S BT | ~ ° od [-}

LY) & B = —_ oN ~ [*) . 8 © ; 5 S |= ~ = ~ |e i =] 2 oa | [= wy oN <¢ [*] 5 FH — “a | ~ co |e S a 8 o A & «© | & . [7] g £ - « RER =) g ~~ «© ag) NIN [x] : = 8 (=) o — R=] = ) s % — |e oc |e cS |e 8 g 2 2 & 8

BEE | 2 SLE [Bl [3EE : |2gE|gE 2 EEF lB [ESE ¢ |ES|E|lZE2| RFT £8 IE2

RICHER IE EE AN EER AE

I=] : z = 8 = 2 0° 3 3 3 Ei

BER LEFEVRE RRR a2 Q : g 2 2 2 3 aE] 3 2 B S lo — oO wv |S —- r= @ 3 aN la = od = = 8 IQ © IN | Q 2 r= < ~ © i= =] eS 2 <Q I

Za 2 2 214] 2| 28 128

SUBSTITUTE SHEET (RULE 26)

3% oo ~ ~ ~ © |e |e |» |n ¥ = a g «~ ~ a oi ELE GCERGRG ~ «~

Fl

S 8 ~ ~ ° eo | ~~ > 5] a E N |e 00 00 a8 § wv LR Ua) ~ ~ % © “ & & ; “ o %0 0 [oy [m a § hs < [ 3) a 8 £2 o on |? ~ Jes |< < aN a § t~ V-J << jen | wl& - gE o ~ o ~ « ~ “ ~ g | ~ 1) ~~ «~ en < ol [>] . °

Esl 3| = slRiziels| 8 8 8 S — ce lo |~ cS |e = =

CS =m

EE = = po Q

EQ < 2 3 ) I m a 8 I

Fe 5 § |g 212 «' 8 ® 2 3 ER: £8 § sk = a ESE gE 23 = = 18 & [= T . 131 ot b= — & 15 [EE(ET|E as |slp|Blslg|E2 [5% = SER Elisa lElElFlE Ele EEE s (elf desl sE sn BIER SES 3 & os |» 5 |B ®|6 8 = 2c ©¢ ald & g x ~ 1 tT |en |\O on |= . nL on ~~ jon jen co |< $d Bl 8| | al 8) SRIERIFE 21 8 gz| g| 2 =| § S588 2| 8

S >) 2 3 8 S132 R 2% 3 = 129

SUBSTITUTE SHEET (RULE 26)

= £ ©} 0 aN = = BE ~ « a [>]

El 3 E

A

RE 9 al ap 8 8 & - on | © 8 8 X a |e ~ [>] 8 E | ow |- = § ~t on rs £5 - = a 8 on © |n ’ [>] 3

HEHEBRIB

8 ] o [--3 [=3 ) [>] ° £3 2 el RB 8 ] oo — put

R= £8

EL

E =] Se $ = = a Rol = 7} =] 2 3 HEE

Oo ‘B 3 & a |e

BS Lg |B g,

IEE RY

8 x Ila Bled « 2 poy 2 4 ™ ~~ 2 rl . 2 3 ga vo) >] =] —~s ° ge 2 = nw 18 8 <= z| §| & 2

Z| 2d = 130

SUBSTITUTE SHEET (RULE 26)

~ Table 35: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula E Peptides. oo

[0125] The peptides at a concentration of 50 ng/ml were shown to increase thie expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 hand the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO4). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and CyS respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity ~ ofunstimulated cells. 131

SUBSTITUTE SHEET (RULE 26)

€ Bla |m no I ll *n “a Y [<2 3 : a 8 £5 |X Sig] diode S ht . s 3 — Sl a len < ln ja {= [2 eo 8 8 l= lo l= lo 22] ~ a len |S o [2 a ERR] SERRE] SEFEEFFEINR [>] Lo

BE |e a |< a le la le |= las lo a gv ~ | o~ ~ | jes a |e 8 3 E Callan] =lalslelnls a Slice Rd] «la |e |s|~ 18 [* . 2 Elnle| els < |e 2 © a gv |v wv A] NON hs t~ [>] . 2° - ;

Eolsle| sialrisls] zRiERSlBlES 8 Yis oc |c c |o = o |e ec |e 18 : =

Ezlaln| =lalglels| spl 2 Vile le cS lo |e oS cs |e |e . o < : : . Q 5 2lEE5 (Ea |5 4 gc 8 © aS gE. g : s |& |B 3 218 5g gE § |B 5 |S |8 281% <|8(g|§|2|E 2 |& & |g [oo

S218 =|8|8 g |.8 £2 |8

EH HR EH

[2] [Vi] ($3 [=} = K

SEF 4B[E|2|a|5 58 BlZ 8 2 wv po

L 9 [an (© % o |§ a |v wo (2 2 81213 s 18 se |8 slo [312 12 le [2 [8 g 8 28185 sIDIRIRIRIZ IE |S

S 2IRIB| sRRIEIS SRISIERIRIE IS

Ih | SFRRE| REEREEEE

EY > |S > ; 132 :

SUBSTITUTE SHEET (RULE 26)

gE " eo fo |= [oo ~ |e b= on 00 0 |= ~ a~ 8 § i -. [ ag] Heal © .

EE |x = ~ |e " - a § wn | ~ oo |en “i ~ [>] . .

SE ss s| 2] A 5 8 sg ~ :

El siz] 2] 3% 2 v 8 s 4 " . = : «kB oo @ ~ lo |n QS ‘0 a § (2) 8 wn jew jes ~~ At

JES] = o 23 12 |e = [8 = = c lo = = [*] °

El 22] 2 sg =] © [= [=] [=] Q 5 8 : an LC 3 T Est E |B] IE g 3 = 2 2g g g e 3] 2 5 8 s a 5 BIE 3 = S 5 8 5 2 & BE Sleld IOBEE |ElelslzlEE |B E

SEVER £18171512 85) 82 . ce Ble = < 21.8 F<) 2 |. BEE 53 EEE]

ELL RLELI EN 3185 fs B 2 81 <o|® @ 218 3 a S| 88 $2 QI 3 AERC 2 218 <7) EB) 3 &| dEREE BE) BE)

D a) < 5 < q = 133

SUBSTITUTE SHEET (RULE 26)

® © ow |= -— ~ vn < N= 3

S Ele ~ is f= I © {a ho oy [R {oo a g PR PE PY = [en |e ~ [|= PRI PA

S

2 En pocgl ~~ al “lls a le |o 2

EER 2k] gl] als gi eg 2a 515] sgl] gf SF > [>] : 3 Ew “ | | als als le] ona a 8 |« a fen =| ale NEL aN fen @ E og} ~ =] 8 sg « a

ELI ] [= = & & |] ] 18 |& 8 Qc °c |s = = oc |e oc = : i)

Exc =lslg| 8] algls] als 5 gv |° o |e =] o c |e o & oo |e 2 § § |B | |8 2 2 gig EB e e |, eg {8 g sg [8 § 8 |e a a 18

Q cS |'E — g B. . 2 S| 18s SEs! 212 318 |3 a] els 8 218 22 Blsi8 |B gg |§ £15 += — Lo | Q 218 & ElE 2/5 3 SIE gl8|8]|e 2|E (8

ERaleilmlE Elf RES EIE(EIE EE: >= (2128 G8 812 |2 a = |= 2 |8 8 i e : = 0 | be 2 2 (2 x ) S Qa 213 |e [8 2 8B IR PA RT a qI= |= > |= |= a vn 1S i= [=] 8 Ble wn |e = oS mn Ie jen T= 18 QQ [oo a [SP < Z |8 g 5 |S 3 3S IS | 213 31318 [9 9 Bigg] 3] S512] RIFE] RLS 134 :

SUBSTITUTE SHEET (RULE 26)

1® £ a lov Joo ~ n |v la fa |e [ea S| o 0 a8 = on |n [en on en jn Jen Jon jen |en on ~ Lo]

S n - B® on wv : << |v. [b= Ug} - len |. vy 0 “a - |= fa < a |e [es < by

S gE — =~ nv) |en MEI) ~ g E ~ fos 8 “ |i © |G |e « © . la 3 “ on 3 — — 0 | N [| «Q : a § en ~~ ele N fen [= ~ ad] oo

S

$$ © & & < (Nm < < oo © — a § Ov aN |e ol vy ~r oo a) ~r 8 . & E — ; «a 5 ~ |Z |e | ~ a « < "

Esl sizizle| 8) shlaRRR al 2 : & co lo o oc | oS |e = oS 8 eS La]

E 3 a “ by av o = S [> 2% . [] O 4 8 g |= i EE LF IB] IgE E fo) } R= a || « 2 o I= IQ 1s B R3, s |& Q bs he g 1% |8 |8 15% g Bg ° 1& o

Eos EEE ls iE EE sed BEN EES Ea lElelt gE EE

QO = w |Z | 8 [7] «3 alia & |& « t=) - 8 —

P23 EEE B| Slap | 8] @ £8 zix@lal 8 S8ielRIg| &| 8&8] 8 4 PR NR - PA Er NL = =) S S < RCE 3 CAERERERE a 51 3 = » > 1» fos 135

SUBSTITUTE SHEET (RULE 26)

gE ~~ ny a «a NN NN |= —-

A E «~ ~ «~ «~ aN CELL ~ 3 [= oe |® on ll 2 le h aE SI A ~ 9 Ll [7-3 IV) pl wo g 2 Ela ~ ln |e — oa fe | a g §|o Q | |F = < | | | 3] [>] w B ~ ps 00 o : 1) «< a) v-) [>] k $ © - 5) a) 3g) ) lg 00 < [= |= & 2 QS wv aT] «a wn [*] ? wv | ~ 1 wy 0 gE 318 S |S 3 S 8 YY |e oc |e o = [>

T eo on on ~ o) - = “ S — ~ <

ES

: r J. 5 . |B |E i = 4 alg £8 2 E = = f] a |g 5] ~ 5 5) 5, n 8 2] = 12 fr ofr IE IEEE PElEs

SeElsiE 413 (8 [Els|3|E E|giE |e [= = — g |g - = © 225% BE Es |SlEEE GEES 8 < 25x] 2 |3 2 12a 8 g wy 2E13] SRIE| =| 3! BIsRE| 88g] 3

I> ~~ |Vo | ~~ ©0 wv ln [DT aN lm J on 2 z|3 © [0 |= ~~ et © a IR Q i= I& ol .

