Patent Application
20090270480
The invention relates to the identification of expression profiles and the nucleic acids indicative of skin-related disorders, such as active psoriasis, and to the use of such expression profiles and nucleic acids in diagnosis of psoriasis and related diseases. The invention further relates to methods for identifying and using candidate agents and/or targets which modulate psoriasis.
Psoriasis vulgaris is a chronic inflammatory skin disease, with an extremely complex underlying pathophysiology. The cellular components include hyperplastic epidermal keratinocytes, infiltrating mononuclear cells including T-cells, neutrophils, dendritic cells, and macrophages (Barker, J N. 1994. Baillieres Clin Rheumatol 8:429-). These disease-mediating cells display abnormal production of several families of protein, such as cytokines, chemokines, adhesion molecules, proteases and proteinase inhibitors. The function of these proteins ranges from innate immunity and inflammation to cell differentiation and proliferation (Barker, J et al., 1991. J Dermatol Sci, 2: 106-; Austin, L M 1999. J Invest Dermatol. 113: 752-). Through clinical and translational studies, it has been shown that at least some of these molecules play critical roles in development and maintenance of psoriasis.
Two cytokines that are thought to be important in the development of Th1 immune responses in psoriasis are interleukin-12 (IL-12) and IL-23. Both cytokines are produced by antigen-presenting cells, such as macrophages and dendritic cells, and function by activating T cells and natural killer cells. IL-12 and IL-23 are members of a heterodimeric family of soluble cytokines that are comprised of p35/p40 protein subunits in IL-12 and p19/p40 protein subunits in IL-23. The IL-12 p40 subunit of either cytokine will bind to the transmembrane IL-12 receptor beta1 (IL-12R1) that is found on the surface of immune cells.
Subsequent binding of IL-12 p35 or IL-23 p19 to their receptor partners, IL-12R2 and IL-23R, respectively, results in immune signaling events that are specific for each cytokine. Thus, interruption of the IL-12 p40/IL-12R1 interaction will prevent the biological activity of both IL-12 and IL-23. The functions of IL-12 have been well characterized and include induction of interferon- (IFN-), differentiation of Th1 cells, and bridging between innate resistance and adaptive immunity (Trinchieri, G. 2003 Interleukin-12 and the regulation of innate resistance and adaptive immunity. Nat Rev Immunol 3: 133146). Although many of the immune consequences of IL-23 are still the subject of active research, IL-23 has been proposed to have functions that are similar, but not identical, to those of IL-12 (Oppmann et al, 2000 Immunity 13: 715-725).
Microarray technology is a powerful tool since it enables analysis of the expression of thousands of genes simultaneously and can also be automated allowing for a high-throughput format. In diseases associated with complex host functions such as these known as autoimmune diseases, such as psoriasis, microarray results can provide a gene expression profile that can be of utility in designing new approaches to disease diagnosis and management. These approaches also serve to identify novel genes and annotating genes of unknown function heretofore unassociated with the disease or condition.
Gene expression can be modulated in several different ways, including by the use of siRNAs, shRNAs, antisense molecules and DNAzymes. SiRNAs and shRNAs both work via the RNAi pathway and have been successfully used to suppress the expression of genes. RNAi was first discovered in worms and the phenomenon of gene silencing related to dsRNA was first reported in plants by Fire and Mello and is thought to be a way for plant cells to combat infection with RNA viruses. In this pathway, the long dsRNA viral product is processed into smaller fragments of 21-25 bp in length by a DICER-like enzyme and then the double-stranded molecule is unwound and loaded into the RNA induced silencing complex (RISC). A similar pathway has been identified in mammalian cells with the notable difference that the dsRNA molecules must be smaller than 30 bp in length in order to avoid the induction of the so-called interferon response, which is not gene specific and leads to the global shut down of protein synthesis in the cell.
Synthetic siRNAs have been successfully designed to selectively target a single gene and can be delivered to cells in vitro or in vivo. ShRNAs are the DNA equivalents of siRNA molecules and have the advantage of being incorporated into a cells' genome where they are replicated during every mitotic cycle.
DNAzymes have also been used to modulate gene expression. DNAzymes are catalytic DNA molecules that cleave single-stranded RNA. They are highly selective for the target RNA sequence and as such can be used to down-regulate specific genes through targeting of the messenger RNA.
Accordingly, there is a need to identify and characterize new gene markers useful in developing methods for diagnosing and treating autoimmune disorders, such as psoriasis, as well as other diseases and conditions.
The present invention relates to a method of diagnosing and/or treating psoriasis and/or related diseases or disorders by identifying and using candidate agents and/or targets which modulate such diseases or disorders. The present invention includes the discovery of a panel of 36 genes that have modified expression levels in patients with psoriasis and/or treated with an agent effective in reducing the symptoms of psoriasis. The modified expression levels constitute a profile that can serve as a biomarker profile indicative of psoriasis and/or the response of a subject to treatment.
In a particular embodiment, the present invention comprises a method of determining the efficacy of the treatment for psoriasis based on the pattern of gene expression of one or more of the 36 genes which constitute the profile. This can be done for a subject, for example, prior to the manifestation of other gross measurements of clinical response. In one embodiment, the method of screening drug candidates includes comparing the level of expression in the absence of the drug candidate to the level of expression in the presence of the drug candidate, wherein the concentration of the drug candidate can vary when present, and wherein the comparison can occur during treatment or after treatment with the drug candidate. In a typical embodiment, the cell specimen expresses at least two expression profile genes. The profile genes may show an increase or decrease.
In one embodiment, the psoriasis-related gene profile is used to create an array-based method for prognostic or diagnostic purposes, the method comprising:
In an alternative embodiment, the present invention comprises a kit for diagnosing psoriasis and/or related diseases or disorders by identifying and using candidate agents and/or targets which modulate such diseases or disorders and for determining the efficacy of the treatment for psoriasis and/or related diseases or disorders based on the pattern of gene expression.
Another embodiment of the present invention relates to agonists and/or antagonists of the transcription of the genes or of the gene products of the psoriasis-related gene panel and a method of using psoriasis-related gene panel antagonists, including antibodies directed toward psoriasis-related gene panel products, to treat psoriasis or related disorders.
In one aspect, the psoriasis-related gene panel antagonist is an antibody that specifically binds psoriasis-related gene panel product. A particular advantage of such antibodies is that they are capable of binding psoriasis-related gene panel product in a manner that prevents its action. The method of the present invention thus employs antibodies having the desirable neutralizing property which makes them ideally suited for therapeutic and preventative treatment of disease states associated with various skin-related disorders in human or nonhuman patients. Accordingly, the present invention is directed to a method of treating psoriasis or a related disease or condition in a patient in need of such treatment which comprises administering to the patient an amount of a neutralizing psoriasis-related gene panel product antibody to inhibit the pulmonary-related disease or condition.
In another aspect, the invention provides methods for modulating activity of a psoriasis-related gene panel gene comprising contacting a cell with an agent (e.g., antagonist or agonist) that modulates (inhibits or enhances) the activity or expression of the psoriasis-related gene panel gene such that activity or expression in the cell is modulated. In a preferred embodiment, the agent is an antibody that specifically binds to the psoriasis-related gene panel. In other embodiments, the modulator is a peptide, peptidomimetic, or other small molecule.
The present invention also provides methods of treating a subject having psoriasis or related disorder wherein the disorder can be ameliorated by modulating the amount or activity of the psoriasis-related gene panel. The present invention also provides methods of treating a subject having a disorder characterized by aberrant activity of the psoriasis-related gene panel product or one of their encoding polynucleotide by administering to the subject an agent that is a modulator of the activity of the psoriasis-related gene panel product or or a modulator of the expression of a psoriasis-related gene panel.
In one embodiment, the modulator is a polypeptide or small molecule compound. In another embodiment, the modulator is a polynucleotide. In a particular embodiment, the psoriasis-related gene panel antagonist is an siRNA molecule, an shRNA molecule, an antisense molecule, a ribozyme, or a DNAzyme capable of preventing the production of psoriasis-related gene panel by cells.
The present invention further provides any invention described herein.
The following definitions are set forth to illustrate and define the meaning and scope of various terms used to describe the invention herein.
