Effectors of innate immunity determination

Abstract

A method of identifying a polynucleotide or pattern of polynucleotides regulated by one or more sepsis or inflammatory inducing agents and inhibited by a peptide is described. A method of identifying a pattern of polynucleotide expression for inhibition of an inflammatory or septic response. The method includes contacting cells with LPS, LTA, CpG DNA and/or intact microbe or microbial components in the presence or absence of a cationic peptide; detecting a pattern of polynucleotide expression for the cells in the presence and absence of the peptide, wherein the pattern in the presence of the peptide represents inhibition of an inflammatory or septic response. Also included are compounds and agents identified by the methods of the invention. In another aspect, the invention provides methods and compounds for enhancing innate immunity in a subject.

Description

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 modem 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 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 factorα (TNF-α) is of extreme importance. TNF-α 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), rhamnose-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-α. 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 Biotechnology 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. E. W. 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; NFκB). 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 α-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 α-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 β-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 inflammatory inducing agents and contacting the polynucleotide or polynucleotides with a cationic peptide either simultaneously or immediately thereafter. Differences 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 (AI1 67887), IL-10 R beta (AA486393), IL-10 R alpha (U00672) 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 (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-κB 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 that is 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.

[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:

[0022] X1X2X3IX4PX4IPX5X2X1 (SEQ ID NO: 4), where X1 is one or two of R, L or K, X2 is one of C, S or A, X3 is one of R or P, X4 is one of A or V and X5 is one of V or W;

[0023] X1LX2X3KX4X2X5X3PX3X1 (SEQ ID NO: 11), where X1 is one or two of D, E, S, T or N, X2 is one or two of P, G or D, X3 is one of G, A, V, L, I or Y, X4 is one of R, K or H and X5 is one of S, T, C, M or R;

[0024] X1X2X3X4WX4WX4X5K (SEQ ID NO: 18), where X1 is one to four chosen from A, P or R, X2 is one or two aromatic amino acids (F, Y and W), X3 is one of P or K, X4 is one, two or none chosen from A, P, Y or W and X5 is one to three chosen from R or P;

[0025] X1X2X3X4X1VX3X4RGX4X3X4X1X3X1 (SEQ ID NO: 25) where X1 is one or two of R or K, X2 is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X3 is C, S, M, D or A and X4 is F, I, V, M or R;

[0026] X1X2X3X4X1VX5X4RGX4X5X4X1X3X1 (SEQ ID NO: 32), where X1 is one or two of R or K, X2 is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X3 is one of C, S, M, D or A, X4 is one of F, I, V, M or R and X5 is one of A, I, S, M, D or R;

[0027] and

[0028] KX1KX2FX2KMLMX2ALKKX3 (SEQ ID NO: 39), where X1 is a polar amino acid (C, S, T, M, N and Q); X2 is one of A, L, S or K and X3 is 1-17 amino acids chosen from G, A, V, L, I, P, F, S, T, K and H;

[0029] KWKX2X1X1X2X2X1X2X2X1X1X2X2IFHTALKPISS (SEQ ID NO: 46), where X1 is a hydrophobic amino acid and X2 is a hydrophilic amino acid.

[0030] Additionally, in another aspect the invention provides isolated cationic peptides KWKSFLRTFKSPVRTVFHTALKPISS (SEQ ID NO: 53) and KWKSYAHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

[0031] Also provided are nucleic acid sequences encoding the cationic peptides of the invention, vectors including such polynucleotides and host cells containing the vectors.

DETAILED DESCRIPTION OF THE INVENTION

[0032] 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.

[0033] “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.

[0034] As used herein, the term “cationic peptide” refers to a sequence of amino acids from about 5 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.

[0035] 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.

(SEQ ID NO: 1)
LL-37       LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES
(SEQ ID NO: 2)
Indolicidin ILPWKWPWWPWRR-NH2
(SEQ ID NO: 3)
Bac2A       RLARIVVIRVAR-NH2

[0036] 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.

[0037] Chemokines, or chemoattractant cytokines, are a subgroup of immune factors that mediate chemotactic and other pro-inflammatory phenomena (See, Schall, 1991, Cytokine 3:165-183). Chemokines are small molecules of approximately 70-80 residues in length and can generally be divided into two subgroups, a which have two N-terminal cysteines separated by a single amino acid (C×C) and β which have two adjacent cysteines at the N terminus (CC). RANTES, MIP- 1α and MIP-1β are members of the β 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 β 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 a 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).

[0038] The monomeric forms of all chemokines characterized thus far share significant structural homology, although the quaternary structures of α and β groups are distinct. While the monomeric structures of the β and α 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 (γ) of chemokines (Yoshida et al., 1995, FEBS Lett. 360:155-159; and Kelner et al., 1994, Science 266:1395-1399).

[0039] 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 β chemokine receptors include: CC CKR-1, which binds RANTES and MIP-1α (Neote et al., 1993, Cell 72: 415-425), CC CKR-4, which binds RANTES, MIP-1α, and MCP-1 (Power et al., 1995, J. Biol. Chem. 270:19495-19500), and CC CKR-5, which binds RANTES, MIP-1α, and MIP-1β (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 α and β 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.

[0040] In one aspect, the present invention provides the use of compounds including cationic 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.

[0041] 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.

[0042] 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.

[0043] 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.

[0044] 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.

[0045] As can be seen in the 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.

[0046] 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), TLR5 (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 (AA 194983), IK cytokine down-regulator of HLA II (R39227), TGF-B inducible early growth response 2 (AI473938), or CD2 (AA927710). The relevance and application of these results are confirmed by an in vivo application to mice.

[0047] 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-α. 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-α and/or interleukins including, but not limited to, IL-1β, IL-6, IL-12 p40, IL-12 p70, and IL-8.

[0048] 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 a 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, CCR5, 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.

[0049] 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 (D8745 1), serine/threonine protein kinase MASK (AB040057), KIAA0912 protein (AB020719), KIAA0239 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 (J03925), Rho-associated kinase 2 (NM—004850), PTD017 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 (Z94155, X81892, U52219, U22491, AF015257, U66579) chemokine (C-C motif) receptor 7 (L31584), tumor necrosis factor receptor superfamily member 17 (Z29575), interferon gamma receptor 2 (U05875), cytokine receptor-like factor 1 (AF059293), class I cytokine receptor (AF053004), coagulation factor II (thrombin) receptor-like 2 (U92971), leukemia inhibitory factor receptor (NM—002310), interferon gamma receptor 1 (AL050337).

[0050] 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).

[0051] 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 5 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.

[0052] 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.

[0053] 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).

[0054] 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.

[0055] 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 a 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.

[0056] 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-γ-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.

[0057] 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.

[0058] In one embodiment, the invention provides an isolated cationic peptides having an amino acid sequence of the general formula (Formula A): X1X2X3IX4PX4IPX5X2X1 (SEQ ID NO: 4), wherein X1 is one or two of R, L or K, X2 is one of C, S or A, X3 is one of R or P, X4 is one of A or V and X5 is one of V or 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).

[0059] In another embodiment, the invention provides an isolated linear cationic peptide having an amino acid sequence of the general formula (Formula B): X1LX2X3KX4X2X5X3PX3X1 (SEQ ID NO: 11), wherein X1 is one or two of D, E, S, T or N, X2 is one or two of P, G or D, X3 is one of G, A, V, L, I or Y, X4 is one of R, K or H and X5 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).

[0060] In another embodiment, the invention provides an isolated linear cationic peptide having an amino acid sequence of the general formula (Formula C): X1X2X3X4WX4WX4X5K (SEQ ID NO: 18) (this formula includes CP12a and CP12d), wherein X1 is one to four chosen from A, P or R, X2 is one or two aromatic amino acids (F, Y and W), X3 is one of P or K, X4 is one, two or none chosen from A, P, Y or W and X5 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).

[0061] In another embodiment, the invention provides an isolated hexadecameric cationic peptide having an amino acid sequence of the general formula (Formula D): X1X2X3X4X1VX3X4RGX4X3X4X1X3X1 (SEQ ID NO: 25) wherein X1 is one or two of R or K, X2 is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X3 is C, S, M, D or A and X4 is F, I, V, M or R. 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).

[0062] In still another embodiment, the invention provides an isolated hexadecameric cationic peptide having an amino acid sequence of the general formula (Formula E): X1X2X3X4X1VX5X4RGX4X5X4X1X3X1 (SEQ ID NO: 32), wherein X1 is one or two of R or K, X2 is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X3 is one of C, S, M, D or A, X4 is one of F, I, V, M or Rand X5 is one of A, I, S, 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).

[0063] In another embodiment, the invention provides an isolated longer cationic peptide having an amino acid sequence of the general formula (Formula F): KX1KX2FX2KMLMX2ALKKX3 (SEQ ID NO: 39), wherein X1 is a polar amino acid (C, S, T, M, N and Q); X2 is one of A, L, S or K and X3 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).

[0064] In yet another embodiment, the invention provides an isolated longer cationic peptide having an amino acid sequence of the general formula (Formula G): KWKX2X1X1X2X2X1X2X2X1X1X2X2IFHTALKPISS (SEQ ID NO: 46), wherein X1 is a hydrophobic amino acid and X2 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).

[0065] 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 KWKSYAHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

[0066] The term “isolated” 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.

[0067] 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.

[0068] A cationic peptide “variant” is an peptide that is an altered form of a 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.

[0069] 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.

[0070] 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 ¼-1 hours at 0° C. After evaporation of the reagents, the peptides are extracted from the polymer with a 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.

[0071] 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.

[0072] 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.

[0073] 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 CaCl2, MgCl2 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.

[0074] “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. aureuis 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.

[0075] 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.

[0076] 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.

[0077] 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).

[0078] The peptide of the invention can be administered parenterally by injection or by gradual infusion over time. 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] 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

[0081] Anti-Sepsis/Anti-Inflammatory Activity

[0082] 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 2.5×106 cells/dish, cultured overnight and then incubated with 100 ng/ml E. coli O111:B4 LPS (Sigma), without (control) or with 50 μg/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, Tex.). 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.

[0083] 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 μg of total RNA and labeled with Cy3 or Cy5 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, Calif.) 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 subgiid and subtracts this for each grid. Analysis was performed with Genespring software (Redwood City, Calif.). 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.

[0084] 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 μg/ml) and LPS (0.1 μg/ml) or LPS alone was incubated with the A549 cells for 4 h and the RNA was isolated. Five μg 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 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
		Control:
	Polynucleotide	Media only	Ratio:	Ratio: LPS + ID
Accession Numbera	Gene Function	Intensity	LPS/control	27/control
AL031983	Unknown	0.032	302.8	5.1
L04510	ADP-	0.655	213.6	1.4
	ribosylation
	factor
D87451	ring finger	3.896	183.7	2.1
	protein 10
AK000869	hypothetical	0.138	120.1	2.3
	protein
U78166	Ric-like	0.051	91.7	0.2
	expressed in
	neurons
AJ001403	mucin 5	0.203	53.4	15.9
	subtype B
	tracheobronchial
AB040057	serine/threonine	0.95	44.3	15.8
	protein
	kinase MASK
Z99756	Unknown	0.141	35.9	14.0
L42243	interferon	0.163	27.6	5.2
	receptor 2
NM_016216	RNA lariat	6.151	22.3	10.9
	debranching
	enzyme
AK001589	hypothetical	0.646	19.2	1.3
	protein
AL137376	Unknown	1.881	17.3	0.6
AB007856	FEM-1-like	2.627	15.7	0.6
	death receptor
	binding protein
AB007854	growth arrest-	0.845	14.8	2.2
	specific 7
AK000353	cytosolic	0.453	13.5	1.0
	ovarian
	carcinoma
	antigen 1
D14539	myeloid/lymphoid	2.033	11.6	3.1
	or mixed-
	lineage
	leukemia
	translocated to 1
X76785	integration site	0.728	11.6	1.9
	for Epstein-Barr
	virus
M54915	pim-1	1.404	11.4	0.6
	oncogene
NM_006092	caspase	0.369	11.0	0.5
	recruitment
	domain 4
J03925	integrin_alpha M	0.272	9.9	4.2
NM_001663	ADP-	0.439	9.7	1.7
	ribosylation
	factor 6
M23379	RAS p21	0.567	9.3	2.8
	protein
	activator
K02581	thymidine	3.099	8.6	3.5
	kinase 1
	soluble
U94831	transmembrane	3.265	7.1	1.5
	9 superfamily
	member 1
X70394	zinc finger	1.463	6.9	1.7
	protein 146
AL137614	hypothetical	0.705	6.8	1.0
	protein
U43083	guanine	0.841	6.6	1.6
	nucleotide
	binding protein
AL137648	DKFZp434J181	1.276	6.5	0.8
	3 protein
AF085692	ATP-binding	3.175	6.5	2.4
	cassette sub-
	family C
	(CFTR/MRP)
	member 3
AK001239	hypothetical	2.204	6.4	1.3
	protein
	FLJ10377
NM_001679	ATPase	2.402	6.3	0.9
	Na+/K+
	transporting
	beta 3
	polypeptide
L24804	unactive	3.403	6.1	1.1
	progesterone
	receptor
U15932	dual specificity	0.854	6.1	2.1
	phosphatase 5
M36067	ligase I DNA—	1.354	6.1	2.2
	ATP-dependent
AL161951	Unknown	0.728	5.8	1.9
M59820	colony	0.38	5.7	2.0
	stimulating
	factor 3
	receptor
AL050290	spermidine/	2.724	5.6	1.4
	spermine N1-
	acetyltransferase
NM_002291	laminin_beta 1	1.278	5.6	1.8
X06614	retinoic acid	1.924	5.5	0.8
	receptor_alpha
AB007896	putative L-type	0.94	5.3	1.8
	neutral amino
	acid transporter
AL050333	DKFZP564B11	1.272	5.3	0.6
	6 protein
AK001093	hypothetical	1.729	5.3	2.0
	protein
NM_016406	hypothetical	1.314	5.2	1.2
	protein
M86546	pre-B-cell	1.113	5.2	2.2
	leukemia
	transcription
	factor 1
X56777	zona pellucida	1.414	5.0	1.4
	glycoprotein 3A
NM_013400	replication	1.241	4.9	2.0
	initiation region
	protein
NM_002309	leukemia	1.286	4.8	1.9
	inhibitory factor
NM_001940	dentatorubral-	2.034	4.7	1.2
	pallidoluysian
	atrophy
U91316	cytosolic acyl	2.043	4.7	1.4
	coenzyme A
	thioester
	hydrolase
X76104	death-	1.118	4.6	1.8
	associated
	protein kinase 1
AF131838	Unknown	1.879	4.6	1.4
AL050348	Unknown	8.502	4.4	1.7
D42085	KIAA0095 gene	1.323	4.4	1.2
	product
X92896	Unknown	1.675	4.3	1.5
U26648	syntaxin 5A	1.59	4.3	1.4
X85750	monocyte to	1.01	4.3	1.1
	macrophage
	differentiation-
	associated
D14043	CD164	1.683	4.2	1.0
	antigen—
	sialomucin
J04513	fibroblast	1.281	4.0	0.9
	growth factor 2
U19796	melanoma-	1.618	4.0	0.6
	associated
	antigen
AK000087	hypothetical	1.459	3.9	1.0
	protein
AK001569	hypothetical	1.508	3.9	1.2
	protein
AF189009	ubiquilin 2	1.448	3.8	1.3
U60205	sterol-C4-	1.569	3.7	0.8
	methyl oxidase-
	like
AK000562	hypothetical	1.166	3.7	0.6
	protein
AL096739	Unknown	3.66	3.7	0.5
AK000366	hypothetical	15.192	3.5	1.0
	protein
NM_006325	RAN member	1.242	3.5	1.4
	RAS oncogene
	family
X51688	cyclin A2	1.772	3.3	1.0
U34252	aldehyde	1.264	3.3	1.2
	dehydrogenase 9
NM_013241	FH1/FH2	1.264	3.3	0.6
	domain-
	containing
	protein
AF112219	esterase	1.839	3.3	1.1
	D/
	formylglutathione
	hydrolase
NM_016237	anaphase-	2.71	3.2	0.9
	promoting
	complex
	subunit 5
AB014569	KIAA0669 gene	2.762	3.2	0.2
	product
AF151047	hypothetical	3.062	3.1	1.0
	protein
X92972	protein	2.615	3.1	1.1
	phosphatase 6
	catalytic
	subunit
AF035309	proteasome	5.628	3.1	1.3
	26S subunit
	ATPase 5
U52960	SRB7 homolog	1.391	3.1	0.8
J04058	electron-	3.265	3.1	1.2
	transfer-
	flavoprotein
	alpha
	polypeptide
M57230	interleukin 6	0.793	3.1	1.0
	signal
	transducer
U78027	galactosidase—	3.519	3.1	1.1
	alpha
AK000264	Unknown	2.533	3.0	0.6
X80692	mitogen-	2.463	2.9	1.3
	activated
	protein kinase 6
L25931	lamin B	2.186	2.7	0.7
	receptor
X13334	CD14 antigen	0.393	2.5	1.1
M32315	tumor necrosis	0.639	2.4	0.4
	factor receptor
	superfamily
	member 1B
NM_004862	LPS-induced	6.077	2.3	1.1
	TNF-alpha
	factor
AL050337	interferon	2.064	2.1	1.0
	gamma
	receptor 1
aAll Accession Numbers in Table 1 through Table 64 refer to GenBank Accession Numbers.

[0085] In Table 2, the cationic peptides at a concentration of 50 μg/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 μg 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.

TABLE 2
Human A549 Epithelial Cell Polynucleotide Expression up-regulated
by E.coli O111:B4 LPS and reduced by Cationic Peptides
		Control:		Ratio:	Ratio:	Ratio:
Accession		Media only	Ratio:	LPS + ID 27/	LPS + ID 16/	LPS + ID 22/
Number	Gene	Intensity	LPS/control	control	control	control
AL031983	Unknown	0.03	302.8	5.06	6.91	0.31
L04510	ADP-	0.66	213.6	1.4	2.44	3.79
	ribosylation
	factor
D87451	ring finger	3.90	183.7	2.1	3.68	4.28
	protein
AK000869	hypothetical	0.14	120.1	2.34	2.57	2.58
	protein
U78166	Ric like	0.05	91.7	0.20	16.88	21.37
X03066	MHC class II	0.06	36.5	4.90	12.13	0.98
	DO beta
AK001904	hypothetical	0.03	32.8	5.93	0.37	0.37
	protein
AB037722	Unknown	0.03	21.4	0.30	0.30	2.36
AK001589	hypothetical	0.65	19.2	1.26	0.02	0.43
	protein
AL137376	Unknown	1.88	17.3	0.64	1.30	1.35
L19185	thioredoxin-	0.06	16.3	0.18	2.15	0.18
	dependent peroxide
	reductase 1
J05068	transcobalamin I	0.04	15.9	1.78	4.34	0.83
AB007856	FEM-1-like	2.63	15.7	0.62	3.38	0.96
	death receptor
	binding protein
AK000353	cytosolic	0.45	13.5	1.02	1.73	2.33
	ovarian
	carcinoma ag 1
X16940	smooth muscle	0.21	11.8	3.24	0.05	2.26
	enteric actin γ2
M54915	pim-1 oncogene	1.40	11.4	0.63	1.25	1.83
AL122111	hypothetical	0.37	10.9	0.21	1.35	0.03
	protein
M95678	phospholipase	0.22	7.2	2.38	0.05	1.33
	C beta 2
AK001239	hypothetical	2.20	6.4	1.27	1.89	2.25
	protein
AC004849	Unknown	0.14	6.3	0.07	2.70	0.07
X06614	retinoic acid	1.92	5.5	0.77	1.43	1.03
	receptor_alpha
AB007896	putative L-type	0.94	5.3	1.82	2.15	2.41
	neutral amino
	acid transporter
AB010894	BAI1-associated	0.69	5.0	1.38	1.03	1.80
	protein
U52522	partner of RAC1	1.98	2.9	1.35	0.48	1.38
AK001440	hypothetical	1.02	2.7	0.43	1.20	0.01
	protein
NM_001148	ankyrin 2—	0.26	2.5	0.82	0.04	0.66
	neuronal
X07173	inter-alpha	0.33	2.2	0.44	0.03	0.51
	inhibitor H2
AF095687	brain and	0.39	2.1	0.48	0.03	0.98
	nasopharyngeal
	carcinoma
	susceptibility
	protein
NM_016382	NKcell	0.27	2.1	0.81	0.59	0.04
	activation
	inducing ligand
	NAIL
AB023198	KIAA0981	0.39	2.0	0.43	0.81	0.92
	protein

EXAMPLE 2

[0086] Neutralization of the Stimulation of Immune Cells

[0087] The ability of compounds to neutralize the stimulation of immune cells by both Gram-negative and Gram-positive bacterial products was tested. Bacterial 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, Mass.). The cells from mouse bone marrow were cultured in 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 μg/ml peptide for 24 hours. The release of cytokines into the culture supernatant was determined by ELISA (R&D Systems, Minneapolis, Minn.). The cell lines, RAW 264.7 and A549, were maintained in DMEM supplemented with 10% fetal calf serum. RAW 264.7 cells were seeded in 24 well plates at a density of 106 cells per well in DMEM and A549 cells were seeded in 24 well plates at a density of 105 cells per well in DMEM and both were incubated at 37° C. in 5% CO2 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, N.J.) containing 14.3 USP units heparin/mI 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×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 5% CO2. 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 (AraLAM) 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 μg 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 μg in 100μl 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 μg E. coli O111:B4 LPS and 10 min later peptide (200 μg) was introduced by intraperitoneal injection. Survival was monitored for 48 hours post injection.

[0088] Hyperproduction of TNF-α has been classically linked to development of sepsis. The three types of LPS, LTA or AraLAM 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-α production stimulated by S. typhimurium, B. cepacia, and E. coli O111:B4 LPS, with the former being affected to a somewhat lesser extent (Table 3). At concentrations as low as 1 μg/ml of peptide (0.25 nM) substantial reduction of TNF-α production was observed in the latter two cases. A different peptide, SEQ ID NO: 3 did not reduce LPS-induced production of TNF-α 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-α production stimulated by E. coli O111:B4 LPS (Table 4). The peptides had a varied ability to reduce TNF-α production although many of them lowered TNF-α by at least 60%.

[0089] 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 μg/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 μg/ml) actually resulted in increased levels of IL-8 (Table 5). This suggests that the peptides have different effects at different concentrations.

[0090] The effect of peptides on inflammatory stimuli was also demonstrated in primary murine cells, in that peptide SEQ ID NO: 1 significantly reduced TNF-α 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-α production (Table 9).

[0091] Consistent with the ability of SEQ ID NO: 1 to prevent LPS-induced production of TNF-α 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. Galactosainine-sensitized mice that were injected with 3 μg of E. coli 0111:B4 LPS were all killed within 4-6 hours. When 200 μg 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 11,12).

[0092] 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-α 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 LTA-induced TNF-α production by RAW 264.7 cells. At a concentration of 1 μg/ml SEQ ID NO: 1 was able to substantially reduce (>75%) the induction of TNF-α production by 1 μg/ml S. aureus LTA. At 20 μg/ml SEQ ID NO: 1, there was >60% inhibition of AraLAM induced TNF-α. 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-α. These results demonstrate that cationic peptides can reduce the pro-inflammatory cytokine response of the immune system to bacterial products.

[0093] Table 3: Reduction by SEQ ID 1 of LPS Induced TNF-α Production in RAW 264.7 Cells.

[0094] 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 0111:B4 LPS in the presence of the indicated concentrations of SEQ ID 1 for 6 hr. The concentrations of TNF-α released into the culture supernatants were determined by ELISA. 100% represents the amount of TNF-α 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-α production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-α 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-α (%)*
1 (μg/ml)	B. cepacia LPS	E. coli LPS	S. typhimurium LPS
0.1	8.5 ± 2.9	0.0 ± 0.6	0.0 ± 0
1	23.0 ± 11.4	36.6 ± 7.5	9.8 ± 6.6
5	55.4 ± 8	65.0 ± 3.6	31.1 ± 7.0
10	63.1 ± 8	75.0 ± 3.4	37.4 ± 7.5
20	71.7 ± 5.8	81.0 ± 3.5	58.5 ± 10.5
50	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-α Production in RAW 264.7 Cells.