Z| SRIF] B| S| TPE E| RRR] 136

SUBSTITUTE SHEET (RULE 26)

Els eg gi” eB «“ E

Ei 8 g 8 g

Ele af" & Ela 8g 8"

Tw |e

Fo) [*)

TS en 5 3 . 8 © El & = 3 B

H

= . £ 215

E-E g 28 <<” 4 137

SUBSTITUTE SHEET (RULE 26)

Table 36: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula F Peptides.

[0126] The peptides at a concentration of 50 pg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells ford h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHUO4). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and CyS5 respectively. The “Ratio ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. 138

SUBSTITUTE SHEET (RULE 26)

oe & © SS) ~ IT ~ |o [em 2 E JAR] «8 @lg = fen [os

S : 2 + E — — 0 i. : 2 § E © ul il © : 2 § £ oe |N | S wo |e ~ n |e. Ia 8 a 8 NN wn el SEA «~ Ne =) > . 2g 8 E| «lo ~| als ¥ |e |= 2 =) a oes on = |e + en jen jon |r

GC) 3 | SUN IR & > © Q a = S814 8 ; = eS = = o [oe 3 . —- ;

ER IB 8] dI% a 314 29 Ss [o |s = oc |e oS Ss |e . [>] 85 2 5 2 oo | 2 8 218 ) . [=] -— — [<8 1 . lle 218 [B| - |g >|E|8|8 ° be g 0 |& Z <5 [8 a

C Ege B 8 go |% § & EI 5 |S oO 2 mw Els @ aR |e 8 g 81818 > o a on QL =] 8 S [3] 2 Q

HEE EE RE LE

2 2 05 © |g 3 Is 9) 2g [s

EBERLE ERE ERIE S|F|R(E 82 un Ta) oo 8 e |v [a al =) 0° [ RIE| 8] 23 21 28s ls g 5 SIRE] S| 28 31 gig 8 = & 139

SUBSTITUTE SHEET (RULE 26)

ew © le ~ on 0 = a j—~ LI : | H «~ : 2 [*] . 23 E olelele]| « oY w| al 9

K) a 8 < [en [= [en on wo | ~ wn 2 [*] 2 4 E nfo Is fe | a ho te 10 ho 8 = g «3 ~ |e en jai aD i) =] = ° ’ . | —- € § £ ~ ho 1% ie < a 3 ny 3 a 5 0 [a |= jn 7] ad a |S LF ~

Ee on | |\o . ~ |\©0 |[o0 | [32 00. ~~ a [an = S [nie |e a) Sil 9 2% o |e |e So |e |e |e oc oc cS 8

Ine] ~ ~ =a) 0 £5 l=: en a “ o 5 HE : 5 15 52) | 8

Io] g = 3 8 ER = 2) Sel 8 Hy 2 |e iz 2 128 lg|E 2 |3|clE 3 |d

EHH RE H EE

© BD 3 E|E|E|a[E SE |E lal BBE |e )F

Q Q [> [=] . E]

ERE EElp|a|ale SBE |E 5d 4 12 5 3| la] = 2 2lslz| 8 cant — Ve] —t I 13 || sllslEl ElplElR] EER| Z < S23 adiSE| TER] 4 = 140

SUBSTITUTE SHEET (RULE 26) ;

8% E = NA CT © ~- « wn

I) a 5 < Qe jn wn = “ oa 2 3 £ =~ ~ ~ n [0 “ 8 8 8 a |e en oa Je oo <9 H =] Po 3 tr — £2 a £ oS < <C leo oe) I a) “ © 3 = o - vol “ < |< bi I pe) 8 8 :

EEE | wilwle|n|e |= wo la:

K a = = oo 4 |N | | EI I . e . e wn [> on |= o~ 0 IN <

Ez =| zalklalk]s 2 a. § v9 Le c |e =] I= cS |e: |s 3 < 2 ou 8 . po g g |B a S E > = 1% 8

K: | § = ! 1s 50 $ — {© & Q 8 7 g 18 8 & — lw o |B g ‘8 2 8 I= g§ |< glen lg 8 @ 2 5 5 = 8 2 8 0 & 3 g § 3 8 Z 88 E © > ° ;

X . = [= — B cER EEE EBB EE aE ElElE 6 g 5 ~N ho Q = SIS 2 oN <tr : 00 % Sl SERB EI!] £2] le! Slg| 2 a jen jen o PAR 2 b-4 : PY g 2 3 Ri bg UN | a a S |8: & i JHE] 2] 8] sf ¢ 2] REDE |R S| 21891 %2 141

SUBSTITUTE SHEET (RULE 26)

ew © - g TE S| = a 28 § le § § “ < | - rl hel Be o k=] ~ a x EGE L «i g A ] © [>] . : °c & © —_ —- 33 & Sd Q pL pil 02 0 el RE fe “x BA g - gS S T * <r. — gag] J 8 = =

S

Ee 2 2 3 2 59 = oS | S

T eo “ A — ~ 00 “00 = on o — oN Dt] Lt [¥] g | 8 |g $ 5 B — 18 2 2 |. 5

B E El2g |& w |B sl ESTEE IEILILIE IS = % 8 co 8 E 3 | 3 O fEEE BESET |B IEEE gl 2 2 2 EIB 5 EIE E & IRE glE Ble

SEILER REI 5 283 2 —_— on [=] 00 AN it pt : 8 2 = a g 8 D: 8 2 e a le 8 2 8 a IS pal oN IN 3 IE g Z AE & sISI515] 2| 28 < 2 2 21213 S| BB 142

SUBSTITUTE SHEET (RULE 26)

eg w PB — — joo |? {on {oo |» 32 ES S = ala ell bel PE Pl bel pe

B 8 2 i t — Lyd I- “ |= © : [=] gE - RCI =< |< S = =I

CRE ee) a Ja [5 a : 3 2% oc NG ala la a

A s 2 4d Elw 00 a |e a fe ds f= 2 2 |< oN oo “|e |0 |N jn jen

A g eB N 2 8 oe - : [>] :

Ess 2 |g 212 Is g Q lo co |e oc le |e o i

Tm ~ oN - [>] B 2 5 2 ¢ g Se 8 a g : 3 a a 2 = = £ £ < S |g" 2 5 S| QM 2 o = |S. 3 IC fg 4g |e 2 8 & 18g [5

CREE EB EE sedi lA

AEERLELEE 2 SlEIEIE5 [) Q [] |.op

SE EIEElgE EEE. 28 EEE EE

J © a [en a lo |e: ~ 2 2 S 2 IR slg IR] Ie iE E| §| Ef z [8 SERERE : — [=] WY |e @ Z ) a 2 IQ 3 NS = - | S| LR 2 |< SEE [EER 143

SUBSTITUTE SHEET (RULE 26)

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Table 37: Up-regulation of Polynucleotide expression in A549 cells induced by

Formula G and additional Peptides. [0127) The peptides at a concentration of 50 pg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labelled cDNA probes and hybridised to Human Operon arrays (PRHUO4). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labelling of cDNA with the dyes Cy3 and Cys5 respectively. The “Ratio

ID#: Control” columns refer to the intensity of polynucleotide expression in peptide- simulated cells divided by the intensity of unstimulated cells. Accession numbers and gene designations are U00115, zinc finger protein; M91036, hemoglobin gamma

G;K000070, hypothetical protein; AF055899, solute carrier family 27; AK001490, hypothetical protein; X97674, nuclear receptor coactivator 2; AB022847, unknown;

AJ275986, transcription factor; D10495, protein kinase C, delta; 136642, EphA7;

M31166, pentaxin-related gene; AF176012, unknown; AF 072756, A kinase anchor protein 4; NM_014439, IL-1 Superfamily z; AJ271351, putative transcriptional regulator; AK000576, hypothetical protein; AJ272265, secreted phosphoprotein 2;

AL122038, hypothetical protein; AK000307, hypothetical protein; AB029001,

KIAA1078 protein; U62437, cholinergic receptor; AF064854, unknown; AL031588, hypothetical protein; X89399, RAS p21 protein activator; D45399, phosphodiesterase; AB037716, hypothetical protein; X79981, cadherin 5; AF034208,

RIG-like 7-1; AL133355, chromosome 21 open reading frame 53; NM_016281,

STE20-like kinase; AF023614, transmembrane activator and CAML interactor; . AF056717, ash2-like; AB029039, KIAA1116 protein; J03634, inhibin, beta A;

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EXAMPLE 5

INDUCTION OF CHEMOKINES IN CELL LINES, WHOLE HUMAN BLOOD,

AND IN MICE BY PEPTIDES

(0128) The murine macrophage cell line RAW 264.7, THP-1 cells (human monocytes), a human epithelial cell line (A549), human bronchial epithelial cells (16HBEo14), and whole human blood were used. HBE cells were grown in MEM with Earle’s. THP-1 cells were grown and maintained in RPMI 1640 medium. The

RAW and A549 cell lines were maintained in DMEM supplemented with’ 10% fetal calf serum. The cells were seeded in 24 well plates at a density of 10° cells per well in DMEM (see above) and A549 cells were seeded in 24 well plates ata density of 10° cells per well in DMEM (see above) and both were incubated at 37°C in 5 % CO; overnight. DMEM was aspirated from cells grown overnight and replaced with fresh medium. After incubation of the cells with peptide, the release of chemokines into the culture supernatant was determined by ELISA (R&D

Systems, Minneapolis, MN). . {0129) Animal studies were approved by the UBC Animal Care Committee (UBC ACC # A01-0008). BALB/c mice were purchased from Charles River

Laboratories and housed in standard animal facilities. Age, sex and weight matched adult mice 1244 149

SUBSTITUTE SHEET (RULE 26)

were anaesthetized with an intraperitoneal injection of Avertin (4.4 mM 2-2-2- tribromoethanol, 2.5% 2-methyl-2-butanol, in distilled water), using 200 pl per 10 g body weight. The instillation was performed using a non-surgical, intratracheal instillation method adapted from Ho and Furst 1973. Briefly, the anaesthetized mouse was placed with its upper teeth hooked over a wire at the top of a support frame with its jaw held open and a spring pushing the thorax forward to position the pharynx, larynx and trachea in a vertical straight line. The airway was illuminated externally and an intubation catheter was inserted into the clearly illuminated tracheal lumen.