An “activity,” a biological activity, and a functional activity of a polypeptide refers to an activity exerted by a gene of the psoriasis-related gene panel in response to its specific interaction with another protein or molecule as determined in vivo, in situ, or in vitro, according to standard techniques. Such activities can be a direct activity, such as an association with or an enzymatic activity on a second protein, or an indirect activity, such as a cellular process mediated by interaction of the protein with a second protein or a series of interactions as in intracellular signaling or the coagulation cascade.
An “antibody” includes any polypeptide or peptide containing molecule that comprises at least a portion of an immunoglobulin molecule, such as but not limited to, at least one complementarity determining region (CDR) of a heavy or light chain or a ligand binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework region, or any portion, fragment or variant thereof. The term “antibody” is further intended to encompass antibodies, digestion fragments, specified portions and variants thereof, including antibody mimetics or comprising portions of antibodies that mimic the structure and/or function of an antibody or specified fragment or portion thereof, including single chain antibodies and fragments thereof. For example, antibody fragments include, but are not limited to, Fab (e.g., by papain digestion), Fab′ (e.g., by pepsin digestion and partial reduction) and F(ab′)2 (e.g., by pepsin digestion), facb (e.g., by plasmin digestion), pFc′ (e.g., by pepsin or plasmin digestion), Fd (e.g., by pepsin digestion, partial reduction and reaggregation), Fv or scFv (e.g., by molecular biology techniques) fragments, are encompassed by the invention (see, e.g., Colligan, et al., eds., Current Protocols in Immunology, John Wiley & Sons, Inc., NY (1994-2001); Colligan et al., Current Protocols in Polypeptide Science, John Wiley & Sons, NY (1997-2001)).
The terms “array” or “microarray” or “biochip” or “chip” as used herein refer to articles of manufacture or devices comprising a plurality of immobilized target elements, each target element comprising a “clone,” “feature,” “spot” or defined area comprising a particular composition, such as a biological molecule, e.g., a nucleic acid molecule or polypeptide, immobilized to a solid surface, as discussed in further detail, below.
“Complement of” or “complementary to” a nucleic acid sequence of the invention refers to a polynucleotide molecule having a complementary base sequence and reverse orientation as compared to a first polynucleotide.
“Identity,” as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including, but not limited to, those described in Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., Siam J. Applied Math., 48:1073 (1988). In addition, values for percentage identity can be obtained from amino acid and nucleotide sequence alignments generated using the default settings for the AlignX component of Vector NTI Suite 8.0 (Informax, Frederick, Md.).
The terms “specifically hybridize to,” “hybridizing specifically to,” “specific hybridization” and “selectively hybridize to,” as used herein refer to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under stringent conditions. The term “stringent conditions” refers to conditions under which a probe will hybridize preferentially to its target subsequence; and to a lesser extent to, or not at all to, other sequences. A “stringent hybridization” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization (e.g., as in array, Southern or Northern hybridizations) are sequence dependent, and are different under different environmental parameters. Alternative hybridization conditions that can be used to practice the invention are described in detail, below. In alternative aspects, the hybridization and/or wash conditions are carried out under moderate conditions, stringent conditions and very stringent conditions, as described in further detail, below. Alternative wash conditions are also used in different aspects, as described in further detail, herein.
The phrases “labeled biological molecule” or “labeled with a detectable composition” or “labeled with a detectable moiety” as used herein refer to a biological molecule, e.g., a nucleic acid, comprising a detectable composition, i.e., a label, as described in detail, below. The label can also be another biological molecule, as a nucleic acid, e.g., a nucleic acid in the form of a stem-loop structure as a “molecular beacon,” as described below. This includes incorporation of labeled bases (or, bases which can bind to a detectable label) into the nucleic acid by, e.g., nick translation, random primer extension, amplification with degenerate primers, and the like. Any label can be used, e.g., chemiluminescent labels, radiolabels, enzymatic labels and the like. The label can be detectable by any means, e.g., visual, spectroscopic, photochemical, biochemical, immunochemical, physical, chemical and/or chemiluminescent detection. The invention can use arrays comprising immobilized nucleic acids comprising detectable labels.
The term “nucleic acid” as used herein refers to a deoxyribonucleotide (DNA) or ribonucleotide (RNA) in either single- or double-stranded form. The term encompasses nucleic acids containing known analogues of natural nucleotides. The term nucleic acid is used interchangeably with gene, DNA, RNA, cDNA, mRNA, oligonucleotide primer, probe and amplification product. The term also encompasses DNA backbone analogues, such as phosphodiester, phosphorothioate, phosphorod ithioate, methyl phosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3′-thioacetal, methylene(methylimino), 3′-N-carbamate, morpholino carbamate, and peptide nucleic acids (PNAs).
The terms “sample” or “sample of nucleic acids” as used herein refer to a sample comprising a DNA or RNA, or nucleic acid representative of DNA or RNA isolated from a natural source. A “sample of nucleic acids” is in a form suitable for hybridization (e.g., as a soluble aqueous solution) to another nucleic acid (e.g., immobilized probes). The sample nucleic acid may be isolated, cloned, or extracted from particular cells or tissues. The cell or tissue sample from which the nucleic acid sample is prepared is typically taken from a patient having or suspected of having psoriasis or a related disease or condition. Methods of isolating cell and tissue samples are well known to those of skill in the art and include, but are not limited to, aspirations, tissue sections, needle biopsies, and the like. Frequently the sample will be a “clinical sample” which is a sample derived from a patient, including sections of tissues such as frozen sections or paraffin sections taken for histological purposes. The sample can also be derived from supernatants (of cells) or the cells themselves taken from patients or from cell cultures, cells from tissue culture and other media in which it may be desirable to detect the response to drug candidates. In some cases, the nucleic acids may be amplified using standard techniques such as PCR, prior to the hybridization. The probe an be produced from and collectively can be representative of a source of nucleic acids from one or more particular (pre-selected) portions of, e.g., a collection of polymerase chain reaction (PCR) amplification products, substantially an entire chromosome or a chromosome fragment, or substantially an entire genome, e.g., as a collection of clones, e.g., BACs, PACs, YACs, and the like (see below).
“Nucleic acids” are polymers of nucleotides, wherein a nucleotide comprises a base linked to a sugar which sugars are in turn linked one to another by an interceding at least bivalent molecule, such as phosphoric acid. In naturally occurring nucleic acids, the sugar is either 2′-deoxyribose (DNA) or ribose (RNA). Unnatural poly- or oliogonucleotides contain modified bases, sugars, or linking molecules, but are generally understood to mimic the complementary nature of the naturally occurring nucleic acids after which they are designed. An example of an unnatural oligonucleotide is an antisense molecule composition that has a phosphorothiorate backbone. An “oligonucleotide” generally refers to a nucleic acid molecule having less than 30 nucleotides.
The term “profile” means a pattern and relates to the magnitude and direction of change of a number of features. The profile may be interpreted stringently, i.e., where the variation in the magnitude and/or number of features within the profile displaying the characteristic is substantially similar to a reference profile or it may be interpreted less stringently, for example, by requiring a trend rather than an absolute match of all or a subset of feature characteristics.
The terms “protein,” “polypeptide,” and “peptide” include “analogs,” or “conservative variants” and “mimetics” or “peptidomimetics” with structures and activity that substantially correspond to the polypeptide from which the variant was derived, as discussed in detail above.
A “polypeptide” is a polymer of amino acid residues joined by peptide bonds, and a peptide generally refers to amino acid polymers of 12 or less residues. Peptide bonds can be produced naturally as directed by the nucleic acid template or synthetically by methods well known in the art.
A “protein” is a macromolecule comprising one or more polypeptide chains. A protein may further comprise substituent groups attached to the side groups of the amino acids not involved in formation of the peptide bonds. Typically, proteins formed by eukaryotic cell expression also contain carbohydrates. Proteins are defined herein in terms of their amino acid sequence or backbone and substituents are not specified, whether known or not.