[0096] 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-α released into the culture supernatants were determined by ELISA. Background levels of TNF-α production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-α 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 μg/ml) Inhibition of TNF-α (%)
SEQ ID 5           65.6 ± 1.6
SEQ ID 6           59.8 ± 1.2
SEQ ID 7           50.6 ± 0.6
SEQ ID 8           39.3 ± 1.9
SEQ ID 9           58.7 ± 0.8
SEQ ID 10          55.5 ± 0.52
SEQ ID 12          52.1 ± 0.38
SEQ ID 13          62.4 ± 0.85
SEQ ID 14          50.8 ± 1.67
SEQ ID 15          69.4 ± 0.84
SEQ ID 16          37.5 ± 0.66
SEQ ID 17          28.3 ± 3.71
SEQ ID 19          69.9 ± 0.09
SEQ ID 20          66.1 ± 0.78
SEQ ID 21          67.8 ± 0.6
SEQ ID 22          73.3 ± 0.36
SEQ ID 23          83.6 ± 0.32
SEQ ID 24          60.5 ± 0.17
SEQ ID 26          54.9 ± 1.6
SEQ ID 27          51.1 ± 2.8
SEQ ID 28          56 ± 1.1
SEQ ID 29          58.9 ± 0.005
SEQ ID 31          60.3 ± 0.6
SEQ ID 33          62.1 ± 0.08
SEQ ID 34          53.3 ± 0.9
SEQ ID 35          60.7 ± 0.76
SEQ ID 36          63 ± 0.24
SEQ ID 37          58.9 ± 0.67
SEQ ID 38          54 ± 1
SEQ ID 40          75 ± 0.45
SEQ ID 41          86 ± 0.37
SEQ ID 42          80.5 ± 0.76
SEQ ID 43          88.2 ± 0.65
SEQ ID 44          44.9 ± 1.5
SEQ ID 45          44.7 ± 0.39
SEQ ID 47          36.9 ± 2.2
SEQ ID 48          64 ± 0.67
SEQ ID 49          86.9 ± 0.69
SEQ ID 53          46.5 ± 1.3
SEQ ID 54          64 ± 0.73

[0097]

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 O111: 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 (μg/ml) Inhibition of IL-8 (%)
0.1              1 ± 0.3
1                32 ± 10
10               60 ± 9
20               47 ± 12
50               40 ± 13
100              0

[0098]

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 (μg/ml) Inhibition of IL-8 (%)
0.1                              6.8 ± 9.6
1                                12.8 ± 24.5
10                               29.0 ± 26.0
50                               39.8 ± 1.6
100                              45.0 ± 3.5

[0099]

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.
SEQ ID 2 (μg/ml) IL-8 (pg/ml)
0                3205
10               1912
50               1458

[0100]

TABLE 8
Reduction by SEQ ID 1 of E. coli LPS induced TNF-α
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 μg/ml of peptide. The supernatant was collected
and tested for levels of TNF-α by ELISA. The data represents the
amount of TNF-α resulting from duplicate wells of bone marrow-
derived macrophages incubated with LPS alone for 6 h (1.1 ± 0 0.09
ng/ml) or 24 h (1.7 ± 0.2 ng/ml). Background levels of TNF-α
were 0.038 ± 0.008 ng/ml for 6 h and 0.06 ± 0.012 ng/ml for 24 h.
	Production of TNF-α (ng/ml)
SEQ ID 1 (μg/ml)	6 hours	24 hours
LPS alone	1.1	1.7
1	0.02	0.048
10	0.036	0.08
100	0.033	0.044
No LPS control	0.038	0.06

[0101]

TABLE 9
Inhibition of E. coli LPS-induced TNF-α production by delayed
addition of SEQ ID 1 to A549 cells. Peptide (20 μg/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-α by ELISA.
The data is presented as the mean of three
experiments + standard error.
Time of addition of SEQ ID 1
after LPS (min) Inhibition of TNF-α (%)
0               98.3 ± 0.3
15              89.3 ± 3.8
30              83 ± 4.6
60              68 ± 8
90              53 ± 8

[0102]

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 μg in 0.1 ml PBS). Peptide, SEQ ID 1,
(200 μg/mouse = 8 mg/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.
				Survival post
D-Galactosamine	E. coli	Peptide or		endotoxin
treatment	0111: B4 LPS	buffer	Total mice	shock
0	3 μg	PBS	5	5 (100%)
20 mg	3 μg	PBS	12	0 (0%)
20 mg	3 μg	SEQ ID 1	12	6 (50%)

[0103]

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 μg in 0.1 ml PBS). Peptide (200 μg/mouse = 8 mg/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.
	E. coli 0111: B4	Number
Peptide Treatment	LPS added	of Mice	Survival (%)
Control (no peptide)	2 μg	5	0
SEQ ID 6	2 μg	5	40
SEQ ID 13	2 μg	5	20
SEQ ID 17	2 μg	5	40
SEQ ID 24	2 μg	5	0
SEQ ID 27	2 μg	5	20

[0104]

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 μg in 0.1 ml PBS).
Peptide (200 μg/mouse = 8 mg/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.
	E. coli
Peptide Treatment	0111:B4 LPS added	Number of Mice	Survival (%)
No peptide	2 μg	10	10
SEQ ID 1	2 μg	6	17
SEQ ID 3	2 μg	6	0
SEQ ID 5	2 μg	6	17
SEQ ID 6	2 μg	6	17
SEQ ID 12	2 μg	6	17
SEQ ID 13	2 μg	6	33
SEQ ID 15	2 μg	6	0
SEQ ID 16	2 μg	6	0
SEQ ID 17	2 μg	6	17
SEQ ID 23	2 μg	6	0
SEQ ID 24	2 μg	6	17
SEQ ID 26	2 μg	6	0
SEQ ID 27	2 μg	6	50
SEQ ID 29	2 μg	6	0
SEQ ID 37	2 μg	6	0
SEQ ID 38	2 μg	6	0
SEQ ID 41	2 μg	6	0
SEQ ID 44	2 μg	6	0
SEQ ID 45	2 μg	6	0

[0105]

TABLE 13
Protection against lethal endotoxaemia in BALB/c mice by SEQ
ID 1. BALB/c mice were injected intraperitoneal with 400 μg E. coli
0111:B4 LPS. Peptide (200 μg/mouse = 8 mg/kg) was injected at a
separate intraperitoneal site and the mice were monitored
for 48 hours and the results were recorded.
	E. coli
Peptide Treatment	0111:B4 LPS	Number of Mice	Survival (%)
No peptide	400 μg	5	0
SEQ ID 1	400 μg	5	100

[0106]

TABLE 14
Peptide inhibition of TNF-α production induced by S. aureus
LTA. RAW 264.7 mouse macrophage cells were stimulated with 1
μg/ml S. aureus LTA in the absence and presence of increasing
concentrations of peptide. The supernatant was collected and tested for
levels of TNF-α by ELISA. Background levels of TNF-α production
by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in
TNF- α levels ranging from 0.037-0.192 ng/ml. The data is
presented as the mean of three or more experiments + standard error.
SEQ ID 1 added (μg/ml) Inhibition of TNF-α (%)
0.1                    44.5 ± 12.5
1                      76.7 ± 6.4
5                      91 ± 1
10                     94.5 ± 1.5
20                     96 ± 1

[0107]

TABLE 15
Peptide inhibition of TNF-α production induced by
Mycobacterium non-capped lipoarabinomannan. RAW 264.7 mouse
macrophage cells were stimulated with 1 μg/ml AraLAM in the
absence and presence of 20 μg/ml peptide or Polymyxin B. The
supernatant was collected and tested for levels of TNF-α by
ELISA. Background levels of TNF-α production by the RAW 264.7
cells cultured with no stimuli for 6 hours resulted in TNF-α 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 μg/ml) Inhibition of TNF-α (%)
No peptide         0
SEQ ID 1           64 ± 5.9
Polymyxin B        15 ± 2

EXAMPLE 3

Assessment of Toxicity of the Cationic Peptides

[0108] 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 calorimetric 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, OD490nm (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 μg 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 calorimetric 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 [3H]-thymidine incorporation assay). In this assay, HBE cells were incubated with 100 μg of peptide for 24 hours, and then 10 μl/well 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, OD490 nm.

[0109] 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.

TABLE 16
Toxicity of the Cationic Peptides as Measured by the LDH
Release Assay. Human HBE bronchial epithelial cells were incubated
with 100 μg/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.
Treatment            LDH Release (OD490 nm)
No cells Control     0.6 ± 0.1
Triton X-100 Control 4.6 ± 0.1
No peptide control   1.0 ± 0.05
SEQ ID 1             1.18 ± 0.05
SEQ ID 3             1.05 ± 0.04
SEQ ID 6             0.97 ± 0.02
SEQ ID 7             1.01 ± 0.04
SEQ ID 9             1.6 ± 0.03
SEQ ID 10            1.04 ± 0.04
SEQ ID 13            0.93 ± 0.06
SEQ ID 14            0.99 ± 0.05
SEQ ID 16            0.91 ± 0.04
SEQ ID 17            0.94 ± 0.04
SEQ ID 19            1.08 ± 0.02
SEQ ID 20            1.05 ± 0.03
SEQ ID 21            1.06 ± 0.04
SEQ ID 22            1.29 ± 0.12
SEQ ID 23            1.26 ± 0.46
SEQ ID 24            1.05 ± 0.01
SEQ ID 26            0.93 ± 0.04
SEQ ID 27            0.91 ± 0.04
SEQ ID 28            0.96 ± 0.06
SEQ ID 29            0.99 ± 0.02
SEQ ID 31            0.98 ± 0.03
SEQ ID 33            1.03 ± 0.05
SEQ ID 34            1.02 ± 0.03
SEQ ID 35            0.88 ± 0.03
SEQ ID 36            0.85 ± 0.04
SEQ ID 37            0.96 ± 0.04
SEQ ID 38            0.95 ± 0.02
SEQ ID 40            2.8 ± 0.5
SEQ ID 41            3.3 ± 0.2
SEQ ID 42            3.4 ± 0.2
SEQ ID 43            4.3 ± 0.2
SEQ ID 44            0.97 ± 0.03
SEQ ID 45            0.98 ± 0.04
SEQ ID 47            1.05 ± 0.05
SEQ ID 48            0.95 ± 0.05
SEQ ID 53            1.03 ± 0.06
Polymyxin B          1.21 ± 0.03

[0110]

TABLE 17
Toxicity of the Cationic Peptides as Measured by the WST-1 Assay.
HBE cells were incubated with 100 μg/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.
Treatment            OD490 nm
No cells Control     0.24 ± 0.01
Triton X-100 Control 0.26 ± 0.01
No peptide control   1.63 ± 0.16
SEQ ID 1             1.62 ± 0.34
SEQ ID 3             1.35 ± 0.12
SEQ ID 10            1.22 ± 0.05
SEQ ID 6             1.81 ± 0.05
SEQ ID 7             1.78 ± 0.10
SEQ ID 9             1.69 ± 0.29
SEQ ID 13            1.23 ± 0.11
SEQ ID 14            1.25 ± 0.02
SEQ ID 16            1.39 ± 0.26
SEQ ID 17            1.60 ± 0.46
SEQ ID 19            1.42 ± 0.15
SEQ ID 20            1.61 ± 0.21
SEQ ID 21            1.28 ± 0.07
SEQ ID 22            1.33 ± 0.07
SEQ ID 23            1.14 ± 0.24
SEQ ID 24            1.27 ± 0.16
SEQ ID 26            1.42 ± 0.11
SEQ ID 27            1.63 ± 0.03
SEQ ID 28            1.69 ± 0.03
SEQ ID 29            1.75 ± 0.09
SEQ ID 31            1.84 ± 0.06
SEQ ID 33            1.75 ± 0.21
SEQ ID 34            0.96 ± 0.05
SEQ ID 35            1.00 ± 0.08
SEQ ID 36            1.58 ± 0.05
SEQ ID 37            1.67 ± 0.02
SEQ ID 38            1.83 ± 0.03
SEQ ID 40            0.46 ± 0.06
SEQ ID 41            0.40 ± 0.01
SEQ ID 42            0.39 ± 0.08
SEQ ID 43            0.46 ± 0.10
SEQ ID 44            1.49 ± 0.39
SEQ ID 45            1.54 ± 0.35
SEQ ID 47            1.14 ± 0.23
SEQ ID 48            0.93 ± 0.08
SEQ ID 53            1.51 ± 0.37
Polymyxin B          1.30 ± 0.13

EXAMPLE 4

[0111] Polynucleotide Regulation by Cationic Peptides

[0112] 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 5.6×106 cells/dish, cultured overnight and then incubated with 50 μg/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, Tex.). The RNA was treated with DNaseI (Clontech, Palo Alto, Calif.) 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% ethanol7 and {fraction (1/10)}th 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 β-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.

[0113] Atlas cDNA Expression Arrays (Clontech, Palo Alto, Calif.), which consist of 588 selected mouse cDNAs spotted in duplicate on positively charged membranes were used for early polynucleotide array studies (Tables 18,19). 32P-radiolabeled CDNA probes prepared from 5 μg total RNA were incubated with the arrays overnight at 71° C. The filters were washed extensively and then exposed to a phosphoimager screen (Molecular Dynamics, Sunnyvale, Calif.) 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, Wash.). 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: β-actin, ubiquitin, ribosomal protein S29, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and Ca2+ binding protein. 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.

[0114] The next polynucleotide arrays used (Tables 21-26) were the Resgen Human cDNA arrays (identification number for the genome is PRHU03-S3), which consist of 7,458 human cDNAs spotted in duplicate. Probes were prepared from 15-20 μg of total RNA and labeled with Cy3 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 Virtek slide reader. The image processing software (Imagene 4.1, Marina Del Rey, Calif.) determines the spot mean intensity, median intensities, and background intensities. Normalization and analysis was performed with Genespring software (Redwood City, Calif.). 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.

[0115] 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 μg 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 2.5×106 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, Calif.) 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, Calif.). 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.

[0116] Semi-quantitative RT-PCR was performed to confirm polynucleotide array results. 1 μg RNA samples were incubated with 1 μl oligodT (500 μg/ml) and 1 μl mixed dNTP stock at 1 mM, in a 12 μl volume with DEPC treated water at 65° C. for 5 min in a thermocycler. 4 μl 5×First Strand buffer, 2 μl 0.1M DTT, and 1 μl RNaseOUT recombinant ribonuclease inhibitor (40 units/μl) were added and incubated at 42° C. for 2 min, followed by the addition of 1 μl (200 units) of Superscript II (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 μM), 0.2 mM dNTP mixture, 1.5 mM MgCl, 1 U of Taq DNA polymerase (New England Biolabs, Missisauga, ON), and 1×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 β-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 β-actin amplification.

[0117] 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, TGFβ receptor 1, G-CSF receptor, and IFNγ 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 Etk1 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-1α, 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 migration 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 cellsa.
The cationic peptides at a concentration of 50 μg/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.
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.
Polynucleotide/		Unstimulated	Ratio peptide:	Accession
Protein	Polynucleotide Function	Intensity	Unstimulatedb	Number
Etk1	Tyrosine-protein kinase	20	43	M68513
	receptor
PDGFRB	Growth factor receptor	24	25	X04367
	Corticotropin releasing	20	23	X72305
	factor receptor
NOTCH4	proto-oncopolynucleotide	48	18	M80456
IL-1R2	Interleukin receptor	20	16	X59769
MCP-3	Chemokine	56	14	S71251
BMP-1	Bone	20	14	L24755
	morphopolynucleotidetic
	protein
Endothelin	Receptor	20	14	U32329
b receptor
c-ret	Oncopolynucleotide	20	13	X67812
	precursor
LIFR	Cytokine receptor	20	12	D26177
BMP-8a	Bone	20	12	M97017
	morphopolynucleotidetic
	protein
Zfp92	Zinc finger protein 92	87	11	U47104
MCSF	Macrophage colony	85	11	X05010
	stimulating factor 1
GCSFR	Granulocyte colony-	20	11	M58288
	stimulating factor receptor
IL-8RB	Chemokine receptor	112	10	D17630
IL-9R	Interleukin receptor	112	6	M84746
Cas	Crk-associated substrate	31	6	U48853
p58/GTA	Kinase	254	5	M58633
CASP2	Caspase precursor	129	5	D28492
IL-1β	Interleukin precursor	91	5	M15131
precursor
SPI2-2	Serine protease inhibitor	62	5	M64086
C5AR	Chemokine receptor	300	4	S46665
L-myc	Oncopolynucleotide	208	4	X13945
IL-10	Interleukin	168	4	M37897
p19ink4	cdk4 and cdk6 inhibitor	147	4	U19597
ATOH2	Atonal homolog 2	113	4	U29086
DNAse1	DNase	87	4	U00478
CXCR-4	Chemokine receptor	36	4	D87747
Cyclin D3	Cyclin	327	3	U43844
IL-7Rα	Interleukin receptor	317	3	M29697
POLA	DNA polymeraseα	241	3	D17384
Tie-2	Oncopolynucleotide	193	3	S67051
DNL1	DNA ligase I	140	3	U04674
BAD	Apoptosis protein	122	3	L37296
GADD45	DNA-damage-inducible	88	3	L28177
	protein
Sik	Src-related kinase	82	3	U16805
integrinα4	Integrin	2324	2	X53176
TGFβR1	Growth factor receptor	1038	2	D25540
LAMR1	Receptor	1001	2	J02870
Crk	Crk adaptor protein	853	2	S72408
ZFX	Chromosomal protein	679	2	M32309
Cyclin E1	Cylcin	671	2	X75888
POLD1	DNA polymerase subunit	649	2	Z21848
Vav	proto-oncopolynucleotide	613	2	X64361
YY (NF-	Transcription factor	593	2	L13968
E1)
JunD	Transcription factor	534	2	J050205
Csk	c-src kinase	489	2	U05247
Cdk7	Cyclin-dependent kinase	475	2	U11822
MLC1A	Myosin light subunit	453	2	M19436
	isoform
ERBB-3	Receptor	435	2	L47240
UBF	Transcription factor	405	2	X60831
TRAIL	Apoptosis ligand	364	2	U37522
LFA-1	Cell adhesion receptor	340	2	X14951
SLAP	Src-like adaptor protein	315	2	U29056
IFNGR	Interferon gamma receptor	308	2	M28233
LIM-1	Transcription factor	295	2	Z27410
ATF2	Transcription factor	287	2	S76657
FST	Follistatin precursor	275	2	Z29532
TIMP3	Protease inhibitor	259	2	L19622
RU49	Transcription factor	253	2	U41671
IGF-1Rα	Insulin-like growth factor	218	2	U00182
	receptor
Cyclin G2	Cyclin	214	2	U95826
fyn	Tyrosine-protein kinase	191	2	U70324
BMP-2	Bone	186	2	L25602
	morphopolynucleotidetic
	protein
Brn-3.2	Transcription factor	174	2	S68377
POU
KIF1A	Kinesin family protein	169	2	D29951
MRC1	Mannose receptor	167	2	Z11974
PAI2	Protease inhibitor	154	2	X19622
BKLF	CACCC Box-binding	138	2	U36340
	protein
TIMP2	Protease inhibitor	136	2	X62622
Mas	Proto-oncopolynucleotide	131	2	X67735
NURR-1	Transcription factor	129	2	S53744

[0118]

TABLE 19
Polynucleotides down-regulated by SEQ ID NO: 1 treatment of RAW
macrophage cellsa.
The cationic peptides at a concentration of 50 μg/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.
Polynucleotide/		Unstimulated	Ratio peptide:	Accession
Protein	Polynucleotide Function	Intensity	Unstimulated	Number
sodium channel	Voltage-gated ion channel	257	0.08	L36179
XRCC1	DNA repair protein	227	0.09	U02887
ets-2	Oncopolynucleotide	189	0.11	J04103
XPAC	DNA repair protein	485	0.12	X74351
EPOR	Receptor precursor	160	0.13	J04843
PEA 3	Ets-related protein	158	0.13	X63190
orphan receptor	Nuclear receptor	224	0.2	U11688
N-cadherin	Cell adhesion receptor	238	0.23	M31131
OCT3	Transcription factor	583	0.24	M34381
PLCβ	phospholipase	194	0.26	U43144
KRT18	Intermediate filament proteins	318	0.28	M11686
THAM	Enzyme	342	0.32	X58384
CD40L	CD40 ligand	66	0.32	X65453
CD86	T-lymphocyte antigen	195	0.36	L25606
oncostatin M	Cytokine	1127	0.39	D31942
PMS2 DNA	DNA repair protein	200	0.4	U28724
IGFBP6	Growth factor	1291	0.41	X81584
MIP-1β	Cytokine	327	0.42	M23503
ATBF1	AT motif-binding factor	83	0.43	D26046
nucleobindin	Golgi resident protein	367	0.43	M96823
bcl-x	Apoptosis protein	142	0.43	L35049
uromodulin	glycoprotein	363	0.47	L33406
IL-12 p40	Interleukin	601	0.48	M86671
MmRad52	DNA repair protein	371	0.54	Z32767
Tob1	Antiproliferative factor	956	0.5	D78382
Ung1	DNA repair protein	535	0.51	X99018
KRT19	Intermediate filament	622	0.52	M28698
	proteins
PLCγ	phospholipase	251	0.52	X95346
Integrin α6	Cell adhesion receptor	287	0.54	X69902
GLUT1	Glucose transporter	524	0.56	M23384
CTLA4	immunoglobin	468	0.57	X05719
	superfamily
FRA2	Fos-related antigen	446	0.57	X83971
MTRP	Lysosome-associated	498	0.58	U34259
	protein

[0119]

TABLE 20
Polynucleotide Expression changes in response to peptide, SEQ ID
NO: 1, could be confirmed by RT-PCR. RAW 264.7 macrophage cells
were incubated with 50 μg/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 β-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.
	Polynucleotide	Array Ratio-*	RT-PCR Ratio-*
	CXCR-4	4.0 ± 1.7	4.1 ± 0.9
	IL-8RB	9.5 ± 7.6	7.1 ± 1.4
	MCP-3	13.5 ± 4.4	4.8 ± 0.88
	IL-10	4.2 ± 2.1	16.6 ± 6.1
	CD14	0.9 ± 0.1	0.8 ± 0.3
	MIP-1B	0.42 ± 0.09	0.11 ± 0.04
	XRCC1	0.12 ± 0.01	0.25 ± 0.093
	MCP-1	Not on array	3.5 ± 1.4

[0120]