Twenty-p of peptide suspension or sterile water was placed in a well at the proximal end of the catheter and gently instilled into the trachea with 200 ul of air. The animals were maintained in an upright position for 2 minutes after instillation to allow the fluid to drain into the respiratory tree. After 4 hours the mice were euthanaised by intraperitoneal injection of 300 mg/kg of pentobarbital. The trachea was exposed; an intravenous catheter was passed into the proximal trachea and tied in place with suture thread. Lavage was performed by introducing 0.75 ml sterile PBS into the lungs via the tracheal cannula and then after a few seconds, withdrawing the fluid.

This was repeated 3 times with the same sample of PBS. The lavage fluid was placed in a tube on ice and the total recovery volume per mouse was approximately 0.5 ml.

The bronchoalveolar lavage (BAL) fluid was centrifuged at 1200 rpm for 10 min, the clear supernatant removed and tested for TNF-a and MCP-1 by ELISA.

[0130] The up-regulation of chemokines by cationic peptides was confirmed in several different systems. The murine MCP-1, a homologue of the human MCP-1, is a member of the B(C-C) chemokine family. MCP-1 has been demonstrated to recruit monocytes, NK cells and some T lymphocytes. When RAW 264.7 macrophage cells and whole human blood from 3 donors were stimulated with increasing concentrations of peptide, SEQ ID NO: 1, they produced significant levels of MCP-1 in their supernatant, as judged by ELISA (Table 36). RAW 264.7 cells stimulated with peptide concentrations ranging from 20-50 pg/ml for 24 hr produced significant levels of MCP-1 (200-400 pg/ml above background). When the cells (24h) and whole blood (4h) were stimulated with 100 pg/ml of LL-37, high levels of MCP-1 were produced.

[0131] The effect of cationic peptides on chemokine induction was also examined in a completely different cell system, AS49 human epithelial cells. Interestingly, although these cells produce MCP-1 in response to LPS, and this response could be antagonized by peptide; there was no production of MCP-1 by A549 cells in direct response to peptide, SEQ ID NO: 1. Peptide SEQ ID NO: 1 at high concentrations, did however induce production of IL-8, a neutrophil specific chemokine (Table 37).

Thus, SEQ ID NO: 1 can induce a different spectrum of responses from different cell types and at different concentrations. A number of peptides from each of the formula groups were tested for their ability to induce IL-8 in A549 cells (Table 38). Many of these peptides at a low concentration, 10 pg/ml induced IL-8 above background levels. At high concentrations (100 pg/ml) SEQ ID NO: 13 was also found to induce

IL-8 in whole human blood (Table 39). Peptide SEQ ID NO: 2 also significantly induced IL-8 in HBE cells (Table 40) and undifferentiated THP-1 cells (Table 41). [0132) BALB/c mice were given SEQ ID NO: 1 or endotoxin-free water by intratracheal instillation and the levels of MCP-1 and TNF-a examined in the bronchioalveolar lavage fluid after 3-4 hr. It was found that the mice treated with 50 pg/ml peptide, SEQ ID NO: 1 produced significantly increased levels of MCP-1 over mice given water or anesthetic alone (Table 42). This was not a pro-inflammatory response to peptide, SEQ ID NO: 1 since peptide did not significantly induce more

TNF-a than mice given water or anesthetic alone. peptide, SEQ ID NO: 1 was also found not to significantly induce TNF-a production by RAW 264.7 cells and bone marrow-derived macrophages treated with peptide, SEQ ID NO: 1 (up to 100 pg/ml) (Table 43). Thus, peptide, SEQ ID NO: 1 selectively induces the production of chemokines without inducing the production of inflammatory mediators such as TNF- o. This illustrates the dual role of peptide, SEQ ID NO: 1 as a factor that can block bacterial product-induced inflammation while helping to recruit phagocytes that can clear infections.

Table 38: Induction of MCP-1 in RAW 264.7 cells and whole human blood.

[0133] RAW 264.7 mouse macrophage cells or whole human blood were stimulated with increasing concentrations of LL-37 for 4 hr. The human blood samples were centrifuged and the serum was removed and tested for MCP-1 by

ELISA along with the supernatants from the RAW 264.7 cells. The RAW cell data presented is the mean of three or more experiments + standard error and the human blood data represents the mean + standard error from three separate donors.

Peptide, SEQ ID NO: 1 Monocyte chemoattractant protein (MCP)-1 (pg/mil)* (ng/ml)

I NCC. Wil

Table 39: Induction of IL-8 in A549 cells and whole human blood.

[0134] A549 cells or whole human blood were stimulated with increasing concentrations of peptide for 24 and 4 hr respectively. The human blood samples were centrifuged and the serum was removed and tested for IL-8 by ELISA along with the supernatants from the A549 cells. The A549 cell data presented is the mean of three or more experiments + standard error and the human blood data represents the mean + standard error from three separate donors. -

Peptide, SEQ ID NO: 1 IL-8 (pg/ml)

Rai

I J. J IL

J 2 NS RCE iF. SE ow [www

I 1 I

Table 40: Induction of IL-8 in A549 cells by Cationic peptides.

[0135] AS49 human epithelial cells were stimulated with 10 pg of peptide for 24 hr. The supernatant was removed and tested for IL-8 by ELISA.

Table 41: Induction by Peptide of IL-8 in human blood.

[0136] Whole human blood was stimulated with increasing concentrations of peptide for 4 hr . The human blood samples were centrifuged and the serum was removed and tested for IL-8 by ELISA. The data shown is the average 2 donors.

SEQ ID NO: 3 (ug/ml) IL-8 (pg/ml)

J EE EL ww

Table 42: Induction of IL-8 in HBE cells.

[0137] Increasing concentrations of the peptide were incubated with HBE cells for 8 h, the supernantant removed and tested for IL-8. The data is presented as the mean of three or more experiments t standard error.

SEQ ID NO: 2 IL-8 (pg/ml) (ng/ml)

Table 43: Induction of IL-8 in undifferentiated THP-1 cells.

[0138] The human monocyte THP-1 cells were incubated with indicated concentrations of peptide for 8 hr. The supernatant was removed and tested for IL-8 by ELISA.

SEQID NO: 3 IL-8 (pg/ml) (ng/ml)

SEQ ID NO: 3 IL-8 (pg/ml) (ng/ml)

IL RR

Table 44: Induction of MCP-1 by Peptide, SEQ ID NO: 1 in mouse airway.

[0139] BALB/c mice were anaesthetised with avertin and given intratracheal - instillation of peptide or water or no instillation (no treatment). The mice were monitored for 4 hours, anaesthetised and the BAL fluid was isolated and analyzed for

MCP-1 and TNF-a concentrations by ELISA. The data shown is the mean of 4 or 5 mice for each condition + standard error. a CE

Table 45: Lack of Significant TNF-a induction by the Cationic Peptides.

[0140] RAW 264.7 macrophage cells were incubated with indicated peptides (40 ug/ml) for 6 hours. The supernatant was collected and tested for levels of TNF-a by

ELISA. The data is presented as the mean of three or more experiments + standard : error.

oo

EXAMPLE 6

CATIONIC PEPTIDES INCREASE SURFACE EXPRESSION

OF CHEMOKINE RECEPTORS

[0141] To analyze cell surface expression of IL-8RB, CXCR-4, CCR2, and LFA- 1, RAW macrophage cells were stained with 10 pg/ml of the appropriate primary antibody (Santa Cruz Biotechnology) followed by FITC-conjugated goat anti-rabbit

IgG [IL-8RB and CXCR-4 (Jackson ImmunoResearch Laboratories, West Grove,

PA)] or FITC-conjugated donkey anti-goat IgG (Santa Cruz). The cells were analyzed using a FACscan, counting 10,000 events and gating on forward and side scatter to exclude cell debris.

[0142] The polynucleotide array data suggested that some peptides up-regulate the expression of the chemokine receptors IL-8RB, CXCR-4 and CCR2 by 10, 4 and 1.4 fold above unstimulated cells respectively. To confirm the polynucleotide array data, the surface expression was examined by flow cytometry of these receptors on RAW cells stimulated with peptide for 4 hr. When 50 pg/ml of peptide was incubated with

RAW cells for 4 hr, [L-8RB was upregulated an average of 2.4-fold above unstimulated cells, CXCR-4 was up-regulated an average of 1.6-fold above unstimulated cells and CCR2 was up-regulated 1.8-fold above unstimulated cells (Table 46). As a control CEMA was demonstrated to cause similar up-regulation.

Bac2A was the only peptide to show significant up-regulation of LFA-1 (3.8 fold higher than control cells).

Table 46: Increased surface expression of CXCR-4, IL-8RB and CCR2 in response to peptides. :

[0143] RAW macrophage cells were stimulated with peptide for 4 hr. The cells were washed and stained with the appropriate primary and FITC-labeled secondary } antibodies. The data shown represents the average (fold change of RAW cells stimulated with peptide from media) + standard error.

SEQID 1.0 1.0 : 1.0 [esl A A A

SEQID (50 1.3 +£0.05 1.3 +0.03 1.3 +0.03

Fl A I

SEQ ID 24+06 1.6 +£0.23 1.8+0.15

Fl A A

SEQID 20+06 Not Done

FE A A a A

J i A

EXAMPLE 7

PHOSPHORYLATION OF MAP KINASES BY CATIONIC PEPTIDES

[0144] The cells were seeded at 2.5x10° - 5 x 10° cells/ml and left overnight. They were washed once in media, serum starved in the morning (serum free media - 4hrs).

The media was removed and replaced with PBS, then sat at 37°C for 15 minutes and then brought to room temp for 15 minutes. Peptide was added (concentrations 0.1ug/ml - 50ug/ml) or HO and incubated 10 min. The PBS was very quickly : removed and replaced with ice-cold radioimmunoprecipitation (RIPA) buffer with inhibitors (NaF, B-glycerophosphate, MOL, Vanadate, PMSF, Leupeptin Aprotinin).