The term “receptor” denotes a molecule having the ability to affect biological activity, in e.g., a cell, as a result of interaction with a specific ligand or binding partner. Cell membrane bound receptors are characterized by an extracellular ligand-binding domain, one or more membrane spanning or transmembrane domains, and an intracellular effector domain that is typically involved in signal transduction. Ligand binding to cell membrane receptors causes changes in the extracellular domain that are communicated across the cell membrane, direct or indirect interaction with one or more intracellular proteins, and alters cellular properties, such as enzyme activity, cell shape, or gene expression profile. Receptors may also be untethered to the cell surface and may be cytosolic, nuclear, or released from the cell altogether. Non-cell associated receptors are termed soluble receptors or ligands.
All publications or patents cited herein are entirely incorporated herein by reference, whether or not specifically designated accordingly, as they show the state of the art at the time of the present invention and/or provide description and enablement of the present invention. Publications refer to any scientific or patent publications, or any other information available in any media format, including all recorded, electronic or printed formats. The following references are entirely incorporated herein by reference: Ausubel, et al., ed., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., NY (1987-2001); Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor, N.Y. (1989); Harlow and Lane, antibodies, a Laboratory Manual, Cold Spring Harbor, N.Y. (1989); Colligan, et al., eds., Current Protocols in Immunology, John Wiley & Sons, Inc., NY (1994-2001); Colligan et al., Current Protocols in Protein Science, John Wiley & Sons, NY (1997-2001).
CNTO 1275 is a human anti-IL-12p40 human IgG1 antibody of Centocor, Inc. that binds to the p40 subunit of human IL-12 and IL-23. CNTO 1275 is in clinical trials for the treatment of psoriasis.
Initial clinical tesing of CNTO 1275 in patients with moderate to severe psoriasis (study designation T01) demonstrated significant clinical improvement after a single IV dose (Kauffman, C L et al., 2004. J Invest Dermatol. 123:1037-1044). A phase I, first in human, nonrandomized open label study demonstrated that a single intravenous infusion of CNTO1275 is generally well tolerated and induces concentration-dependent improvements of psoriatic lesions. While psoriasis is one of the most prevalent T cell-mediated inflammatory disease in humans and among the most common immune mediated inflammatory diseases and disorders, an autoantigen has not been identified. The pathogenesis of psoriasis is thought to depend on the activation of lesional and/or circulating T cells and their secreted products leading to keratinocyte hyperproliferation and angiogenesis with marked ectasia of blood vessels.
In the T01 study, eighteen (18) patients with body surface area ranging from 3% to 35% and at least two plaques located on either the trunk or extremities were treated with a single intravenous infusion. Doses ranged from 0.1 to 5.0 mg per kg. There were no serious adverse events related to CNTO1275. The most commonly reported adverse events included transient decreases in CD4+ and CD16/56+ cells, headache, common cold symptoms and pain at the biopsy site. Twelve of 18 subjects (67%) achieved at least 75% improvement in psoriasis activity and severity index (PASI) between 8 and 16 wk after study administration. Clinical improvements were concentration dependent.
In a similar study, TO2, as described in Example 1, analysis of gene profiling by microarray using skin biopsy samples from subjects in the study, resulted in the identification of a prognostic indicator gene panel which was correlative to efficacy of CNTO 1275 treatment prior to visible clinical improvement as measured by the PASI score.
The present invention provides novel methods for diagnosis of disorders associated with psoriasis, as well as methods for screening for compositions which modulate the symptoms of psoriasis, particularly the psoriatic skin lesions. By “psoriasis,” “psoriatic skin lesions,” “psoriasis-related conditions” or grammatical equivalents as used herein, is meant a disease state or condition which is marked by T cell-mediated inflammatory disease leading to keratinocyte hyperproliferation and angiogenesis with marked ectasia of blood vessels, i.e., erupting cutaneous lesions. Other cutaneous T-cell disorders include: cutaneous T-cell lymphoma.
In the treatment of psoriasis or a related disorder, it would be desirable to limit pathogenic T-cell responses. The IL-12 family of cytokines, IL-12, IL-23, has been identified as being implicated in Th1-driven immune reponses. Therefore, an antagonist of all members (not solely limited to IL-12 or IL-23) which share the common beta (p40) subunit was selected as a first-in-human therapeutic to treat psoriasis.
In one aspect, the expression levels of genes are determined in different patient samples for which diagnosis information is desired, to provide expression profiles. An expression profile of a particular sample is essentially a “fingerprint” of the state of the sample; while two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is unique to the state of the patient sample. That is, normal tissue may be distinguished from lesion tissue and tissue from a treated patient may be distinguished from an untreated patient. By comparing expression profiles of tissue in different disease states that are known, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained.
The identification of sequences (genes) that are differentially expressed in disease tissue allows the use of this information in a number of ways. For example, the evaluation of a particular treatment regime may be evaluated. Similarly, diagnosis may be done or confirmed by comparing patient samples with the known expression profiles. Furthermore, these gene expression profiles (or individual genes) allow screening of drug candidates with an eye to mimicking or altering a particular expression profile; for example, screening can be done for drugs that suppress the angiogenic expression profile.
This may be done by making biochips comprising sets of the important disease genes, which can then be used in these screens. These methods can also be performed on the protein basis; that is, protein expression levels of the psoriasis-related gene product proteins can be evaluated for diagnostic purposes or to screen candidate agents. In addition, the nucleic acid sequences comprising the psoriasis-related gene profile can be used to design a therapeutic including the administration of antisense nucleic acids, or the protein coded for by the gene sequence can be administered as a component of a vaccine.
Thus, the present invention provides information on nucleic acid and protein sequences that are differentially expressed in psoriasis, herein termed “psoriasis-related gene sequences.” As outlined below, psoriasis-related gene sequences include those that are upregulated (i.e., expressed at a higher level) in disorders associated with psoriasis, as well as those that are down-regulated (i.e., expressed at a lower level). In a preferred embodiment, the psoriasis-related gene sequences are from humans; however, as will be appreciated by those in the art, psoriasis-related gene sequences from other organisms may be useful in animal models of disease and drug evaluation; thus, other psoriasis-related gene sequences are provided, from vertebrates, including mammals, including rodents (rats, mice, hamsters, guinea pigs, etc.), primates, farm animals (including sheep, goats, pigs, cows, horses, etc). Psoriasis-related gene sequences from other organisms may be obtained using the techniques known in the art.
Psoriasis-related gene sequences can include both nucleic acid and amino acid sequences. In a preferred embodiment, the psoriasis-related gene sequences are recombinant nucleic acids. By the term “recombinant nucleic acid” herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid by polymerases and endonucleases, in a form not normally found in nature. Thus, an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined, are both considered recombinant for the purposes of this invention. It is understood that once a recombinant nucleic acid is made and reintroduced into a host cell or organism, it will replicate non-recombinantly, i.e., using the in vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinantly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes of the invention.
The invention provides in silico, array-based methods relying on the relative amount of a binding molecule (e.g., nucleic acid sequence) in two or more samples. Also provided are computer-implemented methods for determining the relative amount of a binding molecule (e.g., nucleic acid sequence) in two or more samples and using the determined relative binding amount to diagnose and stage disease, predict responsiveness to a particular therapy, and monitor and enhance therapeutic treatment.
In practicing the methods of the invention, two or more samples of labeled biological molecules (e.g., nucleic acid) are applied to two or more arrays, where the arrays have substantially the same complement of immobilized binding molecule (e.g., immobilized nucleic acid capable of hybridizing to labeled sample nucleic acid). The two or more arrays are typically multiple copies of the same array. However, because each “spot,” “clone” or “feature” on the array has similar biological molecules (e.g., nucleic acids of the same sequence) and the biological molecules (e.g., nucleic acid) in each spot is known, as is typical of nucleic acid and other arrays, it is not necessary that the multiple arrays used in the invention be identical in configuration it is only necessary that the position of each feature on the substrate by known, that is, have an address. Thus, in one aspect, multiple biological molecules (e.g., nucleic acid) samples are comparatively bound to the array (e.g., hybridized simultaneously) and the information gathered is coded so that the results are based on the inherent properties of the freature (e.g., the nucleic acid sequence) and not it's position on the substrate.
