WO2003053351A2 - A NOVEL REGULATORY ELEMENT WITHIN THE IL-Iα PROMOTER AND USES THEREOF - Google Patents

Abstract

A novel regulatory element was identified in the promoter of Interleukin 1 alpha (IL-1α) which mediates activation of the promoter and may be involved in the symptoms and pathogenesis of immune and inflammatory diseases as well as cancer and AIDS. A protein which binds to the regulatory element and activates transcription of IL-1α was also identified. The protein and the regulatory element are used to identify and isolate pharmaceuticals which are used to treat immune and inflammatory diseases as well as cancer and AIDS.

Description

A METHOD FOR THE IDENTIFICATION OF PHARMACEUTICAL AGENTS ACTIVE AGAINST IMMUNE DISEASE, INFECTIOUS DISEASE, CANCER AND

AIDS

FIELD OF THE INVENTION

The present invention is related to a novel regulatory element in the promoter of Interleukin 1 alpha (IL-lα) which mediates activation of the promoter and may be involved in the symptoms and pathogenesis of immune and inflammatory diseases as well as cancer and AIDS. The present invention is further related to a protein which binds to the novel regulatory element and controls transcription of IL-lα.

BACKGROUND OF THE INVENTION

IL-1 is the prototypic pleiotropic cytokine, affecting almost every cell type, often in synergy with other cytokines. Animal models and studies in humans have demonstrated that IL-1 is a highly inflammatory cytokine and that the margin between clinical benefit and toxicity of IL-1 is extremely narrow. There is strong evidence that the production and activity of IL-1 are' tightly regulated by multiple pathways, and agents that inhibit its synthesis are likely to have important clinical impact. In addition to its role in immune regulation and inflammation, IL-1 is important in development as a growth factor and can

"rescue" animals if administered either before or after lethal doses of cyclophosphamide or gamma irradiation.

Tumor necrosis factor alpha (TNFα) and interleukin (IL-1) are the primary proinflammatory cytokines in the pathogenesis of rheumatoid arthritis (RA). TNFα causes inflammation either directly or through induction of IL-1. IL-1 causes cartilage destruction by enhancing the release of enzymes from chondrocytes and by inliibiting matrix synthesis.

There are several members of the IL-1 gene family, all mapping to human chromosome 2: IL-lα, IL-lβ, and IL-1 receptor antagonist (IL-lra). IL-lra is a specific receptor antagonist which is secreted by monocyte/macrophages. There are two IL-1 receptors, the type I receptor (IL-1RI) transduces a signal, whereas the type II receptor (IL-

1RII) binds IL-1, but does not transduce a signal. When IL-1 binds to the receptor, an IL- 1R accessory protein (IL-lRacP) binds and results in high affinity binding. The soluble form of these receptors as well as IL-lra, provide regulation of IL-1 availability and production, acting both intracellularly and extracellularly.

In addition, recent evidence finds a role for IL-lα in idiopathic inflammatory myopathies such as polymyositis, dermatomyositis and inclusion body myositis. The idiopathic inflammatory myopathies encompass a heterogeneous group of disorders of unknown origin, characterized clinically by symmetric proximal muscle weakness and histopathologically by inflammatory exudates in muscle tissue. The most prominent finding was the expression of IL-lα in all patients, but in none of the normal controls. IL-1 Blockade in Inflammation Both IL-lα and IL-lβ, in addition to TNFα, are potential targets for therapeutic intervention in rheumatoid arthritis. Increasingly, the goal in rheumatoid arthritis therapy is to prevent joint damage, as in the case of anti-TNFα therapy (e.g. ENBREL^®). In experimental rodent arthritis, previous results showed that IL-1 plays an important role in cartilage degradation and recent findings indicate that IL-1 blockade is highly effective in limiting joint erosion. However, most of these findings targeted the role of IL-lβ rather than IL-lα. However, these findings do strengthen the idea of targeting IL-1 for autoimmune therapy. IL-lRa is a naturally expressed antagonist of IL-1 and has been shown to be clinically effective and slows progression of bone damage as measured radiographically. Effect of IL-1 on Anti-Inflammatorv Cytokines

Increased production of the proinflammatory cytokines IL-lα, IL-lβ, TNFα and IL- 6, has been demonstrated in multiple animal models of autoimmunity (allergic experimental encephalitis, EAE, collagen-induced arthritis, murine lupus) and human autoimmune diseases, rheumatoid arthritis (RA), juvenile rheumatoid arthritis (JRA), systemic lupus erythematosus (SLE), autoimmune thrombocytopenia and multiple sclerosis

(MS). These proinflammatory cytokines are responsible for direct tissue damage (cartilage and bone destruction, nephritis, and cerebral inflammation).

Natural resolution of EAE is associated with a switch to antigen-specific T helper cells producing IL-4, IL-5 and IL-10 (T helper type 2, Th2). Administration of Th2 T cell lines or IL-4 and IL-10 have been shown to ameliorate the expression of autoimmunity.

Monocytes/macrophages produce both IL-lα and IL-lβ, but IL-lα is the predominant form in other tissue cells (keratinocytes, endothelial cells, epithelial cells). Studies from several laboratories have shown that endothelial cells express mRNA for IL-1. Primary cultures of human umbilical vein endothelial cells (HIJNEC), produce both IL-lα and IL-lβ following stimulation with lipopolysaccharide (LPS), with IL-lα predominating. This is in contrast to LPS-activated monocytes, which produce several fold more IL-lβ. Other stimuli, such as interferon gamma or HIV infection induce primarily IL-lα in monocyte/macrophages, as shown in earlier studies. IL-lβ and TΝFα appear to be potent stimuli for endothelial cells to express IL-1. Endothelial cells do not express IL-lra, in contrast to monocyte/macrophages. This finding is intriguing and points to an important difference in IL-1 regulation in these cells compared with monocyte/macrophages. Lipid metabolism is extensively regulated during the host response to infection. As with other aspects of the host response, these events are mediated by cytokines, including IL-1, IL-6, and interferons. Mouse brown adipose tissue has been shown to contain high levels of IL-lα when compared with brain, lymph nodes, and spleen. The cellular localization of IL-1 α in cultured brown adipocytes was primarily nuclear. Stimulation of adipocytes by noradrenaline or IL- 1 β resulted in a rapid burst of IL- 1 α mRΝA.

Role of IL-lα in differentiation

Much of the proIL-lα produced by cells (macrophages, endothelial cells, epithelial cells, keratinocytes, muscle cells) remains inside the cells where it may act as a messenger and translocate to the nucleus as noted above, or may remain bound to intracellular IL-1RI, and act similarly to a steroid receptor. A nuclear binding domain of pro-IL-lα has been identified between residues 79-85. It is thought that intracellular proIL-lα (31 kD function precursor of mature 17 kD IL-1) regulates cellular differentiation. In vitro, when combined with growth factors such as fibroblast growth factor (FGF), IL-1 acts as a proliferation inhibitory signal. Addition of IL-lα antisense oligonucleotides to endothelial cell cultures has been shown to extend the life span and prevent senescence of endothelial cells.

Previous studies on the pathogenesis of autoimmune disorders have focused on the regulation of interleukin lα (IL-lα) production by human macrophages from blood, spleen and thymus. In acute autoimmune thrombocytopenia (ITP) patients, it was found that IL-1 activity or expression can be increased, while IL-4, an anti-inflammatory cytokine, is strongly decreased. Thus, the sustained production of IL-1 may play a critical role in the perpetuation of anti-platelet antibodies in ITP and is a potent site for future therapeutic manipulation. IL-lα in HIN-1 infection

Previous studies by the inventors have shown that stimuli, such as interferon gamma or HIV infection induce primarily IL-lα in monocyte/macrophages. An IL-lα inhibitor was thought to block the IL-1 dependant maturation of T lymphocytes in ADDS and contribute to the immunodeficiency. Patients with AIDS with more active disease produced more IL-1 than those without. And later in the disease, increased expression of IL-lα occurred and was thought to interfere with proper immune regulation. IL-lα gene and protein structure

There are two distinct fonns of IL-1 : IL-lα and IL-1 β. The human forms are first translated in the form of a precursor of 271 amino acids, then cleaved into a mature form of

159 amino acids with a molecular weight of 17 kD and an iso-electric point of 5.5. Human IL-1 β and IL-lα amino acid sequences are 26% homologous and the nucleotide sequences of their genes are 45% homologous. A certain degree of polymorphism exists for these genes since several allelic forms have been described for IL-lα. This polymorphism may be of clinical importance since a specific IL- 1 α allele may be associated with juvenile polyarthritis.