The plates were shaken on ice for 10-15 min or until the cells were lysed and the lysates collected. The procedure for THP-1 cells was slightly different; more cells (2x10°) were used. They were serum starved overnight, and to stop the reaction 1ml of ice-cold PBS was added then they sat on ice 5-10 min, were spun down then ~ resuspended in RIPA. Protein concentrations were determined using a protein assay (Pierce, Rockford, IL.). Cell lysates (20 pg of protein) were separated by SDS-PAGE and transferred to nitrocellulose filters. The filters were blocked for 1 h with 10 mM

Tris-HCl, pH 7.5, 150 mM NaCl (TBS)/5% skim milk powder and then incubated overnight in the cold with primary antibody in TBS/0.05% Tween 20. After washing for 30 min with TBS/0.05% Tween 20, the filters were incubated for 1 h atroom temperature with 1 pg/ml secondary antibody in TBS. The filters were washed for min with TBS/0.05% Tween 20 and then incubated 1 h at room temperature with horseradish peroxidase-conjugated sheep anti-mouse IgG (1:10,000 in TBS/0.05%

Tween 20). After washing the filters for 30 min with TBS/0.1% Tween 20, immunoreactive bands were visualized by enhanced chemiluminescence (ECL) detection. For experiments with peripheral blood mononuclear cells: The peripheral blood (50-100ml) was collected from all subjects. Mononuclear cells were isolated from the peripheral blood by density gradient centrifugation on Ficoll-Hypaque.

Interphase cells (mononuclear cells) were recovered, washed and then resuspended in recommended primary medium for cell culture (RPMI-1640) with 10% fetal calf serum (FCS) and 1% L-glutamine. Cells were added to 6 well culture plates at 4x10° cells/well and were allowed to adhere at 37° C in 5% CO, atmosphere for 1 hour. The supernatant medium and non-adherent cells were washed off and the appropriate media with peptide was added. The freshly harvested cells were consistently >99% viable as assessed by their ability to exclude trypan blue. After stimulation with peptide, lysates were collected by lysing the cells in RIPA buffer in the presence of various phosphatase- and kinase-inhibitors. Protein content was analyzed and approximately 30 ug of each sample was loaded in a 12% SDS-PAGE gel. The gels were blotted onto nitrocéllulose, blocked for 1 hour with 5% skim milk powder in

Tris buffered saline (TBS) with 1% Triton X 100. Phosphorylation was detected with " phosphorylation-specific antibodies.

[0145] The results of peptide-induced phosphorylation are summarized in Table 46. SEQ ID NO: 2 was found to cause dose dependent phosphorylation of p38 and

ERK 1/2 in the mouse macrophage RAW cell line and the HBE cells. SEQ ID NO: 3 caused phosphorylation of MAP kinases in THP-1 human monocyte cell line and phosphorylation of ERK 1/2 in the mouse RAW cell line.

Table 47: Phosphorylation of MAP kinases in response to peptides.

Cell Line Peptide MAP kinase phosphorylated

I

I a LC EE EA

SED spRos | [

SEG:

WT | Seb sbwor

Table 48: .

[0146] Peptide Phosphorylation of MAP kinases in human blood monocytes.

SEQ ID NO: 1 at 50 ug/ml) was used to promote phosphorylation. p38 phosphorylation ERK1/2 phosphorylation

IE EE A

EXAMPLE 8

CATIONIC PEPTIDES PROTECT AGAINST BACTERIAL INFECTION

BY ENHANCING THE IMMUNE RESPONSE

[0147] BALB/c mice were given 1x 10° Salmonella and cationic peptide (200 pg) by intraperitoneal injection. The mice were monitored for 24 hours at which point they were euthanized, the spleen removed, homogenized and resuspended in PBS and plated on Luria Broth agar plates with Kanamycin (50 ug/ml). The plates were : incubated overnight at 37°C and counted for viable bacteria (Table 49 and 50). CD-1 mice were given 1 x 10® 8. aureus in 5 % porcine mucin and cationic peptide (200 pg) by intraperitoneal injection (Table 51). The mice were monitored for 3 days at which point they were euthanized, blood removed and plated for viable counts. CD-1 male mice were given 5.8 x 10° CFU EHEC bacteria and cationic peptide (200 pg) by intraperitoneal (IP) injection and monitored for 3 days (Table 52). In each of these animal models a subset of the peptides demonstrated protection against infections.

The most protective peptides in the Salmonella model demonstrated an ability to induce a common subset of genes in epithelial cells (Table 53) when comparing the protection assay results in Tables SO and 51 to the gene expression results in Tables 31-37. This clearly indicates that there is a pattern of gene expression that is consistent with the ability of a peptide to demonstrate protection. Many of the cationic peptides were shown not to be directly antimicrobial as tested by the

Minimum Inhibitory Concentration (MIC) assay (Table 54). This demonstrates that the ability of peptides to protect against infection relies on the ability of the peptide to stimulate host innate immunity rather than on direct antimicrobial activity.

Table 49: Effect of Cationic Peptides on Salmonella Infection in BALB/c mice.

[0148] The BALB/c mice were injected IP with Salmonella and Peptide, and 24 h later the animals were euthanized, the spleen removed, homogenized, diluted in PBS and plate counts were done to determine bacteria viability.

Peptide Viable Bacteria in the Spleen Statistical Significance (p

IC I. LL

SEDO | sweeyxw ow

I LL ALN CL

Il NE SA LL SR ‘Table 50: Effect of Cationic Peptides on Salmonella Infection in BALB/c mice.

[0149] The BALB/c mice were injected intraperitoneally with Salmonella and

Peptide, and 24 h later the animals were euthanized, the spleen removed, homogenized, diluted in PBS and plate counts were done to determine bacteria viability.

Table 51. Effect of Cationic Peptides in a Murine S. aureus infection model.

[0150] CD-1 mice were given 1 x 10 bacteria in 5 % porcine mucin via intraperitoneal (IP) injection. Cationic peptide (200 pg) was given via a separate IP injection. The mice were monitored for 3 days at which point they were euthanized, blood removed and plated for viable counts. The following peptides were not effective in controlling S. aureus infection: SEQ ID NO: 48, SEQ ID NO: 26

Treatment CFU/ml (blood) # Mice Survived (3 days)/ Total mice in ll i a

LLL EL

Table 52 Effect of Peptide in a Murine EHEC infection model.

[0151] CD-1 male mice ( 5 weeks old) were given 5.8 x 10° CFU EHEC bacteria via intraperitoneal (IP) injection. Cationic peptide (200 ug) was given via a separate

IP injection. The mice were monitored for 3 days.

Survival (%) conwol [none [25

SEQIDNO:23 |200ug EE : Table 53. Up-regulation of patterns of gene expression in A549 epithelial cells induced by peptides that are active in vivo.

[0152] The peptides SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 13 at concentrations of 50 pg/ml were each shown to increase the expression of a pattern of genes after 4 h treatment. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labelled cDNA probes and hybridised to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second columns for labelling of cDNA (average of Cy3 and Cy5). The Fold Up regulation column refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. The SEQ ID NO: 37 peptide was included as a negative control : that was not active in the murine infection models.

Target (Accession number) Unstimulated relative to Untreated Cells

Cell Intensity | SEQID | SEQID | SEQID | SEQID

Err BE CN ICN ICR

EE CR EE ER AC mmeons | ow | ws | 7 | wn rowers | ov | wi | 3s | | wr

EE ER EN

Tr IC BC CC RC NC

IN NT NE ON I ower | wn | | 5 | mw

ET ER ER EN

Table 54:

[0153] Most cationic peptides studied here and especially the cationic peptides - ~ effective in infection models are not significantly antimicrobial. A dilution series of peptide was incubated with the indicated bacteria overnight in a 96-well plate. The lowest concentration of peptide that killed the bacteria was used as the MIC. The symbol > indicates the MIC is too large to measure. An MIC of 8 ug/ml or less was considered clinically meaningful activity. Abbreviations: E.coli, Escherichia coli,

S.aureus, Staphylococcus aureus; P.aerug, Pseudomonas aeruginosa; S.Typhim,

Salmonella enteritidis ssp. typhimurium; C. rhod, Citobacter rhodensis, EHEC,

Enterohaemorrhagic E.coli.

IC NC J NC CE CI

ML CL EC I I I NL RE

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EXAMPLE 9

USE OF POLYNUCLEOTIDES INDUCED BY BACTERIAL SIGNALLING

MOLECULES IN DIAGNOSTIC/SCREENING

[0154] S. typhimurium LPS and E. coli 0111:B4 LPS were purchased from Sigma

Chemical Co. (St. Louis, MO). LTA (Sigma) from S, aureus, was resuspended in endotoxin free water (Sigma). The Limulus amoebocyte lysate assay (Sigma) was performed on LTA preparations to confirm that lots were not significantly contaminated by endotoxin (i.e. <1 ng/ml, a concentration that did not cause significant cytokine production in the RAW cell assay). The CpG oligodeoxynucleotides were synthesized with an Applied Biosystems Inc., Model 392

DNA/RNA Synthesizer, Mississauga, ON., then purified and resuspended in endotoxin-free water (Sigma). The following sequences were used CpG: 5’-

TCATGACGTTCCTGACGTT-3’ (SEQ ID NO: 57) and nonCpG: 5’-

TTCAGGACTTTCCTCAGGTT-3’ (SEQ ID NO: 58). The nonCpG oligo was tested for its ability to stimulate production of cytokines and was found to cause no significant production of TNF-a or IL-6 and therefore was considered as a negative control. RNA was isolated from RAW 264.7 cells that had been incubated for 4h with medium alone, 100 ng/ml S. typhimurium LPS, 1 pg/ml S. aureus LTA, or 1 HM CpG (concentrations that led to optimal induction of tumor necrosis factor (TNF-a) in

RAW cells). The RNA was used to polynucleotiderate cDNA probes that were hybridized to Clontech Atlas polynucleotide array filters, as described above. The hybridization of the cDNA probes to each immobilized DNA was visualized by autoradiography and quantified using a phosphorimager. Results from at least 2 to 3 independent experiments are summarized in Tables 55-59. It was found that LPS treatment of RAW 264.7 cells resulted in increased expression of more than 60 polynucleotides including polynucleotides encoding inflammatory proteins such as

IL-1, inducible nitric oxide synthase (iNOS), MIP-1a, MIP-13, MIP-2a, CD40, and a variety of transcription factors. When the changes in polynucleotide expression induced by LPS, LTA, and CpG DNA were compared, it was found that all three of these bacterial products increased the expression of pro-inflammatory polynucleotides such as iNOS, MIP-1a, MIP-2a, IL-18, IL-15, TNFR1 and NF-kB to a similar extent (Table 57). Table 57 describes 19 polynucleotides that were up-regulated by the bacterial products to similar extents in that their stimulation ratios differed by less : than 1.5 fold between the three bacterial products. There were also several polynucleotides that were down-regulated by LPS, LTA and CpG to a similar extent.