Amplification of Nucleic Acids
Amplification using oligonucleotide primers can be used to generate nucleic acids used in the compositions and methods of the invention, to detect or measure levels of test or control samples hybridized to an array, and the like. The skilled artisan can select and design suitable oligonucleotide amplification primers. Amplification methods are also well known in the art, and include, e.g., polymerase chain reaction, PCR (PCR PROTOCOLS, A GUIDE TO METHODS AND APPLICATIONS, ed. Innis, Academic Press, N.Y. (1990) and PCR STRATEGIES (1995), ed. Innis, Academic Press, Inc., N.Y., ligase chain reaction (LCR) (see, e.g., Wu (1989) Genomics 4:560; Landegren (1988) Science 241:1077; Barringer (1990) Gene 89:117); transcription amplification (see, e.g., Kwoh (1989) Proc. Natl. Acad. Sci. USA 86:1173); and, self-sustained sequence replication (see, e.g., Guatelli (1990) Proc. Natl. Acad. Sci. USA 87:1874); Q Beta replicase amplification (see, e.g., Smith (1997) J. Clin. Microbiol. 35:1477-1491), automated Q-beta replicase amplification assay (see, e.g., Burg (1996) Mol. Cell. Probes 10:257-271) and other RNA polymerase mediated techniques (e.g., NASBA, Cangene, Mississauga, Ontario); see also Berger (1987) Methods Enzymol. 152:307-316; Sambrook; Ausubel; U.S. Pat. Nos. 4,683,195 and 4,683,202; Sooknanan (1995) Biotechnology 13:563-564.
Hybridizing Nucleic Acids
In practicing the methods of the invention, test and control samples of nucleic acid are hybridized to immobilized probe nucleic acid, e.g., on arrays. In alternative aspects, the hybridization and/or wash conditions are carried out under moderate conditions, stringent conditions and very stringent conditions. An extensive guide to the hybridization of nucleic acids is found in, e.g., Sambrook Ausubel, Tijssen. Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the Tm for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on an array or a filter in a Southern or northern blot is 42° C. using standard hybridization solutions (see, e.g., Sambrook), with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, e.g., Sambrook). Often, a high stringency wash is preceded by a medium or low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example of a low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4× to 6×SSC at 40° C. for 15 minutes.
In alternative aspects of the compositions and methods of the invention, e.g., in practicing comparative nucleic acid hybridization, such as comparative genomic hybridization (CGH) with arrays, the fluorescent dyes Cy3® and Cy5® are used to differentially label nucleic acid fragments from two samples, e.g., the array-immobilized nucleic acid versus the sample nucleic acid, or, nucleic acid generated from a control versus a test cell or tissue. Many commercial instruments are designed to accommodate the detection of these two dyes. To increase the stability of Cy5®, or fluors or other oxidation-sensitive compounds, antioxidants and free radical scavengers can be used in hybridization mixes, the hybridization and/or the wash solutions. Thus, Cy5® signals are dramatically increased and longer hybridization times are possible. See WO 0194630 A2 and U.S. Patent Application No. 20020006622.
To further increase the hybridization sensitivity, hybridization can be carried out in a controlled, unsaturated humidity environment; thus, hybridization efficiency is significantly improved if the humidity is not saturated. See WO 0194630 A2 and U.S. Patent Application No. 20020006622. The hybridization efficiency can be improved if the humidity is dynamically controlled, i.e., if the humidity changes during hybridization. Mass transfer will be facilitated in a dynamically balanced humidity environment. The humidity in the hybridization environment can be adjusted stepwise or continuously. Array devices comprising housings and controls that allow the operator to control the humidity during pre-hybridization, hybridization, wash and/or detection stages can be used. The device can have detection, control and memory components to allow pre-programming of the humidity and temperature controls (which are constant and precise or which flucturate), and other parameters during the entire procedural cycle, including pre-hybridization, hybridization, wash and detection steps. See WO 0194630 A2 and U.S. Patent Application No. 20020006622.
The methods of the invention can comprise hybridization conditions comprising osmotic fluctuation. Hybridization efficiency (i.e., time to equilibrium) can also be enhanced by a hybridization environment that comprises changing hyper-/hypo-tonicity, e.g., a solute gradient. A solute gradient is created in the device. For example, a low salt hybridization solution is placed on one side of the array hybridization chamber and a higher salt buffer is placed on the other side to generate a solute gradient in the chamber. See WO 0194630 A2 and U.S. Patent Application No. 20020006622.
Blocking the Ability of Repetitive Nucleic Acid Sequences to Hybridize
The methods of the invention can comprise a step of blocking the ability of repetitive nucleic acid sequences to hybridize (i.e., blocking “hybridization capacity”) in the immobilized nucleic acid segments. The hybridization capacity of repetitive nucleic acid sequences in the sample nucleic acid sequences can be blocked by mixing sample nucleic acid sequences with unlabeled or alternatively labeled repetitive nucleic acid sequences. Sample nucleic acid sequences can be mixed with repetitive nucleic acid sequences before the step of contacting with the array-immobilized nucleic acid segments. Blocking sequences are for example, Cot-1 DNA, salmon sperm DNA, or specifc repetitive genomic sequences. The repetitive nucleic acid sequences can be unlabeled. A number of methods for removing and/or disabling the hybridization capacity of repetitive sequences using, e.g., Cot-1 are known; see, e.g., Craig (1997) Hum. Genet. 100:472-476; WO 93/18186. Repetitive DNA sequences can be removed from library probes by means of magnetic purification and affinity PCR, see, e.g., Rauch (2000) J. Biochem. Biophys. Methods 44:59-72.
Arrays are generically a plurality of target elements immobilized onto the surface of the plate as defined “spots” or “clusters,” or “features,” with each target element comprising one or more biological molecules (e.g., nucleic acids or polypeptides) immobilized to a solid surface for specific binding (e.g., hybridization) to a molecule in a sample. The immobilized nucleic acids can contain sequences from specific messages (e.g., as cDNA libraries) or genes (e.g., genomic libraries), including a human genome. Other target elements can contain reference sequences and the like. The biological molecules of the arrays may be arranged on the solid surface at different sizes and different densities. The densities of the biological molecules in a cluster and the number of clusters on the array will depend upon a number of factors, such as the nature of the label, the solid support, the degree of hydrophobicity of the substrate surface, and the like. Each feature may comprise substantially the same biological molecule (e.g., nucleic acid), or, a mixture of biological molecules (e.g., nucleic acids of different lengths and/or sequences). Thus, for example, a feature may contain more than one copy of a cloned piece of DNA, and each copy may be broken into fragments of different lengths.
Array substrate surfaces onto which biological molecules (e.g., nucleic acids) are immobilized can include nitrocellulose, glass, quartz, fused silica, plastics and the like, as discussed further, below. The compositions and methods of the invention can incorporate in whole or in part designs of arrays, and associated components and methods, as described, e.g., in U.S. Pat. Nos. 6,344,316; 6,197,503; 6,174,684; 6,159,685; 6,156,501; 6,093,370; 6,087,112; 6,087,103; 6,087,102; 6,083,697; 6,080,585; 6,054,270; 6,048,695; 6,045,996; 6,022,963; 6,013,440; 5,959,098; 5,856,174; 5,843,655; 5,837,832; 5,770,456; 5,723,320; 5,700,637; 5,695,940; 5,556,752; 5,143,854; see also, e.g., WO 99/51773; WO 99/09217; WO 97/46313; WO 96/17958; WO 89/10977; see also, e.g., Johnston (1998) Curr. Biol. 8:R171-174; Schummer (1997) Biotechniques 23:1087-1092; Kern (1997) Biotechniques 23:120-124; Solinas-Toldo (1997) Genes, Chromosomes & Cancer 20:399-407; Bowtell (1999) Nature Genetics Supp. 21:25-32; Epstein (2000) Current Opinion in Biotech. 11:36-41; Mendoza (1999 Biotechniques 27: 778-788; Lueking (1999) Anal. Biochem. 270:103-111; Davies (1999) Biotechniques 27:1258-1261.