The IL-lα gene does not contain sequences corresponding to the classical transcription initiation motif known as the "TATA box", whereas this motif is found in the IL-1 β gene. The main elements regulating IL-lα expression are located upstream on the gene with a positive regulatory element located quite near the transcription initiation site

(147 to -103 bp) and a negative regulatory element much further away (-875 to -3,600 bp).

The transcription of IL-lα, as indeed that of IL-lβ, is stimulated during inflammatory and infectious processes by the immune complexes, certain coagulation and complement cascade proteins, substance P, and viral or bacterial products, in particular LPS. It is also induced or enhanced by certain cytokines of lymphocyte origin, such as the granulocyte-macrophage colony stimulating factor (GM-CSF) and the interferon-gamma (LFΝ-gamma). Monocyte cytokines such as tumor necrosis factor-alpha (TΝF-alpha) also stimulate the production of IL-1 by endothelial cells, by monocytes and by fibroblasts. In addition, IL-lα and IL-lβ, each encourages its own production in endothelial cells and in monocytes.

IL-lα and IL-lβ differ substantially in relation to localization, maturation, and secretion since the former remains mainly intracellular, whilst the main part of the latter is secreted after cleaving by a specific protease. Due to the absence of a signal sequence, the immature forms, referred to as pro-IL-l and pro-IL-lβ remain in the cytosol after their translation and do not accumulate in any cell organelles. Unlike pro-IL-lβ, pro-IL-lα is just as active as the mature form and remains intracellular for the main part and acts at this level. Moreover, IL-lα is only rarely found in the circulation or extracellular biological liquids and only in cases of serious illness when it may have its origin in lysed cells.

IL-lα or pro-IL-lα functions rather like an autocrine intracellular messenger, in particular in endothelial and epithelial cells where it plays a role in the regulation of normal cellular differentiation. It is possible that pro-IL-lα carries out its activities without leaving the cell which produces it. This hypothesis is supported by research showing that the introduction of an IL-lα antisense oligonucleotide modifies the growth of endothelial cell and that complexes composed of pro-IL-lα and the IL-1 receptor bind to the DNA in the nucleus. The origin of these complexes is still disputed. They may either be formed from intracellular receptors or originate from the internalization of membrane complexes. A small fraction of pro-IL-lα, synthesized by monocytes and B lymphocytes, is found at the surface of cells. In fact, myristyl groups bind to the lysines of 10 to 15% of the pro-IL-lα, which allows it to be transported to the surface of the cell where it can anchor by interactions with lectins. This membrane IL-lα is biologically active and its activity is neutralized by anti-IL-lα antibodies but not by anti-IL-lβ antibodies. This activity can therefore be carried out paracrinely on neighboring cells, in particular in inflammatory environments.

In spite of much experimental progress over the last five years, a highly effective and safe new therapeutic agent for the treatment of Rheumatoid arthritis is not yet in hand. Because of the multiple roles which it may have in the pathogenesis, IL-lα is a highly advantageous target for therapy. In addition, IL-lα may be a useful target for the treatment of HIV and cancer.

SUMMARY OF THE INVENTION

One embodiment of the invention is an isolated promoter which has at least one copy of SEQ ID NO:l or a variant thereof. In one embodiment, the at least one copy of

SEQ ID NO: 1 is within SEQ ID NO:4. A further embodiment is an isolated promoter which has at least one copy of SEQ

ID NO:4, a variant or a truncated variant wherein said variant is biologically active as a promoter. In one embodiment, the variant or truncated variant has at least 60% of the activity of SEQ ID NO:4. A further embodiment is a promoter variant or truncated variant that comprises at least one copy of SEQ ID NO: 1.

A further embodiment is a method for the identification of regulators of IL-lα expression by obtaining a promoter comprising at least one copy of SEQ ID NO:l attached to a reporter gene and identifying molecules which up or down-regulate the expression of the reporter. In one embodiment, the promoter comprises SEQ ID NO:4. A further embodiment is a method of identifying a regulator by screening libraries for small molecules and pharmaceuticals which regulate the receptor. In one embodiment, the method of identifying is by one-hybrid technology. In a further embodiment the method is by identifying using computer modeling. In a further embodiment the method of identifying is by administering cell extracts or parts thereof to said promoter construct; and identifying up-or down-regulation of said promoter construct. In one embodiment the regulation is up-regulation. In a further embodiment the regulation is down-regulation.

A further embodiment is an activator or inhibitor of IL-lα identified by the method herein.

A further embodiment is an isolated polypeptide regulator of IL-lα, comprising a sequence selected from- the group consisting of: SEQ ID NO:6, 7, 8, 9, 10, and 11 or a variant thereof wherein said variant has at least about 60% of the activation activity of the full-length protein.

A further embodiment is a method for the treatment of a patient with cancer, autoimmunities, arthritides, and/or viral infections, by administering an inhibitor which binds to the promoter described herein, or a vector expressing said polypeptide to the patient in an amount effective to reduce symptoms of the disease.

A further embodiment is a method for the radioprotection of a patient undergoing treatment with radiotherapy or chemotherapy, by administering the polypeptide of Claim 15, or a vector expressing the polypeptide to the patient in an amount effective to reduce the side effects of the radiotherapy or chemotherapy.

A further embodiment is a method for the identification of promoter elements in the IL-lα promoter, by treating the promoter of Claim 1 with a solution comprising proteins which bind to said promoter; and identifying where the proteins are binding. In a further embodiment the identification is by a method selected from the group consisting of footprinting, DNase I protection and Electro-Mobility Shift Assays.

Further aspects, features and advantages of this invention will become apparent from the detailed description of the preferred embodiments which follow.

BRIEF DESCRIPTION OF THE DRAWINGS

These and other features of the invention will now be described with reference to the drawings of preferred embodiments which are intended to illustrate and not to limit the invention.

Figure 1A is a drawing of the promoter region of IL-lα showing known binding motifs as well as the triple repeat motif region identified herein as a novel regulatory region. Figure IB shows the -224 to +5 footprint region of the gene promoter with both the wild-type (GCC repeats) and mutated (with CAA) sequences. Figure 2 is a DNase protection Assay using the wild-type and mutated IL-lα promoter.

Figure 3 is an electrophoretic mobility shift assay using the wild-type and mutated IL-lα promoter.

Figure 4 is a DNase I protection Assay which identified the transcription factor which bound to the truncated IL- 1 α promoter.

Figure 5 is a comparison between the wild-type (WT) and mutated (Ml 6) relative promoter activity.

Figure 6 is a Competition Assay with NFKB. A. ds footprint oligo, no HEp-2 nuclear extract B. ds footprint oligo + HEp-2 nuclear extract C. ds footprint oligo + nuclear extract + ds cold NFKB (1.75pM), D. ds footprint oligo + nuclear extract + ds cold

NFKB (17.5pM) E. ds footprint oligo + nuclear extract + ds cold WT oligo (1.75pM). F. ds footprint oligo + nuclear extract + ds cold WT oligo (17.5pM)

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT Interleukin lα (IL-lα) is a highly pleiotrophic growth factor which may be involved in a number of normal and disease phenotypes. Studies have shown the presence of IL-lα in patients with various inflammatory conditions, but not in normal patients. In addition, it is known that IL-1 appears to drive the process of tissue destruction, suggesting that IL-lα may be a particularly advantageous target for the treatment of rheumatoid arthritis and other inflammatory conditions.

In addition, IL-lα has also been implicated in the control of growth, inflammation, and differentiation of progenitor cells, suggesting that it may be a target for the treatment of cancer and other diseases involving loss of growth control as well as inflammatory conditions. Finally, recent studies by the inventors have found a role for IL-lα in the pathogenesis of the HIV virus and IL-lα may be involved in other viral infections.

For example, IL-lα, in addition to its role in HIV pathogenesis, has been found to be involved in poxvirus disease (especially Vaccinia virus), measles virus, hantavirus, respiratory syncytial virus, herpes simples virus (and other herpes viruses such as CMN, and EBN), and particularly any viruses which infect macrophages or B cells. In the poxviruses and likely with other viruses, it is believed that part of the pathogenesis is due to inhibition of IL-lα, which allows the virus to multiply without being restricted by the immune system.