It was also found that there were a number of polynucleotides that were differentially regulated in response to the three bacterial products (Table 58), which includes many of these polynucleotides that differed in expression levels by more than 1.5 fold between one or more bacterial products). LTA treatment differentially influenced expression of the largest subset of polynucleotides compared to LPS or CpG, including hyperstimulation of expression of Jun-D, Jun-B, Elk-1 and cyclins G2 and

Al. There were only a few polynucleotides whose expression was altered more by

LPS or CpG treatment. Polynucleotides that had preferentially increased expression due to LPS treatment compared to LTA or CpG treatment included the cAMP response element DNA-binding protein 1 (CRE-BPI), interferon inducible protein 1 and CACCC Box-binding protein BKLF. Polynucleotides that had preferentially increased expression after CpG treatment compared to LPS or LTA treatment included leukemia inhibitory factor (LIF) and protease nexin 1 (PN-1). These results indicate that although LPS, LTA, and CpG DNA stimulate largely overlapping polynucleotide expression responses, they also exhibit differential abilities to regulate certain subsets of polynucleotides.

[0155] The other polynucleotide arrays used are the Human Operon arrays (identification number for the genome is PRHUO04-S1), which consist of about 14,000 human oligos spotted in duplicate. Probes were prepared from 5 ug of total RNA and labeled with Cy3 or CysS labeled dUTP. In these experiments, A549 epithelial cells were plated in 100 mm tissue culture dishes at 2.5 x 10° cells/dish, incubated overnight and then stimulated with 100 ng/ml E. coli O111:B4 LPS for 4 h. Total

RNA was isolated using RNAqueous (Ambion). DNA contamination was removed with DNA-free kit (Ambion). The probes prepared from total RNA were purified and hybridized to printed glass slides overnight at 42°C and washed. After washing, the image was captured using a Perkin Elmer array scanner. The image processing software (Imapolynucleotide 5.0, Marina Del Rey, CA) determines the spot mean intensity, median intensities, and background intensities. An “in house” program was used to remove background. The program calculates the bottom 10 % intensity for each subgrid and subtracts this for each grid. Analysis was performed with

Polynucleotidespring software (Redwood City, CA). The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with LPS compared to control cells can be found in the Tables below. A number of previously unreported changes that would be useful in diagnosing infection are described in Table 60.

[0156] To confirm and assess the functional significance of these changes, the levels of selected mRNAs and proteins were assessed and quantified by densitometry.

Northem blots using a CD14, vimentin, and tristetraprolin-specific probe confirmed similar expression after stimulation with all 3 bacterial products (Table 60). Similarly measurement of the enzymatic activity of nitric oxide synthetase, INOS, using Griess reagent to assess levels of the inflammatory mediator NO, demonstrated comparable levels of NO produced after 24 h, consistent with the similar up-regulation of iNOS expression (Table 59). Western blot analysis confirmed the preferential stimulation of leukaemia inhibitory factor (LIF, a member of the IL-6 family of cytokines) by CpG (Table 59). Other confirmatory experiments demonstrated that LPS up-regulated the expression of TNF-a and IL-6 as assessed by ELISA, and the up-regulated expression of MIP-2q, and IL-1 mRNA and down-regulation of DP-1 and cyclin D mRNA as assessed by Northern blot analysis. The analysis was expanded to a more clinically relevant ex vivo system, by examining the ability of the bacterial elements to stimulate pro-inflammatory cytokine production in whole human blood. It was found that E.

coli LPS, S. typhimurium LPS, and S. aureus LTA all stimulated similar amounts of serum TNF-a, and IL-1B. CpG also stimulated production of these cytokines, albeit to much lower levels, confirming in part the cell line data.

Table 55: Polynucleotides Up-regulated by E. coli 0111:B4 LPS in A549

Epithelial Cells. [01571 E.coliO111:B4 LPS (100 ng/ml) increased the expression of many polynucleotides in A549 cells as studied by polynucleotide microarrays. LPS was : incubated with the A549 cells for 4 h and the RNA was isolated. 5 pg total RNA was used to make Cy3/Cy5 labelled cDNA probes and hybridised onto Human Operon arrays (PRHUO4). The intensity of unstimulated cells is shown in the second column of Table 55. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS simulated cells divided by in the intensity of unstimulated cells.

Accession Gene Control: Ratio: LPS/control la nd

Intensity aldo-keto reductase family 1,

ADP-ribosylation factor eukaryotic translation om | mss | a0 | ws

XE | eomponly | me | dos

EN I I

Accession Control: Ratio: LPS/control

Number Media only

Intensity

I rE RE (Row | ween | #5 |e serine/threonine protein a TL EL

FEM-1-like death receptor procollagen-proline, 2- malate dehydrogenase 2, wom | "wo | wm | wm stress-induced- wos | en | ww ws | mews | we | a

ROS | de [mT ew hypothetical protein . proteasome subunit, beta membrane protein of

Ic I ILE IL

Accession Gene Control: Ratio: LPS/control

Number Media only =] TE TT : translocase of inner mitochondrial membrane 23 :

IEC NN NS IL mucin 5, subtype B,

RAP], GTPase activating calcium and integring binding

I Cc NL EL protein-O- hypothetical protein ovo | roms | os | we cAMP response element- oss | nin | v0 phosphoinositide-3-kinase,

Accession Control: Ratio: LPS/control

Number Media only = "= chromosome 11 open reading

I immunoglobulin superfamily woe |ctimnars|6|w chromosome 11 open reading signal sequence receptor, alpha (translocon-associated arachidonate S-lipoxygenase- human growth factor- regulated tyrosine kinase ow | LL cyclin-dependent kinase

I IC LCN myristoylated alanine-rich : sialic acid binding Ig-like ar EE

OT | sweets | G0 | 6 malignancy-associated

Accession Gene Control: Ratio: LPS/control

Number Media only -] TE TT

Co wemew

CCE RCN mannosyl (alpha-1,3-)- glycoprotein beta-1,2-N-

I CC I ECR branched chain keto acid dehydrogenase El, alpha : 214093 polypeptide hypothetical protein

ICCC CLI FS I: J ribosomal protein 1.34

IC NOLL A EC potassium voltage-gated channel, KQT-like subfamily,

Accession Gene Control: Ratio: LPS/control

Number Media only

Intensity

I EC ER EE major histocompatibility hypothetical protein :

Table 56: Polynucleotides Down-regulated by E. coli 0111:B4 LPS in A549

Epithelial Cells. (0158) E. coli O111:B4 LPS (100 ng/ml) decreased the expression of many polynucleotides in A549 cells as studied by polynucleotide microarrays. LPS was incubated with the A549 cells for 4 h and the RNA was isolated. 5 pg total RNA was used to make Cy3/CyS5 labeled cDNA probes and hybridized onto Human Operon arrays (PRHUO4). The intensity of unstimulated cells is shown in the second column of the Table. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS simulated cells divided by in the intensity of unstimulated cells.

Accession Gene Control: Ratio:

Number Media only | LPS/control = me

CR | Wee mnymeet| Wa | ow

Accession Control: Ratio:

Number Media only | LPS/control

Intensity inhibitor of DNA binding 2, dominant

El

Ia I ICL

I LN TLL NL

Homo sapiens mRNA for NUP98-HOXD13 an | antes | wa | ow

I LL WL ICL erythrocyte membrane protein band 7.2

EN hare

X-ray repair complementing defective eukaryotic translation initiation factor 4E

EE a= EE

I i LE IL 5(3)-deoxyribonucleotidase; RB-associated

I TC) I ICL

ADOT | pom | ws | ow

EE | odes || om

I TO LLC LN

Accession Gene Control: Ratio:

Number Media only | LPS/control = [Ee

I CL I

Human ribosomal protein L12 pseudogene,

I LL I C2

ASE | hn ope Xe | om nuclear factor IX (CCAAT-binding

B-cell translocation gene 1, anti- mitogen-activated protein kinase kinase

I LL I IL phosphoinositide-3-kinase, regulatory

H.sapiens (MARI11) MUCSAC mRNA for

IE CS I DL

PERBI11 family member in MHC class I

Accession : Gene Control: Ratio: = EF

Intensity

TsO we Ss bape | 0 | 0%

I ET LC CEA

ICC LO LI R.A

IC NC ICL NCA

ATPase, Ca++ transporting, plasma

IC SY I NC

LCCC I. FC BL

SES | dweswnc | a1 | ow

Table 57: Polynucleotides expressed to similar extents after stimulation by the bacterial products LPS, LTA, and CpG DNA. {01591 Bacterial products (100 ng/ml S. typhimurium LPS, 1pug/ml S. aureus LTA or 1 uM CpG) were shown to potently induce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of control, unstimulated cells is shown in the second column. The “Ratio

LPS/LTA/CpG: Control” column refers to the intensity of polynucleotide expression in bacterial product-simulated cells divided by the intensity of unstimulated cells.