TABLE 21
Polynucleotides up-regulated by peptide treatment of A549 epithelial cellsa.
The cationic peptides at concentrations of 50 μg/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#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	Ratio Peptide: Unstimulated	Accession
Polynucleotide/Protein	Intensity	ID 2	ID 3	ID 19	ID 1	Number
IL-1 R antagonist homolog 1	0.00	3086	1856	870		AI167887
IL-10 R beta	0.53	2.5	1.6	1.9	3.1	AA486393
IL-11 R alpha	0.55	2.4	1.0	4.9	1.8	AA454657
IL-17 R	0.54	2.1	2.0	1.5	1.9	AW029299
TNF R superfamily, member 1B	0.28	18	3.0	15	3.6	AA150416
TNF R superfamily, member 5	33.71	3.0	0.02			H98636
(CD40LR)
TNF R superfamily, member 11b	1.00	5.3	4.50	0.8		AA194983
IL-8	0.55	3.6	17	1.8	1.1	AA102526
interleukin enhancer binding factor 2	0.75	1.3	2.3	0.8	4.6	AA894687
interleukin enhancer binding factor 1	0.41	2.7		5.3	2.5	R56553
cytokine inducible SH2-containing	0.03	33	44	39	46	AA427521
protein
IK cytokine, down-regulator of	0.50	3.1	2.0	1.7	3.3	R39227
HLA II
cytokine inducible SH2-containing	0.03	33	44	39	46	AA427521
Protein
IK cytokine, down-regulator of	0.50	3.1	2.0	1.7	3.3	R39227
HLA II
small inducible cytokine subfamily	1.00	3.9			2.4	AI922341
A (Cys-Cys), member 21
TGFB inducible early growth	0.90	2.4	2.1	0.9	1.1	AI473938
response 2
NK cell R	1.02	2.5	0.7	0.3	1.0	AA463248
CCR6	0.14	4.5	7.8	6.9	7.8	N57964
cell adhesion molecule	0.25	4.0	3.9	3.9	5.1	R40400
melanoma adhesion molecule	0.05	7.9	20	43	29.1	AA497002
CD31	0.59	2.7	3.1	1.0	1.7	R22412
integrin, alpha 2 (CD49B, alpha 2	1.00	0.9	2.4	3.6	0.9	AA463257
subunit of VLA-2 receptor
integrin, alpha 3 (antigen CD49C,	0.94	0.8	2.5	1.9	1.1	AA424695
alpha 3 subunit of VLA-3 receptor)
integrin, alpha E	0.01	180	120	28	81	AA425451
integrin, beta 1	0.47	2.1	2.1	7.0	2.6	W67174
integrin, beta 3	0.55	2.7	2.8	1.8	1.0	AA037229
integrin, beta 3	0.57	2.6	1.4	1.8	2.0	AA666269
integrin, beta 4	0.65	0.8	2.2	4.9	1.5	AA485668
integrin beta 4 binding protein	0.20	1.7	5.0	6.6	5.3	AI017019
calcium and integrin binding protein	0.21	2.8	4.7	9.7	6.7	AA487575
disintegrin and metalloproteinase	0.46	3.1		2.2	3.8	AA279188
domain 8
disintegrin and metalloproteinase	0.94	1.1	2.3	3.6	0.5	H59231
domain 9
disintegrin and metalloproteinase	0.49	1.5	2.1	3.3	2.2	AA043347
domain 10
disintegrin and metalloproteinase	0.44	1.9	2.3	2.5	4.6	H11006
domain 23
cadherin 1, type 1, E-cadherin	0.42	8.1	2.2	2.4	7.3	H97778
(epithelial)
cadherin 12, type 2 (N-cadherin 2)	0.11	13	26	9.5		AI740827
protocadherin 12	0.09	14.8	11.5	2.6	12.4	AI652584
protocadherin gamma subfamily C, 3	0.34	3.0	2.5	4.5	9.9	R89615
catenin (cadherin-associated	0.86	1.2	2.2	2.4		AA025276
protein), delta 1
laminin R 1 (67 kD, ribosomal	0.50	0.4	2.0	4.4	3.0	AA629897
protein SA)
killer cell lectin-like receptor	0.11	9.7	9.0	4.1	13.4	AA190627
subfamily C, member 2
killer cell lectin-like receptor	1.00	3.2	1.0	0.9	1.3	W93370
subfamily C, member 3
killer cell lectin-like receptor	0.95	2.3	1.7	0.7	1.1	AI433079
subfamily G, member 1
C-type lectin-like receptor-2	0.45	2.1	8.0	2.2	5.3	H70491
CSF 3 R	0.40	1.9	2.5	3.5	4.0	AA458507
macrophage stimulating 1 R	1.00	1.7	2.3	0.4	0.7	AA173454
BMP R type IA	0.72	1.9	2.8	0.3	1.4	W15390
formyl peptide receptor 1	1.00	3.1	1.4	0.4		AA425767
CD2	1.00	2.6	0.9	1.2	0.9	AA927710
CD36	0.18	8.2	5.5	6.2	2.5	N39161
vitamin D R	0.78	2.5	1.3	1.1	1.4	AA485226
Human proteinase activated R-2	0.54	6.1	1.9	2.2		AA454652
prostaglandin E receptor 3 (subtype	0.25	4.1	4.9	3.8	4.9	AA406362
EP3)
PDGF R beta polypeptide	1.03	2.5	1.0	0.5	0.8	R56211
VIP R 2	1.00	3.1			2.0	AI057229
growth factor receptor-bound	0.51	2.2	2.0	2.4	0.3	AA449831
protein 2
Mouse Mammary Turmor Virus	1.00	6.9		16		W93891
Receptor homolog
adenosine A2a R	0.41	3.1	1.8	4.0	2.5	N57553
adenosine A3 R	0.83	2.0	2.3	1.0	1.2	AA863086
T cell R delta locus	0.77	2.7	1.3		1.8	AA670107
prostaglandin E receptor 1 (subtype	0.65	7.2		6.0	1.5	AA972293
EP1)
growth factor receptor-bound	0.34		3.0	6.3	2.9	R24266
protein 14
Epstein-Barr virus induced	0.61	1.6	2.4		8.3	AA037376
polynucleotide 2
complement component receptor 2	0.22	26	4.5	2.6	18.1	AA521362
endothelin receptor type A	0.07	12	14	14	16	AA450009
v-SNARE R	0.56	11	12	1.8		AA704511
tyrosine kinase, non-receptor, 1	0.12	7.8	8.5	10	8.7	AI936324
receptor tyrosine kinase-like orphan	0.40	7.3	5.0	1.6	2.5	N94921
receptor 2
protein tyrosine phosphatase, non-	1.02	1.0	13.2	0.5	0.8	AA682684
receptor type 3
protein tyrosine phosphatase, non-	0.28	3.5	4.0	0.9	5.3	AA434420
receptor type 9
protein tyrosine phosphatase, non-	0.42	2.9	2.4	2.2	3.0	AA995560
receptor type 11
protein tyrosine phosphatase, non-	1.00	2.3	2.2	0.8	0.5	AA446259
receptor type 12
protein tyrosine phosphatase, non-	0.58	1.7	2.4	3.6	1.7	AA679180
receptor type 13
protein tyrosine phosphatase, non-	0.52	3.2	0.9	1.9	6.5	AI668897
receptor type 18
protein tyrosine phosphatase,	0.25	4.0	2.4	16.8	12.8	H82419
receptor type, A
protein tyrosine phosphatase,	0.60	3.6	3.2	1.6	1.0	AA045326
receptor type, J
protein tyrosine phosphatase,	0.73	1.2	2.8	3.0	1.4	R52794
receptor type, T
protein tyrosine phosphatase,	0.20	6.1	1.2	5.6	5.0	AA644448
receptor type, U
protein tyrosine phosphatase,	1.00	5.1			2.4	AA481547
receptor type, C-associated protein
phospholipase A2 receptor 1	0.45	2.8	2.2	1.9	2.2	AA086038
MAP kinase-activated protein	0.52	2.1	2.7	1.1	1.9	W68281
kinase 3
MAP kinase kinase 6	0.10	18	9.6		32	H07920
MAP kinase kinase 5	1.00	3.0	5.2	0.8	0.2	W69649
MAP kinase 7	0.09		11.5	12	33	H39192
MAP kinase 12	0.49	2.1	1.7	2.2	2.0	AI936909
G protein-coupled receptor 4	0.40	3.7	3.0	2.4	2.5	AI719098
G protein-coupled receptor 49	0.05		19	19	27	AA460530
G protein-coupled receptor 55	0.08	19	15	12		N58443
G protein-coupled receptor 75	0.26	5.2	3.1	7.1	3.9	H84878
G protein-coupled receptor 85	0.20	6.8	5.4	4.9	5.0	N62306
regulator of G-protein signalling 20	0.02	48	137	82		AI264190
regulator of G-protein signalling 6	0.27		3.7	8.9	10.6	R39932
BCL2-interacting killer (apoptosis-	1.00	1.9		5.2		AA291323
inducing)
apoptosis inhibitor 5	0.56	2.8	1.6	2.4	1.8	AI972925
caspase 6, apoptosis-related	0.79	0.7	2.6	1.3	2.8	W45688
cysteine protease
apoptosis-related protein PNAS-1	0.46	2.2	1.4	2.3	2.9	AA521316
caspase 8, apoptosis-related	0.95	2.2	1.0	0.6	2.0	AA448468
cysteine protease

[0121]

TABLE 22
Polynucleotides down-regulated by peptide treatment of A549 epithelial
cellsa.
The cationic peptides at concentrations of 50 μg/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	Ratio Peptide: Unstimulated	Accession
Polynucleotide/Protein	Intensity	ID 2	ID 3	ID 19	ID 1	Number
TLR 1	3.22	0.35	0.31	0.14	0.19	AI339155
TLR 2	2.09	0.52	0.31	0.48	0.24	T57791
TLR 5	8.01	0.12	0.39			N41021
TLR 7	5.03	0.13	0.11	0.20	0.40	N30597
TNF receptor-associated factor 2	0.82	1.22	0.45	2.50	2.64	T55353
TNF receptor-associated factor 3	3.15	0.15		0.72	0.32	AA504259
TNF receptor superfamily, member 12	4.17	0.59	0.24		0.02	W71984
TNF R superfamily, member 17	2.62		0.38	0.55	0.34	AA987627
TRAF and TNF receptor-associated	1.33	0.75	0.22	0.67	0.80	AA488650
protein
IL-1 receptor, type I	1.39	0.34	0.72	1.19	0.34	AA464526
IL-2 receptor, alpha	2.46	0.41	0.33	0.58		AA903183
IL-2 receptor, gamma (severe combined	3.34	0.30	0.24		0.48	N54821
immunodeficiency)
IL-12 receptor, beta 2	4.58	0.67	0.22			AA977194
IL-18 receptor 1	1.78	0.50	0.42	0.92	0.56	AA482489
TGF beta receptor III	2.42	0.91	0.24	0.41	0.41	H62473
leukotriene b4 receptor (chemokine	1.00		1.38	4.13	0.88	AI982606
receptor-like 1)
small inducible cytokine subfamily A	2.26	0.32		0.44	1.26	AA495985
(Cys-Cys), member 18
small inducible cytokine subfamily A	2.22	0.19	0.38	0.45	0.90	AI285199
(Cys-Cys), member 20
small inducible cytokine subfamily A	2.64	0.38	0.31	1.53		AA916836
(Cys-Cys), member 23
small inducible cytokine subfamily B	3.57	0.11	0.06	0.28	0.38	AI889554
(Cys-X-Cys), member 6 (granulocyte
chemotactic protein 2)
small inducible cytokine subfamily B	2.02	0.50	1.07	0.29	0.40	AA878880
(Cys-X-Cys), member 10
small inducible cytokine A3	2.84	1.79	0.32	0.35		AA677522
(homologous to mouse Mip-1a)
cytokine-inducible kinase	2.70	0.41	0.37	0.37	0.34	AA489234
complement component C1q receptor	1.94	0.46	0.58	0.51	0.13	AI761788
cadherin 11, type 2, OB-cadherin	2.00	0.23	0.57	0.30	0.50	AA136983
(osteoblast)
cadherin 3, type 1, P-cadherin	2.11	0.43	0.53	0.10	0.47	AA425217
(placental)
cadherin, EGF LAG seven-pass G-type	1.67	0.42	0.41	1.21	0.60	H39187
receptor 2, flamingo (Drosophila)
homolog
cadherin 13, H-cadherin (heart)	1.78	0.37	0.40	0.56	0.68	R41787
selectin L (lymphocyte adhesion	4.43	0.03	0.23	0.61		H00662
molecule 1)
vascular cell adhesion molecule 1	1.40	0.20	0.72	0.77	0.40	H16591
intercellular adhesion molecule 3	1.00	0.12	0.31	2.04	1.57	AA479188
integrin, alpha 1	2.42	0.41	0.26		0.56	AA450324
integrin, alpha 7	2.53	0.57	0.39	0.22	0.31	AA055979
integrin, alpha 9	1.16	0.86	0.05	0.01	2.55	AA865557
integrin, alpha 10	1.00	0.33	0.18	1.33	2.25	AA460959
integrin, beta 5	1.00	0.32	1.52	1.90	0.06	AA434397
integrin, beta 8	3.27	0.10	1.14	0.31	0.24	W56754
disintegrin and metalloproteinase	2.50	0.40	0.29	0.57	0.17	AI205675
domain 18
disintegrin-like and metalloprotease	2.11	0.32	0.63	0.47	0.35	AA398492
with thrombospondin type 1 motif, 3
disintegrin-like and metalloprotease	1.62	0.39	0.42	1.02	0.62	AI375048
with thrombospondin type 1 motif, 5
T-cell receptor interacting molecule	1.00	0.41	1.24	1.41	0.45	AI453185
diphtheria toxin receptor (heparin-	1.62	0.49	0.85	0.62	0.15	R45640
binding epidermal growth factor-like
growth factor)
vasoactive intestinal peptide receptor 1	2.31	0.43	0.31	0.23	0.54	H73241
Fc fragment of IgG, low affinity IIIb,	3.85	−0.20	0.26	0.76	0.02	H20822
receptor for (CD16)
Fc fragment of IgG, low affinity IIb,	1.63	0.27	0.06	1.21	0.62	R68106
receptor for (CD32)
Fc fragment of IgE, high affinity I,	1.78	0.43	0.00	0.56	0.84	AI676097
receptor for; alpha polypeptide
leukocyte immunoglobulin-like	2.25	0.44	0.05	0.38	0.99	N63398
receptor, subfamily A
leukocyte immunoglobulin-like	14.21			1.10	0.07	AI815229
receptor, subfamily B (with TM and
ITIM domains), member 3
leukocyte immunoglobulin-like	2.31	0.75	0.43	0.19	0.40	AA076350
receptor, subfamily B (with TM and
ITIM domains), member 4
leukocyte immunoglobulin-like	1.67	0.35	0.60	0.18	0.90	H54023
receptor, subfamily B
peroxisome proliferative activated	1.18	0.38	0.85	0.87	0.26	AI739498
receptor, alpha
protein tyrosine phosphatase, receptor	2.19	0.43		1.06	0.46	N49751
type, f polypeptide (PTPRF), interacting
protein (liprin), α1
protein tyrosine phosphatase, receptor	1.55	0.44	0.64	0.30	0.81	H74265
type, C
protein tyrosine phosphatase, receptor	2.08	0.23	0.37	0.56	0.48	AA464542
type, E
protein tyrosine phosphatase, receptor	2.27	0.02	0.44		0.64	AA464590
type, N polypeptide 2
protein tyrosine phosphatase, receptor	2.34	0.11	0.43	0.24	0.89	AI924306
type, H
protein tyrosine phosphatase, receptor-	1.59	0.63	0.34	0.72	0.35	AA476461
type, Z polypeptide 1
protein tyrosine phosphatase, non-	1.07	0.94	0.43	0.25	1.13	H03504
receptor type 21
MAP kinase 8 interacting protein 2	1.70	0.07	0.85	0.47	0.59	AA418293
MAP kinase kinase kinase 4	1.27	0.37	0.79	1.59	−5.28	AA402447
MAP kinase kinase kinase 14	1.00	0.34	0.66	2.10	1.49	W61116
MAP kinase 8 interacting protein 2	2.90	0.16	0.35	0.24	0.55	AI202738
MAP kinase kinase kinase 12	1.48	0.20	0.91	0.58	0.68	AA053674
MAP kinase kinase kinase kinase 3	2.21	0.45	0.20	1.03	0.41	AA043537
MAP kinase kinase kinase 6	2.62	0.37	0.38		0.70	AW084649
MAP kinase kinase kinase kinase 4	1.04	0.96	0.09	0.29	2.79	AA417711
MAP kinase kinase kinase 11	1.53	0.65	0.41	0.99	0.44	R80779
MAP kinase kinase kinase 10	1.32	1.23	0.27	0.50	0.76	H01340
MAP kinase 9	2.54	0.57	0.39	0.16	0.38	AA157286
MAP kinase kinase kinase 1	1.23	0.61	0.42	0.81	1.07	AI538525
MAP kinase kinase kinase 8	0.66	1.52	1.82	9.50	0.59	W56266
MAP kinase-activated protein kinase 3	0.52	2.13	2.68	1.13	1.93	W68281
MAP kinase kinase 2	0.84	1.20	3.35	0.02	1.31	AA425826
MAP kinase kinase kinase 7	1.00	0.97		1.62	7.46	AA460969
MAP kinase 7	0.09		11.45	11.80	33.43	H39192
MAP kinase kinase 6	0.10	17.83	9.61		32.30	H07920
regulator of G-protein signalling 5	3.7397	0.27	0.06	0.68	0.18	AA668470
regulator of G-protein signalling 13	1.8564	0.54	0.45	0.07	1.09	H70047
G protein-coupled receptor	1.04	1.84	0.16	0.09	0.96	R91916
G protein-coupled receptor 17	1.78	0.32	0.56	0.39	0.77	AI953187
G protein-coupled receptor kinase 7	2.62		0.34	0.91	0.38	AA488413
orphan seven-transmembrane receptor,	7.16	1.06	0.10	0.11	0.14	AI131555
chemokine related
apoptosis antagonizing transcription	1.00	0.28	2.50	1.28	0.19	AI439571
factor
caspase 1, apoptosis-related cysteine	2.83	0.44		0.33	0.35	T95052
protease (interleukin 1, beta,
convertase)
programmed cell death 8 (apoptosis-	1.00	1.07	0.35	1.94	0.08	AA496348
inducing factor)

[0122]

TABLE 23
Pro-inflammatory polynucleotides up-regulated by peptide treatment of
A549 cells.
The cationic peptides at concentrations of 50 μg/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#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.
	Unstim	Ratio Peptide: Unstimulated	Accession
Polynucleotide/Protein and function	Intensity	ID 2	ID 3	ID 19	ID 1	Number
IL-11 Rα; Receptor for pro-	0.55	2.39	0.98	4.85	1.82	AA454657
inflammatory cytokine, inflammation
IL-17 R; Receptor for IL-17, an inducer	0.54	2.05	1.97	1.52	1.86	AW029299
of cytokine production in epithelial cells
small inducible cytokine subfamily A,	1.00	3.88			2.41	AI922341
member 21; a chemokine
CD31; Leukocyte and cell to cell	0.59	2.71	3.13	1.01	1.68	R22412
adhesion (PECAM)
CCR6; Receptor for chemokine MIP-3α	0.14	4.51	7.75	6.92	7.79	N57964
integrin, alpha 2 (CD49B, alpha 2	1.00	0.89	2.44	3.62	0.88	AA463257
subunit of VLA-2 receptor; Adhesion to
leukocytes
integrin, alpha 3 (antigen CD49C, alpha	0.94	0.79	2.51	1.88	1.07	AA424695
3 subunit of VLA-3 receptor);
Leukocyte Adhesion
integrin, alpha E; Adhesion	0.01	179.33	120.12	28.48	81.37	AA425451
integrin, beta 4; Leukocyte adhesion	0.65	0.79	2.17	4.94	1.55	AA485668
C-type lectin-like receptor-2;Leukocyte	0.45	2.09	7.92	2.24	5.29	H70491
adhesion

[0123]

TABLE 24
Pro-inflammatory polynucleotides down-regulated by peptide treatment
of A549 cells.
The cationic peptides at concentrations of 50 μg/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#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.
	Unstim	Ratio Peptide:Unstimulated	Accession
Polynucleotide/Protein; Function	Intensity	ID 2	ID 3	ID 19	ID 1	Number
Toll-like receptor (TLR) 1; Response to gram	3.22	0.35	0.31	0.14	0.19	AI339155
positive bacteria
TLR 2; Response to gram positive bacteria and	2.09	0.52	0.31	0.48	0.24	T57791
yeast
TLR 5; May augment other TLR responses,	8.01	0.12	0.39			N41021
Responsive to flagellin
TLR 7: Putative host defence mechanism	5.03	0.13	0.11	0.20	0.40	N30597
TNF receptor-associated factor 2; Inflammation	0.82	1.22	0.45	2.50	2.64	T55353
TNF receptor-associated factor 3; Inflammation	3.15	0.15		0.72	0.32	AA504259
TNF receptor superfamily, member 12;	4.17	0.59	0.24		0.02	W71984
Inflammation
TNF R superfamily, member 17; Inflammation	2.62		0.38	0.55	0.34	AA987627
TRAF and TNF receptor-associated protein;	1.33	0.75	0.22	0.67	0.80	AA488650
TNF signalling
small inducible cytokine subfamily A, member	2.26	0.32		0.44	1.26	AA495985
18; Chemokine
small inducible cytokine subfamily A, member	2.22	0.19	0.38	0.45	0.90	AI285199
20; Chemokine
small inducible cytokine subfamily A, member	2.64	0.38	0.31	1.53		AA916836
23; Chemokine
small inducible cytokine subfamily B, member	3.57	0.11	0.06	0.28	0.38	AI889554
6 (granulocyte chemotactic protein); Chemokine
small inducible cytokine subfamily B, member	2.02	0.50	1.07	0.29	0.40	AA878880
10; Chemokine
small inducible cytokine A3 (homologous to	2.84	1.79	0.32	0.35		AA677522
mouse Mip-1α); Chemokine
IL-12 receptor, beta 2; Interleukin and	4.58	0.67	0.22			AA977194
Interferon receptor
IL-18 receptor 1; Induces IFN-γ	1.78	0.50	0.42	0.92	0.56	AA482489
selectin L (lymphocyte adhesion molecule 1);	4.43	0.03	0.23	0.61		H00662
Leukocyte adhesion
vascular cell adhesion molecule 1; Leukocyte	1.40	0.20	0.72	0.77	0.40	H16591
adhesion
intercellular adhesion molecule 3; Leukocyte	1.00	0.12	0.31	2.04	1.57	AA479188
adhesion
integrin, alpha 1; Leukocyte adhesion	2.42	0.41	0.26		0.56	AA450324

[0124]

TABLE 25
Anti-inflammatory polynucleotides up-regulated by peptide treatment of
A549 cells.
The cationic peptides at concentrations of 50 μg/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#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.
	Unstim	Ratio Peptide: Unstimulated	Accession
Polynucleotide/Protein; Function	Intensity	ID 2	ID 3	ID 19	ID 1	Number
IL-1 R antagonist homolog 1; Inhibitor of septic	0.00	3085.96	1855.90	869.57		AI167887
shock
IL-10 R beta; Receptor for cytokine synthesis	0.53	2.51	1.56	1.88	3.10	AA486393
inhibitor
TNF R, member 1B; Apoptosis	0.28	17.09	3.01	14.93	3.60	AA150416
TNF R, member 5; Apoptosis (CD40L)	33.71	2.98	0.02			H98636
TNF R, member 11b; Apoptosis	1.00	5.29	4.50	0.78		AA194983
IK cytokine, down-regulator of HLA II; Inhibits	0.50	3.11	2.01	1.74	3.29	R39227
antigen presentation
TGFB inducible early growth response 2; anti-	0.90	2.38	2.08	0.87	1.11	AI473938
inflammatory cytokine
CD2; Adhesion molecule, binds LFAp3	1.00	2.62	0.87	1.15	0.88	AA927710

[0125]

TABLE 26
Anti-inflammatory polynucleotides down-regulated by peptide treatment
of A549 cells.
The cationic peptides at concentrations of 50 μg/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#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.
	Unstim	Ratio Peptide: Unstimulated	Accession
Polynucleotide/Protein; Function	Intensity	ID 2	ID 3	ID 19	ID 1	Number
MAP kinase 9	2.54	0.57	0.39	0.16	0.38	AA157286

[0126]

TABLE 27
Polynucleotides up-regulated by SEQ ID NO: 6, in primary human
macrophages. The peptide SEQ ID NO: 6 at a concentration of 50
μg/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.
		Ratio
	Control:	peptide
	Unstimulated	treated:
Gene (Accession Number)	cells	control
proteoglycan 2 (Z26248)	0.69	9.3
Unknown (AK001843)	26.3	8.2
phosphorylase kinase alpha 1 (X73874)	0.65	7.1
actinin, alpha 3 (M86407)	0.93	6.9
DKFZP586B2420 protein (AL050143)	0.84	5.9
Unknown (AL109678)	0.55	5.6
transcription factor 21 (AF047419)	0.55	5.4
Unknown (A433612)	0.62	5.0
chromosome condensation 1-like (AF060219)	0.69	4.8
Unknown (AL137715)	0.66	4.4
apoptosis inhibitor 4 (U75285)	0.55	4.2
TERF1 (TRF1)-interacting nuclear factor 2	0.73	4.2
(NM_012461)
LINE retrotransposable element 1 (M22333)	6.21	4.0
1-acylglycerol-3-phosphate O-acyltransferase 1	0.89	4.0
(U56417)
Vacuolar proton-ATPase, subunit D; V-	1.74	4.0
ATPase, subunit D (X71490)
KIAA0592 protein (AB011164)	0.70	4.0
potassium voltage-gated channel KQT-like	0.59	3.9
subfamily member 4 (AF105202)
CDC14 homolog A (AF000367)	0.87	3.8
histone fold proteinCHRAC17 (AF070640)	0.63	3.8
Cryptochrome 1 (D83702)	0.69	3.8
pancreatic zymogen granule membrane
associated protein (AB035541)	0.71	3.7
Sp3 transcription factor (X68560)	0.67	3.6
hypothetical protein FLJ20495 (AK000502)	0.67	3.5
E2F transcription factor 5, p130-binding	0.56	3.5
(U31556)
hypothetical protein FLJ20070 (AK000077)	1.35	3.4
glycoprotein IX (X52997)	0.68	3.4
KIAA1013 protein (AB023230)	0.80	3.4
eukaryotic translation initiation factor 4A,	2.02	3.4
isoform 2 (AL137681)
FYN-binding protein (AF198052)	1.04	3.3
guanine nucleotide binding protein, gamma	0.80	3.3
transducing activity polypeptide 1 (U41492)
glypican 1 (X54232)	0.74	3.2
mucosal vascular addressin cell adhesion	0.65	3.2
molecule 1 (U43628)
lymphocyte antigen (M38056)	0.70	3.2
H1 histone family, member 4 (M60748)	0.81	3.0
translational inhibitor protein p14.5 (X95384)	0.78	3.0
hypothetical protein FLJ20689 (AB032978)	1.03	2.9
KIAA1278 protein (AB03104)	0.80	2.9
unknown (AL031864)	0.95	2.9
chymotrypsin-like protease (X71877)	3.39	2.9
calumenin (NM_001219)	2.08	2.9
protein kinase, cAMP-dependent, regulatory,	7.16	2.9
type I, beta (M65066)	7.16	2.9
POU domain, class 4, transcription factor 2	0.79	2.8
(U06233)
POU domain, class 2, associating factor 1	1.09	2.8
(Z49194)
KIAA0532 protein (AB011104)	0.84	2.8
unknown (AF068289)	1.01	2.8
unknown (AL117643)	0.86	2.7
cathepsin E (M84424)	15.33	2.7
matrix metalloproteinase 23A (AF056200)	0.73	2.7
interferon receptor 2 (L42243)	0.70	2.5
MAP kinase kinase 1 (L11284)	0.61	2.4
protein kinase C, alpha (X52479)	0.76	2.4
c-Cbl-interacting protein (AF230904)	0.95	2.4
c-fos induced growth factor (Y12864)	0.67	2.3
cyclin-dependent kinase inhibitor 1B (S76988)	0.89	2.2
zinc finger protein 266 (X78924)	1.67	2.2
MAP kinase 14 (L35263)	1.21	2.2
KIAA0922 protein (AB023139)	0.96	2.1
bone morphogenetic protein 1 (NM_006129)	1.10	2.1
NADH dehydrogenase 1 alpha subcomplex, 10	1.47	2.1
(AF087661)
bone morphogenetic protein receptor, type IB	0.50	2.1
(U89326)
interferon regulatory factor 2 (NM 002199)	1.46	2.0
protease, serine, 21 (AB031331)	0.89	2.0

[0127]