Thus, the studies herein were aimed at understanding the role of interleukin lα in the control of growth and differentiation. In particular, studies were aimed at the growth and differentiation of pancreatic duct cells and progenitor cells, neural progenitor cells, epithelial cells, endothelial cells, and adipocytes, because all of these cell types produce interleukin lα. Previous studies have primarily addressed the production of IL-lα by macrophages and its effects on inflammation, thus very little was known about its regulation and role in other cells, particularly in the above mentioned cell types which primarily produce IL-lα (not IL-lβ). The intracellular and intranuclear localization suggests that IL-lα has regulatory functions different from other pro-inflammatory cytokines.

The focus on IL-lα is primarily based on a) its presence in stem and progenitor cells, b) its rapid production and release upon activation by HIN-1 and possibly other viruses, more rapid and in larger amounts than IL-lβ, c) the gap in knowledge of the noninflammatory functions of IL-lα, d) its potential in growth regulation of stem cells, and e) its potential as a target for anti-inflammatory therapy.

Since observations suggest that IL-lα may be uniquely linked to the pathogenesis of chronic inflammatory diseases and cancer, the studies herein are directed towards the molecular mechanisms of IL-lα repression and activation in cis and in trans. The molecular mechanisms, production and activity of IL-lα can be controlled at multiple levels, including transcriptional activation, post-transcriptional mRNA stabilization, posttranscriptional activation and release. Thus, these aspects are identified and used to treat disease linked to IL-lα.

General Techniques

The embodiments described herein can be practiced in conjunction with any method or protocol known in the art and described in the scientific and patent literature. The various compositions (e.g., natural or synthetic compounds, polypeptides, peptides, nucleic acids, antibodies, constructs) used in the embodiment described herein can be isolated from a variety of sources, genetically engineered, amplified, expressed recombinantly and combinations thereof. Alternatively, these compounds can be synthesized in vitro by well- known chemical synthesis tecliniques, particularly polypeptides and polynucleotides which may also be synthesized commercially. One embodiment is an IL-lα promoter. The IL-lα promoter identified herein is a truncated version of the IL-lα promoter which comprises the triple repeat motif sequence identified herein, which, in spite of being truncated or a variant, has high activity. The truncated or variant promoter may include any or all of nucleotides -224 to +5 (SEQ ID NO:4) of the promoter sequence deposited in the NCBI genbank by Furitani et al. (Nucleic Acids Research Vol. 14 (8) pp 3167-3179, 1986). Alternatively, the promoter construct may contain the nucleotides from -224 to +5 of the promoter sequence deposited in the NCBI genbank' by Furitani et al. Alternatively, the promoter construct may have from -65 to -41 of the promoter sequence deposited in the NCBI genbank by Furitani et al., corresponding to the triple repeat motif of SEQ ID NO:l. Preferably, the promoter construct contains at least sequences -65 to -41, but less than the full-length promoter construct. Preferably, the promoter construct is 90-98% identical in the region from -65 to -41 and from about 50% to 95% identical to the region from -224 to +5. Alternatively, the promoter may be about 65% to about 98% identical to the region from -224 to +5, including 70% identical, 75%, 80%, 85%, 90%, and 95%. One variant of the promoter construct still has full promoter activity. Alternatively the variant promoter has from about

50 to 99% of activity of the promoter from -224 to + 5 (SEQ ID NO:4), including 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, and 99%. Variants of the promoter may include deletions, base changes or additions of nucleotides, preferably the deletion, base change or addition comprises multiple of 3 nucleotides which correspond to amino acids, corresponding to the addition, deletion or change of an amino acid. Alternatively, nucleotides may be added, deleted or changed on either side of SEQ ID NO:l or at either end of the promoter SEQ ID NO:4. Other variants may include the addition of copies of activation sequences, such as the triple repeat motif described herein.

It is envisioned that the promoter described herein may be advantageous particularly for use in virally infected cells, in cancer cells, and in arthritic or autoimmune cells. In particular, the promoter may be used to express a therapeutic protein in diseased cells, including but not limited to rheumatoid arthritis, HIV-infected cells, and cancer cells.

The IL-lα promoter and variant described herein may be used to identify elements of the promoter which activate or repress IL-lα. Alternatively, the IL-lα promoter or variant may be used to design antisense or triple helix forming (TFO) polynucleotides which can be used to inhibit the activity of the IL-lα promoter. The IL-lα promoter described herein can be used to identify other protein factors which bind to the IL-lα promoter and activate or repress transcription of IL-lα. Thus, a further aspect is methods of identifying activators, repressors or promoter elements which affect IL-lα transcription using the described variant or truncated promoter.

Further aspects of the embodiment are proteins or other factors which affect transcription of IL-lα. These may be transcriptional activators or repressors, or they may be proteins which bind directly to the IL-lα protein and affect the activity of the factor. Alternatively, these may be promoter elements which, when included in a promoter, up- regulate or down-regulate transcription.

One embodiment is an activator of IL-lα expression or activity. Preferably, the activator is a transcription factor which binds to the IL-lα promoter. One activator which has been identified and isolated herein, specifically binds to the novel transcription activation signal identified in the promoter of IL-lα and activates expression. The signal in the promoter is a triple repeat motif sequence identified herein as SEQ ID NO:l. Other activators can be identified using the methods described herein as well as the expression constructs which include the truncated promoter identified herein as having activity for the expression of IL-lα (SEQ ID NO:4). A further embodiment is a repressor of IL-lα expression or activity. One aspect is a transcription factor which binds to the IL-lα promoter and represses transcription of IL- lα or an alternative protein which is operatively linked to the promoter. Alternatively, the repressor is a protein which binds directly to the IL-lα protein. Alternatively, the repressor is an antibody, polynucleotide, or small molecule which inhibits expression or activity of

IL-lα. For example, a 7 kD repressor was identified in cells which were infected with HIV. This repressor may be used to down-regulate expression or activity of IL-lα by administering the protein or an expression vector which expresses the protein. Alternatively, this repressor may be used to identify the binding site in the promoter or may be used to produce peptides or antibodies which repress IL-lα.

Other embodiments are proteins, peptides, polynucleotides or vectors which express proteins, peptides or polynucleotides which can be used to treat diseases such as autoimmune diseases, cancer, AIDS, skin diseases or wounds, and the side effects of chemotherapy or radiotherapy. The various aspects and embodiments will be described in greater detail below and with reference to the figures and examples.

Inhibition of IL-lα gene expression or activity

Inhibition of IL-lα activity or expression may be mediated in any way known to one of skill in the art. In one embodiment, antibodies are used to inhibit the activity of the protein. The antibodies may be any antibodies or antibody fragments which still allow binding to the IL-lα promoter with little or no cross-reactivity with other human proteins.

It is envisioned that binding of the antibodies will keep the IL-lα from acting at the cellular level. The antibodies may be produced by any method known to one of skill in the art. Thus, one embodiment is a method for the treatment of cancer, autoimmune disease or viral infections using anti-IL-lα antibodies. One aspect is antibodies which inhibit the interaction of an activator of IL-lα transcription with the IL-lα promoter, including the triple repeat motif region of the promoter. A further embodiment is antibodies which inhibit the interaction of the activator protein identified herein using the IL-lα promoter. A further embodiment is the inhibition of IL-lα expression using antisense oligonucleotides or TFOs. The antisense oligonucleotides and TFOs may be identified and produced using methods known to one of skill in the art. In one embodiment, the antisense oligonucleotides and TFOs at least partially comprise the sequence or a homologous sequence to that of SEQ ID NO:l. In a further embodiment, the antisense oligonucleotides and TFOs at least partially comprise the sequence or the homologous sequence to that of SEQ ID NO:4 (-224 to +5). The antisense oligonucleotides or TFOs may include universal, degenerate, artificial, or unnatural base analogs. Many of these have been found to increase the binding affinity and/or stacking properties of the oligonucleotides.

Triple helix forming nucleotides recognize the double-helical DNA by sequence- specific binding in the major groove; they are among the most specific ligands of double- stranded DNA, together with some recently described small molecules such as synthetic hairpin oligoamides that bind in the minor groove. Thus, triplex-based approaches are an attractive means to achieve targeted gene regulation and gene manipulation both in vitro and in vivo. In a variety of cell-free applications, triplex formation has been used successfully. In living cells triple-helix forming oligonucleotides (TFOs) have been used to target specific DNA modifications resulting in site-specific mutagenesis and the inhibition of gene expression. Mutations can be induced by using a TFO conjugated to a DNA- damaging agent, both on an exogenous plasmid vector and an endogenous chromosomal locus; the mutations are localized around the triplex site. Intracellular inhibition of transcription initiation induced by TFOs has been reported for various clinically relevant genes. In one example, triplex-induced inhibition of transcription elongation in cell cultures was best effected using oligonucleotide analogues containing N3'-P5' phosphoramidate (np) linkages.