Accession Control [Ratio Ratio Ratio Protein/polynucleotide mumber [Unstim. [LPS: LTA: pG:

EERE

El CO cI A CA LS

J cl NL LE Lc

Call CI CI SA LN LR cl LO J LI RR

Siac CN CN LA CA LR

OTE 0 [5 Jn men

Sl LC EI LI 2 il CN J LI I 0:

Qo pr p pr fm

LN LC CN I LI A

J Cc CI TR J CR

Sa CCI CS EI SI UN

Accession|{Control [Ratio . |Ratio Ratio Protein/polynucleotide number [Unstim. [LPS: LTA: pG: #5333

Table 58: Polynucleotides that were differentially regulated by the bacterial products LPS, LTA, and CpG DNA.

[0160] Bacterial products (100 ng/ml S. typhimurium LPS, 1pg/ml S. aureus LTA or 1 uM CpG) were shown to potently induce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of control, unstimulated cells is shown in the second column. The “Ratio

LPS/LTA/CpG: Control” column refers to the intensity of polynucleotide expression in bacterial product-simulated cells divided by the intensity of unstimulated cells.

Accession [Unstim. [Ratio [Ratio Ratio Protein/polynucleotide number ontrol |LPS: LTA: pG: =A

SEAL CC I CON

[38847 [2 ’. 1.0 hepatoma transmembrane kinase

A A i

EA oI EI J LS LS a I I J

Cl CI J CI JO

Accession [Unstim. [Ratio Ratio Ratio Protein/polynucleotide oumber [Control [LPS: LTA: pG:

SEE a

CE JR E.R os pr [8 pp wo aa CO LN A LN LL

Sal I JS SU J

SE LT J J ON LL

Sa CI CIN CO LN Lc Ls eo}

La I CN CI CN LON 36340 [2 3 CACCC Box- binding protein nl A A nl

CAA IN I JR A oc

SALLE CCIM LIN J LL

Table 59: Confirmation of Table 57 and 58 Array Data. [01611 a) Total RNA was isolated from unstimulated RAW macrophage cells and cells treated for 4 hr with 100 ng/ml S. typhimurium LPS, 1 ug/ml §. aureus LTA, 1 uM CpG DNA or media alone and Northern blots were performed the membrane was probed for GAPDH, CD14, vimentin, and tristetraprolin as described previously [Scott et al]. The hybridization intensities of the Northern blots were compared to

GAPDH to look for inconsistencies in loading. These experiments were repeated at least three times and the data shown is the average relative levels of each condition compared to media (as measured by densitometry) + standard error.

[0162] bb) RAW 264.7 cells were stimulated with 100 ng/ml S. typhimurium LPS, 1 ug/ml S. aureus LTA, 1 uM CpG DNA or media alone for 24 hours. Protein lysates were prepared, run on SDS PAGE gels and western blots were performed to detect

LIF (R&D Systems). These experiments were repeated at least three times and the data shown is the relative levels of LIF compared to media (as measured by densitometry) + standard error.

[0163] c) Supernatant was collected from RAW macrophage cells treated with 100 : ng/ml S. typhimurium LPS, 1 pg/ml S. aureus LTA, 1 uM CpG DNA, or media alone for 24 hours and tested for the amount of NO formed in the supematant as estimated from the accumulation of the stable NO metabolite nitrite with the Griess reagent as described previously [Scott, et al]. The data shown is the average of three experiments + standard error.

Ee

Tem | 1 | gsw0s | sais | wsais

IE LC NL N= NEL

Table 60. Pattern of Gene expression in A549 Human Epithelial cells up- regulated by bacterial signalling molecules (ILPS).

[0164] E. coli O111:B4 LPS (100 ng/ml) increased the expression of many polynucleotides in A549 cells as studied by polynucleotide microarrays. LPS was incubated with the A549 cells for 4 h and the RNA was isolated. 5 pg total RNA was used to make Cy3/CyS5 labelled cDNA probes and hybridised onto Human Operon arrays (PRHUO4). The examples of polynucleotide expression changes in LPS simulated cells represent a greater than 2-fold intensity level change of LPS treated cells from untreated cells.

: EXAMPLE 10

ALTERING SIGNALING TO PROTECT

AGAINST BACTERIAL INFECTIONS

[0165] The Salmonella Typhimurium strain SL1344 was obtained from the

American Type Culture Collection (ATCC; Manassas, VA) and grown in Luria-

Bertani (LB) broth. For macrophage infections, 10 ml LB in a 125 mL flask was inoculated from a frozen glycerol stock and cultured overnight with shaking at 37°C to stationary phase. RAW 264.7 cells (1x10° cells/well) were seeded in 24 well plates.

Bacteria were diluted in culture medium to give a nominal multiplicity of infection (MOI) of approximately 100, bacteria were centrifuged onto the monolayer at 1000 rpm for 10 minutes to synchronize infection, and the infection was allowed to proceed for 20 min in a 37°C, 5% CO; incubator. Cells were washed 3 times with PBS to remove extracellular bacteria and then incubated in DMEM + 10% FBS containing 100 pg/ml gentamicin (Sigma, St. Louis, MO) to kill any remaining extracellular bacteria and prevent re-infection. After 2 h, the gentamicin concentration was lowered to 10 ug/ml and maintained throughout the assay. Cells were pretreated with inhibitors for 30 min prior to infection at the following concentrations: 50 uM PD 98059 (Calbiochem), 50 uM U 0126 (Promega), 2 mM diphenyliodonium (DPI), 250 uM acetovanillone (apocynin, Aldrich), 1 mM ascorbic acid (Sigma), 30 mM N- acetyl cysteine (Sigma), and 2 mM N°L-monomethyl arginine (L-NMMA,

Molecular Probes) or 2 mM N°-D-monomethyl arginine (D-NMMA, Molecular

Probes). Fresh inhibitors were added immediately after infection, at 2 h, and 6-8 h post-infection to ensure potency. Control cells were treated with equivalent volumes of dimethylsulfoxide (DMSO) per mL of media. Intracellular survival/replication of

S. Typhimurium SL1344 was determined using the gentamicin-resistance assay, as previously described. Briefly, cells were washed twice with PBS to remove gentamicin, lysed with 1% Triton X-100/0.1% SDS in PBS at 2 h and 24 h post- infection, and numbers of intracellular bacteria calculated from colony counts on LB agar plates. Under these infection conditions, macrophages contained an average of 1 bacterium per cell as assessed by standard plate counts, which permitted analysis of macrophages at 24 h post-infection. Bacterial filiamentation is related to bacterial stress. NADPH oxidase and iNOS can be activated by MEK/ERK signaling. The results (Table 61) clearly demonstrate that the alteration of cell signaling is a method whereby intracellular Salmonella infections can be resolved. Thus since bacteria to up-regulate multiple genes in human cells, this strategy of blocking signaling represents a general method of therapy against infection,

Table 61: Effect of the Signaling Molecule MEK on Intracellular Bacteria in IFN-y- primed RAW cells.

A I

Ww

MEK inhibitor U 0126 Decrease bacterial filamentation (bacterial stress)

TE | ee drones on

MEK inhibitor PD 98059 Decrease bacterial filamentation (bacterial stress)®

NADPH oxidase inhibitor® Decrease bacterial filamentation (bacterial stress) ee

EXAMPLE 11

ANTI-VIRAL ACTIVITY

[0166] SDF-1, a C-X-C chemokine is a natural ligand for HIV-1 coreceptor-

CXCR4. The chemokine receptors CXCR4 and CCRS are considered to be potential targets for the inhibition of HIV-1 replication. The crystal structure of SDF-1 exhibits antiparallel B-sheets and a positively charged surface, features that are critical in binding to the negatively charged extracellular loops of CXCR4. These findings suggest that chemokine derivatives, small-size CXCR4 antagonists, or agonists mimicking the structure or ionic property of chemokines may be useful agents for the treatment of X4 HIV-1 infection. It was found that the cationic peptides inhibited

SDF-1 induced T-cell migration suggesting that the peptides may act as CXCR4 antagonists. The migration assays were performed as follows. Human Jurkat T cells were resuspended to 5 x 10° / ml in chemotaxis medium (RPMI 1640 / 10mM Hepes / 0.5 % BSA). Migration assays were performed in 24 well plates using 5 um polycarbonate Transwell inserts (Costar). Briefly, peptide or controls were diluted in chemotaxis medium and placed in the lower chamber while 0.1 mi cells (5 x 10% / mi) was added to the upper chamber. After 3 hr at 37°C, the number of cells that had migrated into the lower chamber was determined using flow cytometry. The medium from the lower chamber was passed through a FACscan for 30 seconds, gating on forward and side scatter to exclude cell debris. The number of live cells was - compared to a “100 % migration control” in which 5 x 10° /ml cells had been pipetted directly into the lower chamber and then counted on the FACscan for 30 seconds.

The results demonstrate that the addition of peptide results in an inhibition of the migration of Human Jurkat T-cells (Table 62) probably by influencing CXCR4 expression (Tables 63 and 64).

Table 62: Peptide inhibits the migration of human Jurkat-T cells:

Migration (%)

Experiment Positive SDF-1 SDF-1+SEQ 1D | Negative control control (100 ng/ml) 1 (50 pg/ml)

Table 63: Corresponding polynucleotide array data to Table 56:

Unstimulated Ratio Accession

Polynucl Polynucleotide Intensity peptide: Number eotide / Function Unstimulated

Protein

CXCR-4 Chemokine receptor D87747

Table 64: Corresponding FACs data to Tables 62 and 63:

Concentration Fold Increase in Protein

Peptide (ng/ml) Expression

CXCR+4

SQDNOT| To | ewww

SEQ ID 50 1.3 +£0.03

NO:1

EXAMPLE 12

SYNERGISTIC COMBINATIONS

[0167] Methods And Materials

[0168] S. aureus was prepared in phosphate buffered solution (PBS) and 5% porcine mucin (Sigma) to a final expected concentration of 1-4x10” CFU/ml. 100 pl of §. aureus (mixed with 5% porcine mucin) was injected intraperitoneally (IP) into each CD-1 mouse (6~8 weeks female weighing 20-25 g (Charles River)). Six hours after the onset of infection, 100 pl of the peptide was injected (50-200 pg total) IP along with 0.1 mg/kg Cefepime. After 24 hours, animals were sacrificed and heart puncture was performed to remove 100 pl of blood. The blood was diluted into 1ml

PBS containing Heparin. This was then further diluted and plated for viable colony counts on Mueller-Hinton agar plates (10°, 102, 103, & 10). Viable colonies, colony-forming units (CFU), were counted after 24 hours. Each experiment was carried out 2 minimum of three times. Data is presented as the average CFU + standard error per treatment group (8-10 mice / group).