Substrate Surfaces
Substrate surfaces that can be used in the compositions and methods of the invention include, for example, glass (see, e.g., U.S. Pat. No. 5,843,767), ceramics, and quartz. The arrays can have substrate surfaces of a rigid, semi-rigid or flexible material. The substrate surface can be flat or planar, be shaped as wells, raised regions, etched trenches, pores, beads, filaments, or the like. Substrate surfaces can also comprise various materials such as nitrocellulose, paper, crystalline substrates (e.g., gallium arsenide), metals, metalloids, polacryloylmorpholide, various plastics and plastic copolymers, Nylon®, Teflon®, polyethylene, polypropylene, latex, polymethacrylate, poly(ethylene terephthalate), rayon, nylon, poly(vinyl butyrate), and cellulose acetate. The substrates may be coated and the substate and the coating may be functionalized to, e.g., enable conjugation to an amine.
Arrays Comprising Calibration Sequences
The invention comtemplates the use of arrays comprising immobilized calibration sequences for normalizing the results of array-based hybridization reactions, and methods for using these calibration sequences, e.g., to determine the copy number of a calibration sequence to “normalize” or “calibrate” ratio profiles. The calibration sequences can be substantially the same as a unique sequence in an immobilized nucleic acid sequence on an array. For example, a “marker” sequence from each “spot” or “biosite” on an array (which is present only on that spot, making it a “marker” for that spot) is represented by a corresponding sequence on one or more “control” or “calibration” spot(s).
The “control spots” or “calibration spots” are used for “normalization” to provide information that is reliable and repeatable. Control spots can provide a consistent result independent of the labeled sample hybridized to the array (or a labeled binding molecule from a sample). The control spots can be used to generate a “normalization” or “calibration” curve to offset possible intensity errors between the two arrays (or more) used in the in silico, array-based methods of the invention.
One method of generating a control on the array would be to use an equimolar mixture of all the biological molecules (e.g., nucleic acid sequences) spotted on the array and generating a single spot. This single spot would have equal amounts of the biological molecules (e.g., nucleic acid sequences) from all the other spots on the array. Multiple control spots can be generated by varying the concentration of the equimolar mixture.
Samples and Specimens
The sample nucleic acid may be isolated, cloned, or extracted from particular cells, tissues, or other specimens. The cell or tissue sample from which the nucleic acid sample is prepared is typically taken from a patient having or suspected of having psoriasis or a related condition. Methods of isolating cell and tissue samples are well known to those of skill in the art and include, but are not limited to, aspirations, tissue sections, needle biopsies, and the like. Frequently, the sample will be a “clinical sample” which is a sample derived from a patient, including whole blood, or sections of tissues, such as frozen sections or paraffin sections taken for histological purposes. The sample can also be derived from supernatants (of cells) or the cells themselves taken from patients or from cell cultures, cells from tissue culture and other media in which it may be desirable to detect the response to drug candidates. In some cases, the nucleic acids may be amplified using standard techniques such as PCR, prior to the hybridization.
In one embodiment, the present invention is a post-treatment method of monitoring disease resolution. The method includes (1) taking a cutaneous lesion or other specimen from an individual diagnosed with psorasis or a related disease or disorder, (2) measuring the expression levels of the profile genes of the panel, (3) comparing the post-treatment expression level of the genes with a pre-treatment reference profile for the individual, and (4) determining the prognosis for resolution of the psoriatic lesion by monitoring at least one constituent of the psoriasis-related gene profile.
In another embodiment, the present invention is a diagnostic method for psoriasis and the reference standard (sample) is taken from an uninvolved site and the test sample from a suspect lesion.
Methods of Assessing Biomarker Utility
The diagnostic and prognostic utility of the present biomarker gene panel for assessing a patient's response to treatment, prognosis, or presence, extent, severity or stage of disease can be validated by using other means for assessing a patient's state of health or disease. For example, gross measurement of disease may be assessed and recorded by certain imaging methods, such as but not limited to: physician evaluation, imaging by photographic, radiometric, or magnetic resonance technology. General indices of health or disease further include serum or blood composition (protein, liver enzymes, pH, electrolytes, red cell volume, hematocrit, hemoglobin, or specific protein). However, in some diseases, the etiology is still poorly understood. Psoriasis is an example of one such disease.
The most common variety of psoriasis is called plaque type. Patients with plaque-type psoriasis have stable, slowly enlarging plaques, which remain basically unchanged for long periods of time. The most common areas for plaque psoriasis to occur are the elbows, knees, gluteal cleft, and the scalp. Involvement tends to be symmetric. Inverse psoriasis affects the intertriginous regions including the axilla, groin, submammary region, and navel; it also tends to affect the scalp, palms, and soles. The individual lesions are sharply demarcated plaques but may be moist due to their location. Plaque psoriasis generally develops slowly and runs an indolent course. It rarely remits spontaneously.
Eruptive psoriasis (guttate psoriasis) is most common in children and young adults. It develops acutely in individuals without psoriasis or in those with chronic plaque psoriasis. Patients present with many small erythematous, scaling papules, frequently after upper respiratory tract infection with -hemolytic streptococci. The differential diagnosis should include pityriasis rosea and secondary syphilis. Pustular psoriasis is another variant. Patients may have disease localized to the palms and soles or generalized and associated with fever, malaise, diarrhea, and arthralgias.
About half of all patients with psoriasis have fingernail involvement, appearing as punctate pitting, nail thickening, or subungual hyperkeratosis. About 5 to 10% of patients with psoriasis have associated joint complaints, and these are most often found in patients with fingernail involvement. Although some have the coincident occurrence of classic rheumatoid arthritis, many have joint disease that falls into one of three types associated with psoriasis: (1) asymmetric inflammatory arthritis most commonly involving the distal and proximal interphalangeal joints and less commonly the knees, hips, ankles, and wrists; (2) a seronegative rheumatoid arthritis-like disease; a significant portion of these patients go on to develop a severe destructive arthritis; or (3) disease limited to the spine (psoriatic spondylitis).
The etiology of psoriasis is still poorly understood, but there is clearly a genetic component to the disease. Over 50% of patients with psoriasis report a positive family history. Psoriasis has been linked to HLA-Cw6 and, to a lesser extent, to HLA-DR7. Psoriatic lesions are characterized by infiltration of skin with activated T cells, which appear to have a role in the pathophysiology of psoriasis. Presumably, cytokines from activated T cells elaborate growth factors that stimulate keratinocyte hyperproliferation. Agents that inhibit T cell activation, clonal expansion, or release of proinflammatory cytokines are often effective for the treatment of severe psoriasis.
Treatment of psoriasis depends on the type, location, and extent of disease. All patients should be instructed to avoid excess drying or irritation of their skin and to maintain adequate cutaneous hydration. Most patients with localized, plaque-type psoriasis can be managed with midpotency topical glucocorticoids, although their long-term use is often accompanied by loss of effectiveness (tachyphylaxis) and atrophy of the skin. A topical vitamin D analogue (calcipotriene) and a retinoid (tazarotene) are also efficacious in the treatment of psoriasis and have largely replaced other topical agents, such as coal tar, salicylic acid, and anthralin.
Ultraviolet light, natural or artificial, is an effective therapy for patients with widespread psoriasis. Ultraviolet B (UV-B) light is effective alone, or may be combined with coal tar or anthralin. The combination of the ultraviolet A (UV-A) spectrum with either oral or topical psoralens (PUVA) is also extremely effective for the treatment of psoriasis, but long-term use may be associated with an increased incidence of squamous cell cancer and melanoma of the skin.
Various other agents can be used for severe, widespread psoriatic disease. Oral glucocorticoids should not be used for the treatment of psoriasis due to the potential for developing life-threatening pustular psoriasis when therapy is discontinued. Methotrexate is an effective agent, especially in patients with psoriatic arthritis; however, liver toxicity and bone marrow suppression limit its use. The synthetic retinoid, acitretin, is effective in some patients with severe psoriasis. It is a potent teratogen and should not be used in women of childbearing potential. The evidence implicating psoriasis as a T cell-mediated disorder has directed therapeutic efforts to immunoregulation. Cyclosporine is highly effective in selected patients with severe disease, but nephrotoxicity and hypertension complicate its use.
Infliximab and etanercept, tumor necrosis factor (TNFalpha) antagonists, are now approved for psoriatic arthritis. Other TNFalpha antagonists and other agents targeting proinflammatory cytokines, T cell activation, and lymphocyte trafficking may be useful in suppressing the inflammation characteristic of psoriasis.