A further embodiment is repressor proteins which specifically act on and repress the IL-lα promoter which may also be used to treat disease. The repressor proteins may be identified herein using the promoter described herein in any assay known to one of skill in the art, including 1 -hybrid assays, affinity columns comprising parts of the promoter,

EMSA, footprinting, gel shift assays(band shift assays), and assays which identify components of cell extracts which inhibit the activity of the IL-lα promoter constructs herein.

A further embodiment is pharmaceutical or small molecule inhibitors which may be identified using computer modeling or high throughput testing techniques. For example, the small molecules may be assayed for the ability to inhibit the thymocyte proliferation assay described herein using the promoter or a promoter variant described herein. A further embodiment is a promoter site which has an inhibitory or repressive effect on IL-lα expression. The promoter site may be identified using methods known to one of skill in the art, including, but not limited to, gel shift assays, or one hybrid techniques. Alternatively, the sites may be identified by identifying repressor proteins and using them to locate a binding site on the promoter using methods known to one of skill in the art.

Such promoter sites may be targeted with pharmaceuticals or small molecules to identify treatments for cancer, arthritidies, autoimmunities, and viral infections. For example the site at which the approximately 7 kD protein binds is determined using a gel shift assay using the promoter described herein. After identification of the protein inhibitors or activators as well as the promoter sites, the function can be confirmed using any method known to one of skill in the art, including one of the following methods: a thymocite proliferation assay or the identification of up-regulation or down-regulation of the promoter constructs herein.

The inhibitors and methods above may be used for the treatment of a variety of diseases including cancer, preferably those which use IL-lα as a growth stimulatory promoter, viral infections, preferably AIDS and AIDS-related illnesses, sepsis, autoimmune diseases, preferably rheumatoid arthritis, juvenile rheumatoid arthritis, lupus, fibrositis, myositis, fibromyalgia and related diseases.

The development of an effective way to selectively suppress IL-lα will provide insight into its role in the proliferation of progenitor cells and could lead to more efficient expansion of these cells in vitro for transplantation studies. Such methodology is used therapeutically in autoimmune diseases such as rheumatoid arthritis and juvenile rheumatoid arthritis. Further, the methodology is used to further understand the control of growth and differentiation of other tissue cells, including vascular endothelium. epithelium and fat cells.

Previous studies have shown that IL-lα and IL-lβ directly inhibit IL-4 expression in human T cells, suggesting that IL-1 may be a major determinant of T cell helper phenotype (Thl versus Th2) through enhancing IL-2 production and receptor expression and inhibiting IL-4 production. Inhibition of the production of IL-4, an anti-inflammatory cytokine, may contribute to inadequate down-regulation of inflammation, leading to autoimmune diseases. Thus inhibition of IL-lα at any point may allow normal control of inflammation in disease states such as rheumatoid arthritis. The events following environmental stimuli (e.g. infection, trauma) are coordinated by cytokines and receptors and other mediators to provide protection to the organism, repair, and return to homeostasis. Failure to appropriately return to a quiescent, noninflammatory state may be caused by individual differences in cytokine regulatory circuits. The analysis of IL-lα promoter polymorphisms, is used to provide insight into these individual differences associated with autoimmune disease. Activation of IL-lα gene expression or activity

IL-lα may be involved in the processes of radioprotection and may offer a cancer patient protection from the side effects of radiotherapy or chemotherapy if given prior to or during radiotherapy or chemotherapy.

IL-lα may also be involved in the processes of skin and blood vessel regeneration or healing and may contribute to the process if given topically, locally, or even systemically.

Thus, one embodiment is a method for the identification of activators of IL- lα activity or expression. Such methods will be comparable to those described for identifying repressors, except that the opposite result will be sought, namely the activation of IL-lα. For example, proteins, peptides, small molecules, nutriceuticals, and polynucleotides may be tested in the thymocyte proliferation assay to identify those which activate expression of IL-lα . A further embodiment is the use of the activator identified herein (comprising sequences selected from the group consisting of SEQ ID Nos:6 to 11), a variant, or a truncated variant to activate IL-l . Preferably, the variant or truncated variant retain at least 60% of the activation activity, including at least 70%, 75%, 80%, 85%, 90%, 95%, and 99% of the activation activity.

A further embodiment is the identification of activation sites in the IL-lα promoter. The sites may be identified by any method known to one of skill in the art. One aspect of this embodiment is the triple repeat motif region identified herein (SEQ ID NO:l). When a copy of this region was cloned into the promoter its presence increased the transcription of IL-lα. Thus, transcription factors which activate by binding to the triple repeat motif region can be identified using promoter constructs herein and testing fractionated cellular extracts for activity in the thymocyte proliferation assay. Alternatively, one-hybrid techniques are performed using the triple repeat motif region. Methods of identification of repressors or activators of IL-lα Proteins

Activators or repressors may be identified by any method known to one of skill in the art, including, but not limited to: 1 hybrid, 2 hybrid, and the isolation of proteins from fractionated supernatants which act on thymocyte proliferation assays. Alternatively, repressors or activators may be identified by screening small molecule or pharmaceutical libraries. Alternatively, repressors or activators may be identified using computer modeling.

Repressor or activation sites

Identification of repressor and activator sites may be by way of any method known to one of skill in the art, including, but not limited to: using promoter sequence bound affinity columns, DNase 1 footprinting, and gel shift assays.

Assays which can be used to confirm that any proteins, small molecules, or promoter sites are indeed involved in activation or repression of IL-lα include expression assays using the promoter expression constructs herein or thymocyte proliferation assays. Methods of treatment of patients with proteins, vectors or nucleic acids of the preferred embodiment.

For treatment of the disease, the proteins, polynucleotides, or small molecules may be administered as pharmaceutical preparations alone or may be expressed by vectors. Alternatively, the proteins, polynucleotides, or small molecules may be carried within liposomes or the equivalent.

In providing a patient with the pharmaceutical preparations, the dosage of the administered agent will vary depending upon such factors as the patient's age, weight, height, sex, general medical condition, previous medical history, and the like. In addition, the dosage will vary depending on the therapeutic moiety and the desired effect of the pharmaceutical or the disease which is being treated. The effective dose may be lowered if the pharmaceutical preparation is administered in combination with a second therapy.

The pharmaceutical preparation may be injected via arteries, arterioles, capillaries, sinuses, lymphatic ducts, epithelial cell perfusable space or the like. When administering the pharmaceutical preparation by injection, the administration may be by continuous infusion, or by single or multiple boluses.

The pharmaceutical preparation may be administered either alone or in combination with one or more additional immunosuppressive, chemotherapeutic, anti-inflammatory, or anti-viral agents. The administration may be for either a "prophylactic" or a "therapeutic" purpose.

A composition is said to be "pharmacologically acceptable" if its administration can be tolerated by a recipient patient. Such an agent is said to be administered in a "therapeutically effective amount" if the amount administered is physiologically significant. One or multiple doses of the pharmaceutical composition may be given over a period of hours, days, weeks, or months as the conditions suggest. An agent is physiologically significant if its presence results in a detectable change in the physiology of a recipient patient. The term "pharmaceutically effective amount" refers to an amount effective in treating or ameliorating an IL-1 mediated disease in a patient. The term

"pharmaceutically acceptable carrier, adjuvant, or excipient" refers to a non-toxic carrier, adjuvant, or excipient that may be administered to a patient, together with a compound of the preferred embodiment, and which does not destroy the pharmacological activity thereof. The term "pharmaceutically acceptable derivative" means any pharmaceutically acceptable salt, ester, or salt of such ester, of a compound of the preferred embodiments or any other compound which, upon administration to a recipient, is capable of providing (directly or indirectly) a compound of the preferred embodiment. Pharmaceutical compositions of this invention comprise any of the compounds of the present invention, and pharmaceutically acceptable salts thereof, with any acceptable carrier, adjuvant, excipient, or vehicle. The pharmaceutical preparation of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby these materials, or their functional derivatives, are combined in admixture with a pharmaceutically acceptable carrier vehicle. Suitable vehicles and their formulation, inclusive of other human proteins, e.g., human serum albumin, are described, for example, in Remington's Pharmaceutical Sciences (18^th ed., Gem aro, Ed., Mack, Easton Pa. (1990)).