TABLE 28
Polynucleotides down-regulated by SEQ ID NO: 6,
in primary human macrophages.
The peptide SEQ ID NO: 6 at a concentration of 50 μg/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 of Peptide: Control” columns refer to the
intensity of polynucleotide expression in peptide-simulated cells
divided by the intensity of unstimulated cells.
		Ratio
	Control:	peptide
	Unstimulated	treated:
Gene (Accession Number)	cells	control
Unknown (AL049263)	17	0.06
integrin-linked kinase (U40282)	2.0	0.13
KIAA0842 protein (AB020649)	1.1	0.13
Unknown (AB037838)	13	0.14
Granulin (AF055008)	8.6	0.14
glutathione peroxidase 3 (NM_002084)	1.2	0.15
KIAA0152 gene product (D63486)	0.9	0.17
TGFB1-induced anti-apoptotic factor 1 (D86970)	0.9	0.19
disintegrin protease (Y13323)	1.5	0.21
proteasome subunit beta type 7 (D38048)	0.7	0.22
cofactor required for Sp1 transcriptional	0.9	0.23
activation subunit 3 (AB033042)
TNF receptor superfamily, member 14 (U81232)	0.8	0.26
proteasome 26S subunit non-ATPase 8 (D38047)	1.1	0.28
proteasome subunit beta type, 4 (D26600)	0.7	0.29
TNF receptor superfamily member 1B (M32315)	1.7	0.29
cytochrome c oxidase subunit Vic (X13238)	3.3	0.30
S100 calcium-binding protein A4 (M80563)	3.8	0.31
proteasome subunit alpha type, 6 (X59417)	2.9	0.31
proteasome 26S subunit non-ATPase, 10	1.0	0.32
(AL031177)
MAP kinase kinase kinase 2 (NM_006609)	0.8	0.32
ribosomal protein L11 (X79234)	5.5	0.32
matrix metalloproteinase 14 (Z48481)	1.0	0.32
proteasome subunit beta type, 5 (D29011)	1.5	0.33
MAP kinase-activated protein kinase 2 (U12779)	1.5	0.34
caspase 3 (U13737)	0.5	0.35
jun D proto-oncogene (X56681)	3.0	0.35
proteasome 26S subunit, ATPase, 3 (M34079)	1.3	0.35
IL-1 receptor-like 1 (AB012701)	0.7	0.35
interferon alpha-inducible protein (AB019565)	13	0.35
SDF receptor 1 (NM_012428)	1.6	0.35
Cathepsin D (M63138)	46	0.36
MAP kinase kinase 3 (D87116)	7.4	0.37
TGF, beta-induced, (M77349)	1.8	0.37
TNF receptor superfamily, member 10b	1.1	0.37
(AF016266)
proteasome subunit beta type, 6 (M34079)	1.3	0.38
nuclear receptor binding protein (NM_013392)	5.2	0.38
Unknown (AL050370)	1.3	0.38
protease inhibitor 1 alpha-1-antitrypsin (X01683)	0.7	0.40
proteasome subunit alpha type, 7 (AF054185)	5.6	0.40
LPS-induced TNF-alpha factor (NM_004862)	5.3	0.41
transferrin receptor (X01060)	14	0.42
proteasome 26S subunit non-ATPase 13	1.8	0.44
(AB009398)
MAP kinase kinase 5 (U25265)	1.3	0.44
Cathepsin L (X12451)	15	0.44
IL-1 receptor-associated kinase 1 (L76191)	1.7	0.45
MAP kinase kinase kinase kinase 2 (U07349)	1.1	0.46
peroxisome proliferative activated receptor delta	2.2	0.46
(AL022721)
TNF superfamily, member 15 (AF039390)	16	0.46
defender against cell death 1 (D15057)	3.9	0.46
TNF superfamily member 10 (U37518)	287	0.46
cathepsin H (X16832)	14	0.47
protease inhibitor 12 (Z81326)	0.6	0.48
proteasome subunit alpha type, 4 (D00763)	2.6	0.49
proteasome 26S subunit ATPase, 1 (L02426)	1.8	0.49
proteasome 26S subunit ATPase, 2 (D11094)	2.1	0.49
caspase 7 (U67319)	2.4	0.49
matrix metalloproteinase 7 (Z11887)	2.5	0.49

[0128]

TABLE 29
Polynucleotides up-regulated by SEQ ID NO: 1, in HBE cells.
The peptide SEQ ID NO: 1 at a concentration of 50 μg/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 (PRHU04). 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.
		Control:
Accession		Unstimulated	Ratio peptide
Number	Gene	cells	treated: control
AL110161	Unknown	0.22	5218.3
AF131842	Unknown	0.01	573.1
AJ000730	solute carrier family	0.01	282.0
Z25884	chloride channel 1	0.01	256.2
M93426	protein tyrosine phosphatase receptor-	0.01	248.7
	type, zeta
X65857	olfactory receptor, family 1, subfamily	0.01	228.7
	D, member 2
M55654	TATA box binding protein	0.21	81.9
AK001411	hypothetical protein	0.19	56.1
D29643	dolichyl-diphosphooligosaccharide-	1.56	55.4
	protein glycosyltransferase
AF006822	myelin transcription factor 2	0.07	55.3
AL117601	Unknown	0.05	53.8
AL117629	DKFZP434C245 protein	0.38	45.8
M59465	tumor necrosis factor, alpha-induced	0.50	45.1
	protein 3
AB013456	aquaporin 8	0.06	41.3
AJ131244	SEC24 related gene family, member A	0.56	25.1
AL110179	Unknown	0.87	24.8
AB037844	Unknown	1.47	20.6
Z47727	polymerase II polypeptide K	0.11	20.5
AL035694	Unknown	0.81	20.4
X68994	H.sapiens CREB gene	0.13	19.3
AJ238379	hypothetical protein	1.39	18.5
NM_003519	H2B histone family member	0.13	18.3
U16126	glutamate receptor, ionotropic kainate 2	0.13	17.9
U29926	adenosine monophosphate deaminase	0.16	16.3
AK001160	hypothetical protein	0.39	14.4
U18018	ets variant gene 4	0.21	12.9
D80006	KIAA0184 protein	0.21	12.6
AK000768	hypothetical protein	0.30	12.3
X99894	insulin promoter factor 1,	0.26	12.0
AL031177	Unknown	1.09	11.2
AF052091	unknown	0.28	10.9
L38928	5,10-methenyltetrahydrofolate	0.22	10.6
	synthetase
AL117421	unknown	0.89	10.1
AL133606	hypothetical protein	0.89	9.8
NM_016227	membrane protein CH1	0.28	9.6
NM_006594	adaptor-related protein complex 4	0.39	9.3
U54996	ZW10 homolog, protein	0.59	9.3
AJ007557	potassium channel,	0.28	9.0
AF043938	muscle RAS oncogene	1.24	8.8
AK001607	unknown	2.74	8.7
AL031320	peroxisomal biogenesis factor 3	0.31	8.4
D38024	unknown	0.31	8.3
AF059575	LIM homeobox TF	2.08	8.2
AF043724	hepatitis A virus cellular receptor 1	0.39	8.1
AK002062	hypothetical protein	2.03	8.0
L13436	natriuretic peptide receptor	0.53	7.8
U33749	thyroid transcription factor 1	0.36	7.6
AF011792	cell cycle progression 2 protein	0.31	7.6
AK000193	hypothetical protein	1.18	6.8
AF039022	exportin, tRNA	0.35	6.8
M17017	interleukin 8	0.50	6.7
AF044958	NADH dehydrogenase	0.97	6.5
U35246	vacuolar protein sorting	0.48	6.5
AK001326	tetraspan 3	1.59	6.5
M55422	Krueppel-related zinc finger protein	0.34	6.4
U44772	palmitoyl-protein thioesterase	1.17	6.3
AL117485	hypothetical protein	0.67	5.9
AB037776	unknown	0.75	5.7
AF131827	unknown	0.69	5.6
AL137560	unknown	0.48	5.2
X05908	annexin A1	0.81	5.1
X68264	melanoma adhesion molecule	0.64	5.0
AL161995	neurturin	0.86	4.9
AF037372	cytochrome c oxidase	0.48	4.8
NM_016187	bridging integrator 2	0.65	4.8
AL137758	unknown	0.57	4.8
U59863	TRAF family member-associated NFKB	0.46	4.7
	activator
Z30643	chloride channel Ka	0.70	4.7
D16294	acetyl-Coenzyme A acyltransferase 2	1.07	4.6
AJ132592	zinc finger protein 281	0.55	4.6
X82324	POU domain TF	1.73	4.5
NM_016047	CGI-110 protein	1.95	4.5
AK001371	hypothetical protein	0.49	4.5
M60746	H3 histone family member D	3.05	4.5
AB033071	hypothetical protein	4.47	4.4
AB002305	KIAA0307 gene product	1.37	4.4
X92689	UDP-N-acetyl-alpha-D-	0.99	4.4
	galactosamine: polypeptide N-
	acetylgalactosaminyltransferase 3
AL049543	glutathione peroxidase 5	1.62	4.3
U43148	patched homolog	0.96	4.3
M67439	dopamine receptor D5	2.61	4.2
U09850	zinc finger protein 143	0.56	4.2
L20316	glucagon receptor	0.75	4.2
AB037767	a disintegrin-like and metalloprotease	0.69	4.2
NM_017433	myosin IIIA	99.20	4.2
D26579	a disintegrin and metalloprotease	0.59	4.1
	domain 8
L10333	reticulon 1	1.81	4.1
AK000761	unknown	1.87	4.1
U91540	NK homeobox family 3, A	0.80	4.1
Z17227	interleukin 10 receptor, beta	0.75	4.0

[0129]

TABLE 30
Polynucleotides down-regulated by Peptide (50 μg/ml), SEQ ID NO: 1, in
HBE cells.
The peptide SEQ ID NO: 1 at a concentration of 50 μg/ml was shown to
decrease 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 hybridized to Human Operon
arrays (PRHU04). The intensity of polynucleotides in unstimulated cells
in shown is 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.
		Control:	Ratio of SEQ
Accession		Unstimulated	ID NO: 1-
Number	Gene	Cells	treated: control
AC004908	Unknown	32.4	0.09
S70622	G1 phase-specific gene	43.1	0.10
Z97056	DEAD/H box polypeptide	12.8	0.11
AK002056	hypothetical protein	11.4	0.12
L33930	CD24 antigen	28.7	0.13
X77584	thioredoxin	11.7	0.13
NM_014106	PRO1914 protein	25.0	0.14
M37583	H2A histone family member	22.2	0.14
U89387	polymerase (RNA) II polypeptide D	10.2	0.14
D25274	ras-related C3 botulinum toxin substrate 1	10.3	0.15
J04173	phosphoglycerate mutase 1	11.4	0.15
U19765	zinc finger protein 9	8.9	0.16
X67951	proliferation-associated gene A	14.1	0.16
AL096719	profilin 2	20.0	0.16
AF165217	tropomodulin 4	14.6	0.16
NM_014341	mitochondrial carrier homolog 1	11.1	0.16
AL022068	Unknown	73.6	0.17
X69150	ribosomal protein S18	42.8	0.17
AL031577	Unknown	35.0	0.17
AL031281	Unknown	8.9	0.17
AF090094	Human mRNA for ornithine decarboxylase	10.3	0.17
	antizyme,
AL022723	HLA-G histocompatibility antigen, class I, G	20.6	0.18
U09813	ATP synthase, H+ transporting mitochondrial	9.8	0.18
	F0 complex
AF000560	Homo sapiens TTF-I interacting peptide 20	20.2	0.19
NM_016094	HSPC042 protein	67.2	0.19
AF047183	NADH dehydrogenase	7.5	0.19
D14662	anti-oxidant protein 2 (non-selenium glutathione	8.1	0.19
	peroxidase, acidic calcium-independent
	phospholipas
X16662	annexin A8	8.5	0.19
U14588	paxillin	11.3	0.19
AL117654	DKFZP586D0624 protein	12.6	0.20
AK001962	hypothetical protein	7.7	0.20
L41559	6-pyruvoyl-tetrahydropterin	9.1	0.20
	synthase/dimerization cofactor of hepatocyte
	nuclear factor 1 alpha
NM_016139	16.7 Kd protein	21.0	0.21
NM_016080	CGI-150 protein	10.7	0.21
U86782	26S proteasome-associated pad1 homolog	6.7	0.21
AJ400717	tumor protein, translationally-controlled 1	9.8	0.21
X07495	homeo box C4	31.0	0.21
AL034410	Unknown	7.3	0.22
X14787	thrombospondin 1	26.2	0.22
AF081192	purine-rich element binding protein B	6.8	0.22
D49489	protein disulfide isomerase-related protein	11.0	0.22
NM_014051	PTD011 protein	9.3	0.22
AK001536	Unknown	98.0	0.22
X62534	high-mobility group protein 2	9.5	0.22
AJ005259	endothelial differentiation-related factor 1	6.7	0.22
NM_000120	epoxide hydrolase 1, microsomal	10.0	0.22
M38591	S100 calcium-binding protein A10	23.9	0.23
AF071596	immediate early response 3	11.5	0.23
X16396	methylene tetrahydrofolate dehydrogenase	8.3	0.23
AK000934	ATPase inhibitor precursor	7.6	0.23
AL117612	Unknown	10.7	0.23
AF119043	transcriptional intermediary factor 1 gamma	7.3	0.23
AF037066	solute carrier family 22 member 1-like antisense	7.6	0.23
AF134406	cytochrome c oxidase subunit	13.3	0.23
AE000661	Unknown	9.2	0.24
AL157424	synaptojanin 2	7.2	0.24
X56468	tyrosine 3-monooxygenase/tryptophan 5-	7.2	0.24
	monooxygenase activation protein,
U39318	ubiquitin-conjugating enzyme E2D 3	10.7	0.24
AL034348	Unknown	24.4	0.24
D26600	proteasome subunit beta type 4	11.4	0.24
AB032987	Unknown	16.7	0.24
J04182	lysosomal-associated membrane protein 1	7.4	0.24
X78925	zinc finger protein 267	16.1	0.25
NM_000805	gastrin	38.1	0.25
U29700	anti-Mullerian hormone receptor, type II	12.0	0.25
Z98200	Unknown	13.4	0.25
U07857	signal recognition particle	10.3	0.25
L05096	Homo sapiens ribosomal protein L39	25.3	0.25
AK001443	hypothetical protein	7.5	0.25
K03515	glucose phosphate isomerase	6.2	0.25
X57352	interferon induced transmembrane protein 3	7.5	0.26
J02883	colipase pancreatic	5.7	0.26
M24069	cold shock domain protein	6.3	0.26
AJ269537	chondroitin-4-sulfotransferase	60.5	0.26
AL137555	Unknown	8.5	0.26
U89505	RNA binding motif protein 4	5.5	0.26
U82938	CD27-binding protein	7.5	0.26
X99584	SMT3 homolog 1	12.8	0.26
AK000847	Unknown	35.8	0.27
NM_014463	Lsm3 protein	7.8	0.27
AL133645	Unknown	50.8	0.27
X78924	zinc finger protein 266	13.6	0.27
NM_004304	anaplastic lymphoma kinase	15.0	0.27
X57958	ribosomal protein L7	27.9	0.27
U63542	Unknown	12.3	0.27
AK000086	hypothetical protein	8.3	0.27
X57138	H2A histone family member N	32.0	0.27
AB023206	KIAA0989 protein	6.5	0.27
AB021641	gonadotropin inducible transcriptn repressor-1,	5.5	0.28
AF050639	NADH dehydrogenase	5.5	0.28
M62505	complement component 5 receptor 1	7.5	0.28
X64364	basigin	5.8	0.28
AJ224082	Unknown	22.5	0.28
AF042165	cytochrome c oxidase	20.4	0.28
AK001472	anillin	10.9	0.28
X86428	protein phosphatase 2A subunit	12.7	0.28
AF227132	candidate taste receptor T2R5	5.1	0.28
Z98751	Unknown	5.3	0.28
D21260	clathrin heavy polypeptide	8.3	0.28
AF041474	actin-like 6	15.1	0.28
NM_005258	GTP cyclohydrolase I protein	7.6	0.28
L20859	solute carrier family 20	9.6	0.29
Z80783	H2B histone family member	9.0	0.29
AB011105	laminin alpha 5	7.1	0.29
AL008726	protective protein for beta-galactosidase	5.2	0.29
D29012	proteasome subunit	12.6	0.29
X63629	cadherin 3 P-cadherin	6.8	0.29
X02419	plasminogen activator urokinase	12.9	0.29
X13238	cytochrome c oxidase	8.0	0.29
X59798	cyclin D1	12.7	0.30
D78151	proteasome 26S subunit	7.6	0.31*
AF054185	proteasome subunit	18.8	0.31
J03890	surfactant pulmonary-associated protein C	5.5	0.32
M34079	proteasome 26S subunit,	5.2	0.33

[0130]

TABLE 31
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula A Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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.
Accession		control-	control-	ID 5:	ID 6:	ID 7:	ID 8:	ID 9:	ID 10:
Number	Gene	Cy3	Cy5	control	control	control	control	control	control
U12472	glutathione S-	0.09	0.31	13.0	3.5	4.5	7.0	4.3	16.4
	transferase
X66403	cholinergic	0.17	0.19	7.8	9.9	6.0	6.4	5.0	15.7
	receptor
AK001932	unknown	0.11	0.25	19.4	4.6	9.9	7.6	8.1	14.5
X58079	S100 calcium-	0.14	0.24	12.2	7.6	8.1	4.3	4.5	13.2
	binding protein
U18244	solute carrier	0.19	0.20	6.1	9.7	11.9	5.0	3.7	10.6
	family 1
U20648	zinc finger	0.16	0.13	5.3	6.2	5.6	3.1	6.8	9.5
	protein
AB037832	unknown	0.10	0.29	9.0	4.2	9.4	3.1	2.6	8.7
AC002542	unknown	0.15	0.07	10.5	15.7	7.8	10.1	11.7	8.2
M89796	membrane-	0.15	0.14	2.6	6.1	7.6	3.5	13.3	8.1
	spanning 4-
	domains,
	subfamily A
AF042163	cytochrome c	0.09	0.19	3.9	3.2	7.6	6.3	4.9	7.9
	oxidase
AL032821	Vanin 2	0.41	0.23	2.5	5.2	3.2	2.1	4.0	7.9
U25341	melatonin	0.04	0.24	33.1	5.1	23.3	6.6	4.1	7.6
	receptor 1B
U52219	G protein-	0.28	0.20	2.1	6.2	6.9	2.4	3.9	7.1
	coupled receptor
X04506	apolipoprotein B	0.29	0.32	7.9	3.4	3.3	4.8	2.6	7.0
AB011138	ATPase type IV	0.12	0.07	3.5	12.9	6.6	6.4	21.3	6.9
AF055018	unknown	0.28	0.22	3.8	6.9	5.0	2.3	3.1	6.8
AK002037	hypothetical	0.08	0.08	2.9	7.9	14.1	7.9	20.1	6.5
	protein
AK001024	guanine	0.16	0.11	7.7	11.9	5.0	10.3	6.0	6.3
	nucleotide-
	binding protein
AF240467	TLR-7	0.11	0.10	20.4	9.0	3.4	9.4	12.9	6.1
AF105367	glucagon-like	0.15	0.35	23.2	2.6	3.0	10.6	2.9	5.7
	peptide 2
	receptor
AL009183	TNFR	0.46	0.19	10.6	4.7	3.7	2.8	6.5	5.7
	superfamily,
	member 9
X54380	pregnancy-zone	0.23	0.08	4.7	11.9	7.2	12.7	3.8	5.5
	protein
AL137736	unknown	0.22	0.15	2.1	7.2	3.3	7.1	4.6	5.5
X05615	thyroglobulin	0.28	0.42	6.3	2.7	7.7	2.4	3.1	5.4
D28114	myelin-	0.24	0.08	2.5	15.9	13.0	7.1	13.7	5.4
	associated
	protein
AK000358	microfibrillar-	0.28	0.28	8.7	4.2	7.2	3.2	2.4	5.3
	associated
	protein 3
AK001351	unknown	0.12	0.22	3.9	7.6	8.7	3.9	2.3	5.2
U79289	unknown	0.14	0.27	2.5	2.7	2.8	2.0	4.3	5.1
AB014546	ring finger	0.12	0.34	6.8	2.4	4.1	2.7	2.0	5.0
	protein
AL117428	DKFZP434A236	0.10	0.07	2.8	16.1	12.8	9.7	14.2	4.9
	protein
AL050378	unknown	0.41	0.14	3.5	8.7	11.7	3.5	7.0	4.9
AJ250562	transmembrane	0.13	0.10	5.2	5.7	14.2	3.8	10.3	4.8
	4 superfamily
	member 2
NM_001756	corticosteroid	0.28	0.13	4.0	7.9	6.5	14.9	5.6	4.8
	binding globulin
AL137471	hypothetical	0.29	0.05	3.7	18.0	6.2	7.2	16.3	4.7
	protein
M19684	protease	0.41	0.14	3.5	4.6	5.4	2.8	9.4	4.7
	inhibitor 1
NM_001963	epidermal	0.57	0.05	3.4	6.2	1.8	32.9	14.7	4.4
	growth factor
NM_000910	neuropeptide Y	0.62	0.36	3.1	2.7	2.3	2.6	3.1	4.4
	receptor
AF022212	Rho GTPase	0.19	0.02	9.0	45.7	25.6	12.4	72.2	4.4
	activating
	protein 6
AK001674	cofactor required	0.11	0.13	8.4	6.5	7.9	4.5	7.4	4.3
	for Sp1
U51920	signal	0.23	0.27	3.4	3.8	2.1	4.1	8.8	4.2
	recognition
	particle
AK000576	hypothetical	0.27	0.06	4.4	14.7	7.4	14.1	8.6	4.2
	protein
AL080073	unknown	0.17	0.20	21.6	3.9	4.3	8.8	2.6	4.1
U59628	paired box gene 9	0.34	0.06	3.4	14.1	5.4	7.9	4.9	4.1
U90548	butyrophilin,	0.41	0.31	2.3	4.7	5.5	6.8	3.4	4.1
	subfamily 3,
	member A3
M19673	cystatin SA	0.43	0.26	2.3	8.5	4.5	2.5	4.1	3.8
AL161972	ICAM 2	0.44	0.37	2.0	3.6	2.0	2.7	5.5	3.8
X54938	inositol 1,4,5-	0.32	0.22	3.9	3.3	6.2	3.1	4.4	3.7
	trisphosphate 3-
	kinase A
AB014575	KIAA0675 gene	0.04	0.13	46.2	4.5	10.2	8.0	6.2	3.4
	product
M83664	MHC II, DP beta 1	0.57	0.29	2.9	2.1	2.0	3.1	6.6	3.4
AK000043	hypothetical	0.34	0.14	2.7	7.1	3.7	9.4	8.8	3.3
	protein
U60666	testis specific	0.21	0.11	9.9	9.0	4.1	5.5	13.0	3.3
	leucine rich
	repeat protein
AK000337	hypothetical	0.49	0.19	4.3	5.1	4.7	10.6	7.1	3.3
	protein
AF050198	putative	0.34	0.15	7.0	6.3	3.6	5.6	11.9	3.3
	mitochondrial
	space protein
AJ251029	odorant-binding	0.28	0.12	4.4	9.4	7.2	8.8	7.1	3.2
	protein 2A
X74142	forkhead box	0.12	0.33	19.5	4.5	8.4	6.4	4.4	3.2
	G1B
AB029033	KIAA1110	0.35	0.24	3.1	2.2	5.6	5.2	3.1	3.1
	protein
D85606	cholecystokinin	0.51	0.14	4.3	3.9	4.6	3.5	7.2	3.1
	A receptor
X84195	acylphosphatase	0.32	0.19	4.8	3.7	5.0	11.2	9.8	3.0
	2 muscle type
U57971	ATPase Ca++	0.29	0.13	2.2	7.9	1.8	6.3	4.8	3.0
	transporting
	plasma
	membrane 3
J02611	apolipoprotein D	0.28	0.10	2.8	11.0	3.7	10.3	8.4	3.0
AF071510	lecithin retinol	0.07	0.05	7.9	3.8	11.7	46.0	16.3	3.0
	acyltransferase
AF131757	unknown	0.10	0.08	4.8	9.0	44.3	9.3	10.7	3.0
L10717	IL2-inducible T-	0.45	0.21	2.5	4.9	2.8	10.9	4.5	2.9
	cell kinase
L32961	4-aminobutyrate	0.64	0.32	3.6	2.9	3.2	5.3	2.3	2.9
	aminotransferase
NM_003631	poly (ADP-	0.46	0.41	9.7	3.9	4.1	3.8	2.8	2.7
	ribose)
	glycohydrolase
AF098484	pronapsin A	0.28	0.14	3.7	3.7	5.6	11.6	3.7	2.5
NM_009589	arylsulfatase D	0.73	0.16	3.2	5.6	6.0	48.6	7.2	2.4
M14764	TNFR	0.49	0.15	2.3	3.5	10.6	13.6	6.8	2.2
	superfamily,
	member 16
AL035250	endothelin 3	0.52	0.14	2.1	7.3	4.8	4.5	3.7	2.2
M97925	defensin, alpha	0.33	0.07	4.0	14.7	7.8	9.4	3.5	2.1
	5, Paneth cell-
	specific
D43945	transcription	0.46	0.19	6.6	2.9	8.2	4.0	3.5	2.1
	factor EC
D16583	histidine	0.46	0.09	3.2	13.8	4.2	8.8	13.7	2.1
	decarboxylase

[0131]