Psoriasis patients are commonly evaluated using the Psoriasis Area and Severity Index (PASI) and Physician Global Assessment (PGA). The PASI (3) evaluates the degree of erythema, thickness, and scaling of psoriatic plaques, and estimates the extent of involvement of each of these components in four separate body areas (head, trunk, upper and lower extremities). The PASI composite score, ranging from 0-72, provides a subjective measure and relies on estimates of the involved body surface area (BSA). The PGA is a six-point score that summarizes the overall quality (erythema, scaling and thickness) and extent (BSA) of plaques relative to the baseline assessment. A patient's response is rated as worse, poor (0-24%), fair (25-49%), good (50-74%), excellent (75-99%), or cleared (100%).
More recently, the National Psoriasis Foundation's (NPF's) Medical Advisory Board developed a five-component method: the NPF-Psoriasis Score (NPF—PS). The equally weighted primary endpoints of the NPF-PS, which contribute to a total score ranging from 0 to 30, include induration of two target lesions, BSA, physician's static global assessment, patient's global assessment, and pruritus (Kreuger, G. 1999. National Psoriasis Foundation Psoriasis Forum 5:1-5). The NPF-PS gives equal weight to the patient and investigator global assessments of clinical severity. Secondly, although pruritus is a complaint of 79% of psoriasis patients, neither the PASI nor PGA includes measurements of pruritus.
Other immunologically mediated skin disorders include pemphigus vulgaris. immunologically pemphigus vulgaris, pemphigus foliaceus, paraneoplastic pemphigus, bullous pemphigoid, pemphigoid gestationis, dermatitis herpetiformis, linear iga disease, epidermolysis bullosa acquisita, cicatricial pemphigoid, dermatomyositis, lupus erythematosus, scleroderma and morphea. Dermatomyositis, lupus erythematosus, scleroderma and morphea are classified as autoimmune systemic diseases with prominent cutaneous features.
When an eruption is characterized by elevated lesions, papules (<1 cm), or plaques (>1 cm), in association with scale, it is referred to as a papulosquamous lesion. The most common papulosquamous diseases—psoriasis, tinea, pityriasis rosea, and lichen planus—are primary cutaneous disorders. When psoriatic lesions are accompanied by arthritis, the possibility of psoriatic arthritis or Reiter's disease should be considered. A history of oral ulcers, conjunctivitis, uveitis, and/or urethritis points to the latter diagnosis. In guttate psoriasis, there is an acute onset of small, widely scattered, uniform lesions, often in association with a streptococcal infection. Lithium, beta blockers, HIV infection, and a rapid taper of systemic glucocorticoids are also known to exacerbate psoriasis.
Whenever the diagnosis of pityriasis rosea or lichen planus is made, it is important to review the patient's medications because the eruption can be treated by simply discontinuing the offending agent. Pityriasis rosea-like drug eruptions are seen most commonly with beta blockers, angiotensin-converting enzyme (ACE) inhibitors, gold, and metronidazole, while the drugs that can produce a lichenoid eruption include gold, antimalarials, thiazides, quinidine, phenothiazines, sulfonylureas, and ACE inhibitors. Lichen planus-like lesions are also observed in chronic graft-versus-host disease.
In its early stages, cutaneous T cell lymphoma (CTCL) may be confused with ezcema or psoriasis, but it often fails to respond to the appropriate therapy for those inflammatory diseases. CTCL can develop within lesions of large-plaque parapsoriasis and is suggested by an increase in the thickness of the lesions. The diagnosis of CTCL is established by skin biopsy in which collections of atypical T lymphocytes are found in the epidermis and dermis. As the disease progresses, cutaneous tumors and lymph node involvement may appear.
In secondary syphilis, there are scattered red-brown papules with thin scale. The eruption often involves the palms and soles and can resemble pityriasis rosea. Associated findings are helpful in making the diagnosis and include annular plaques on the face, nonscarring alopecia, condyloma lata (broad-based and moist), and mucous patches as well as lymphadenopathy, malaise, fever, headache, and myalgias. The interval between the primary chancre and the secondary stage is usually 4 to 8 weeks, and spontaneous resolution without appropriate therapy is seen.
Thus, the method of the invention, in so far as the analytical methods of the invention predict responders to Th1-type disease, can be used to assess and recommend therapeutic treatment for patients presenting with various cutaneous symptoms.
Although most of the genes in the panel have been reported to be aberrantly expressed in psoriatic skin previously, the expression patterns of the genes over the course of treatment have not been studied in the treatment of psoriasis, and none has been identified as having predictive value. The panel of gene expression biomarkers disclosed here permits the generation of methods for rapid and reliable diagnostic tools that predict the clinical outcome of a psoriasis trial, or prognostic tools for tracking the efficacy of psoriasis therapy. Diagnostic and prognostic methods based on detecting these genes in a sample are provided. These compositions may be used, for example, for the prevention and treatment of a range of immune-mediated inflammatory diseases.
As used herein, the term “antagonists” refer to substances which inhibit or neutralize the biologic activity of the gene product of the psoriasis-related gene panel of the invention. Such antagonists accomplish this effect in a variety of ways. One class of antagonists will bind to the gene product protein with sufficient affinity and specificity to neutralize the biologic effects of the protein. Included in this class of molecules are antibodies and antibody fragments (such as, for example, F(ab) or F(ab′)2 molecules). Another class of antagonists comprises fragments of the gene product protein, muteins or small organic molecules, i.e., peptidomimetics, that will bind to the cognate binding partners or ligands of the gene product, thereby inhibiting the biologic activity of the specific interaction of the gene product with its cognate ligand or receptor. The psoriasis-related gene antagonist may be of any of these classes as long as it is a substance that inhibits at least one biological activity of the gene product.
Antagonists include antibodies directed to one or more regions of the gene product protein or fragments thereof, antibodies directed to the cognate ligand or receptor, and partial peptides of the gene product or its cognate ligand which inhibit at least one biological activity of the gene product. Another class of antagonists include siRNAs, shRNAs, antisense molecules and DNAzymes targeting the gene sequence as known in the art are disclosed herein.
Suitable antibodies include those that compete for binding to psoriasis-related gene products with monoclonal antibodies that block psoriasis-related gene product activation or prevent psoriasis-related gene product binding to its cognate ligand, or prevent psoriasis-related gene product signalling.
A therapeutic targeting the inducer of the psoriasis-related gene product may provide better chances of success. Gene expression can be modulated in several different ways including by the use of siRNAs, shRNAs, antisense molecules and DNAzymes. Synthetic siRNAs, shRNAs, and DNAzymes can be designed to specifically target one or more genes and they can easily be delivered to cells in vitro or in vivo.
The present invention encompasses antisense nucleic acid molecules, i.e., molecules that are complementary to a sense nucleic acid encoding a psoriasis-related gene product polypeptide, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be complementary to an entire coding strand, or to only a portion thereof, e.g., all or part of the protein coding region (or open reading frame). An antisense nucleic acid molecule can be antisense to all or part of a non-coding region of the coding strand of a nucleotide sequence encoding a psoriasis-related gene product polypeptide. The non-coding regions (“5′ and 3′ untranslated regions”) are the 5′ and 3′ sequences that flank the coding region and are not translated into amino acids.
The invention also provides chimeric or fusion proteins. As used herein, a “chimeric protein” or “fusion protein” comprises all or part (preferably biologically active) of a psoriasis-related gene product polypeptide operably linked to a heterologous polypeptide (i.e., a polypeptide other than the same psoriasis-related gene product polypeptide). Within the fusion protein, the term “operably linked” is intended to indicate that the psoriasis-related gene product polypeptide and the heterologous polypeptide are fused in-frame to each other. The heterologous polypeptide can be fused to the amino-terminus or the carboxyl-terminus of the psoriasis-related gene product polypeptide. In another embodiment, a psoriasis-related gene product polypeptide or a domain or active fragment thereof can be fused with a heterologous protein sequence or fragment thereof to form a chimeric protein, where the polypeptides, domains or fragments are not fused end to end but are interposed within the heterologous protein framework.