[0169] Experiments were carried out with peptide and sub-optimal Cefepime given 6 hours after the onset of systemic S. aureus infection (Figure 1). The data in Figure 1 is presented as the mean + standard error of viable counts from blood taken from the mice 24 hrs after the onset of infection. The combination of sub optimal antibiotic (cefepime) dosing and SEQ ID NO: 7 resulted in improved therapeutic efficacy. The + ability of the peptides to work in combination with sub-optimal concentrations of an antibiotic in 2 murine infection model is an important finding, It suggests the potential for extending the life of antibiotics in the clinic and reducing incidence of antibiotic resistance.

[0170] SEQ ID NO: 1, as an example, induced phosphorylation and activation of the mitogen activated protein kinases, ERK1/2 and p38 in human peripheral blood- derived monocytes and a human bronchial epithelial cell line but not in B- or T- . lymphocytes. Phosphorylation was not dependent on the G-protein coupled receptor,

FPRL-1, which was previously proposed to be the receptor for SEQ ID NO: 1- induced chemotaxis on human monocytes and T cells. Activation of ERK1/2 and p38 was markedly increased by the presence of granulocyte macrophage-colony stimulating factor (GM-CSF), but not macrophage-colony stimulating factor (M-

CSF). Exposure to SEQ ID NO: 1 also led to the activation of Elk-1, a transcription factor that is downstream of and activated by phosphorylated ERK 1/2, as well as the up-regulation of various Elk-1 controlled genes. The ability of SEQ ID NO: 1 to signal through these pathways has broad implications in immunity, monocyte activation, proliferation and differentiation.

[0171] Methods And Materials

[0172] SEQ ID NO: 1 (sequence : LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES), was synthesized by Fmoc [(N-(9-fluorenyl) methoxycarbonyl)] chemistry at the Nucleic Acid/Protein Synthesis (NAPS) Unit at UBC. Human recombinant granulocyte-macrophage colony- stimulating factor (GM-CSF), interleukin-4 (IL-4) and macrophage colony- stimulating factor (M-CSF) were purchased from Research Diagnostics Inc. (Flanders, NJ, USA). Pertussis toxin was supplied by List Biological Laboratories Inc. (Campbell, CA, USA).

[0173] Blood monocytes were prepared using standard techniques. Briefly, 100ml of fresh human venous blood was collected in sodium heparin Vacutainer collection tubes (Becton Dickinson, Mississauga, ON, Canada) from volunteers according to

UBC Clinical Research Ethics Board protocol C02-0091. The blood was mixed, at a 1:1 ratio, with RPMI 1640 media [supplemented with 10% v/v fetal calf serum (FBS), 1% L-glutamine, | nM sodium pyruvate] in an E-toxa-clean (Sigma-Aldrich,

Oakville, ON, Canada) washed, endotoxin-free bottle. PBMC were separated using

Ficoll-Paque Plus (Amersham Pharmacia Biotech, Baie D’Urf¢, PQ, Canada) at room temperature and washed with phosphate buffered saline (PBS). Monocytes were enriched with the removal of T-cells by rosetting with fresh sheep red blood cells (UBC animal care unit) pre-treated with Vibrio cholerae neuraminidase (Calbiochem

Biosciences Inc., La Jolla, CA, USA) and repeat separation by Ficoll Paque Plus. The enriched monocytes were washed with PBS, then cultured (approximately 2-3 x 10 per well) for 1 hour at 37 °C followed by the removal of non-adherent cells; monocytes were >95% pure as determined by flow cytometry (data not shown). B- lymphocytes were isolated by removing non-adherent cells and adding them to a new plate for one hour at 37°C. This was repeated a total of three times. Any remaining monocytes adhered to the plates, and residual non-adherent cells were primarily B cells. Cells were cultured in Falcon tissue culture 6-well plates (Becton Dickinson,

Mississauga, ON, Canada). The adherent monocytes were cultured in 1 mi media at 37°C in which SEQ ID NO: 1 and/or cytokines dissolved in endotoxin-free water (Sigma-Aldrich, Oakville, ON, Canada) were added. Endotoxin-free water was added as a vehicle control. For studies using pertussis toxin the-media was replaced with 1 ml of fresh media containing 100 ng/ml of toxin and incubated for 60 min at 37°C.

SEQ ID NO: 1 and cytokines were added directly to the media containing pertussis toxin. For the isolation of T lymphocytes, the rosetted T cells and sheep red blood cells were resuspended in 20 ml PBS and 10 ml of distilled water was added to lyse the latter. The cells were then centrifuged at 1000 rpm for 5 min after which the supernatant was removed. The pelleted T cells were promptly washed in PBS and increasing amounts of water were added until all sheep red blood cells had lysed. The remaining T cells were washed once in PBS, and viability was confirmed using a 0.4% Trypan blue solution. Primary human blood monocytes and T cells were cultured in RPMI 1640 supplemented with 10% v/v heat-inactivated FBS, 1% v/v L-

glutamine, 1 nM sodium pyruvate (GIBCO Invitrogen Corporation, Burlington, ON, - Canada). For each experiment between two and eight donors were used.

[0174] The simian virus 40-transformed, immortalized 16HBE4o- bronchial epithelial cell line was a generous gift of Dr. D. Gruenert (University of California,

San Francisco, CA). Cells were routinely cultured to confluence in 100% humidity and 5% CO; at 37°C. They were grown in Minimal Essential media with Earles' salts (GIBCO Invitrogen Corporation, Burlington, ON, Canada) containing 10% FBS (Hyclone), 2mM L-glutamine. For experiments, cells were grown on Costar

Transwell inserts (3-um pore size, Fischer Scientific) in 24-well plates. Cells were seeded at 5x10* cells per 0.25 ml of media on the top of the inserts while 0.95 ml of media was added to the bottom of the well and cultured at 37°C and 5% CO..

Transmembrane resistance was measured daily with a Millipore voltohmeter and inserts were used for experiments typically after 8 to 10 days, when the resistance was 500-700 ohms. The cells were used between passages 8 and 20.

[0175] Western Immunoblotting

[0176] After stimulation, cells were washed with ice-cold PBS containing 1mM vanadate (Sigma). Next 125ul of RIPA buffer (50 mM Tris-HCI, pH 7.4, NP-40 1%, sodium deoxycholate 0.25%, NaCl 150 mM, EDTA 1 mM, PMSF 1 mM, Aprotinin, leupeptin, pepstatin 1 pg/ml each, sodium orthovanadate 1 mM, NaF 1 mM) was added and the cells were incubated on ice until they were completely lysed as assessed by visual inspection. The lysates were quantitated using a BCA assay (Pierce). 30 pg of lysate was loaded onto 1.5mm thick gels, which were run at 100 volts for approximately 2 hours. Proteins were transferred to nitrocellulose filters for 75 min at 70 V. The filters were blocked for 2 hours at room temperature with 5% skim milk in TBST (10 mM Tris-HCl pH 8, 150 mM NaCl, 0.1% Tween-20). The filters were then incubated overnight at 4°C with the anti-ERK 1/2-P or anti-p38-P (Cell Signaling Technology, Ma) monoclonal antibodies. Immunoreactive bands were detected using horseradish peroxidase-conjugated sheep anti-mouse IgG antibodies (Amersham Pharmacia, New Jersey) and chemiluminescence detection (Sigma, Mo).

To quantify bands, the films were scanned and then quantified by densitometry using the software program, ImageJ. The blots were reprobed with a B-actin antibody (ICN

Biomedical Incorporated, Ohio) and densitometry was performed to allow correction for protein loading,

[0177] Kinase Assay

[0178] An ERKI/2 activity assay was performed using a non-radioactive kit (Cell

Signaling Technology). Briefly, cells were treated for 15 min and lysed in lysis buffer. . Equal amounts of proteins were immunoprecipitated with an immobilized phospho-

ERK1/2 antibody that reacts only with the phosphorylated (i.e. active) form of

ERK1/2. The immobilized precipitated enzymes were then used for the kinase assay using Elk-1 followed by Western blot analysis with antibodies that allow detection and quantitation of phosphorylated substrates.

[0179] Quantification of IL-8

[0180] Human IL-8 from supernatants of 16HBE40- cells was measured by using the commercially available enzyme-linked immunosorbent assay kit (Biosource) according to the manufacturer's instructions.

[0181] Semiquantitative RT-PCR

[0182] Total RNA from two independent experiments was isolated from 16HBE4o0- cells using RNaqueous (Ambion) as described by the manufacturer.

The samples were DNase treated, and then cDNA synthesis was accomplished by - using a first-strand cDNA synthesis kit (Gibco). The resultant cDNAs were used as a template in PCRs for various cytokine genes MCP-1 (5%-

TCATAGCAGCCACCTTCATTC-3' (SEQ ID NO:59), 5'-

TAGCGCAGATTCTTGGGTTG-3 (SEQ ID NO:60)), MCP-3, (5*-

TGTCCTTTCTCAGAGTGGTTCT-3' (SEQ ID NO:61), 5'"TGCTTCCATAGGGACATCATA-3' (SEQ ID NO:62)) IL-6, (5'-ACCTGAACCTTCCAAAGATGG-3' (SEQ ID NO:63), 5'-

GCGCAGAATGAGATGAGTTG-3' (SEQ ID NO:64)), and IL-8,(5'-

GTGCAGAGGGTTGTGGAGAAG-3' (SEQ ID NO:65), 5'-

TTCTCCCGTGCAATATCTAGG-3' (SEQ ID NO:66))Each RT-PCR reaction was performed in at least duplicate. Results were analysed in the linear phase of amplification and normalized to the housekeeping control, glyceraldehyde-3-phosphate dehydrogenase. Reactions were verified for RNA amplification by including controls without reverse transcriptase.

[0183] Results

[0184] A. Peptides induce ERK 1/2 and p38 phosphorylation in peripheral blood ‘ derived monocytes.