In order to form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of the pharmaceutical preparation, together with a suitable amount of carrier veliicle. Liposomes and vectors The polypeptides, polynucleotides, or small molecules may be administered within liposomes. The liposomes may be produced in a solution containing the pharmaceutical preparation (polypeptides, polynucleotide or small molecules) so that the substance is encapsulated during polymerization. Alternatively the liposomes may be polymerized first and the pharmaceutical preparation added later by resuspending the polymerized liposomes in a solution of the pharmaceutical preparation and sonicating to affect encapsulation.

Alternatively, the polypeptides or polynucleotides may be admimstered as part of a vector. For example, the repressor or activator protein may be expressed by a vector containing the gene construct controlled by a promoter. The promoter may be constitutive or may be controlled such that it will be expressed in a tissue specific or cell-specific manner. The vector may be a plasmid, a retrovirus, or a viral vector and may be admimstered as naked DNA (or RNA) or may be administered as part of a viral particle. Studies of immune abnormalities in AIDS patients led to the development and study of the promoter of IL-lα. These studies showed a dramatic, selective increase in the production of IL-lα produced in AIDS patients, especially in the symptomatic phase of the disease. The studies showed that HIV can directly upregulate the IL-lα gene. A novel regulatory motif and a regulatory protein for the IL-lα gene were identified using DNA footprinting.

EXAMPLES To produce a vector which could be used to study the activation of the IL-lα promoter, the IL-lα promoter was cloned into two expression vectors containing two different reporter genes (see Examples 1 to 3). A mutated IL-lα promoter was used as the control.

Example 1 Synthesis and cloning of the 5' upstream promoter fragment of the IL-lα gene and method of cloning the fragment into pUC19. An IL-lα genomic DNA fragment containing the region -1425 to +5 was synthesized by PCR using primers prepared according to the published DNA sequence of the IL-lα gene deposited in the NCBI gene bank by Furitani et al (Nucleic Acids Research Vol. 14 (8) pp 3167-3179, 1986). The following primers were designed to create EcoRI restriction sites: forward primer 5' CTCGAGTCTGGTGCTACACTTAC 3' (SEQ ID NO:2), and reverse primer 5' TCTGGCTGGAGCTTAAGCCTGAG 3' (SEQ ID NO:3). A 1.4Kb DNA fragment was amplified and cloned into pUC19 at the Eco Rl sites. Example 2 Cloning IL-lα into the pSV2CAT reporter gene vector.

The IL-lα promoter-reporter gene construct was produced as follows: the 1.4Kb DNA fragment replaced the SV40 early gene promoter at the Kpn 1/HdIII MCS (Multiple Cloning Site) in the pSV2CAT vector. Promoter fragments of different sizes were constructed using Bal 1 enzyme partial digestion and these fragments were ligated into the reporter vector using blunt end methods. One of these deleted mutants (-258 to +5) with high activity was used in the subsequent studies. This fragment was sequenced using the dideoxy DNA sequenase kit (USB version 2.0) to confirm the sequence. A base pair change from C— »A at position -48 was identified and compared with the published sequence (Furitani et al).

CLONED SEQUENCE:

GGT ACC CGA CTACAT GTT TGT CAT CTTATAAAGCAAAGGGGT GAATAA ATGAAC CAAATCAATAAC TTC TGGAAT ATC TGC AAA CAACAATAATAT CAGCTATGC CAT CTTTCACTATTTTAGCCAGTATCGAGTTGAATGAAC ATAGAAAAATAC AAAACT GAATTC TTC CCT GTAAAT TCC CC GTTT TGA CGACGCACTTGTAGC CAC GTAGCCACGCCTACTTAA GACAATTACAAA AGGCGAAGAAGACTGACT CAGGCT TAA GCT T (SEQIDNO:4)

MUTATED CLONED SEQUENCE

GGT ACC CGA CTA CAT GTT TGT CAT CTT ATA AAG CAA AGG GGT GAA TAAATG AAC CAAATC AAT AAC TTC TGG AAT ATC TGC AAA CAA CAA TAA TAT CAG CTA TGC CAT CTT TCA CTA TTT TAG CCA GTA TCG AGT TGA ATG AAC ATA GAAAAATAC AAAACT GAATTC TTC CCT GTAAAT TCC CC GTTT TGA CGA CGC ACT TGT ACAAAC GTA CAAACG CCT ACT TAAGAC AAT TAC AAAAGGCGAAGAAGA CTGACT CAG GCTTAA GCT T (SEQ ID NO:5), (Bold letters showbase changes introduced)

The constructs were produced using the commercially available pCAT-Basic Vector from Promega which is better defined than the previously used vector. The constructs produced were named pCATTL-l WT/BIZ (represents the wild type, genomic sequence) and p CA TIL- ϊ M16/BIZ (represents the mutated sequence).

The IL-lα DNA fragments with Kpnl/Hdlll restriction ends were 'filled in' to create blunt ends and cloned into the pCAT-Basic Vector at the Pstl site. When expression was tested in a variety of cell lines (T cell, myelomonocytic, and epithelial tumor cell lines), the vector with the non-mutated IL-lα promoter showed strong activity.

The mutation reduced the activity of the promoter approximately 90% and confirmed that the activity was dependent on this portion of the sequence. Thus, the mutated fragment provided a control reagent for experiments.

Example 3 Cloning IL-1 αWT (wild type, unmodified sequence) and IL-1αM (mutated sequence) into a the pGL3 luciferase vector

An IL-lα genomic DNA fragment containing the region -258 to +5 (according to Furutani et al.) was cloned into the Multiple Cloning Site (MCS) of the pGL3 luciferase vector (Promega, Madison, WI). A 263bp promoter (-258 to +5) was cloned into the Sma 1/ Xho I sites (pIL-lαD24LUC-WT). The 263bp wild type and mutated fragment was sequenced and their orientation confirmed using the ALFexpress automated sequencer (Amersham, Piscataway, NJ). When compared to the published Furutani et al. sequence, an additional base pair change from A-»G at position -221 was noticed. Both of these promoters were used in this study.

Example 4 Promoter Activation in cell lines Chimeric genes of the 5' upstream human interleukin lα promoter/enhancer region were constructed and cloned into reporter gene vectors using the CAT reporter gene as in Example 2. Transfection of this construct into human peripheral blood mononuclear cells (PBMC), a T cell tumor cell line (CCRF) and a promonocytic tumor cell line (U937) showed promoter activation. Strong promoter activation was found using a 260bp construct, spanning -224 to +5 of the human IL-lα (pIL-lαD24CAT) gene promoter (Fig.

1). Optimal promoter activity was seen with a -224 to +5 fragment of the IL-lα gene in the macrophage and T cell lines. Transfection of the construct into HEL/DAMI was performed using TransIT-LTl. The construct showed constitutive promoter activity and an enhanced response (4-5 fold) induced by adding IL-1, IL-3 or thrombopoietin (TPO). The regulatory elements identified in the IL-lα promoter was used to identify regions to target as well as regulatory factors. The pIL-lαD24LUC-WT (WT) promoter of Example 3 was transfected into

HEL/DAMI, CCRF, and HEp-2 target cells by using lipofectamine (Invitrogen, Carlsbad, CA). The construct showed constitutive promoter activity and an enhanced response induced by adding recombinant IL-lα (Fig. 5).

Example 5

Identification of novel response elements

From DNase I footprinting and Electro-Mobility Shift Assays in macrophage and T cell lines a 27 base pair region was identified with possible regulatory elements (see Fig. 2). Nuclear extracts from these cells were isolated to study transcription factor interaction with double stranded DNA molecules. These experiments using the DNase I protection and

Electro-Mobility Shift Assays revealed novel response elements (see Figs. 2 and 3). These elements were in close proximity to the transcription start site.

Example 6 Characterization of the Response elements

To further characterize the response elements, a 27 bp double stranded oligonucleotide was synthesized that corresponded to the area of protection. This area was sequenced and revealed a triple repeat motif element spanning from position -65 to -41 (T TGT AGC CAC GTA GCC ACG CCT ACT)(SEQ ID NO:l) (see also Figure 1).