TABLE 32
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula B Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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.
Accession			control-	ID 12:	ID 13:	ID 14:	ID 15:	ID 16:	ID 17:
Number	Gene	control-Cy3	Cy5	control	control	control	control	control	control
AL157466	unknown	0.05	0.06	18.0	21.4	16.7	5.2	6.8	8.6
AB023215	KIAA0998 protein	0.19	0.07	14.8	10.6	7.9	14.4	6.6	16.1
AL031121	unknown	0.24	0.09	14.1	5.7	3.8	5.5	2.8	4.6
NM_016331	zinc finger protein	0.16	0.08	12.8	7.2	11.0	5.3	11.2	9.7
M14565	cytochrome P450	0.16	0.12	10.6	12.5	5.0	3.6	10.1	6.3
U22492	G protein-coupled	0.28	0.07	10.4	8.9	4.8	10.8	6.6	3.6
	receptor 8
U76010	solute carrier	0.14	0.07	9.7	18.6	3.7	4.8	5.6	8.9
	family 30
AK000685	unknown	0.51	0.10	9.0	3.1	2.8	3.9	15.3	3.0
AF013620	Immunoglobulin	0.19	0.18	8.5	2.6	6.2	5.7	8.2	3.8
	heavy variable 4-4
AL049296	unknown	0.61	0.89	8.1	3.2	2.7	3.2	2.7	2.0
AB006622	KIAA0284 protein	0.47	0.28	7.5	5.0	2.8	11.1	5.5	4.6
X04391	CD5 antigen	0.22	0.13	7.2	16.7	2.7	7.7	6.1	5.9
AK000067	hypothetical	0.80	0.35	7.1	4.6	2.1	3.2	8.5	2.2
	protein
AF053712	TNF superfamily—	0.17	0.08	6.9	17.7	3.0	6.2	12.3	5.2
	member 11
X58079	S100 calcium-	0.14	0.24	6.7	6.7	5.9	6.5	5.3	2.5
	binding protein A1
M91036	hemoglobin—	0.48	0.36	6.7	14.2	2.1	2.9	2.7	4.8
	gamma A
AF055018	unknown	0.28	0.22	6.3	10.7	2.7	2.6	4.6	6.5
L17325	pre-T/NK cell	0.19	0.29	6.1	4.4	6.5	4.7	4.0	4.0
	associated protein
D45399	phosphodiesterase	0.21	0.18	6.1	4.6	5.0	2.8	10.8	4.0
AB023188	KIAA0971 protein	0.29	0.13	5.9	10.6	3.6	3.4	10.6	7.2
NM_012177	F-box protein	0.26	0.31	5.9	5.5	3.8	2.8	3.0	6.8
D38550	E2F TF 3	0.43	0.39	5.8	3.4	2.1	4.5	2.5	2.4
AL050219	unknown	0.26	0.04	5.7	17.0	3.1	9.2	30.3	16.1
AL137540	unknown	0.67	0.79	5.5	3.2	3.9	10.9	2.9	2.3
D50926	KIAA0136 protein	0.57	0.21	5.4	5.6	2.0	3.3	4.4	3.2
AL137658	unknown	0.31	0.07	5.4	12.1	2.6	10.8	3.9	8.6
U21931	fructose-	0.48	0.14	5.4	4.1	2.9	3.6	6.0	3.2
	bisphosphatase 1
AK001230	DKFZP586D211	0.43	0.26	5.0	4.6	2.1	2.2	2.5	2.7
	protein
AL137728	unknown	0.67	0.47	5.0	5.9	2.2	6.8	5.9	2.1
AB022847	unknown	0.39	0.24	4.5	2.2	3.5	4.3	3.8	3.7
X75311	mevalonate kinase	0.67	0.22	4.3	4.0	2.0	8.3	4.0	5.1
AK000946	DKFZP566C243	0.36	0.29	4.1	3.8	3.9	5.4	25.8	2.7
	protein
AB023197	KIAA0980 protein	0.25	0.30	4.0	8.3	2.1	8.8	2.2	4.9
AB014615	fibroblast growth	0.19	0.07	3.9	3.3	7.0	3.4	2.2	7.7
	factor 8
X04014	unknown	0.29	0.16	3.8	2.5	2.2	3.0	5.5	3.1
U76368	solute carrier	0.46	0.17	3.8	3.8	2.8	3.2	4.2	3.0
	family 7
AB032436	unknown	0.14	0.21	3.8	2.7	6.1	3.2	4.5	2.6
AB020683	KIAA0876 protein	0.37	0.21	3.7	4.2	2.2	5.3	2.9	9.4
NM_012126	carbohydrate	0.31	0.20	3.7	5.2	3.2	3.4	3.9	2.5
	sulfotransferase 5
AK002037	hypothetical	0.08	0.08	3.7	17.1	4.6	12.3	11.0	8.7
	protein
X78712	glycerol kinase	0.17	0.19	3.6	2.5	4.5	5.3	2.2	3.3
	pseudogene 2
NM_014178	HSPC156 protein	0.23	0.12	3.5	8.4	2.9	6.9	14.4	5.5
AC004079	homeo box A2	0.31	0.11	3.5	7.0	2.1	2.0	7.3	9.1
AL080182	unknown	0.51	0.21	3.4	3.5	2.2	2.1	2.9	2.4
M91036	hemoglobin	0.22	0.02	3.4	26.3	5.8	6.8	30.4	21.6
	gamma G
AJ000512	serum/glucocortico	0.27	0.43	3.3	2.1	4.9	2.3	3.9	2.7
	id regulated kinase
AK002140	hypothetical	0.28	0.14	3.3	9.9	2.8	2.1	16.6	7.2
	protein
AL137284	unknown	0.22	0.04	3.3	7.2	4.1	6.0	12.2	3.7
Z11898	POU domain—	0.12	0.29	3.2	3.7	8.2	2.5	6.6	2.2
	class 5 TF 1
AB017016	brain-specific	0.27	0.29	3.1	2.8	2.5	2.8	3.3	5.5
	protein
X54673	Solute-carrier	0.34	0.08	2.9	12.0	2.2	10.4	7.4	5.9
	family 6
AL033377	unknown	0.40	0.22	2.6	2.6	2.6	2.3	4.5	2.2
X85740	CCR4	0.34	0.05	2.6	2.3	2.6	2.5	12.5	5.2
AB010419	core-binding factor	0.59	0.20	2.5	12.8	2.0	2.8	2.9	5.9
AL109726	uknown	0.14	0.15	2.3	9.0	4.3	4.4	2.6	3.7
NM_012450	sulfate transporter 1	0.15	0.10	2.2	3.1	8.2	9.9	4.7	5.9
J04599	biglycan	0.39	0.30	2.1	3.3	6.6	2.2	2.7	5.4
AK000266	hypothetical	0.49	0.35	2.1	3.5	3.5	6.6	4.3	4.0
	protein

[0132]

TABLE 33
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula C Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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.
Accession		control-	control-	ID 19:	ID 20:	ID 21:	ID 22:	ID 23:	ID 24:
Number	Gene	Cy3	Cy5	control	control	control	control	control	control
NM_014139	sodium channel	0.04	0.05	31.6	25.2	18.0	9.7	22.2	11.2
	voltage-gated,
X84003	TATA box binding	0.47	0.07	31.8	12.7	2.5	2.8	18.0	14.2
	protein
AF144412	lens epithelial cell	0.25	0.07	23.9	8.0	6.8	3.4	16.2	3.5
	protein
AL080107	unknown	0.11	0.06	17.8	34.4	12.4	6.2	5.4	7.9
AF052116	unknown	0.34	0.07	15.5	3.9	9.2	3.0	6.9	2.7
AB033063	unknown	0.46	0.13	15.2	10.3	4.0	2.6	7.2	11.2
AK000258	hypothetical protein	0.27	0.07	13.9	8.0	3.5	3.4	26.5	11.5
NM_006963	zinc finger protein	0.10	0.08	12.8	6.8	6.2	5.9	17.2	1241.2
NM_014099	PRO1768 protein	0.30	0.06	12.3	17.4	5.4	5.4	19.5	3.4
AK000996	hypothetical protein	0.17	0.07	10.0	8.0	9.7	7.4	20.7	16.3
M81933	cell division cycle	0.13	0.21	8.8	7.8	19.6	15.6	4.8	3.8
	25A
AF181286	unknown	0.05	0.22	8.8	2.7	12.0	35.6	5.9	2.3
AJ272208	IL-1R accessory	0.22	0.17	8.8	2.9	5.0	3.2	9.8	7.3
	protein-like 2
AF030555	fatty-acid-Coenzyme	0.10	0.39	8.7	2.2	11.3	9.9	3.0	2.1
	A ligase
AL050125	unknown	0.23	0.07	8.6	14.3	5.2	2.8	18.7	8.3
AB011096	KIAA0524 protein	0.21	0.08	8.5	24.4	4.7	6.8	10.4	7.5
J03068	N-acylaminoacyl-	0.54	0.21	8.3	2.4	2.2	4.1	3.0	6.0
	peptide hydrolase
M33906	MHC class II, DQ	0.14	0.08	7.6	4.5	15.2	6.1	7.5	7.9
	alpha 1
AJ272265	secreted	0.21	0.09	7.6	9.0	3.3	4.9	18.8	14.5
	phosphoprotein
J00210	interferon alpha 13	0.41	0.07	7.2	15.0	2.8	3.1	11.0	4.3
AK001952	hypothetical protein	0.42	0.21	6.9	4.9	2.5	3.1	7.6	4.5
X54131	protein tyrosine	0.09	0.20	6.4	6.5	7.7	15.0	5.6	4.1
	phosphatase,
	receptor type,
AF064493	LIM binding domain 2	0.46	0.14	5.9	5.6	2.2	2.9	8.5	5.8
AL117567	DKFZP566O084	0.44	0.22	5.8	3.3	2.9	2.3	5.7	14.9
	protein
L40933	phosphoglucomutase 5	0.16	0.03	5.6	11.0	4.8	3.5	8.5	76.3
M27190	regenerating islet-	0.19	0.28	5.3	3.0	3.8	3.6	5.8	3.6
	derived 1 alpha
AL031121	unknown	0.24	0.09	5.3	3.8	3.2	3.9	3.0	27.9
U27655	regulator of G-	0.24	0.29	5.0	9.0	4.5	8.3	4.2	4.5
	protein signalling
AB037786	unknown	0.12	0.03	4.7	54.1	2.8	2.3	2.2	11.0
	myosin-binding	0.29	0.13	4.7	6.5	6.0	2.4	6.7	6.3
	protein C
AB010962	matrix	0.08	0.12	4.7	6.2	2.4	4.7	10.9	4.2
	metalloproteinase
AL096729	unknown	0.36	0.13	4.7	7.7	3.2	2.4	6.3	6.2
AB018320	Arg/Ab1-interacting	0.16	0.18	4.6	7.1	3.0	3.3	5.8	8.9
	protein
AK001024	guanine nucleotide-	0.16	0.11	4.6	2.0	9.8	2.6	7.6	14.1
	binding protein
AJ275355	unknown	0.15	0.08	4.6	17.3	5.4	9.2	5.1	5.5
U21931	fructose-	0.48	0.14	4.6	4.3	2.6	2.1	8.4	9.6
	bisphosphatase 1
X66403	cholinergic receptor	0.17	0.19	4.4	9.0	10.9	9.3	5.1	6.7
X67734	contactin2	0.25	0.09	4.3	6.8	3.1	5.8	7.9	8.4
U92981	unknown	0.20	0.23	4.3	3.2	4.8	5.6	5.4	6.3
X68879	empty spiracles	0.05	0.08	4.3	2.0	12.3	2.7	5.6	4.7
AL137362	unknown	0.22	0.22	4.2	4.1	2.7	4.1	9.3	4.2
NM_001756	corticosteroid	0.28	0.13	4.1	10.6	3.9	2.7	10.3	5.5
	binding globulin
U80770	unknown	0.31	0.14	4.1	4.1	23.3	2.7	7.0	10.1
AL109792	unknown	0.16	0.19	4.0	4.5	4.3	8.8	8.7	3.9
X65962	cytochrome P-450	0.33	0.05	3.8	25.3	5.7	5.1	19.8	12.0
AK001856	unknown	0.40	0.21	3.8	7.0	2.6	3.1	2.9	7.8
AL022723	MHC, class I, F	0.55	0.18	3.7	5.7	4.4	2.3	3.3	5.2
D38449	putative G protein	0.18	0.09	3.5	11.1	13.3	5.8	4.8	5.2
	coupled receptor
AL137489	unknown	0.74	0.26	3.3	2.9	2.6	3.3	2.5	5.4
AB000887	small inducible	0.76	0.18	3.3	5.0	2.6	2.4	5.9	10.3
	cytokine subfamily A
NM_012450	sulfate transporter 1	0.15	0.10	3.3	9.0	10.0	10.9	4.6	8.7
U86529	glutathione S-	0.55	0.15	3.2	6.8	4.4	2.3	9.3	5.1
	transferase zeta 1
AK001244	unknown	0.79	0.31	3.2	5.5	2.3	2.3	3.9	2.8
AL133602	unknown	0.16	0.21	3.1	7.8	8.7	2.6	4.1	5.6
AB033080	cell cycle	0.31	0.31	3.1	4.6	3.0	3.5	2.2	4.2
	progression 8 protein
AF023466	putative glycine-N-	0.27	0.18	3.1	5.0	4.2	7.4	10.1	3.8
	acyltransferase
AL117457	cofilin 2	0.68	0.53	3.0	4.6	3.3	2.4	7.4	3.4
AC007059	unknown	0.37	0.35	3.0	5.7	3.1	2.4	2.6	2.4
U60179	growth hormone	0.34	0.21	2.9	3.5	2.3	3.1	8.0	4.7
	receptor
M37238	phospholipase C,	0.60	0.36	2.9	2.0	3.2	2.1	2.9	4.6
	gamma 2
L22569	cathepsin B	0.32	0.12	2.9	2.1	6.2	3.0	13.1	16.7
M80359	MAP/microtubule	0.37	0.76	2.9	3.1	6.1	7.6	2.1	3.3
	affinity-regulating
	kinase 3
S70348	Integrin beta 3	0.58	0.31	2.6	4.8	4.1	2.6	2.6	2.6
L13720	growth arrest-	0.36	0.26	2.4	2.5	6.8	4.8	3.9	3.7
	specific 6
AL049423	unknown	0.33	0.30	2.4	3.7	3.8	2.8	2.9	3.4
AL050201	unknown	0.68	0.29	2.2	3.1	3.7	3.0	3.0	2.2
AF050078	growth arrest	0.87	0.33	2.1	8.4	2.5	2.2	2.6	4.4
	specific 11
AK001753	hypothetical protein	0.53	0.28	2.1	5.0	2.2	2.8	3.6	4.6
X05323	unknown	0.39	0.13	2.1	7.8	2.6	2.4	21.5	3.5
AB014548	KIAA0648 protein	0.61	0.30	2.0	2.4	4.8	3.4	4.9	3.9

[0133]

TABLE 34
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula D Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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.
Accession		control-	control-	ID 26:	ID 27:	ID 28:	ID 29:	ID 30:	ID 31:
Number	Gene	Cy3	Cy5	control	control	control	control	control	control
U68018	MAD	0.13	0.71	11.2	2.2	8.0	2.3	6.7	25.6
	homolog 2
NM_016015	CGI-68	0.92	1.59	2.3	2.3	3.5	3.7	3.4	22.9
	protein
AF071510	lecithin retinol	0.07	0.05	15.4	10.3	5.3	44.1	2.1	21.2
	acyltransferase
AC005154	unkown	0.17	1.13	2.7	7.2	12.6	6.4	3.3	20.6
M81933	cell division	0.13	0.21	4.3	3.1	3.2	4.3	5.6	18.2
	cycle 25 A
AF124735	LIM HOX	0.17	0.21	2.1	4.4	5.9	5.2	7.6	17.0
	gene 2
AL110125	unknown	0.30	0.08	5.0	2.7	6.8	10.2	2.8	12.0
NM_004732	potassium	0.15	0.16	7.6	4.0	3.4	2.2	2.9	11.4
	voltage-gated
	channel
AF030555	fatty-acid-	0.10	0.39	10.5	2.2	6.4	3.0	5.1	10.7
	Coenzyme A
	ligase_long-
	chain 4
AF000237	1-	1.80	2.37	3.4	2.5	2.4	2.1	3.7	9.9
	acylglycerol-
	3-phosphate
	O-
	acyltransferase 2
AL031588	hypothetical	0.40	0.26	5.8	20.2	2.8	4.7	5.6	9.1
	protein
AL080077	unknown	0.15	0.21	2.4	2.0	11.9	3.8	2.3	8.7
NM_014366	putative	0.90	2.52	2.4	4.3	2.4	2.6	3.0	8.6
	nucleotide
	binding
	protein—
	estradiol-
	induced
AB002359	phosphoribos	0.81	2.12	3.2	2.7	5.5	2.5	2.8	6.9
	ylformylglyci
	namidine
	synthase
U33547	MHC class II	0.14	0.16	2.5	5.3	4.5	5.0	3.1	6.6
	antigen HLA-
	DRB6
	mRNA—
AL133051	unknown	0.09	0.07	7.7	6.3	5.4	23.1	5.4	6.5
AK000576	hypothetical	0.27	0.06	7.1	9.3	5.0	6.9	2.9	6.2
	protein
AF042378	spindle pole	0.36	0.39	3.3	3.0	9.5	4.5	3.4	6.2
	body protein
AF093265	Homer	0.67	0.53	2.7	13.3	6.5	5.0	2.9	6.2
	neuronal
	immediate
	early gene_3
D80000	Segregation of	1.01	1.56	3.6	2.5	4.9	3.2	6.3	6.1
	mitotic
	chromosomes 1
AF035309	proteasome	3.61	4.71	2.7	6.6	5.2	4.9	2.7	6.0
	26S subunit
	ATPase 5
M34175	adaptor-	4.57	5.13	3.2	3.1	4.0	4.6	2.7	6.0
	related protein
	complex 2
	beta 1 subunit
AB020659	KLAA0852	0.18	0.37	4.1	7.6	5.7	4.8	2.5	5.7
	protein
NM_004862	LPS-induced	2.61	3.36	3.8	4.8	4.1	4.9	3.2	5.6
	TNF-alpha
	factor
U00115	zinc finger	0.51	0.07	18.9	2.2	3.5	7.2	21.2	5.6
	protein 51
AF088868	fibrousheathin	0.45	0.20	4.7	10.0	3.2	6.4	6.0	5.6
	II
AK001890	unknown	0.42	0.55	2.4	3.5	3.6	2.3	2.2	5.6
AL137268	KIAA0759	0.49	0.34	3.8	2.3	5.0	3.5	3.3	5.4
	protein
X63563	polymerase II	1.25	1.68	2.5	8.1	3.4	4.8	5.2	5.4
	polypeptide B
D12676	CD36 antigen	0.35	0.39	2.9	3.4	2.6	2.2	3.5	5.3
AK000161	hypothetical	1.06	0.55	3.4	8.7	2.1	6.7	2.9	5.1
	protein
AF052138	unknown	0.64	0.51	2.9	2.8	2.7	5.2	3.6	5.0
AL096803	unknown	0.36	0.03	20.1	18.3	3.7	19.3	16.1	4.9
S49953	DNA-binding	0.70	0.15	3.7	4.0	2.1	6.6	4.0	4.8
	transcriptional
	activator
X89399	RAS p21	0.25	0.10	8.5	14.9	4.8	18.6	4.3	4.8
	protein
	activator
AJ005273	antigenic	0.70	0.10	7.6	11.1	2.8	9.9	12.0	4.6
	determinant of
	recA protein
AK001154	hypothetical	1.70	0.96	2.4	4.4	2.9	8.9	2.4	4.5
	protein
AL133605	unknown	0.26	0.15	12.4	4.2	4.4	3.3	3.3	4.1
U71092	G protein-	0.53	0.06	19.0	9.1	2.2	12.0	3.3	4.1
	coupled
	receptor 24
AF074723	RNA	0.67	0.54	4.0	3.2	3.1	3.4	6.0	4.0
	polymerase II
	transcriptional
	regulation
	mediator
AL137577	unknown	0.32	0.12	31.4	6.2	5.3	10.1	25.3	3.9
AF151043	hypothetical	0.48	0.35	2.6	2.2	2.0	3.3	2.2	3.8
	protein
AF131831	unknown	0.67	0.81	2.1	7.0	3.5	3.2	3.9	3.7
D50405	histone	1.52	2.62	3.1	7.2	2.9	4.1	2.8	3.7
	deacetylase 1
U78305	protein	1.21	0.20	4.7	13.0	3.5	5.9	4.2	3.7
	phosphatase
	1D
AL035562	paired box	0.24	0.01	30.2	81.9	5.6	82.3	6.2	3.7
	gene 1
U67156	mitogen-	1.15	0.30	6.6	3.0	2.2	2.3	2.5	3.6
	activated
	protein kinase
	kinase kinase 5
AL031121	unknown	0.24	0.09	5.2	3.7	2.3	6.5	9.1	3.6
U13666	G protein-	0.34	0.14	3.8	5.4	3.1	3.3	2.8	3.6
	coupled
	receptor 1
AB018285	KIAA0742	0.53	0.13	14.9	13.9	5.9	18.5	15.2	3.5
	protein
D42053	site-1 protease	0.63	0.40	2.6	7.1	5.6	9.2	2.6	3.5
AK001135	Sec23-	0.29	0.53	5.7	4.5	3.4	2.6	11.3	3.4
	interacting
	protein p125
AL137461	unknown	0.25	0.02	23.8	9.0	2.7	59.2	12.5	3.3
NM_006963	zinc finger	0.10	0.08	3.2	7.6	3.7	7.9	11.2	3.2
	protein 22
AL137540	unknown	0.67	0.79	3.9	2.6	5.6	4.2	3.5	3.1
AL137718	unknown	0.95	0.18	4.7	8.0	4.0	13.3	3.0	3.1
AF012086	RAN binding	1.20	0.59	4.6	4.0	2.0	4.6	3.6	3.1
	protein 2-like 1
S57296	HER2/neu	0.59	0.17	7.3	12.1	2.3	20.0	22.2	3.0
	receptor
NM_013329	GC-rich	0.16	0.08	6.9	14.3	9.7	3.3	7.2	3.0
	sequence
	DNA-binding
	factor
	candidate
AF038664	UDP-	0.15	0.03	13.4	22.2	5.4	15.8	17.6	3.0
	Gal: betaGlcN
	Ac beta 1_4-
	galactosyltransferase
AF080579	Homo sapiens	0.34	1.03	3.3	3.0	6.7	2.1	2.9	2.9
	integral
	membrane
	protein
AK001075	hypothetical	0.67	0.10	2.1	2.6	2.6	8.9	2.2	2.9
	protein
AB011124	KIAA0552	0.46	0.04	9.6	72.0	6.0	33.9	13.6	2.9
	gene product
J03068	N-	0.54	0.21	2.2	5.0	2.4	5.2	3.6	2.8
	acylaminoacyl-
	peptide
	hydrolase
D87120	osteoblast	0.87	0.87	2.2	2.0	4.7	2.3	2.0	2.8
	protein
AB006537	IL-1R	0.17	0.07	2.9	7.0	14.5	5.3	6.6	2.8
	accessory
	protein
L34587	transcription	2.49	1.23	2.2	16.3	5.0	15.8	5.5	2.7
	elongation
	factor B
D31891	SET domain—	1.02	0.29	3.9	6.0	4.3	4.9	6.6	2.7
	bifurcated_1
D00760	proteasome	4.97	4.94	4.1	2.6	2.0	2.8	2.7	2.7
	subunit_alpha
	type_2
AC004774	distal-less	0.25	0.12	2.3	6.3	3.8	5.2	5.2	2.6
	homeo box 5
AL024493	unknown	1.46	0.54	4.8	13.5	2.1	11.6	6.8	2.6
AB014536	copine III	1.80	1.29	3.2	9.5	3.8	6.8	2.6	2.6
X59770	IL-1R type II	0.59	0.16	9.6	4.7	3.9	3.2	4.9	2.5
AF052183	unknown	0.65	0.76	4.0	3.7	2.3	5.0	3.0	2.5
AK000541	hypothetical	0.92	0.27	4.5	13.9	3.6	18.1	4.3	2.5
	protein
U88528	cAMP	1.37	0.86	3.1	5.4	2.1	2.8	2.1	2.4
	responsive
	element
	binding
	protein
M97925	defensin alpha	0.33	0.07	4.6	35.9	2.0	7.8	6.5	2.4
	5_Paneth
	cell-specific
NM_013393	cell division	1.38	0.94	3.1	5.8	2.1	4.2	2.6	2.3
	protein FtsJ
X62744	MHC class II	0.86	0.32	4.0	4.7	2.3	2.9	6.1	2.3
	DM alpha
AF251040	putative	0.64	0.30	6.7	3.4	2.9	3.9	5.7	2.2
	nuclear
	protein
AK000227	hypothetical	1.49	0.43	3.4	7.1	2.3	3.3	9.1	2.1
	protein
U88666	SFRS protein	1.78	0.37	3.4	5.9	2.6	8.4	6.1	2.0
	kinase 2

[0134]