In yet another embodiment, the fusion protein is an immunoglobulin fusion protein in which all or part of a psoriasis-related gene product polypeptide is fused to sequences derived from a member of the immunoglobulin protein family. The immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand (soluble or membrane-bound) and a protein on the surface of a cell (receptor), to thereby suppress signal transduction in vivo. The immunoglobulin fusion protein can be used to affect the bioavailability of a cognate ligand of a psoriasis-related gene product polypeptide. Inhibition of ligand/receptor interaction can be useful therapeutically, both for treating proliferative and differentiative disorders and for modulating (e.g., promoting or inhibiting) cell survival. A preferred embodiment of an immunoglobulin chimeric protein is a CH1 domain-deleted immunoglobulin or “mimetibody” having an active polypeptide fragment interposed within a modified framework region as taught in co-pending application PCT WO/04002417. Moreover, the immunoglobulin fusion proteins of the invention can be used as immunogens to produce antibodies directed against a psoriasis-related gene product polypeptide in a subject, to purify ligands and in screening assays to identify molecules that inhibit the interaction of receptors with ligands.
Compositions and Their Uses
In accordance with the invention, the neutralizing anti-psoriasis-related gene product antagonists, such as monoclonal antibodies, described herein can be used to inhibit psoriasis-related gene product activity. Additionally, such antagonists can be used to inhibit the pathogenesis or psoriasis and -related inflammatory diseases amenable to such treatment, which may include, but are not limited to, rheumatic diseases. The individual to be treated may be any mammal and is preferably a primate, a companion animal which is a mammal and most preferably a human patient. The amount of antagonist administered will vary according to the purpose it is being used for and the method of administration.
The psoriasis-related gene antagonists may be administered by any number of methods that result in an effect in tissue in which pathological activity is desired to be prevented or halted. Further, the anti-psoriasis-related gene product antagonists need not be present locally to impart an effect on the psoriasis-related gene product activity, therefore, they may be administered wherever access to body compartments or fluids containing psoriasis-related gene product is achieved. In the case of inflamed, malignant, or otherwise compromised tissues, these methods may include direct application of a formulation containing the antagonists. Such methods include intravenous administration of a liquid composition, transdermal administration of a liquid or solid formulation, oral, topical administration, or interstitial or inter-operative administration. Administration may be affected by the implantation of a device whose primary function may not be as a drug delivery vehicle.
For antibodies, the preferred dosage is about 0.1 mg/kg to 100 mg/kg of body weight (generally about 10 mg/kg to 20 mg/kg). If the antibody is to act in the brain, a dosage of about 50 mg/kg to 100 mg/kg is usually appropriate. Generally, partially human antibodies and fully human antibodies have a longer half-life within the human body than other antibodies. Accordingly, the use of lower dosages and less frequent administration is often possible. Modifications, such as lipidation, can be used to stabilize antibodies and to enhance uptake and tissue penetration (e.g., into the brain). A method for lipidation of antibodies is described by Cruikshank et al. ((1997) J. Acquired Immune Deficiency Syndromes and Human Retrovirology 14:193).
The psoriasis-related gene product antagonist nucleic acid molecules can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (U.S. Pat. No. 5,328,470), or by stereotactic injection (see, e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
Agents, or modulators that have a stimulatory or inhibitory effect on activity or expression of a psoriasis-related gene product polypeptide as identified by a screening assay described herein, can be administered to individuals to treat (prophylactically or therapeutically) disorders associated with aberrant activity of the polypeptide. In conjunction with such treatment, the pharmacogenomics (i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug) of the individual may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug. Thus, the pharmacogenomics of the individual permits the selection of effective agents (e.g., drugs) for prophylactic or therapeutic treatments based on a consideration of the individual's genotype. Such pharmacogenomics can further be used to determine appropriate dosages and therapeutic regimens. Accordingly, the activity of a psoriasis-related gene product polypeptide, expression of a psoriasis-related gene product nucleic acid, or mutation content of a psoriasis-related gene product gene in an individual can be determined to thereby select an appropriate agent(s) for therapeutic or prophylactic treatment of the individual.
Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, e.g., Linder (1997) Clin. Chem. 43(2):254-266. In general, two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body are referred to as “altered drug action.” Genetic conditions transmitted as single factors altering the way the body acts on drugs are referred to as “altered drug metabolism.” These pharmacogenetic conditions can occur either as rare defects or as polymorphisms. For example, glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited enzymopathy in which the main clinical complication is hemolysis after ingestion of oxidant drugs (anti-malarials, sulfonamides, analgesics, nitrofurans) and consumption of fava beans.
As an illustrative embodiment, the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action. The discovery of genetic polymorphisms of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19) has provided an explanation as to why some patients do not obtain the expected drug effects or show exaggerated drug response and serious toxicity after taking the standard and safe dose of a drug. These polymorphisms are expressed in two phenotypes in the population, the extensive metabolizer (EM) and poor metabolizer (PM). The prevalence of PM is different among different populations. For example, the gene coding for CYP2D6 is highly polymorphic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, a PM will show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite morphine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplification.
Thus, the activity of a psoriasis-related gene product polypeptide, expression of a nucleic acid encoding the polypeptide, or mutation content of a gene encoding the polypeptide in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual. In addition, pharmacogenetic studies can be used to apply genotyping of polymorphic alleles encoding drug-metabolizing enzymes to the identification of an individual's drug responsiveness phenotype. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with a modulator of activity or expression of the polypeptide, such as a modulator identified by one of the exemplary screening assays described herein.
The present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant expression or activity of a psoriasis-related gene product polypeptide and/or in which the psoriasis-related gene product polypeptide is involved.
The present invention provides a method for modulating or treating at least one psoriasis-related gene product related disease or condition, in a cell, tissue, organ, animal, or patient, as known in the art or as described herein, using at least one psoriasis-related gene product antagonist.
Compositions of psoriasis-related gene product antagonist may find therapeutic use in the treatment of psoriasis or related conditions, such as asthma, scleroderma, idiopathic pulmonary fibrosis.
The present invention also provides a method for modulating or treating at least one immune related disease, in a cell, tissue, organ, animal, or patient including, but not limited to, at least one of rheumatoid arthritis, juvenile rheumatoid arthritis, systemic onset juvenile rheumatoid arthritis, psoriatic arthritis, ankylosing spondilitis, gastric ulcer, seronegative arthropathies, osteoarthritis, inflammatory bowel disease, ulcerative colitis, systemic lupus erythematosis, antiphospholipid syndrome, iridocyclitis/uveitis/optic neuritis, idiopathic pulmonary fibrosis, systemic vasculitis/wegener's granulomatosis, sarcoidosis, orchitis/vasectomy reversal procedures, allergic/atopic diseases, allergic rhinitis, eczema, allergic contact dermatitis, allergic conjunctivitis, hypersensitivity pneumonitis, transplants, organ transplant rejection, graft-versus-host disease, systemic inflammatory response syndrome, sepsis syndrome, gram positive sepsis, gram negative sepsis, culture negative sepsis, fungal sepsis, neutropenic fever, urosepsis, meningococcemia, trauma/hemorrhage, burns, ionizing radiation exposure, acute pancreatitis, adult respiratory distress syndrome, rheumatoid arthritis, alcohol-induced hepatitis, chronic inflammatory pathologies, sarcoidosis, Crohn's pathology, sickle cell anemia, diabetes, nephrosis, atopic diseases, hypersensitivity reactions, allergic rhinitis, hay fever, perennial rhinitis, conjunctivitis, endometriosis, urticaria, systemic anaphalaxis, dermatitis, pernicious anemia, hemolytic disease, thrombocytopenia, graft rejection of any organ or tissue, kidney transplant rejection, heart transplant rejection, liver transplant rejection, pancreas transplant rejection, lung transplant rejection, bone marrow transplant (BMT) rejection, skin allograft rejection, cartilage transplant rejection, bone graft rejection, small bowel transplant rejection, fetal thymus implant rejection, parathyroid transplant rejection, xenograft rejection of any organ or tissue, allograft rejection, anti-receptor hypersensitivity reactions, Graves disease, Raynoud's disease, type B insulin-resistant diabetes, myasthenia gravis, antibody-meditated cytotoxicity, type III hypersensitivity reactions, systemic lupus erythematosus, POEMS syndrome (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes syndrome), antiphospholipid syndrome, pemphigus, scleroderma, mixed connective tissue disease, idiopathic Addison's disease, diabetes mellitus, chronic active hepatitis, primary billiary cirrhosis, vitiligo, vasculitis, post-MI cardiotomy syndrome, type IV hypersensitivity, contact dermatitis, hypersensitivity pneumonitis, allograft rejection, granulomas due to intracellular organisms, drug sensitivity, metabolic/idiopathic, Wilson's disease, hemachromatosis, alpha-1-antitrypsin deficiency, diabetic retinopathy, hashimoto's thyroiditis, osteoporosis, hypothalamic-pituitary-adrenal axis evaluation, primary biliary cirrhosis, thyroiditis, encephalomyelitis, cachexia, cystic fibrosis, familial hematophagocytic lymphohistiocytosis, dermatologic conditions, psoriasis, alopecia, nephrotic syndrome, nephritis, glomerular nephritis, acute renal failure, hemodialysis, uremia, toxicity, preeclampsia, okt3 therapy, anti-cd3 therapy, cytokine therapy, chemotherapy, radiation therapy (e.g., including but not limited toasthenia, anemia, cachexia, and the like), chronic salicylate intoxication, and the like. See, e.g., the Merck Manual, 12th-17th Editions, Merck & Company, Rahway, N.J. (1972, 1977, 1982, 1987, 1992, 1999), Pharmacotherapy Handbook, Wells et al., eds., Second Edition, Appleton and Lange, Stamford, Conn. (1998, 2000), each entirely incorporated by reference.