Example 7

Production of a mutated promoter with only one triple repeat

A mutated promoter with two of the triple repeat elements disrupted, leaving one of the repeat elements closest to the start site intact (pIL-lαD24LUC-M16), was constructed to introduce CAA point mutations at positions -60 to -58 and -52 to -50 using the forward primer 5' CGACGCACTTGTACAAACGTA CAAACGCCTACTTAAGAC 3' (SEQ ID

NO: 12), reverse primer 5' GTCTTAAGTAGGCGTTTGTACGTT TGTACAAGTGCGTCG 3'(SEQ ID NO: 13). As in Example 3, its orientation was confirmed and sequencing performed, again confirming the two pase pair changes at -48 and -221. A 90% decrease in activity was observed using the mutated promoter in CCRF, DAMI, HEp-2 and U937 tumor cell lines. In addition, this mutated promotoer was not inducible by the addition of the recombinant IL-lα (Fig. 5).

In the following examples, similar studies were performed using the endothelial cells from different source tissues. The cell cultures exposed to different stimuli (pro- or anti-inflammatory cytokines, chemokines) provide a model to study endothelial cell activation in response to cytokines.

Example 8 Identification of additional regulatory regions in the IL-lα promoter

As mentioned previously, in contrast to other cytokine gene promoters, few studies have examined the IL-lα promoter. This promoter does not contain a typical TATA box, but TACAAA sequences are noted at position -31 and -112. There are several potential transcription binding factor sites including a GM-CSF promoter sequence, adenovirus 2 major late promoter sequence, NF IL-6, gamma interferon responsive element, CREB, NFKB, T cell factor-1, and AP-1 sequences. The footprint sequence (SEQ ID NO: 1) was analyzed for known regulatory elements using NCBI and the transcription factor TESS databases. The results suggested a possible match with NFKB:

Footprint - TTGTAGCCACGTAGCCACGCCTACT

NFKB GGCGACTTTCCC (SEQ ID NO: 16)

DNA Competition Assay:

DNA competition experiments were performed using oligonucleotides representing a NFKB consensus sequence with the wild-type promoter. Unlabeled NFKB did not alter the DNA/protein complex formation while unlabeled wild-type promoter exhibited complete competition of the DNA/protein complex formation. Complete competition with the wild type was seen with the lowest concentration of 1.75 pM (see Fig 6).

The functional relevance of these or other sequences in this promoter is unknown. As shown in Example 4, optimal promoter activity was seen with a -224 to +5 fragment of the IL-lα gene in macrophage and T cell lines. From DNase I footprinting and Electro- Mobility Shift Assays in macrophage and T cell lines, a 27 base pair region with possible regulatory elements was identified (novel triple repeat at -65 to -41).

The reporter gene vectors with the 5' upstream human IL-l promoter/enhancer region from Examples 1 to 3 are used in the following experiments. The construct is transfected into endothelial cells from different tissues and the cell cultures are exposed to different stimuli (pro- or anti-inflammatory cytokines or chemokines) and promoter activation is assessed. Nuclear extracts from these cells are isolated to study transcription factor interaction with double stranded DNA molecules. These experiments are performed using the DNase I protection and Electro-Mobility Shift Assays and reveal novel response elements.

Example 9 Identification of other promoter active regions Repressor sites are identified by DNase 1 footprinting using extracts from cells which do not express IL-lα. The goal of these experiments is to find a selective, effective mode of IL-lα blockade. IL-lα synthesis by antisense oligonucleotides has been reported, and blocking of IL-lα after its production using a monoclonal antibody or IL-1 receptor antagonist has been used previously. However, the identification of specific regions of the promoter necessary for activation or which can be used for repression may identify specific promoter regions which can be targeted with therapeutics.

The regions are identified as follows: The previously isolated 5' upstream regulatory region of the IL-lα gene (pIL-lα) and chimeric promoter\reporter gene vectors are used. Initially, using the most active promoter construct, 229bp-pIL-lα/CAT (comprising -224 to +5 transcriptional start site), macrophage lines (DAMI, U937), endothelial cells (microvascular lines), epithelial cell lines, neuronal stem cells, and adipocytes (obtained from ATTC) are transfected and promoter activation determined with and without additional stimuli appropriate for the given cell types (e.g. cytokines, growth factors, PMA, LPS). These experiments determine if cell types other than the previously tested macrophage and T cell lines also mediate IL-lα production through these promoter element(s) and therefore may be activated by similar transcription factors in these non- lymphoid/myeloid cell types.

The IL-lα promoter constructs are transfected into cultured cells, and activity is assessed by the levels of expression of the luciferase or CAT reporter gene. In Example 10, promoter variants are constructed to identify the parts of the promoter necessary for activation or repression.

Example 10 Production of promoter variants Promoter variants are constructed which have truncations of the regions which are not necessary for activity. More specifically, promoter truncations 5' and 3' to the -224 to +5 transcriptional start site are produced. In addition, variants are produced to identify the importance of the two TACAAA sequences at positions -31 and -112. Mutants which still contain the 27 base pair region with the important TACAAA site are produced. These variants contain deletion of other parts of the promoter. These mutants are used to identify important up and down-regulatory regions of the promoter. In addition, to produce a more active promoter, the 27 base pair repeat element and any other "activation" region are repeated in the sequence. Alternatively, repressor elements are identified and removed. To produce a less active promoter, the repressor regions are repeated and activation regions are mutated.

In order to use the information obtained about IL-lα and its promoter, in Examples 10 and 11, repressors are identified which may be used to treat autoimmune disease, cancer or viral diseases.

Example 11

Identification of a novel IL-lα promoter binding factor

An affinity column was produced by binding oligonucleotides of the triple repeat motif region identified in Example 6. These oligonucleotides were synthesized and linked to cyanogen bromide activated sepharose following the vendor's protocol (Amersham Pharmacia Biotech, Piscataway, New Jersey). Supematants from a human epithelial cell line, Hep-2, were partially purified and applied to the column. Those proteins which bound were isolated as follows: After washing the column extensively, the proteins were eluted, run on an acrylamide gel and a Southwestern was performed with radiolabelled oligonucleotides of the triple repeat (see Figure 3). Of the four protein bands on the gel, only the band which appeared to be a smeared band or a doublet was positive. However, all of the eluted proteins bound to DNA in a gel shift assay. Thus, the smeared or doublet band was isolated and subjected to amino acid sequencing using the core facility at Cal

Tech (California Institute of Technology). The other proteins were saved for further characterization.

In this way, a novel IL-lα promoter binding factor was identified as binding to the triple repeat region of the IL-lα promoter. Amino acid sequencing was performed by enzymatically cleaving the purified protein or proteins, isolating the peaks which were produced and sequencing these peaks which corresponded to peptides. The following four sequences were identified and BLAST searches were performed to identify possible homologies, and activities for the peptide or peptides. Since it was not clear whether there was one protein, two proteins, or multiple proteins in the band all sequences were analyzed independently as follows:

1. TF IL-1 band 3, peak 46 was a mixed sequence with: AVFLTLHGTLVE (SEQ ID NO:6). A BLAST search showed that this sequence shows homology to various potassium channel proteins. A d RTYGQADFTPLE (SEQ ID NO:7).

2. TF IL-1 band 3, peak 46: QALLXA (SEQ ID NO:8). This amino acid sequence shows no significant similarity or homology when searched with BLAST.

3. TF IL-1 band 3, peak 47: ATYAQTDWGLF (SEQ ID NO:9). This amino acid sequence shows homology to a human hairless protein as well as a number of bacterial and viral proteins when searched using BLAST.

4. TF IL-1 band 3, peak 47: QVSGSINTDQPE (SEQ ID NO:10). 5. TF IL-1 band 3, peak 48: EVTEDTEKLITXIYXDY (SEQ ID NO: 11). This sequence shows homology to human gene (KIAA1351) and WD40 repeat domain 11 protein. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and tφ-asp (GH-WD), which may facilitate formation of heterotrimeric or multiproteic complexes. According to a search with BLAST, members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Table 1 : Peptide Sequences

These protein sequences may correspond to one protein, two proteins, or multiple proteins. Therefore, the BLAST searches were performed assuming that each was from a different protein. However, it is likely that one or more of the sequences will be found to constitute the same protein. For example, SEQ ID NOs: 6 and 7 may be from the same protein. Alternatively, all of the sequences (SEQ ID NOs: 6-11) may be from the same protein. This information is clarified as more sequence is included.

However, from the data obtained from the BLAST search, a number of options are available for the use of the peptides and sequences above. Homologs may be identified in other species, genus, or even families by searching databases with the known sequences alone, in pairs, or in groups. Alternatively, primers can be produced which may be degenerate or identical. These primers can be used to identify homologs using PCR or the primers may be used as probes to search libraries for homologs. In addition, methods may be envisioned in which the full-length proteins or fragments may be used to treat diseases.