TABLE 35
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula E Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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.
Accession		control-	control-	ID 33:	ID 34:	ID 35:	ID 36:	ID 37:	ID 38:
Number	Gene	Cy3	Cy5	control	control	control	control	control	control
AL049689	Novel human	0.25	0.05	2.7	26.5	3.3	21.7	5.4	37.9
	mRNA
AK000576	hypothetical	0.27	0.06	3.0	19.1	3.9	23.0	3.1	28.3
	protein
X74837	mannosidase,	0.10	0.07	5.6	10.0	10.8	12.3	12.0	19.9
	alpha class 1A
	member 1
AK000258	hypothetical	0.27	0.07	14.0	11.1	7.9	16.1	6.2	18.9
	protein
X89067	transient receptor	0.20	0.14	3.7	2.2	2.4	2.6	8.0	18.1
AL137619	unknown	0.16	0.08	6.3	6.7	10.8	10.5	7.9	16.5
NM_003445	zinc finger	0.17	0.07	4.0	23.6	2.9	13.6	4.3	14.4
	protein
X03084	complement	0.36	0.15	2.4	3.1	2.9	7.7	3.4	13.7
	component 1
U27330	fucosyltransferase 5	0.39	0.08	2.4	2.5	2.6	12.1	3.5	13.0
AF070549	unknown	0.16	0.09	2.7	4.7	7.9	10.3	4.2	12.6
AB020335	sel-1-like	0.19	0.24	2.9	2.6	2.0	7.3	4.7	12.4
M26901	renin	0.09	0.12	14.9	2.2	7.3	12.0	20.8	12.0
Y07828	ring finger	0.09	0.06	9.0	26.6	8.9	16.0	3.6	11.6
	protein
AK001848	hypothetical	0.21	0.07	6.2	8.2	2.7	5.2	5.5	10.9
	protein
NM_016331	zinc finger	0.16	0.08	7.6	5.1	7.0	25.5	5.5	10.9
	protein
U75330	neural cell	0.42	0.08	2.5	3.6	2.0	5.8	6.2	9.9
	adhesion
	molecule 2
AB037826	unknown	0.16	0.11	3.8	6.0	3.4	13.4	6.0	9.8
M34041	adrenergic alpha-	0.30	0.13	4.5	4.5	3.7	8.6	5.6	9.8
	2B-receptor
D38449	putative G	0.18	0.09	2.3	25.8	11.7	2.3	3.2	9.5
	protein coupled
	receptor
AJ250562	transmembrane 4	0.13	0.10	10.0	8.4	2.2	8.1	16.3	9.1
	superfamily
	member 2
AK001807	hypothetical	0.18	0.12	4.2	5.3	4.6	3.2	4.0	8.3
	protein
AL133051	unknown	0.09	0.07	5.1	13.6	6.0	9.1	2.2	8.2
U43843	Neuro-d4	0.61	0.10	2.0	6.4	2.3	16.6	2.2	8.1
	homolog
NM_013227	aggrecan 1	0.28	0.15	7.5	3.1	2.5	6.9	8.5	7.8
AF226728	somatostatin	0.23	0.17	7.0	3.6	3.1	5.5	3.5	7.7
	receptor-
	interacting
	protein
AK001024	guanine	0.16	0.11	3.9	12.3	2.7	7.4	3.3	7.0
	nucleotide-
	binding protein
AC002302	unknown	0.13	0.14	16.1	5.8	5.8	2.6	9.6	6.2
AB007958	unknown	0.17	0.27	2.0	2.3	11.3	3.3	3.0	6.1
AF059293	cytokine	0.19	0.22	3.6	2.5	10.2	3.8	2.7	5.9
	receptor-like
	factor 1
V01512	v-fos	0.27	0.21	6.7	3.7	13.7	9.3	3.7	5.4
U82762	sialyltransferase 8	0.23	0.15	3.2	6.5	2.7	9.2	5.7	5.4
U44059	thyrotrophic	0.05	0.13	22.9	7.1	12.5	7.4	9.7	5.4
	embryonic factor
X05323	antigen identified	0.39	0.13	4.3	2.5	2.2	7.4	2.8	5.1
	by monoclonal
	antibody
U72671	ICAM 5,	0.25	0.14	5.3	2.7	3.7	10.0	3.2	4.8
AL133626	hypothetical	0.26	0.25	2.2	4.2	2.9	3.0	2.6	4.7
	protein
X96401	MAX binding	0.31	0.29	6.9	2.3	4.9	3.1	2.9	4.6
	protein
AL117533	unknown	0.05	0.26	8.2	2.7	11.1	2.5	11.9	4.5
AK001550	hypothetical	0.10	0.30	8.0	2.0	4.9	2.1	7.8	4.5
	protein
AB032436	Homo sapiens	0.14	0.21	5.1	2.2	9.1	4.5	6.4	4.4
	BNPI mRNA
AL035447	hypothetical	0.28	0.23	4.3	3.7	8.7	5.2	3.7	4.2
	protein
U09414	zinc finger	0.28	0.25	4.0	2.2	4.7	3.3	7.2	4.2
	protein
AK001256	unknown	0.09	0.08	5.3	6.5	31.1	12.7	6.4	4.1
L14813	carboxyl ester	0.64	0.21	2.7	6.2	3.1	2.1	3.4	3.9
	lipase-like
AF038181	unknowan	0.06	0.18	34.1	6.4	4.5	8.7	11.3	3.9
NM_001486	glucokinase	0.21	0.08	3.0	2.2	6.5	12.4	5.7	3.9
AB033000	hypothetical	0.24	0.22	3.4	3.3	7.1	5.5	4.5	3.8
	protein
AL117567	DKFZP566O084	0.44	0.22	2.2	2.7	3.9	4.0	4.5	3.7
	protein
NM_012126	carbohydrate	0.31	0.20	5.5	5.4	3.8	5.5	2.6	3.5
	sulfotransferase 5
AL031687	unknown	0.16	0.27	5.9	2.6	3.4	2.3	4.9	3.5
X04506	apolipoprotein B	0.29	0.32	5.4	4.4	6.9	5.5	2.1	3.5
NM_006641	CCR 9	0.35	0.11	3.3	3.3	2.2	16.5	2.3	3.5
Y00970	acrosin	0.12	0.14	8.2	8.8	3.1	6.2	17.5	3.4
X67098	rTS beta protein	0.19	0.26	2.4	3.1	7.8	3.5	4.4	3.3
U51990	pre-mRNA	0.56	0.19	2.2	3.0	2.8	13.7	2.9	3.0
	splicing factor
AF030555	fatty-acid-	0.10	0.39	3.5	6.9	13.3	4.4	7.5	2.9
	Coenzyme A
AL009183	TNFR	0.46	0.19	6.0	4.1	2.8	8.6	2.6	2.8
	superfamily,
	member 9
AF045941	sciellin	0.16	0.21	11.6	2.4	2.8	2.2	4.1	2.8
AF072756	A kinase anchor	0.33	0.07	2.5	5.3	3.9	32.7	2.3	2.7
	protein 4
X78678	ketohexokinase	0.10	0.20	18.0	3.5	4.1	2.5	14.6	2.6
AL031734	unknown	0.03	0.39	43.7	2.3	41.7	4.0	10.8	2.5
D87717	KIAA0013 gene	0.35	0.42	4.2	2.3	3.6	2.6	2.9	2.5
	product
U01824	solute carrier	0.42	0.29	4.8	2.3	4.2	7.1	4.2	2.4
	family 1
AF055899	solute carrier	0.14	0.31	9.5	12.3	7.4	4.7	6.6	2.3
	family 27
U22526	lanosterol	0.09	0.45	4.1	3.4	10.4	2.2	17.9	2.3
	synthase
AB032963	unknown	0.19	0.34	6.3	6.1	2.9	2.1	5.7	2.2
NM_015974	lambda-crystallin	0.17	0.25	11.4	2.8	5.9	2.4	5.8	2.2
X82200	stimulated transacting	0.23	0.15	8.2	3.4	3.0	2.8	11.3	2.2
	factor
AL137522	unknown	0.12	0.26	12.1	3.7	12.6	6.9	4.3	2.2
Z99916	crystallin, beta	0.28	0.65	2.5	2.1	3.6	2.2	2.6	2.1
	B3
AF233442	ubiquitin specific	0.41	0.31	2.6	3.6	3.6	4.5	3.4	2.1
	protease 21
AK001927	hypothetical	0.24	0.52	7.6	5.6	5.0	2.5	4.1	2.0
	protein

[0135]

TABLE 36
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula F Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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 “Ratio ID#: Control” columns refer
to the intensity of polynucleotide expression in peptide-simulated cells divided by the
intensity of unstimulated cells.
				Ratio	Ratio	Ratio	Ratio	Ratio
Accession		control-	control-	ID 40:	ID 42:	ID 43:	ID 44:	ID 45:
Number	Gene	Cy3	Cy5	control	control	control	control	control
AF025840	polymerase	0.34	0.96	3.4	2.0	2.0	2.1	4.3
	epsilon 2
AF132495	CGI-133 protein	0.83	0.67	3.0	2.2	2.6	2.8	5.1
AL137682	hypothetical	0.73	0.40	2.0	5.3	4.8	2.9	8.2
	protein
U70426	regulator of G-	0.23	0.25	3.1	3.0	5.3	3.1	12.2
	protein signalling
	16
AK001135	Sec23-interacting	0.29	0.53	3.2	2.6	3.3	14.4	5.2
	protein p125
AB023155	KIAA0938 protein	0.47	0.21	2.7	4.8	8.1	4.2	10.4
AB033080	cell cycle	0.31	0.31	4.4	2.2	5.9	4.3	6.9
	progression 8
	protein
AF061836	Ras association	0.29	0.31	3.2	2.5	11.1	18.8	6.8
	domain family 1
AK000298	hypothetical	0.48	0.27	3.3	2.2	7.1	5.6	7.7
	protein
L75847	zinc finger protein	0.35	0.52	3.2	3.0	4.0	3.0	3.9
X97267	protein tyrosine	0.19	0.24	4.1	9.3	2.4	4.2	8.3
	phosphatase
Z11933	POU domain class	0.09	0.23	8.7	2.5	3.6	4.3	8.2
	3 TF 2
AB037744	unknown	0.37	0.57	2.6	2.9	2.7	3.0	3.1
U90908	unknown	0.12	0.16	11.8	7.7	3.4	7.8	11.2
AL050139	unknown	0.29	0.60	5.2	2.4	3.3	3.0	2.8
AB014615	fibroblast growth	0.19	0.07	5.4	3.5	8.5	3.2	22.7
	factor 8
M28825	CD1A antigen	0.51	0.36	4.1	2.6	2.0	4.6	4.4
U27330	fucosyltransferase 5	0.39	0.08	3.3	2.1	24.5	8.2	19.3
NM_006963	zinc finger protein	0.10	0.08	10.4	12.6	12.3	29.2	20.5
AF093670	peroxisomal	0.44	0.53	4.0	2.6	2.6	4.3	2.9
	biogenesis factor
AK000191	hypothetical	0.50	0.18	2.3	3.6	4.4	2.2	8.2
	protein
AB022847	unknown	0.39	0.24	2.1	6.9	4.5	2.8	6.2
AK000358	microfibrillar-	0.28	0.28	5.7	2.0	3.5	5.2	5.2
	associated protein 3
X74837	mannosidase—	0.10	0.07	13.1	18.4	23.6	16.3	20.8
	alpha class 1A
AF053712	TNF superfamily—	0.17	0.08	11.3	9.3	13.4	10.6	16.6
	member 11
AL133114	DKFZP586P2421	0.11	0.32	8.5	3.4	4.9	5.3	4.3
	protein
AF049703	E74-like factor 5	0.22	0.24	5.1	6.0	3.3	2.7	5.4
AL137471	hypothetical	0.29	0.05	4.0	15.0	10.1	2.7	25.3
	protein
AL035397	unknown	0.33	0.14	2.3	2.8	10.6	4.6	9.3
AL035447	hypothetical	0.28	0.23	3.8	6.8	2.7	3.0	5.7
	protein
X55740	CD73	0.41	0.61	2.1	3.3	2.9	3.2	2.1
NM_004909	taxol resistance	0.20	0.22	3.9	2.9	6.5	3.2	5.6
	associated gene 3
AF233442	ubiquitin specific	0.41	0.31	2.9	4.7	2.7	3.5	3.9
	protease
U92980	unknown	0.83	0.38	4.2	4.1	4.8	2.3	3.1
AF105424	myosin heavy	0.30	0.22	2.8	3.3	4.4	2.3	5.3
	polypeptide-like
M26665	histatin 3	0.29	0.26	7.9	3.5	4.6	3.5	4.5
AF083898	neuro-oncological	0.20	0.34	18.7	3.8	2.2	3.6	3.5
	ventral antigen 2
AJ009771	ariadne—	0.33	0.06	2.3	17.6	15.9	2.5	20.3
	Drosophila—
	homolog of
AL022393	hypothetical	0.05	0.33	32.9	2.4	3.0	69.4	3.4
	protein P1
AF039400	chloride channel—	0.11	0.19	8.4	2.9	5.1	18.1	5.9
	calcium activated—
	family member 1
AJ012008	dimethylarginine	0.42	0.43	5.1	3.3	3.2	6.2	2.6
	dimethylaminohydrolase 2
AK000542	hypothetical	0.61	0.24	2.1	4.5	5.0	3.7	4.4
	protein
AL133654	unknown	0.27	0.40	2.8	2.1	2.5	2.5	2.6
AL137513	unknown	0.43	0.43	6.4	3.2	3.8	2.3	2.3
U05227	GTP-binding	0.38	0.36	5.0	3.1	3.1	2.2	2.8
	protein
D38449	putative G protein	0.18	0.09	5.8	6.7	6.7	9.1	10.4
	coupled receptor
U80770	unknown	0.31	0.14	3.9	3.8	6.6	3.1	6.8
X61177	IL-5R alpha	0.40	0.27	2.6	4.4	9.8	8.1	3.6
U35246	vacuolar protein	0.15	0.42	5.8	2.8	2.6	4.5	2.2
	sorting 45A
AB017016	brain-specific	0.27	0.29	6.0	2.6	3.4	3.1	3.1
	protein p25 alpha
X82153	cathepsin K	0.45	0.20	4.2	5.2	4.8	4.4	4.6
AC005162	probable	0.12	0.28	11.9	3.4	6.8	18.7	3.2
	carboxypeptidase
	precursor
AL137502	unknown	0.22	0.16	3.9	4.9	7.3	3.9	5.3
U66669	3-	0.30	0.40	10.3	3.5	5.2	2.3	2.1
	hydroxyisobutyryl-
	Coenzyme A
	hydrolase
AK000102	unknown	0.39	0.30	2.8	5.3	5.2	4.1	2.8
AF034970	docking protein 2	0.28	0.05	3.3	8.5	15.7	4.0	17.3
AK000534	hypothetical	0.13	0.29	6.8	2.3	4.0	20.6	2.9
	protein
J04599	biglycan	0.39	0.30	4.0	3.7	4.0	4.8	2.8
AL133612	unknown	0.62	0.33	2.7	3.4	5.2	3.0	2.5
D10495	protein kinase C	0.18	0.10	12.0	20.7	8.7	6.8	8.1
	delta
X58467	cytochrome P450	0.07	0.24	15.4	4.7	7.9	34.4	3.4
AF131806	unknown	0.31	0.25	2.6	3.4	5.7	7.0	3.2
AK000351	hypothetical	0.34	0.13	4.0	6.9	5.5	2.8	6.3
	protein
AF075050	hypothetical	0.55	0.09	2.7	17.8	5.1	2.2	8.3
	protein
AK000566	hypothetical	0.15	0.35	6.7	2.2	6.8	6.4	2.1
	protein unknown
U43328	cartilage linking	0.44	0.19	2.5	6.2	6.9	7.8	3.8
	protein 1
AF045941	sciellin	0.16	0.21	6.8	7.5	4.8	6.9	3.4
U27655	regulator of G-	0.24	0.29	5.5	4.9	2.9	4.9	2.4
	protein signalling 3
AK000058	hypothetical	0.25	0.15	5.0	9.7	16.4	2.7	4.5
	protein
AL035364	hypothetical	0.32	0.26	4.4	4.2	7.3	2.8	2.6
	protein
AK001864	unknown	0.40	0.25	3.7	3.7	4.6	3.2	2.6
AB015349	unknown	0.14	0.24	10.5	2.8	3.7	8.0	2.7
V00522	MHC class II DR	0.62	0.22	4.8	3.9	4.7	2.5	3.0
	beta 3
U75330	neural cell	0.42	0.08	2.1	9.6	13.2	3.3	7.8
	adhesion molecule 2
NM_007199	IL-1R-associated	0.15	0.25	8.7	7.8	8.6	16.1	2.5
	kinase M
D30742	calcium/calmodulin-	0.28	0.09	6.2	28.7	7.4	2.4	6.8
	dependent
	protein kinase IV
X05978	cystatin A	0.63	0.17	2.7	4.8	9.4	2.2	3.6
AF240467	TLR-7	0.11	0.10	13.8	13.3	4.7	7.7	4.9

[0136]

TABLE 37
Up-regulation of Polynucleotide expression in A549 cells induced by
Formula G and additional Peptides.
The peptides at a concentration of 50 μg/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 (PRHU04). 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 Cy5 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; L36642, EphA7; M31166, pentaxin-related gene; AF176012,
unknown; AF072756, 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;
U80764, unknown; AB032963, unknown; X82835, sodium channel, voltage-gated, type IX
Accession	control-	control-	ID 53:	ID 54:	ID 47:	ID 48:	ID 49:	ID 50:	ID 51:	ID 52:
Number	Cy3	Cy5	control	control	control	control	control	control	control	control
U00115	0.51	0.07	27.4	7.3	2.4	3.1	4.8	8.3	3.5	20.0
M91036	0.22	0.02	39.1	32.5	5.2	2.2	37.0	6.0	16.2	18.0
AK000070	0.36	0.18	3.8	7.6	2.6	15.1	12.2	9.9	17.2	15.3
AF055899	0.14	0.31	6.7	3.7	9.7	10.0	2.2	16.7	5.4	14.8
AK001490	0.05	0.02	14.1	35.8	3.2	28.6	25.0	20.2	56.5	14.1
X97674	0.28	0.28	3.2	3.7	4.0	10.7	3.3	3.1	4.0	13.2
AB022847	0.39	0.24	4.1	4.4	4.5	2.7	3.7	10.4	5.0	11.3
AJ275986	0.26	0.35	5.8	2.3	5.7	2.2	2.5	9.7	4.3	11.1
D10495	0.18	0.10	8.0	3.4	4.6	2.0	6.9	2.5	12.7	10.3
L36642	0.26	0.06	5.8	14.2	2.6	4.1	8.9	3.4	6.5	6.6
M31166	0.31	0.12	4.8	3.8	12.0	3.6	9.8	2.4	8.8	6.4
AF176012	0.45	0.26	3.1	2.9	2.8	2.6	2.3	6.9	3.0	5.8
AF072756	0.33	0.07	9.9	9.3	4.4	4.3	3.2	4.9	11.9	5.4
NM_014439	0.47	0.07	12.0	7.1	3.3	3.3	4.7	5.9	5.0	5.4
AJ271351	0.46	0.12	3.4	3.5	2.3	4.7	2.3	2.7	6.9	5.2
AK000576	0.27	0.06	7.4	15.7	2.9	4.7	9.0	2.4	8.2	5.1
AJ272265	0.21	0.09	6.2	7.9	2.3	3.7	10.3	4.5	4.6	4.7
AL122038	0.46	0.06	6.7	4.5	2.6	4.3	16.4	6.5	26.6	4.6
AK000307	0.23	0.09	3.7	4.0	4.3	3.2	5.3	2.9	13.1	4.4
AB029001	0.52	0.21	14.4	4.3	4.6	4.4	4.8	21.9	3.2	4.2
U62437	0.38	0.13	12.6	6.5	4.2	6.7	2.2	3.7	4.8	3.9
AF064854	0.15	0.16	2.6	2.9	6.2	8.9	14.4	5.0	9.1	3.9
AL031588	0.40	0.26	8.3	5.2	2.8	3.3	5.3	9.0	5.6	3.4
X89399	0.25	0.10	15.8	12.8	7.4	4.2	16.7	6.9	12.7	3.3
D45399	0.21	0.18	3.0	4.7	3.3	4.4	8.7	5.3	5.1	3.3
AB037716	0.36	0.40	5.1	7.5	2.6	2.1	3.5	3.1	2.4	2.8
X79981	0.34	0.10	4.7	7.2	3.2	4.6	6.5	5.1	5.8	2.7
AF034208	0.45	0.24	2.7	10.9	2.1	3.7	2.3	5.9	2.2	2.5
AL133355	0.22	0.23	2.3	3.4	7.3	2.7	3.3	4.3	2.8	2.5
NM_016281	0.40	0.19	6.6	10.6	2.1	2.8	5.0	11.2	10.6	2.5
AF023614	0.11	0.42	2.2	2.2	6.0	7.5	5.0	2.7	2.0	2.4
AF056717	0.43	0.62	4.3	3.2	5.1	4.0	4.6	9.7	3.1	2.2
AB029039	0.79	0.49	2.7	3.3	3.7	2.0	2.3	2.4	4.8	2.2
J03634	0.40	0.12	3.7	2.3	2.3	4.0	10.5	4.1	9.1	2.2
U80764	0.31	0.18	2.3	7.4	4.2	2.3	5.1	3.3	8.8	2.1
AB032963	0.19	0.34	4.0	7.3	5.0	3.0	2.9	6.7	3.8	2.1
X82835	0.25	0.38	2.0	2.7	2.9	7.7	3.3	3.1	3.5	2.0

EXAMPLE 5

[0137] Induction of Chemokines in Cell Lines, Whole Human Blood, and in Mice By Peptides

[0138] 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 106 cells per well in DMEM (see above) and A549 cells were seeded in 24 well plates at a density of 105 cells per well in DMEM (see above) and both were incubated at 37° C. in 5% CO2 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, Minn.).

[0139] 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 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 μl 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-μl 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 μl 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-α and MCP-1 by ELISA.

[0140] 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 β (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 μg/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 μg/ml of LL-37, high levels of MCP-1 were produced.

[0141] The effect of cationic peptides on chemokine induction was also examined in a completely different cell system, A549 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 μg/ml induced IL-8 above background levels. At high concentrations (100 μg/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).

[0142] BALB/c mice were given SEQ ID NO: 1 or endotoxin-free water by intratracheal instillation and the levels of MCP-1 and TNF-α examined in the bronchioalveolar lavage fluid after 3-4 hr. It was found that the mice treated with 50 μg/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-α a than mice given water or anesthetic alone. peptide, SEQ ID NO: 1 was also found not to significantly induce TNF-α production by RAW 264.7 cells and bone marrow-derived macrophages treated with peptide, SEQ ID NO: 1 (up to 100 μg/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-α. 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.
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 in the mean of three or more experiments ± standard
error and the human blood data represents the mean ± standard
error from three separate donors.
	Monocyte chemoattractant
Peptide, SEQ ID NO: 1	protein (MCP)-1 (pg/ml)*
(μg/ml)	RAW cells	Whole blood
0	135.3 ± 16.3	112.7 ± 43.3
10	165.7 ± 18.2	239.3 ± 113.3
50	367 ± 11.5	371 ± 105
100	571 ± 17.4	596 ± 248.1

[0143]

TABLE 39
Induction of IL-8 in A549 cells and whole human blood.
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)
(μg/ml)	A549 cells	Whole blood
0	172 ± 29.1	660.7 ± 126.6
1	206.7 ± 46.1
10	283.3 ± 28.4	945.3 ± 279.9
20	392 ± 31.7
50	542.3 ± 66.2	1160.3 ± 192.4
100	1175.3 ± 188.3

[0144]

TABLE 40
Induction of IL-8 in A549 cells by Cationic peptides.
A549 human epithelial cells were stimulated with 10 μg
of peptide for 24 hr. The supernatant was
removed and tested for IL-8 by ELISA.
Peptide (10 ug/ml) IL-8 (ng/ml)
No peptide         0.164
LPS, no peptide    0.26
SEQ ID NO: 1       0.278
SEQ ID NO: 6       0.181
SEQ ID NO: 7       0.161
SEQ ID NO: 9       0.21
SEQ ID NO: 10      0.297
SEQ ID NO: 13      0.293
SEQ ID NO: 14      0.148
SEQ ID NO: 16      0.236
SEQ ID NO: 17      0.15
SEQ ID NO: 19      0.161
SEQ ID NO: 20      0.151
SEQ ID NO: 21      0.275
SEQ ID NO: 22      0.314
SEQ ID NO: 23      0.284
SEQ ID NO: 24      0.139
SEQ ID NO: 26      0.201
SEQ ID NO: 27      0.346
SEQ ID NO: 28      0.192
SEQ ID NO: 29      0.188
SEQ ID NO: 30      0.284
SEQ ID NO: 31      0.168
SEQ ID NO: 33      0.328
SEQ ID NO: 34      0.315
SEQ ID NO: 35      0.301
SEQ ID NO: 36      0.166
SEQ ID NO: 37      0.269
SEQ ID NO: 38      0.171
SEQ ID NO: 40      0.478
SEQ ID NO: 41      0.371
SEQ ID NO: 42      0.422
SEQ ID NO: 43      0.552
SEQ ID NO: 44      0.265
SEQ ID NO: 45      0.266
SEQ ID NO: 47      0.383
SEQ ID NO: 48      0.262
SEQ ID NO: 49      0.301
SEQ ID NO: 50      0.141
SEQ ID NO: 51      0.255
SEQ ID NO: 52      0.207
SEQ ID NO: 53      0.377
SEQ ID NO: 54      0.133

[0145]

TABLE 41
Induction by Peptide of IL-8 in human blood.
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 (μg/ml) IL-8 (pg/ml)
0                    85
10                   70
100                  323

[0146]

TABLE 42
Induction of IL-8 in HBE cells.
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 ± standard error.
SEQ ID NO: 2
(μg/ml) IL-8 (pg/ml)
0       552 ± 90
0.1     670 ± 155
1       712 ± 205
10      941 ± 15
50      1490 ± 715

[0147]

TABLE 43
Induction of IL-8 in undifferentiated THP-1 cells.
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.
SEQ ID NO: 3
(μg/ml) IL-8 (pg/ml)
0       10.6
10      17.2
50      123.7

[0148]

TABLE 44
Induction of MCP-1 by Peptide, SEQ ID NO: 1 in mouse airway.
BALB/c mice were anaesthetised with avertin and
given intratracheal installation of peptide or water or
no installation (no treatment). The mice were monitored
for 4 hours, anaesthetised and the BAL fluid was
isolated and analyzed for MCP-1 and TNF-α
concentrations by ELISA. The data shown is the mean
of 4 or 5 mice for each condition ± standard error.
	Condition	MCP-1 (pg/ml)	TNF-α (pg/ml)
	Water	16.5 ± 5	664 ± 107
	peptide	111 ± 30	734 ± 210
	Avertin	6.5 ± 0.5	393 ± 129

[0149]

TABLE 45
Lack of Significant TNF-α induction by the Cationic
Peptides. RAW 264.7 macrophage cells were
incubated with indicated peptides (40 μg/ml)
for 6 hours. The supernatant was collected
and tested for levels of TNF-α by ELISA.
The data is presented as the mean of three or
more experiments + standard error.
Peptide Treatment         TNF-α (pg/ml)
Media background          56 ± 8
LPS treatment, No peptide 15207 ± 186
SEQ ID NO: 1              274 ± 15
SEQ ID NO: 5              223 ± 45
SEQ ID NO: 6              297 ± 32
SEQ ID NO: 7              270 ± 42
SEQ ID NO: 8              166 ± 23
SEQ ID NO: 9              171 ± 33
SEQ ID NO: 10             288 ± 30
SEQ ID NO: 12             299 ± 65
SEQ ID NO: 13             216 ± 42
SEQ ID NO: 14             226 ± 41
SEQ ID NO: 15             346 ± 41
SEQ ID NO: 16             341 ± 68
SEQ ID NO: 17             249 ± 49
SEQ ID NO: 19             397 ± 86
SEQ ID NO: 20             285 ± 56
SEQ ID NO: 21             263 ± 8
SEQ ID NO: 22             195 ± 42
SEQ ID NO: 23             254 ± 58
SEQ ID NO: 24             231 ± 32
SEQ ID NO: 26             281 ± 34
SEQ ID NO: 27             203 ± 42
SEQ ID NO: 28             192 ± 26
SEQ ID NO: 29             242 ± 40
SEQ ID NO: 31             307 ± 71
SEQ ID NO: 33             196 ± 42
SEQ ID NO: 34             204 ± 51
SEQ ID NO: 35             274 ± 76
SEQ ID NO: 37             323 ± 41
SEQ ID NO: 38             199 ± 38
SEQ ID NO: 43             947 ± 197
SEQ ID NO: 44             441 ± 145
SEQ ID NO: 45             398 ± 90
SEQ ID NO: 48             253 ± 33
SEQ ID NO: 49             324 ± 38
SEQ ID NO: 50             311 ± 144
SEQ ID NO: 53             263 ± 40
SEQ ID NO: 54             346 ± 86

EXAMPLE 6

[0150] Cationic Peptides Increase Surface Expression of Chemokine Receptors

[0151] To analyze cell surface expression of IL-8RB, CXCR-4, CCR2, and LFA-1, RAW macrophage cells were stained with 10 μg/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.