[0185] To determine if peptide induced the activation of the MAP kinases,

ERK 1/2 and/or p38, peripheral blood derived monocytes were treated with 50 ug/mi

SEQIDNO: 1 or water (as a vehicle control) for 15 min. To visualize the activated (phosphorylated) form of the kinases, Western blots were performed with antibodies specific for the dually phosphorylated form of the kinases (phosphorylation on

Thr202+Tyr204 and Thr180+Tyr182 for ERK 1/2 and p38 respectively). The gels - were re-probed with an antibody for B-actin to normalize for loading differences. In all, an increase in phosphorylation of ERK 1/2 (n=8) and p38 (n=4) was observed in response to SEQ ID NO: 1 treatment (Figure 2).

[0186] Figure 2 shows exposure to SEQ ID NO: 1 induces phosphorylation of : ERK1/2 and p38. Lysates from human peripheral blood derived monocytes were exposed to 50 pg/ml of SEQ ID NO: 1 for 15 minutes. A) Antibodies specific for the phosphorylated forms of ERK and p38 were used to detect activation of ERK 1/2 and p38. All donors tested showed increased phosphorylation of ERK1/2 and p38 in response to SEQ ID NO: 1 treatment . One representative donor of eight. Relative amounts of phosphorylation of ERK (B) and p38(C) were determined by dividing the intensities of the phosphorylated bands by the intensity of the corresponding control band as described in the Materials and Methods. :

[0187] B. Peptide induced activation of ERK 1/2 is greater in human serum than in fetal bovine serum.

[0188] We were able to demonstrate that LL-37 induced phosphorylation of

ERK1/2 did not occur in the absence of serum and the magnitude of phosphorylation was dependent upon the type of serum present such that activation of ERK 1/2 was far superior in human serum (HS) than in fetal bovine serum (FBS).

[0189] Figure 3 shows LL-37 induced phosphorylation of ERK 1/2 does not occur in the absence of serum and the magnitude of phosphorylation is dependent upon the type of serum present. Human blood derived monocytes were treated with 50 pg/ml of LL-37 for 15 minutes. Lysates were run on a 12% acrylamide gel then transferred to nitrocellulose membrane and probed with antibodies specific for the phosphorylated (active) form of the kinase. To normalize for protein loading, the blots were reprobed with B-actin. Quantification was done with Image] software. The

Figure 3 inset demonstrates that LL-37 is unable to induce MAPK activation in human monocytes under serum free conditions. Cells were exposed to 50 mg/ml of

LL-37 (+), or endotoxin free water (-) as a vehicle control, for 15 minutes. (A) After exposure to LL-37 in media containing 10% fetal calf serum, phosphorylated ERK 1/2 : was detectable, however, no phosphorylation of ERK 1/2 was detected in the absence of serum (n=3). (B) Elk-1, a transcription factor downstream of ERK 1/2, was activated (phosphorylated) upon exposure to 50 pg/ml of LL-37 in media containing 10% fetal calf serum, but not in the absence of serum (n=2).

[0191] C. Peptide induced activation of ERK 1/2 and p38 is dose dependent and demonstrates synergy with GM-CSF.

[0192] GM-CSF, IL-4, or M-CSF (each at 100ng/ml) was added concurrently with

SEQ ID NO: 1 and phosphorylation of ERK 1/2 was measured in freshly isolated human blood monocytes. ERK1/2 phosphorylation was evident when cells were treated with 50 ug/ml of SEQ ID NO: 1 (8.3 fold increase over untreated, n=9) but not at lower concentrations (n=2). In the presence of 100 ng/m! GM-CSF, SEQ ID NO: 1- induced ERK1/2 phosphorylation increased markedly (58 fold greater than untreated, n=>5). Furthermore, in the presence of GM-CSF, activation of ERK 1/2 occurred in response to concentrations of 5 and 10 pg/ml of SEQ ID NO: 1, respectively, in the two donors tested (Fig 4). This demonstrates that SEQ ID NO: 1 induced activation of

ERK 1/2 occurred at a lower threshold in the presence of GM-CSF, a cytokine found locally at sites of infection.

[0193] Figure 4 shows LL-37 induced activation of ERK 1/2 occurs at lower concentrations and is amplified in the presence of certain cytokines. When freshly isolated monocytes were stimulated in media containing both GM-CSF (100ng/mi) and IL-4 (100ng/ml) LL-37 induced phosphorylation of ERK1/2 was apparent at concentrations as low as 5 ug/ml. This synergistic activation of ERK1/2 seems to be due primarily to GM-CSF.

[0194] D. Activation of ERK1/2 leads to transcription of Elk-1 controlled genes and secretion of IL-8

[0195] IL-8 release is governed, at least in part, by activation of the ERK 1/2 and p38 kinases. In order to determine if peptide could induce IL-8 secretion the human bronchial cell line, 16HBE40-, was grown to confluency in Transwell filters, which allows for cellular polarization with the creation of distinct apical and basal surfaces.

When the cells were stimulated with SOug/ml of SEQ ID NO: 1 on the apical surface for four hours a statistically significant increase in the amount of IL-8 released into the apical supernatant was detected (Fig. 5). To determine the downstream transcriptional effects of peptide-induced MAP kinase activation, the expression of genes known to be regulated by ERK 1/2 or p38 was assessed by RT-PCR. RT-PCR was performed on RNA isolated from 16HBE4o- cells, treated for four hours with 50ug/ml of SEQ ID NO: 1 in the presence of serum, from two independent experiments. MCP-1 and IL-8 have been demonstrated to be under the transcriptional control of both ERK 1/2 and p38, consistent with this they are up-regulated 2.4 and 4.3 fold respectively. Transcription of MCP-3 has not previously been demonstrated to be influenced by the activation of the mitogen activated protein kinases, consistent with this, expression is not affected by peptide treatment. (Fig. 5). These data are consistent with the hypothesis that activation of the activation of the ERK1/2 and p38 signaling pathways has functional effects on transcription of cytokine genes with immunomodulatory functions. The inset to Figure 3B also demonstrates that peptide induced the phosphorylation of transcription facor Elk-1 in a serum dependent manner.

[0196] Figure 5 shows peptide affects both transcription of various cytokine genes : and release of IL-8 in the 16HBE4o0- human bronchial epithelial cell line. Cells were : grown to confluency on a semi-permeable membrane and stimulated on the apical surface with 50 ug/ml of SEQ ID NO: 1 for four hours. A) SEQ ID NO: 1 treated cells produced significantly more IL-8 than controls, as detected by ELISA in the supernatant collected from the apical surface, but not from the basolateral surface.

Mean + SE of three independent experiments shown, asterisk indicates p=0.002. B)

RNA was collected from the above experiments and RT-PCR was performed. A number of cytokine genes known to be regulated by either ERK 1/2 or p38 were up- regulated upon stimulation with peptide. The average of two independent experiments is shown.

[0197] Although the invention has been described with reference to the presently preferred embodiment, it should be understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims.

Claims (23)

WHAT IS CLAIMED IS:

1. The use of a peptide as set forth in SEQ ID NO:1-4, 11, 18, 25, 32, 39, 46, 53 or 54, in a method of making a medicament for use in a method of stimulating innate immunity in a subject.

2. The use of claim 1, wherein the innate immunity is evidenced by host immune cell activation, proliferation, differentiation or MAP kinase pathway activation.

3. The use of claim 2, wherein the MAP kinases are MEK and/or ERK.

4. The use of claim 1, further comprising administering GM-CSF to the subject.

5. The use of an antibiotic in combination with a peptide as set forth in SEQ ID NO:1-4, 7,11, 18, 25, 32, 39, 46, 53 or 54 in a method of making a medicament for use in a method of stimulating innate immunity in a subject having or at risk of having an infection.

6. The use of claim 1, wherein the peptide contains at least one amino acid that is a D- enantiomer.

7. The use of claim 1, wherein the peptide is cyclic.

8. The use of claim 1, wherein the peptide sequence is reversed.

9. The use of claim 1, wherein the medicament further comprises an antibiotic.

10. The use of claim 9, wherein the antibiotic is selected from aminoglycosides, penicillins, cephalosporins, cerbacephems, cephamycins, chloramphenicols, glycylcyclines, licosamides, aminocclitols, cationic antimicrobial peptides, lipopeptides, poymyxins, streptogramins, oxazoladinones, lincosamides, fluoroquinolones, carbapenems, tetracyclines, macrolides, beta-lactams carbapenems, monobactams, quinolones, tetracyclines, or glycopeptides.

11. The use of claim 5, wherein the peptide has anti-inflammatory activity.

12. The use of claim 5, wherein the peptide has anti-sepsis activity. 200 Amended sheet7/05/2007

WO .2005/025607 PCT/CA2004/001602

13. The use of claim §, wherein the peptide contains at least one amino acid that is a D- enantiomer.

14. The use of claim 5, wherein the peptide is cyclic.

15. The use of claim 5, wherein the peptide sequence is reversed.

16. The use of claim 5, wherein the antibiotic is selected from aminoglycosides, penicillins, cephalosporins, cerbacephems, cephamycins, chloramphenicols, glycylcyclines, licosamides, aminocclitols, cationic antimicrobial peptides, lipopeptides, poymyxins, streptogramins, oxazoladinones, lincosamides, fluoroquinolones, carbapenems, tetracyclines, macrolides, beta-lactams carbapenems, monobactams, quinolones, tetracyclines, or glycopeptides.

17. The use of GM-CSF in combination with a peptide as set forth in SEQ [D NO: 1-4, 7, 11, 18, 25, 32, 39, 46, 53 or 54 in a method of making a medicament for use in a method of stimulating innate immunity in a subject having or at risk of having an infection.

18. The use of claim 17, wherein the peptide has anti-inflammatory activity.

19. The use of claim 17, wherein the peptide has anti-sepsis activity.

20. The use of claim 17, wherein the peptide contains at least one amino acid that is a D- enantiomer.

21. The use of claim 17, wherein the peptide is cyclic.

22. The use of claim 17, wherein the peptide sequence is reversed.

23. A peptide as set forth in SEQ ID NO:1-4, 11, 18, 25, 32, 39, 46, 53 or 54 for stimulating innate immunity in a subject. 201 Amended sheet7/05/2007