For example, SEQ ID NO: 9 is homologous to a human hairless protein which may contain one or more Zinc fingers and SEQ ID NO: 6 is homologous to a potassium channel protein. Treatments which already exist for hair loss such as minoxidil are channel blockers. Thus, the full-length protein, active fragments or active variants of SEQ ID NO:9 and/or 6 may be used to treat alopecia, hairlessness, or hair loss in humans and mammals. Alternatively, SEQ ID Nos: 6 and 9 may be parts of the same protein which is involved in hair loss and may be used to treat hair loss.

In a further example, the full-length protein corresponding to SEQ ID NO:l 1 (human KIAA1351 protein) or variants or fragments, may be used to treat diseases related to cell cycle progression and apoptosis (such as cancer), diseases related to signal transduction, and diseases related to abnormal gene regulation. Preferably variants for fragments which still contain the WD repeats.

In a further example, SEQ ID NO: 6 shows some homology to an antiterminator protein, which affects the termination of transcription. This can lead to mutations due to the fact that transcription is not terminated in the normal manner. Thus, the full length protein corresponding to SEQ ID NO:6 or active variants or fragments may be used to treat cancer and autoimmune disease.

Example 12

Identification of repressors, an IL-lα repressor involved in AIDS, and the binding site of the IL-lα repressor involved in AIDS

In previous studies of autoimmune diseases and in published studies of chronic HIV infection, the focus has been on the regulation of IL-1 α production by human macrophages from blood, spleen and thymus. This cytokine was found to be selectively increased and, in contrast to IL-lβ and TNFα, showed sustained production in HIV-infected macrophage cultures and in cultures of synovial cells from patients with rheumatoid arthritis. For this reason, transcriptional control was studied in the mononuclear cell fraction.

The mononuclear cell fraction was isolated from a patient with AIDS, the cells were fractionated and a crude extract was isolated (Berman, et al. 1987, Clinical Immunology and Immunopathology, Vol. 42, pages 133-140). The extract was then fractionated by MW and charge and the fractions were assayed for IL-lα activity. IL-lα activity was analyzed in the different fractions using the murine thymocyte proliferation assay with PHA. Briefly, 10⁶ BALB/c thymocytes in 100 μl complete medium were placed in microtiter plates together with 50 μl of a 1:100 dilution of PHA-P. Each sample was tested in triplicate. Cultures were incubated for 48 hrs and pulsed with 0.5 μCi [³H]thymidine (6.7 Ci/mmol) for 24 hours. To assay IL-1 activity in the supernatant and column fractions, 25 ml aliquots were added. To measure IL-1 activity, 25 μl of the column fractions was added to the thymocyte proliferation assay together with 100 units of human IL-1. An approximately 7 kD protein which aggregates was identified and subsequently sequenced.

The sequence data identified a contiguous sequence of amino acids which showed homology to SLT-3, a protein which belongs to the semaphorin family. Other semaphorin proteins have been found in the nervous system and are thought to be involved in inhibiting axon growth.

The binding site for the repressor protein (the approximately 7 kD) is identified using the promoter construct described herein in a DNase 1 footprinting assay and binding is confirmed by Southwestern.

Other repressors of IL-lα production are identified using the expression constructs from Examples 1 to 3 or by using a one hybrid technique.

Example 13 Treatment of autoimmune disease with repressors

The repressors identified in Example 11 are administered to a patient with Rheumatoid Arthritis systemically or locally, intravenously, intramuscularly, parentally, enterally, or by mode of inhalation at a concentration sufficient to inhibit IL-lα activity. The concentration necessary to inhibit IL-lα expression in the cells or area of interest is determined. A reduction in the symptoms and the effects of the autoimmune disease are identified. Alternatively, a reduction in TNFα and IL-lα is used to determine efficacy.

Example 14 Treatment of autoimmune disease with antisense or triple helix formers For inhibition of promoter mediated activation, triple helix-forming oligonucleotides (TFOs) which bind with high affinity and specificity to homopurine- homopyrimidine sequences in DNA are identified and produced which are specific to important regions of the promoter. TFOs have been used to inhibit transcription of target genes in various experimental systems. The ability of 3'-amino-modified phosphodiester TFOs directed at sites in the IL-lα promoter element and at sites flanking this motif located either upstream or downstream of the promoter element to repress expression are analyzed using the promoter\reporter constructs already produced as well as new truncated and mutated promoter constructs. If promoter activation is inhibited in this system, the specificity of IL-lα inhibition is tested in different target cells in vitro. If selective inhibition of IL-lα gene expression is accomplished, this methodology is used to study the effect of selective IL-lα blockade on cell growth (stem cells, endothelial cells, epithelial cells, adipocytes) and expression of differentiated functions. Increased IL-lβ secretion has been reported to be associated with a polymorphism in the IL-lβ gene and previously, polymorphisms in a tandem repeat region of intron 6 of IL-lα have also been described. Because a variable number of tandem repeats in a regulatory region (SP1 binding site, a viral enhancer) could have regulatory consequences by predisposing individuals to develop inflammatory disease, polymorphisms in IL-lα which predispose a patient to RA are identified. A polymorphism in the IL-lα promoter at position -885 upstream from the transcription start site has been found to be associated with Juvenile rheumatoid arthritis.

In Example 15 polymorphisms are identified in patients which may be used for treatment and diagnosis.

Example 15 Identification of promoter mutations in patients

These studies identify polymorphisms of the IL-lα gene located in the 5' upstream promoter region. In preliminary studies, single base substitutions in the IL-lα gene have been observed. Thus, a larger number of samples from JRA patients (n=20) are tested. In addition, a number of samples from children with other autoimmune diseases (genomic DNA band for ITP, type 1 diabetes, is available) are also sequenced to determine disease association. Control samples from individuals without known autoimmune/inflammatory diseases or family histories are included. The studies address whether the base changes found are associated with functional differences in gene activation.

Method: the region to be analyzed is amplified by PCR of purified genomic DNA using the following primers (5'-3'):

+AAAATATACATGGCTTAAACTC (-894) (SEQ ID NO: 14) -AAGAGAAAAACAACAACAG (+89) (SEQ ID NO: 15)

Samples containing the correct fragment are cleaned using QIAquick and used in the AutoCycle sequencing kit (Amersham/Pharmacia) on the ALFexpress DNA sequencer

(Pharmacia/Molecular Dynamics). Mutations that are identified are analyzed and correlated with the presence and absence of disease. Any correlative mutations are noted as polymorphisms.

This information is used to produce a diagnostic test to identify the polymorphisms or SNPs in patient samples. Example 16 Interleukin lα gene regulation in megakaryocyte lineage

IL-1 gene regulation and cytokine secretion patterns in megakaryocytes were analyzed, using the human cell lines HEL and DAMI, which have strong megakaryocytic features. Cytokine production was observed in HEL/DAMI cell lines, both unstimulated and stimulated with PMA. High levels of IL-1 and IL-6 were detected by ELISA, but no production of IFNγ or IL-4 was observed.

Presently it is not known if human pancreatic ductal precursor cells of insulin- secreting beta cells produce IL-lα. However, pancreatic islets are known to express IL-1, but it is not known if this cytokine is also present in the precursor cells. Thus, the expression of IL-lα will be analyzed in these cells in Example 15.

Example 17 Expression of IL-lα in stem cell and pancreatic beta cell physiology

Recent studies have shown the presence of IL-lα and IL-lβ in human and rat neural progenitor cells. The role of IL-lα in these cells is not known, but based on its "rescue" function for hematopoietic stem cells (hemopoietin 1 is IL-lα), IL-1 likely plays a growth regulatory role in stem cells, perhaps directly as a factor for self-renewal, or a signal for differentiation, or indirectly by promoting factor production by surrounding cells. Neural stem cells, the self-renewing precursors of neurons and glia, are the focus of intensive research aimed at developing transplantation strategies to repair diseased or injured nervous system. Recently, both blood stem cell potential for migration and differentiation into brain tissue and brain derived progenitor potential to form blood cells have been reported. Progenitor cells for replacement of insulin-producing cells in type 1 diabetes have been identified in pancreatic duct tissue. In order for these cells to be used for the treatment of diabetes, they need to be isolated and propagated.