[0152] 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 μg/ml of peptide was incubated with RAW cells for 4 hr, IL-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.
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.
	Concen-
	tration	Fold Increase in Protein Expression
	Peptide	(μg/ml)	IL-8RB	CXCR-4	CCR2
	SEQ ID	10	1.0	1.0	1.0
	NO: 1
	SEQ ID	50	1.3 ± 0.05	1.3 ± 0.03	1.3 ± 0.03
	NO: 1
	SEQ ID	100	2.4 ± 0.6	1.6 ± 0.23	1.8 ± 0.15
	NO: 1
	SEQ ID	100	2.0 ± 0.6	Not Done	4.5
	NO: 3
	CEMA	50	1.6 ± 0.1	1.5 ± 0.2	1.5 ± 0.15
		100	3.6 ± 0.8	Not Done	4.7 ± 1.1

EXAMPLE 7

[0153] Phosphorylation of Map Kinases by Cationic Peptides

[0154] The cells were seeded at 2.5×105-5×105 cells/ml and left overnight. They were washed once in media, serum starved in the morning (serum free media−4 hrs). 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 0.1 μg/ml-50 μg/ml) or H2O 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 (2×106) were used. They were serum starved overnight, and to stop the reaction 1 ml 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, Ill.). Cell lysates (20 μg 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 at room temperature with 1 μg/ml secondary antibody in TBS. The filters were washed for 30 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 (50-100 ml) 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 4×106 cells/well and were allowed to adhere at 37° C. in 5% CO2 atmosphere for 1 hour. The supenatant 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 μg of each sample was loaded in a 12% SDS-PAGE gel. The gels were blotted onto nitrocellulose, 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.

[0155] 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 ERK1/2 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 ERK1/2 in the mouse RAW cell line.

TABLE 47
Phosphorylation of MAP kinases in response to peptides.
	MAP kinase
	phosphorylated
	Cell Line	Peptide	p38	ERK1/2
	RAW 264.7	SEQ ID NO: 3	−	+
		SEQ ID NO: 2	+	+
	HBE	SEQ ID NO: 3		+
		SEQ ID NO: 2	+	+
	THP-1	SEQ ID NO: 3	+	+
		SEQ ID NO: 2

[0156]

TABLE 48
Peptide Phosphorylation of MAP kinases in human
blood monocytes. SEQ ID NO: 1 at 50 μg/ml) was
used to promote phosphorylation.
	p38 phosphorylation	ERK1/2 phosphorylation
	15 minutes	60 minutes	15 minutes	60 minutes
	+	−	+	+

EXAMPLE 8

[0157] Cationic Peptides Protect Against Bacterial Infection by Enhancing the Immune Response

[0158] BALB/c mice were given 1×105 Salmonella and cationic peptide (200 μg) 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 μg/ml). The plates were incubated overnight at 37° C. and counted for viable bacteria (Table 49 and 50). CD-1 mice were given 1×108 S. aureus in 5% porcine mucin and cationic peptide (200 μg) 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 5.8×106 CFU EHEC bacteria and cationic peptide (200 μg) 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 50 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. 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
		Viable Bacteria	Statistical
	Peptide	in the Spleen	Significance (p
	Treatment	(CFU/ml)	value)
	Control	2.70 ± 0.84 × 105
	SEQ ID NO: 1	1.50 ± 0.26 × 105	0.12
	SEQ ID NO: 6	2.57 ± 0.72 × 104	0.03
	SEQ ID NO: 13	3.80 ± 0.97 × 104	0.04
	SEQ ID NO: 17	4.79 ± 1.27 × 104	0.04
	SEQ ID NO: 27	1.01 ± 0.26 × 105	0.06

[0159]

TABLE 50
Effect of Cationic Peptides on Salmonella Infection in
BALB/c mice. 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.
Peptide Treatment Viable Bacteria in the Spleen (CFU/ml)
Control           1.88 ± 0.16 × 104
SEQ ID NO: 48     1.98 ± 0.18 × 104
SEQ ID NO: 26     7.1 ± 1.37 × 104
SEQ ID NO: 30     5.79 ± 0.43 × 103
SEQ ID NO: 37     1.57 ± 0.44 × 104
SEQ ID NO: 5      2.75 ± 0.59 × 104
SEQ ID NO: 7      5.4 ± 0.28 × 103
SEQ ID NO: 9      1.23 ± 0.87 × 104
SEQ ID NO: 14     2.11 ± 0.23 × 103
SEQ ID NO: 20     2.78 ± 0.22 × 104
SEQ ID NO: 23     6.16 ± 0.32 × 104

[0160]

TABLE 51
Effect of Cationic Peptides in a Murine S. aureus
infection model. CD-1 mice were given 1 × 108
bacteria in 5% porcine mucin via intraperitoneal (IP)
injection. Cationic peptide (200 μg) 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
		# Mice Survived (3 days)/
		Total mice in
Treatment	CFU/ml (blood)	group
No Peptide	7.61 ± 1.7 × 103	6/8
SEQ ID NO: 1	0	4/4
SEQ ID NO: 27	2.25 ± 0.1 × 102	3/4
SEQ ID NO: 30	1.29 ± 0.04 × 102	4/4
SEQ ID NO: 37	9.65 ± 0.41 × 102	4/4
SEQ ID NO: 5	3.28 ± 1.7 × 103	4/4
SEQ ID NO: 6	1.98 ± 0.05 × 102	3/4
SEQ ID NO: 7	3.8 ± 0.24 × 103	4/4
SEQ ID NO: 9	2.97 ± 0.25 × 102	4/4
SEQ ID NO: 13	4.83 ± 0.92 × 103	3/4
SEQ ID NO: 17	9.6 ± 0.41 × 102	4/4
SEQ ID NO: 20	3.41 ± 1.6 × 103	4/4
SEQ ID NO: 23	4.39 ± 2.0 × 103	4/4

[0161]

TABLE 52
Effect of Peptide in a Murine EHEC infection model.
CD-1 male mice (5 weeks old) were given 5.8 × 106
CFU EHEC bacteria via intraperitoneal (IP) injection.
Cationic peptide (200 μg) was given via a separate IP
injection. The mice were monitored for 3 days.
	Treatment	Peptide	Survival (%)
	control	none	25
	SEQ ID NO: 23	200 μg	100

[0162]

TABLE 53
Up-regulation of patterns of gene expression in A549 epithelial cells
induced by peptides that are active in vivo.
The peptides SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 13 at
concentrations of 50 μg/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.
	Fold Up regulation of Gene Expression
	relative to Untreated Cells
	Unstimulated	SEQ ID	SEQ ID	SEQ ID	SEQ ID
Target (Accession number)	Cell Intensity	NO: 30	NO: 7	NO: 13	NO: 37
Zinc finger protein (AF061261)	13	2.6	9.4	9.4	1.0
Cell cycle gene (S70622)	1.62	8.5	3.2	3.2	0.7
IL-10 Receptor (U00672)	0.2	2.6	9	4.3	0.5
Transferase (AF038664)	0.09	12.3	9.7	9.7	0.1
Homeobox protein (AC004774)	0.38	3.2	2.5	2.5	1.7
Forkhead protein (AF042832)	0.17	14.1	3.5	3.5	0.9
Unknown (AL096803)	0.12	4.8	4.3	4.3	0.6
KIAA0284 Protein (AB006622)	0.47	3.4	2.1	2.1	1.3
Hypothetical Protein (AL022393)	0.12	4.4	4.0	4.0	0.4
Receptor (AF112461)	0.16	2.4	10.0	10.0	1.9
Hypothetical Protein (AK002104)	0.51	4.7	2.6	2.6	1.0
Protein (AL050261)	0.26	3.3	2.8	2.8	1.0
Polypeptide (AF105424)	0.26	2.5	5.3	5.3	1.0
SPR1 protein (AB031480)	0.73	3.0	2.7	2.7	1.3
Dehydrogenase (D17793)	4.38	2.3	2.2	2.2	0.9
Transferase (M63509)	0.55	2.7	2.1	2.1	1.0
Peroxisome factor (AB013818)	0.37	3.4	2.9	2.9	1.4

[0163]

TABLE 54
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 μg/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.
	MIC (μg/ml)
	E.	S.	P.	S.
Peptide	coli	aureus	aerug.	typhim.	C. rhod.	EHEC
Polymyxin	0.25	16	0.25	0.5	0.25	0.5
Gentamicin	0.25	0.25	0.25	0.25	0.25	0.5
SEQ ID NO: 1	32	>	96	64	8	4
SEQ ID NO: 5	128	>	>	>	64	64
SEQ ID NO: 6	128	>	>	128	64	64
SEQ ID NO: 7	>	>	>	>	>	>
SEQ ID NO: 8	>	>	>	>	>	>
SEQ ID NO: 9	>	>	>	>	>	>
SEQ ID NO: 10	>	>	>	>	>	64
SEQ ID NO: 12	>	>	>	>	>	>
SEQ ID NO: 13	>	>	>	>	>	>
SEQ ID NO: 14	>	>	>	>	>	>
SEQ ID NO: 15	128	>	>	>	128	64
SEQ ID NO: 16	>	>	>	>	>	>
SEQ ID NO: 17	>	>	>	>	>	>
SEQ ID NO: 19	8	16	16	64	4	4
SEQ ID NO: 2	4	16	32	16	64
SEQ ID NO: 20	8	8	8	8	16	8
SEQ ID NO: 21	64	64	96	64	32	32
SEQ ID NO: 22	8	12	24	8	4	4
SEQ ID NO: 23	4	8	8	16	4	4
SEQ ID NO: 24	16	16	4	16	16	4
SEQ ID NO: 26	0.5	32	64	2	2	0.5
SEQ ID NO: 27	8	64	64	16	2	4
SEQ ID NO: 28	>	>	>	64	64	128
SEQ ID NO: 29	2	>	>	16	32	4
SEQ ID NO: 30	16	>	128	16	16	4
SEQ ID NO: 31	>	>	128	>	>	64
SEQ ID NO: 33	16	32	>	16	64	8
SEQ ID NO: 34	8	>	>	32	64	8
SEQ ID NO: 35	4	128	64	8	8	4
SEQ ID NO: 36	32	>	>	32	32	16
SEQ ID NO: 37	>	>	>	>	>	>
SEQ ID NO: 38	0.5	32	64	4	8	4
SEQ ID NO: 40	4	32	8	4	4	2
SEQ ID NO: 41	4	64	8	8	2	2
SEQ ID NO: 42	1.5	64	4	2	2	1
SEQ ID NO: 43	8	128	16	16	8	4
SEQ ID NO: 44	8	>	128	128	64	64
SEQ ID NO: 45	8	>	128	128	16	16
SEQ ID NO: 47	4	>	16	16	4	4
SEQ ID NO: 48	16	>	128	16	1	2
SEQ ID NO: 49	4	>	16	8	4	4
SEQ ID NO: 50	8	>	16	16	16	8
SEQ ID NO: 51	4	>	8	32	4	8
SEQ ID NO: 52	8	>	32	8	2	2
SEQ ID NO: 53	4	>	8	8	16	8
SEQ ID NO: 54	64	>	16	64	16	32

EXAMPLE 9

[0164] Use of Polynucleotides Induced by Bacterial Signalling Molecules in Diagnostic/Screening

[0165] 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-α 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 μg/ml S. aureus LTA, or 1 μM CpG (concentrations that led to optimal induction of tumor necrosis factor (TNF-α) 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 β, inducible nitric oxide synthase (iNOS), MIP-1α, MIP-1β, MIP-2α, 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-1α, MIP-2α, IL-1β, IL-15, TNFR1 and NF-κB 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 A1. 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.

[0166] The other polynucleotide arrays used are 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 5 μg 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 2.5×106 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, Calif.) 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, Calif.). 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.

[0167] To confirm and assess the functional significance of these changes, the levels of selected mRNAs and proteins were assessed and quantified by densitometry. Northern blots using a CD 14, 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-α and IL-6 as assessed by ELISA, and the up-regulated expression of MEP-2α, and IL-1β 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-α, and IL-1β. 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 O111: B4 LPS
in A549 Epithelial Cells.
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 μg total RNA was used to make Cy3/Cy5
labelled cDNA probes and hybridised onto Human
Operon arrays (PRHU04). 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.
		Control:	Ratio:
Acession		Media only	LPS/
Number	Gene	Intensity	control
D87451	ring finger protein 10	715.8	183.7
AF061261	C3H-type zinc finger protein	565.9	36.7
D17793	aldo-keto reductase family 1,	220.1	35.9
	member C3
M14630	prothymosin, alpha	168.2	31.3
AL049975	Unknown	145.6	62.3
L04510	ADP-ribosylation factor	139.9	213.6
	domain protein 1, 64 kD
U10991	G2 protein	101.7	170.3
U39067	eukaryotic translation	61.0	15.9
	initiation factor 3, subunit 2
X03342	ribosomal protein L32	52.6	10.5
NM_004850	Rho-associated, coiled-coil	48.1	11.8
	containing protein kinase 2
AK000942	Unknown	46.9	8.4
AB040057	serine/threonine protein	42.1	44.3
	kinase MASK
AB020719	KIAA0912 protein	41.8	9.4
AB007856	FEM-1-like death receptor	41.2	15.7
	binding protein
J02783	procollagen-proline, 2-	36.1	14.1
	oxoglutarate 4-dioxygenase
AL137376	Unknown	32.5	17.3
AL137730	Unknown	29.4	11.9
D25328	phosphofructokinase, platelet	27.3	8.5
AF047470	malate dehydrogenase 2,	25.2	8.2
	NAD
M86752	stress-induced-	22.9	5.9
	phosphoprotein 1
M90696	cathepsin S	19.6	6.8
AK001143	Unknown	19.1	6.4
AF038406	NADH dehydrogenase	17.7	71.5
AK000315	hypothetical protein	17.3	17.4
	FLJ20308
M54915	pim-1 oncogene	16.0	11.4
D29011	proteasome subunit, beta	15.3	41.1
	type, 5
AK000237	membrane protein of	15.1	9.4
	cholinergic synaptic vesicles
AL034348	Unknown	15.1	15.8
AL161991	Unknown	14.2	8.1
AL049250	Unknown	12.7	5.6
AL050361	PTD017 protein	12.6	13.0
U74324	RAB interacting factor	12.3	5.2
M22538	NADH dehydrogenase	12.3	7.6
D87076	KIAA0239 protein	11.6	6.5
NM_006327	translocase of inner	11.5	10.0
	mitochondrial membrane 23
	(yeast) homolog
AK001083	Unknown	11.1	8.6
AJ001403	mucin 5, subtype B,	10.8	53.4
	tracheobronchial
M64788	RAP1, GTPase activating	10.7	7.6
	protein 1
X06614	retinoic acid receptor, alpha	10.7	5.5
U85611	calcium and integring binding	10.3	8.1
	protein
U23942	cytochrome P450, 51	10.1	10.2
AL031983	Unknown	9.7	302.8
NM_007171	protein-O-	9.5	6.5
	mannosyltransferase 1
AK000403	hypothetical protein	9.5	66.6
	FLJ20396
NM_002950	ribophorin I	9.3	35.7
L05515	cAMP response element-	8.9	6.2
	binding protein CRE-BPa
X83368	phosphoinositide-3-kinase,	8.7	27.1
	catalytic, gamma polypeptide
M30269	nidogen (enactin)	8.7	5.5
M91083	chromosome 11 open reading	8.2	6.6
	frame 13
D29833	salivary proline-rich protein	7.7	5.8
AB024536	immunoglobulin superfamily	7.6	8.0
	containing leucine-rich repeat
U39400	chromosome 11 open reading	7.4	7.3
	frame 4
AF028789	unc119 (C.elegans) homolog	7.4	27.0
NM_003144	signal sequence receptor,	7.3	5.9
	alpha (translocon-associated
	protein alpha)
X52195	arachidonate 5-lipoxygenase-	7.3	13.1
	activating protein
U43895	human growth factor-	6.9	6.9
	regulated tyrosine kinase
	substrate
L25876	cyclin-dependent kinase	6.7	10.3
	inhibitor 3
L04490	NADH dehydrogenase	6.6	11.1
Z18948	S100 calcium-binding protein	6.3	11.0
D10522	myristoylated alanine-rich	6.1	5.8
	protein kinase C substrate
NM_014442	sialic acid binding Ig-like	6.1	7.6
	lectin 8
U81375	solute carrier family 29	6.0	6.4
AF041410	malignancy-associated	5.9	5.3
	protein
U24077	killer cell immunoglobulin-	5.8	14.4
	like receptor
AL137614	hypothetical protein	4.8	6.8
NM_002406	mannosyl (alpha-1,3-)-	4.7	5.3
	glycoprotein beta-1,2-N-
	acetylglucosaminyltransferase
AB002348	KIAA0350 protein	4.7	7.6
AF165217	tropomodulin 4 (muscle)	4.6	12.3
Z14093	branched chain keto acid	4.6	5.4
	dehydrogenase E1, alpha
	polypeptide
U82671	caltractin	3.8	44.5
AL050136	Unknown	3.6	5.0
NM_005135	solute carrier family 12	3.6	5.0
AK001961	hypothetical protein	3.6	5.9
	FLJ11099
AL034410	Unknown	3.2	21.3
S74728	antiquitin 1	3.1	9.2
AL049714	ribosomal protein L34	3.0	19.5
	pseudogene 2
NM_014075	PRO0593 protein	2.9	11.5
AF189279	phospholipase A2, group IIE	2.8	37.8
J03925	integrin, alpha M	2.7	9.9
NM_012177	F-box protein Fbx5	2.6	26.2
NM_004519	potassium voltage-gated	2.6	21.1
	channel, KQT-like subfamily,
	member 3
M28825	CD1A antigen, a polypeptide	2.6	16.8
X16940	actin, gamma 2, smooth	2.4	11.8
	muscle, enteric
X03066	major histocompatibility	2.2	36.5
	complex, class II, DO beta
AK001237	hypothetical protein	2.1	18.4
	FLJ10375
AB028971	KIAA1048 protein	2.0	9.4
AL137665	Unknown	2.0	7.3

[0168]

TABLE 56
Polynucleotides Down-regulated by E. coli O111: B4
LPS in A549 Epithelial Cells.
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 μg 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 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.
		Control:
		Media
		only	Ratio:
Accession		Inten-	LPS/
Number	Gene	sity	control
NM_017433	myosin IIIA	167.8	0.03
X60484	H4 histone family member E	36.2	0.04
X60483	H4 histone family member D	36.9	0.05
AF151079	hypothetical protein	602.8	0.05
M96843	inhibitor of DNA binding 2, dominant	30.7	0.05
	negative helix-loop-helix protein
S79854	deiodinase, iodothyronine, type III	39.4	0.06
AB018266	matrin 3	15.7	0.08
M33374	NADH dehydrogenase	107.8	0.09
AF005220	Homo sapiens mRNA for	105.2	0.09
	NUP98-HOXD13
	fusion protein, partial cds
Z80783	H2B histone family, member L	20.5	0.10
Z46261	H3 histone family, member A	9.7	0.12
Z80780	H2B histone family, member H	35.3	0.12
U33931	erythrocyte membrane protein band 7.2	18.9	0.13
	(stomatin)
M60750	H2B histone family, member A	35.8	0.14
Z83738	H2B histone family, member E	19.3	0.15
Y14690	collagen, type V, alpha 2	7.5	0.15
M30938	X-ray repair complementing defective	11.3	0.16
	repair in Chinese hamster cells 5
L36055	eukaryotic translation initiation	182.5	0.16
	factor 4E binding protein 1
Z80779	H2B histone family, member G	54.3	0.16
AF226869	5(3)-deoxyribonucleotidase; RB-	7.1	0.18
	associated KRAB repressor
D50924	KIAA0134 gene product	91.0	0.18
AL133415	vimentin	78.1	0.19
AL050179	tropomyosin 1 (alpha)	41.6	0.19
AJ005579	RD element	5.4	0.19
M80899	AHNAK nucleoprotein	11.6	0.19
NM_004873	BCL2-associated athanogene 5	6.2	0.19
X57138	H2A histone family, member N	58.3	0.20
AF081281	lysophospholipase I	7.2	0.22
U96759	von Hippel-Lindau binding protein 1	6.6	0.22
U85977	Human ribosomal protein L12	342.6	0.22
	pseudogene, partial cds
D13315	glyoxalase I	7.5	0.22
AC003007	Unknown	218.2	0.22
AB032980	RU2S	246.6	0.22
U40282	integrin-linked kinase	10.1	0.22
U81984	endothelial PAS domain protein 1	4.7	0.23
X91788	chloride channel,	9.6	0.23
	nucleotide-sensitive, 1A
AF018081	collagen, type XVIII, alpha 1	6.9	0.24
L31881	nuclear factor I/X (CCAAT-binding	13.6	0.24
	transcription factor)
X61123	B-cell translocation gene 1, anti-	5.3	0.24
	proliferative
L32976	mitogen-activated protein kinase kinase	6.3	0.24
	kinase 11
M27749	immunoglobulin lambda-like	5.5	0.24
	polypeptide 3
X57128	H3 histone family, member C	9.0	0.25
X80907	phosphoinositide-3-kinase, regulatory	5.8	0.25
	subunit, polypeptide 2
Z34282	H. sapiens (MAR11) MUC5AC mRNA	100.6	0.26
	for mucin (partial)
X00089	H2A histone family, member M	4.7	0.26
AL035252	CD39-like 2	4.6	0.26
X95289	PERB11 family member in MHC class I	27.5	0.26
	region
AJ001340	U3 snoRNP-associated 55-kDa protein	4.0	0.26
NM_014161	HSPC071 protein	10.6	0.27
U60873	Unknown	6.4	0.27
X91247	thioredoxin reductase 1	84.4	0.27
AK001284	hypothetical protein FLJ10422	4.2	0.27
U90840	synovial sarcoma, X breakpoint 3	6.6	0.27
X53777	ribosomal protein L17	39.9	0.27
AL035067	Unknown	10.0	0.28
AL117665	DKFZP586M1824 protein	3.9	0.28
L14561	ATPase, Ca++ transporting, plasma	5.3	0.28
	membrane 1
L19779	H2A histone family, member O	30.6	0.28
AL049782	Unknown	285.3	0.28
X00734	tubulin, beta, 5	39.7	0.29
AK001761	retinoic acid induced 3	23.7	0.29
U72661	ninjurin 1	4.4	0.29
S48220	deiodinase, iodothyronine, type I	1,296.1	0.29
AF025304	EphB2	4.5	0.30
S82198	chymotrypsin C	4.1	0.30
Z80782	H2B histone family, member K	31.9	0.30
X68194	synaptophysin-like protein	7.9	0.30
AB028869	Unknown	4.2	0.30
AK000761	Unknown	4.3	0.30