Thus, the role of IL-lα in cell types which naturally produce predominantly IL-lα without apparent pro-inflammatory stimuli is analyzed with the view of using IL-lα to propagate the cells. The consequences of IL-lα blockade on cell proliferation and expression of differentiation markers or functions are measured. The method of blocking will depend on the preceding studies. If triple helix-forming oligonucleotides are determined to be effective in Example 10, this will be the method of choice. Alternatively, anti-sense oligonucleotides to block mRNA translation, monoclonal anti-IL-lα antibody, or IL-1 receptor antagonist (ra) will be used.

Example 18

Role of IL-lα in Neural Stem Cells

The above preliminary studies of both adult rat neural progenitor cells and human embryonic progenitor cells have shown the presence of IL-lα mRNA and protein, but the function of IL-lα in these cells is unknown. To explore the role of IL-lα as a growth factor, rIL-lα (over a broad dose range) is added to neural stem cells in tissue culture at a concentration which inhibits IL-lα synthesis or activity, as described in Example 10. To measure the effect of these treatments, proliferation of cells in culture is assessed by ³H- thymidine incorporation into DNA and by counting viable cells after days 1, 3, and 5 of treatment. Further, (especially if no growth effect is apparent), the expression of stem cell (nestin) and differentiation markers (neuronal, glial) is examined by immunocytochemistry.

Example 19 IL-lα Regulation in Endothelial Cells, Adherent Synovial Fluid Cells, Macrophages and Adipocytes Although IL-lα and IL-lβ production have a potent effect on immune and inflammatory activation of blood cells, very little is known about the regulation of IL-1 α in other tissues. In addition, IL-lα has a sustained presence in RA and immune-mediated diseases. Thus, the regulatory stimuli and elements for IL-1 production are analyzed by activation of the IL-lα promoter constructs. A large number of studies have addressed the effects of IL-1 (and TNFα) on endothelial cells. These two cytokines affect endothelial endothelial cell function in a prothrombotic, proinflammatory sense, e.g. induction of PGI₂ (vasodilation), tissue factor, PAF, thrombomodulin/protein C, inhibitor of plasminogen activator (thrombosis), adhesion molecules (ICAM-1, ELAM-1, VCAM-1), and chemotactic cytokines (IL-8), MCP, CSFs. The antithrombotic properties of endothelial cells are profoundly altered by exposure to IL-1. Thrombin formation is facilitated on the endothelial cell surface by newly synthesized thromboplastic gene transcription and by suppression of thrombomodulin gene transcription. IL-1 and TNFα also induce platelet activating factor synthesis. There are conflicting reports regarding the capacity of IL-1 to induce von Willebrand factor. IL-1 shifts the fibrinolytic properties of endothelial cells by increasing plasminogen activator inhibitor 1 production while leaving unchanged or decreasing tissue type plasminogen activator. Thus, the effect of blocking IL-lα in these cells is evaluated for a role in growth inhibition or stimulation as well as on the expression of the differentiated functions expressed above. IL-lα is inhibited using the methods identified herein.

In addition, the production of IL-lα and the effect of inhibition are studied in adipocyte lines (from ATTC). With the intriguing effects of pro-inflammatory cytokines on adipocyte lipid metabolism and the abundant nuclear presence of IL-lα in these cells, blocking of IL-lα may provide new insight on its role in the control of fat tissue.

Example 20 Identification of activators or anti-repressors

Using the functional DNA binding sites in the IL-lα promoter identified above, nuclear proteins from different cellular sources (lymphoid and myeloid) are analyzed using DNase I footprinting methodology and electrophoretic mobility shift assay (EMSA). Previously, these studies have demonstrated 'footprints' of the IL-lα promoter with human myelomonocytic cell lines (U937 and DAMI) and with T cell lines (Jurkat and CCRF).

The major footprint has a unique sequence, not previously reported to date. To screen for less tightly bound factors, exonuclease III footprinting is performed. This method can detect partially protected sites whereas DNase I footprinting requires >80% protection by DNA binding proteins. In addition, footprints of a larger upstream fragment (1 kb) are examined for potential activity in these cell types.

The experiments described above determine the functional sites in the IL-lα upstream promoter that are active and regulated by different stimuli. The next steps will be aimed toward characterization of the DNA binding proteins for these sites. The motif which was found to be active in macrophage and T cell lines herein does not have a known

DNA binding sequence. Supersliifts with antibodies to NfkB or SP1, as well as competition by these factors in the footprinting analysis or in EMSA with the corresponding fragment of the promoter have been negative.

Since the motif appears to be novel or the associated DNA binding protein appears to be novel, studies are directed toward isolation and characterization of the protein using DNA affinity chromatography with multimers of the responsive element, HPLC, SDS- polyacrylamide gel electrophoresis, and protein sequencing.

Example 21 Pre-treatment of a cancer patient with IL-lα, IL-lα activators or IL-lα anti- repressors

Previous results indicate that IL-lα may have a radioprotective role in the ability of normal cells to survive various forms of radiotherapy or chemotherapy. Thus, the activators or anti-repressors identified in Example 20 are administered to a patient with Cancer systemically or locally, intravenously, intramuscularly, parentally, enterally, or by mode of inlialation in an amount effective to activate IL-lα expression prior to the start of chemotherapy or radiotherapy. Activation of IL-1 α is identified. The concentration necessary to activate IL-lα expression in the cells or area of interest are determined. A reduction in side effects of chemotherapy and radiotherapy are analyzed.

Example 22

Treatment of a wound or damaged skin with IL-lα, IL-lα activators or IL-lα anti- repressors

Previous results indicate that IL-lα may have a healing or regenerative effect on skin cells and blood vessels. Thus, the activators or anti-repressors identified in Example 20 are administered to a patient with a wound or damaged skin systemically or locally, intravenously, intramuscularly, parentally, enterally, or by mode of inlialation in an amount effective to activate IL-lα expression in skin and blood vessels. Preferably, the administration is topically. Activation of IL-1 α is identified. The concentration necessary to activate IL-lα expression in the cells or area of interest are determined.

Claims

WHAT IS CLAIMED IS:

1. An isolated promoter comprising at least one copy of SEQ ID NO:l or a variant thereof.

2. The isolated promoter of Claim 1 wherein said at least one copy of SEQ ID NO: 1 is within SEQ ID NO:4.

3. An isolated promoter comprising SEQ ID NO: 4, a variant or a truncated variant wherein said variant is active as a promoter.

4. The isolated promoter of Claim 3 wherein said variant or truncated variant has at least 60% of the activity of SEQ ID NO:4.

5. The isolated promoter of Claim 4 wherein said promoter is a variant or truncated variant that comprises at least one copy of SEQ ID NO: 1.

6. A method for the identification of regulators of IL-lα expression comprising: obtaining a promoter comprising at least one copy of SEQ ID NO:l attached to a reporter gene; and identifying molecules which up or down-regulate the expression of the reporter.

7. The method of Claim 6 wherein said promoter comprises SEQ ID NO:4.

8. The method of Claim 6 wherein said identifying is by screening libraries for small molecules and phamiaceuticals which regulate the receptor.

9. The method of Claim 6 wherein said identifying is by one-hybrid technology.

10. The method of Claim 6 wherein said identifying is by computer modeling.

11. The method of Claim 6 wherein said identifying is by administering cell extracts or parts thereof to said promoter construct; and identifying up-or down-regulation of said promoter construct.

12. The method of Claim 6 wherein said regulation is up-regulation.

13. The method of Claim 6 wherein said regulation is down-regulation.

14. An activator or inhibitor of IL-lα identified by the method of Claim 6.

15. An isolated polypeptide regulator of IL-lα, comprising a sequence selected from the group consisting of: SEQ ID NO:6, 7, 8, 9, 10, and 11 or a variant thereof wherein said variant has at least about 60% of the activation activity of the full-length protein corresponding to SEQ ID NO:6, 7, 8, 9, 10, or 11.

16. A method for the radioprotection of a patient undergoing treatment with radiotherapy or chemotherapy: comprising: administering the polypeptide of Claim 15, or a vector expressing the polypeptide to the patient in an amount effective to reduce the side effects of the radiotherapy or chemotherapy.

17. A method for the identification of promoter elements in the IL-lα promoter, comprising: treating the promoter of Claim 1 with a solution comprising proteins which bind to said promoter; and identifying where the proteins are binding.

18. The method of Claim 17, wherein the identification is by a method selected from the group consisting of footprinting, DNase I protection and Electro-Mobility Shift Assays.