[0169]

TABLE 57
Polynucleotides expressed to similar extents after stimulation by the
bacterial products LPS, LTA, and CpG DNA.
Bacterial products (100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA or 1 μM
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.
	Control	Ratio	Ratio	Ratio
Accession	Unstim.	LPS:	LTA:	CpG:
number	Intensity	Control	Control	Control	Protein/polynucleotide
M15131	20	82	80	55	IL-1β
M57422	20	77	64	90	tristetraprolin
X53798	20	73	77	78	MIP-2α
M35590	188	50	48	58	MIP-1β
L28095	20	49	57	50	ICE
M87039	20	37	38	45	iNOS
X57413	20	34	40	28	TGFβ
X15842	20	20	21	15	c-rel proto-oncopolynucleotide
X12531	489	19	20	26	MIP-1α
U14332	20	14	15	12	IL-15
M59378	580	10	13	11	TNFR1
U37522	151	6	6	6	TRAIL
M57999	172	3.8	3.5	3.4	NF-κB
U36277	402	3.2	3.5	2.7	I-κB (alpha subunit)
X76850	194	3	3.8	2.5	MAPKAP-2
U06924	858	2.4	3	3.2	Stat 1
X14951	592	2	2	2	CD18
X60671	543	1.9	2.4	2.8	NF-2
M34510	5970	1.6	2	1.4	CD14
X51438	2702	1.3	2.2	2.0	vimentin
X68932	4455	0.5	0.7	0.5	c-Fms
Z21848	352	0.5	0.6	0.6	DNA polymerase
X70472	614	0.4	0.6	0.5	B-myb

[0170]

TABLE 58
Polynucleotides that were differentially regulated by the bacterial
products LPS, LTA, and CpG DNA.
Bacterial products (100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA or 1 μM
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.
	Unstim.	Ratio	Ratio	Ratio
Accession	Control	LPS:	LTA:	CpG:
number	Intensity	Control	Control	Control	Protein/polynucleotide
X72307	20	1.0	23	1.0	hepatocyte growth factor
L38847	20	1.0	21	1.0	hepatoma transmembrane kinase
					ligand
L34169	393	0.3	3	0.5	thrombopoietin
J04113	289	1	4	3	Nur77
Z50013	20	7	21	5	H-ras proto-oncopolynucleotide
X84311	20	4	12	2	Cyclin A1
U95826	20	5	14	2	Cyclin G2
X87257	123	2	4	1	Elk-1
J05205	20	18	39	20	Jun-D
J03236	20	11	19	14	Jun-B
M83649	20	71	80	42	Fas 1 receptor
M83312	20	69	91	57	CD40L receptor
X52264	20	17	23	9	ICAM-1
M13945	573	2	3	2	Pim-1
U60530	193	2	3	3	Mad related protein
D10329	570	2	3	2	CD7
X06381	20	55	59	102	Leukemia inhibitory factor (LIF)
X70296	20	6.9	13	22	Protease nexin 1 (PN-1)
U36340	20	38	7	7	CACCC Box-binding protein
					BKLF
S76657	20	11	6	7	CRE-BPI
U19119	272	10	4	4	interferon inducible protein 1

[0171]

TABLE 59
Confirmation of Table 57 and 58 Array Data.
	Relative levels
Product	Untreated	LPS	LTA	CpG
CD14a	1.0	2.2 ± 0.4	1.8 ± 0.2	1.5 ± 0.3
Vimentina	1.0	1.2 ± 0.07	1.5 ± 0.05	1.3 ± 0.07
Tristetraprolina	1.0	5.5 ± 0.5	5.5 ± 1.5	9.5 ± 1.5
LIFb	1.0	2.8 ± 1.2	2.7 ± 0.6	5.1 ± 1.6
NOc	8 ± 1.5	47 ± 2.5	20 ± 3	21 ± 1.5
a Total RNA was isolated from unstimulated RAW macrophage cells and cells treated for 4 hr with 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, 1 μM 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.
b RAW 264.7 cells were stimulated with 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, 1 μM 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.
c Supernatant was collected from RAW macrophage cells treated with 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, 1 μM CpG DNA, or media alone for 24 hours and tested for the amount of NO formed in the supernatant 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.

[0172]

TABLE 60
Pattern of Gene expression in A549 Human Epithelial cells
up-regulated by bacterial signalling molecules (LPS).
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 μg total RNA was used to
make Cy3/Cy5 labelled cDNA probes and hybridised onto
Human Operon arrays (PRHU04). 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.
Accession Number Gene
AL050337         interferon gamma receptor 1
U05875           interferon gamma receptor 2
NM_002310        leukemia inhibitory factor receptor
U92971           coagulation factor II (thrombin) receptor-like 2
Z29575           tumor necrosis factor receptor superfamily
                 member 17
L31584           Chemokine receptor 7
J03925           cAMP response element-binding protein
M64788           RAP1, GTPase activating protein
NM_004850        Rho-associated kinase 2
D87451           ring finger protein 10
AL049975         Unknown
U39067           eukaryotic translation initiation factor 3, subunit 2
AK000942         Unknown
AB040057         serine/threonine protein kinase MASK
AB020719         KIAA0912 protein
AB007856         FEM-1-like death receptor binding protein
AL137376         Unknown
AL137730         Unknown
M90696           cathepsin S
AK001143         Unknown
AF038406         NADH dehydrogenase
AK000315         hypothetical protein FLJ20308
M54915           pim-1 oncogene
D29011           proteasome subunit, beta type, 5
AL034348         Unknown
D87076           KIAA0239 protein
AJ001403         mucin 5, subtype B, tracheobronchial
J03925           integrin, alpha M

EXAMPLE 10

[0173] Altering Signaling to Protect Against Bacterial Infections

[0174] 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 (1×105 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% CO2 incubator. Cells were washed 3 times with PBS to remove extracellular bacteria and then incubated in DMEM+10% FBS containing 100 μg/mnl gentarnicin (Sigma, St. Louis, Mo.) to kill any remaining extracellular bacteria and prevent re-infection. After 2 h, the gentamicin concentration was lowered to 10 μg/ml and maintained throughout the assay. Cells were pretreated with inhibitors for 30 min prior to infection at the following concentrations: 50 μM PD 98059 (Calbiochem), 50 μM U 0126 (Promega), 2 mM diphenyliodonium (DPI), 250 μM acetovanillone (apocynin, Aldrich), 1 mM ascorbic acid (Sigma), 30 mM N-acetyl cysteine (Sigma), and 2 mM NG-L-monomethyl arginine (L-NMMA, Molecular Probes) or 2 mM NG-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-γ-primed RAW cells.
Treatmenta Effectb
0          None
MEK        Decrease bacterial filamentation (bacterial stress)c
inhibitor  Increase in the number of intracellular S. Typhimurium
U 0126
MEK        Decrease bacterial filamentation (bacterial stress)c
inhibitor  Increase in the number of intracellular S. Typhimurium
PD 98059
NADPH      Decrease bacterial filamentation (bacterial stress)c
oxidase    Increase in the number of intracellular S. Typhimurium
inhibitord

EXAMPLE 11

[0175] Anti-Viral Activity

[0176] SDF-1, a C-X-C chemokine is a natural ligand for HIV-1 coreceptor-CXCR4. The chemokine receptors CXCR4 and CCR5 are considered to be potential targets for the inhibition of HIV-1 replication. The crystal structure of SDF-1 exhibits antiparallel β-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 5×106/ml in chemotaxis medium (RPMI 1640/10 mM Hepes/0.5% BSA). Migration assays were performed in 24 well plates using 5 μm polycarbonate Transwell inserts (Costar). Briefly, peptide or controls were diluted in chemotaxis medium and placed in the lower chamber while 0.1 ml cells (5×106/ml) 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 5×105 /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 (%)
	Positive	SDF-1	SDF-1 + SEQ 1D	Negative
Experiment	control	(100 ng/ml)	1 (50 μg/ml)	control
1	100%	32%	0%	<0.01%
2	100%	40%	0%	0%

[0177]

TABLE 63
Corresponding polynucleotide array data to Table 56:
	Poly-		Ratio
Polynucleotide /	nucleotide	Unstimulated	peptide:	Accession
Protein	Function	Intensity	Unstimulated	Number
CXCR-4	Chemokine	36	4	D87747
	receptor

[0178]

TABLE 64
Corresponding FACs data to Tables 62 and 63:
			Fold Increase in Protein
		Concentration	Expression
	Peptide	(μg/ml)	CXCR-4
	SEQ ID NO: 1	10	No change
	SEQ ID NO: 1	50	1.3 ± 0.03
	SEQ ID NO: 1	100	1.6 ± 0.23
	SEQ ID NO: 3	100	1.5 ± 0.2

[0179] 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

1. 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 comprising contacting the polynucleotide or polynucleotides with one or more sepsis or inflammatory inducing agents, contacting the polynucleotide or polynucleotides with a cationic peptide either simultaneously or immediately thereafter, and determining a change in expression, wherein a change is indicative of a polynucleotide or pattern of polynucleotides that is regulated by a sepsis or inflammatory inducing agent and reduced by a cationic peptide.

2. The method of claim 1, wherein the sepsis or inflammatory inducing agent is LPS, LTA or CpG DNA, bacterial components or whole cells, or related agents.

3. The method of claim 1, comprising determining the level of expression of the polynucleotide prior to and following contacting with the sepsis or inflammatory inducing agent.

4. A polynucleotide or polynucleotide pattern identified by the method of claim 1.

5. A polynucleotide of claim 3, wherein the polynucleotide encodes a polypeptide involved in an inflammatory or septic response.

6. A method of identifying an agent that blocks sepsis or inflammation comprising combining a polynucleotide of claim 5 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 the inflammatory or septic response.

7. The method of claim 6, wherein the effect is inhibition of the inflammatory or septic response.

8. An agent identified by the method of claim 6.

9. The agent of claim 8, wherein the agent is a peptide, peptidomimetic, chemical compound, nucleic acid molecule or a polypeptide.

10. The agent of claim 8, wherein the peptide is selected from SEQ ID NO:4-54.

11. A method of identifying a pattern of polynucleotide expression for inhibition of an inflammatory or septic response comprising: contacting cells with LPS, LTA, CpG DNA and/or intact bacteria or bacterial components in the presence or absence of a cationic peptide; detecting a pattern of polynucleotide expression for the cells in the presence and absence of the peptide, wherein the pattern in the presence of the peptide represents inhibition of an inflammatory or septic response.

12. The method of claim 11, further comprising contacting cells with one or more compounds suspected of inhibiting an inflammatory or septic response and identifying a compound that provides a pattern of polynucleotide expression similar to a pattern obtained with a cationic peptide that inhibits an inflammatory or septic response.

13. A compound identified by the method of claim 11.

14. A method of identifying an agent that enhances innate immunity comprising: 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.

15. The method of claim 14, wherein the agent does not stimulate a septic reaction.

16. The method of claim 14, wherein the agent inhibits the inflammatory or septic response.

17. The method of claim 14, wherein the agent blocks the inflammatory or septic response.

18. The method as in any of claims 16 or 17, wherein the agent increases the expression of an anti-inflammatory encoding polynucleotide.

19. The method of claim 18, wherein the anti-inflammatory gene is selected from a subset that includes IL-1 R antagonist homolog 1 (AI167887), IL-10 R beta (AA486393), IL-10 R alpha (U00672), TNF Receptor member 1B (AA150416), TNF receptor member 5 (H98636), TNF receptor member 11b (AA194983), IK cytokine down-regulator of HLA II (R39227), TGFB inducible early growth response 2 (AI473938), CD2 (AA927710), glucocorticoid-related polynucleotides (AK000892), or IL-10 (M5 762720.

20. The method of claim 19, wherein the agent inhibits the expression of TNF-alpha.

21. The method of claim 19, wherein the agent inhibits the expression of interleukins.

22. The method of claim 23, wherein the interleukin is IL-8.

23. The method of claim 16, wherein the agent is a peptide.

24. The method of claim 23, wherein the peptide is selected from SEQ ID NO: 4-54.

25. An agent identified by the method of claim 14.

26. An agent of claim 25, wherein the agent is a peptide, peptidomimetic, chemical compound, or a nucleic acid molecule.

27. A method of identifying a pattern of polynucleotide expression for identification of a compound that selectively enhances innate immunity comprising: 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 that is similar to the pattern observed in the presence of the cationic peptide, is indicative of a compound that enhances innate immunity.

28. A compound identified by the method of claim 27.

29. The method of claim 27, wherein the compound does not stimulate a septic reaction.

30. The method of claim 27, wherein the polynucleotide expression pattern includes expression of pro-inflammatory polynucleotides.

31. The method of claim 30, wherein the pro-inflammatory polynucleotides include ring finger protein 10 (D87451), serine/threonine protein kinase MASK (AB040057), KIAA0912 protein (AB020719), KIAA0239 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 (J03925), Rho-associated kinase 2 (NM—004850), PTD017 protein (AL050361) unknown genes (AK00143, AK034348, AL049250, AL16199, AL031983), retinoic acid receptor (X06614), G protein-coupled receptors (Z94155, X81892, U52219, U22491, AF015257, U66579) chemokine (C-C motif) receptor 7 (L31584), tumor necrosis factor receptor superfamily member 17 (Z29575), interferon gamma receptor 2 (U05875), cytokine receptor-like factor I (AF059293), class I cytokine receptor (AF053004), coagulation factor II (thrombin) receptor-like 2 (U92971), leukemia inhibitory factor receptor (NM—002310), interferon gamma receptor 1 (AL050337) or any combination thereof.

32. The method of claim 27, wherein the expression pattern includes expression of polynucleotides encoding chemokines.

33. The method of claim 27, wherein the expression pattern includes expression of cell differentiation factors.

34. The method of claim 27, wherein the polynucleotide expression pattern includes expression of cell surface receptors.

35. The method of claim 34, wherein the cell surface receptors include chemokine receptors or integrin receptors.

36. A method of identifying an agent that is capable of selectively enhancing innate immunity comprising: contacting a cell containing a polynucleotide or polynucleotides that encode a polypeptide involved in innate immunity, with an agent of interest, wherein expression of the polynucleotide or polynucleotides in the presence of the agent is modulated as compared with expression in the absence of the agent and wherein the modulated expression results in enhancement of innate immunity.

37. The method of claim 26 in which the pattern of expression is utilized in screening for compounds that enhance innate immunity.

38. A compound of claim 28, wherein the compound stimulates chemokine or chemokine receptor expression.

39. A compound of claim 38, wherein the chemokine or chemokine receptor is CXCR4, CCR5, CCR2, CCR6, MIP-1 alpha, IL-8, MCP-1, MCP-2, MCP-3, MCP-4, or MCP-5.

40. A compound of claim 28, wherein the compound is a peptide, peptidomimetic, chemical compound, or a nucleic acid molecule.

41. A method of identifying an agent that is capable of both suppressing or blocking septic or inflammatory responses and enhancing innate immunity comprising: contacting a cell containing i) a polynucleotide or polynucleotides that encode a polypeptide capable of suppressing inflammatory or septic responses and ii) a polynucleotide or polynucleotides that encode a polypeptide involved in innate immunity, with an agent of interest, wherein expression of in the presence of the agent is modulated as compared with expression of the polynucleotide or polynucleotides in the absence of the agent and wherein the modulated expression results in suppression of inflammatory or septic responses and enhancement of innate immunity.

42. A method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject comprising 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.

43. A method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject comprising identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by a decrease in polynucleotide expression of at least 2 polynucleotides in Table 56 as compared to a non-infected subject.

44. A method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject comprising identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by a polynucleotide expression of at least 2 polynucleotides in Table 57 as compared to a non-infected subject.

45. The method of any of claims 30, 31 or 32, wherein the state of infection is due to a bacteria, virus, fungus or parasitic agent.

46. The method of any of claims 30, 31 or 32, wherein the state of infection is due to a Gram positive or Gram negative bacteria.

47. A polynucleotide expression pattern of a subject having a state of infection identified by the method of claim 31.

48. A cationic peptide that is an antagonist of CXCR-4.

49. A method of identifying a cationic peptide that is an antagonist of CXCR-4 comprising contacting T cells with SDF-1 in the presence of absence of a test peptide and measuring chemotaxis, wherein a decrease in chemotaxis in the presence of the test peptide is indicative of a peptide that is an antagonist of CXCR-4.

50. An isolated cationic peptide comprising the general formula X1X2X3IX4PX4IPX5X2X1 (SEQ ID NO: 4), wherein X1 is one or two of R, L or K, X2 is one of C, S or A, X3 is one of R or P, X4 is one of A or V and X5 is one of V or W.

51. The cationic peptide of claim 38, wherein the peptide is selected from the group consisting of: LLCRIVPVIPWCK (SEQ ID NO: 5), LRCPIAPVIPVCKK (SEQ ID NO: 6), KSRIVPAIPVSLL (SEQ ID NO: 7), KKSPIAPAIPWSR (SEQ ID NO: 8), RRARWVPAIPVARR (SEQ ID NO: 9) and LSRIAPAIPWAKL (SEQ ID NO: 10).

52. The peptide of claim 38, wherein the peptide has anti-inflammatory activity.

53. The peptide of claim 38, wherein the peptide has anti-sepsis activity.

54. An isolated cationic peptide comprising the general formula X1LX2X3KX4X2X5X3PX3X1 (SEQ ID NO: 11), wherein X1 is one or two of D, E, S, T or N, X2 is one or two of P, G or D, X3 is one of G, A, V, L, I or Y, X4 is one of R, K or H and X5 is one of S, T, C, M or R.

55. The cationic peptide of claim 42, wherein the peptide is selected from the group consisting of: DLPAKRGSAPGST (SEQ ID NO: 12), SELPGLKHPCVPGS (SEQ ID NO: 13), TTLGPVKRDSIPGE (SEQ ID NO: 14), SLPII(HDRLPATS (SEQ ID NO: 15), ELPLKRGRVPVE (SEQ ID NO: 16) and NLPDLKKPRVPATS (SEQ ID NO: 17).

56. The peptide of claim 42, wherein the peptide has anti-inflammatory activity.

57. The peptide of claim 42, wherein the peptide has anti-sepsis activity.

58. An isolated cationic peptide comprising the general formula X1X2X3X4WX4WX4X5K (SEQ ID NO: 18), wherein X1 is one to four chosen from A, P or R, X2 is one or two aromatic amino acids (F, Y and W), X3 is one of P or K, X4 is one, two or none chosen from A, P, Y or W and X5 is one to three chosen from R or P.

59. The cationic peptide of claim 46, wherein the peptide is selected from the group consisting of: RPRYPWWPWWPYRPRK (SEQ ID NO: 19), RRAWWKAWWARRK (SEQ ID NO: 20), RAPYVYPWAWARPRK (SEQ ID NO: 21), RPAWKYWWPWPWPRRK (SEQ ID NO: 22), RAAFKWAWAWWRRK (SEQ ID NO: 23) and RRRWKWAWPRRK (SEQ ID NO: 24).

60. The peptide of claim 46, wherein the peptide has anti-inflammatory activity.

61. The peptide of claim 46, wherein the peptide has anti-sepsis activity.

62. An isolated cationic peptide comprising the general formula X1X2X3X4X1VX3X4RGX4X3X4X1X3X1 (SEQ ID NO: 25) wherein X1 is one or two of R or K, X2 is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X3 is C, S, M, D or A and X4 is F, I, V, M or R.

63. The cationic peptide of claim 50, wherein the peptide is selected from the group consisting of: RRMCIHVCVRGVCRRKCRK (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).

64. The peptide of claim 50, wherein the peptide has anti-inflammatory activity.

65. The peptide of claim 50, wherein the peptide has anti-sepsis activity.

66. An isolated cationic peptide comprising the general formula X1X2X3X4X1VX5X4RGX4X5X4X1X3X1 (SEQ ID NO: 32), wherein X1 is one or two of R or K, X2 is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X3 is one of C, S, M, D or A, X4 is one of F, I, V, M or Rand X5 is one of A, I, S, M, D or R.

67. The cationic peptide of claim 54, wherein the peptide is selected from the group consisting of: 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).

68. The peptide of claim 54, wherein the peptide has anti-inflammatory activity.

69. The peptide of claim 54, wherein the peptide has anti-sepsis activity.

70. An isolated cationic peptide comprising the general formula KX1KX2FX2KMLMX2ALKKX3 (SEQ ID NO: 39), wherein X1 is a polar amino acid (C, S, T, M, N and Q); X2 is one of A, L, S or K and X3 is 1-17 amino acids chosen from G, A, V, L, I, P, F, S, T, K and H.

71. The cationic peptide of claim 58, wherein the peptide is selected from the group consisting of: 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).

72. The peptide of claim 58, wherein the peptide has anti-inflammatory activity.

73. The peptide of claim 58, wherein the peptide has anti-sepsis activity.

74. An isolated cationic peptide comprising the general formula KWKX2X1X1X2X2XX2X2X1X1X2X2IFHTALKPISS (SEQ ID NO: 46), wherein X1 is a hydrophobic amino acid and X2 is a hydrophilic amino acid.

75. The cationic peptide of claim 62, wherein the peptide is selected from the group consisting of: 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).

76. The peptide of claim 62, wherein the peptide has anti-inflammatory activity.

77. The peptide of claim 62, wherein the peptide has anti-sepsis activity.

78. An isolated cationic peptide comprising the sequence KWKSFLRTFKSPVRTVFHTALKPISS (SEQ ID NO: 53).

79. An isolated cationic peptide comprising the sequence KWKSYAHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

80. The method of claim 28, wherein the agent is a Zinc finger protein (AF061261); Cell cycle gene (S70622); IL-10 Receptor U00672); Transferase (AF038664); Homeobox protein (AC004774); Forkhead protein (AF042832); Unknown (AL096803); KIAA0284 Protein (AB006622); Hypothetical Protein (AL022393); Receptor (AF112461); Hypothetical Protein (AK002104); Protein (AL050261); Polypeptide (AF105424); SPR1 protein (AB031480); Dehydrogenase (D17793); Transferase (M63509); and Peroxisome factor (AB013818).

81. The polynucleotide expression pattern of a subject having a state of infection identified by claim 56 wherein the genes upregulated are Accession number D87451 -ring finger protein 10; Accession number AL049975, Unknown; Accession number U39067, eukaryotic translation initiation factor 3 subunit 2; Accession number AK000942, Unknown; Accession number AB040057, serine/threonine protein kinase MASK; Accession number AB020719, KIAA0912 protein; Accession number AB007856, FEM-1-like death receptor binding protein; Accession number AL137376, Unknown; Accession number AL137730, Unknown; Accession number M90696, cathepsin S; Accession number AK00143, Unknown; Accession number AF038406, NADH dehydrogenase; Accession number AK000315, hypothetical protein FLJ20308; Accession number M54915, pim-1 oncogene; Accession number D29011, proteasome subunit beta type 5; Accession number AL034348, Unknown; Accession number D87076, KIAA0239 protein; Accession number AJ001403, tracheobronchial mucin 5 subtype B; Accession number J03925, integrin alpha M, Rho-associated kinase 2 (NM—004850), PTD017 protein (AL050361) unknown genes (AK00143, AK034348, AL049250, AL16199, AL031983), retinoic acid receptor (X06614), G protein-coupled receptors (Z94155, X81892, U52219, U22491, AF015257, U66579) chemokine (C-C motif) receptor 7 (L31584), tumor necrosis factor receptor superfamily member 17 (Z29575), interferon gamma receptor 2 (U05875), cytokine receptor-like factor 1 (AF059293), class I cytokine receptor (AF053004), coagulation factor 11 (thrombin) receptor-like 2 (U92971), leukemia inhibitory factor receptor (NM—002310), interferon gamma receptor 1 (AL050337), or any combination thereof.

82. The method of claim 32, wherein the chemokines include CXCR4, CXCR1, CXCR2, CCR2, CCR4, CCR5, CCR6, MIP-1 alpha, MDC, MIP-3 alpha, MCP-1, MCP-2, MCP-3, MCP-4, MCP-5, and RANTES.

83. The method of claim 33, wherein the cell differentiation factors include TGFβ inducible early growth response 2 (AI473938), zinc finger proteins (AF061261, U00115, X78924), and transcription factors (U31556, ALI37681, X68560).

84. A compound of claim 38, wherein the compound modifies kinase activity.

85. A compound of claim 84, wherein the kinase is selected from MAP kinase kinase 3 (D87116), MAP kinase kinase 6 (H07920), MAP kinase kinase 5 (W69649), MAP kinase 7 (H39192), MAP kinase 12 (AI936909), MAP kinase-activated protein kinase 3 (W68281), or MAP kinase kinase 1 (L11284).

86. A compound of claim 21, wherein the compound decreases proteasome subunit expression.

87. A compound of claim 86, wherein the proteasome subunit includes polynucleotides with accession numbers D11094, L02426, D00763, AB009398, AF054185, M34079, M34079, or AL031177.

88. An isolated cationic peptide that reduces polynucleotide expression of SDF-1 receptor.