The present invention also provides a method for modulating or treating at least one malignant disease in a cell, tissue, organ, animal or patient, including, but not limited to, at least one of: leukemia, acute leukemia, acute lymphoblastic leukemia (ALL), B-cell, T-cell or FAB ALL, acute myeloid leukemia (AML), acute promyelocytic leukemia (APL), chromic myelocytic leukemia (CML), chronic lymphocytic leukemia (CLL), hairy cell leukemia, myelodyplastic syndrome (MDS), a lymphoma, Hodgkin's disease, a malignamt lymphoma, non-hodgkin's lymphoma, Burkitt's lymphoma, multiple myeloma, Kaposi's sarcoma, colorectal carcinoma, pancreatic carcinoma, nasopharyngeal carcinoma, malignant histiocytosis, paraneoplastic syndrome/hypercalcemia of malignancy, solid tumors, adenocarcinomas, sarcomas, malignant melanoma, hemangioma, metastatic disease, cancer related bone resorption, cancer related bone pain, and the like.
Disorders characterized by aberrant expression or activity of the psoriasis-related gene product polypeptides are further described elsewhere in this disclosure.
In one aspect, the invention provides a method for at least substantially preventing in a subject, a disease or condition associated with an aberrant expression or activity of a psoriasis-related gene product polypeptide, by administering to the subject an agent that modulates expression or at least one activity of the polypeptide. Subjects at risk for a disease that is caused or contributed to by aberrant expression or activity of a psoriasis-related gene product can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression. Depending on the type of aberrancy, for example, an agonist or antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein.
Another aspect of the invention pertains to methods of modulating expression or activity of psoriasis-related gene or gene product for therapeutic purposes. The modulatory method of the invention involves contacting a cell with an agent that modulates one or more of the activities of the polypeptide. An agent that modulates activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring cognate ligand of the polypeptide, a peptide, a peptidomimetic, or other small molecule. In one embodiment, the agent stimulates one or more of the biological activities of the polypeptide. In another embodiment, the agent inhibits one or more of the biological activities of the psoriasis-related gene or gene product polypeptide. Examples of such inhibitory agents include antisense nucleic acid molecules and antibodies and other methods described herein. These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject). As such, the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant expression or activity of a psoriasis-related gene product polypeptide. In one embodiment, the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulate (e.g., up-regulates or down-regulates) expression or activity. Inhibition of activity is desirable in situations in which activity or expression is abnormally high or up-regulated and/or in which decreased activity is likely to have a beneficial effect.
While having described the invention in general terms, the embodiments of the invention will be further disclosed in the following examples which should not be construed as limiting the scope of the claims.
The study (Protocol C379T02) design was a phase I, double blind, placebo-controlled study for the evaluation of safety and pharmacology of single subcutaneous administrations of human monoclonal antibody to IL-12 (CNTO1275) in subjects with moderate to severe psoriasis vulgaris. This study was conducted at multiple centers in Florida, New Jersey, and Pennsylvania. Twenty-one subjects were randomized to active or placebo treatment within 1 of 4 sequential escalating dose cohorts (0.3 mg/kg, 0.75 mg/kg, 1.5 mg/kg, or 3.0 mg/kg) across the 3 sites. Each subject received a single subcutaneous injection and remained in the clinic for at least 8 hours following administration of the study agent. Subjects returned for periodic follow-up visits over a 24-week period and subjects were required to have at least 4 weeks of follow-up. Subjects participated for up to 28 weeks including the 4 weeks prior to the test agent administration. Subjects (ages 18-65) with moderate to severe plaque psoriasis involving >3% body surface area (BSA) and who were generally in good health were admitted to the study.
Skin biopsy samples were taken from trial subjects 24 hours before (baseline) and 1 week after treatment. A representative biopsy target lesion, located on the trunk or extremities with adequate dermis and SC tissue, was identified by the investigator to be used for biopsy analysis. A 6-mm punch biopsy was obtained at baseline and 1 week after administration of test agent. There were 4 samples from 2 non-responders both at day 0 and at week 1. These samples were excluded from the analysis. The data described below is based on samples from patients who showed improvement in their psoriatic condition after treatment with the anti-IL-12p40.
Total RNA was isolated from these skin biopsies using RNeasy kit (Qiagen, Valencia, Calif.). RNA quality was assessed using the BioAnalyzer (Agilent, South Plainfield, N.J.). Only high quality RNA is used for microarray analysis that contains 8160 unique human cDNA clones collected from IMAGE consortium and Incyte Genomices (Santa Clara, Calif.). RNA amplification, probe synthesis and labeling, cDNA chip hybridization and washing were performed as described previously (Salunga, et a1.1999. In: M. Schena (Ed.), DNA microarrays a practical approach, Oxford University Press, Oxford, pp. 121-137). An Agilent Image Scanner was used to scan the cDNA chips (Palo Alto, Calif.). Fluorescence intensity for each feature of the array was obtained by using ImaGene software (BioDiscovery, Los Angeles, Calif.).
A total of 24 samples were analyzed from 5 treatment groups (placebo, 0.3 mg/kg, 0.75 mg/kg, 1.5 mg/kg and 3.0 mg/kg) and 2 timepoints (baseline and week 1) from these groups as shown in Table 1.
Using GeneSpring™ software version 6.0 (Silicon Genetics, Redwood City, Calif.), the average intensity for each feature was further normalized across all samples. Chip-to-chip normalization was performed by dividing the average intensity of each clone by the median intensity of a chip. The intensity of each clone was then normalized to the median intensity of that clone in the control group. The baseline values in this study were the average of all day 0 samples before the treatment. The statistical comparison of anti-IL-12p40 treated groups vs. placebo within each dosing group (except the 1.5 mg/kg for it only has two samples) was done by one-way ANOVA (P<0.05) on the log2 transformed normalized intensity.
Subsequently, statistical pairwise analysis also used a p-value of 0.05. These parameters result in the possibility that 350-400 genes could be identified by chance out of the universe of possible genes. However, the genes identified appear credibly related to the disease because their expression patterns are consistent with clinical response; being relatively constant in the pre-treatment samples, down-regulated after treatment, and, finally, many were known immune response genes, e.g., IL1F5, IL1F9, ILRN, IL8, and have been previously associated with inflammatory conditions. Thus, they are believed to be authentic psoriasis-related gene biomarkers.
Tables 2A-F list the 26 genes that showed significant changes by statistical test in at least one dosing group comparison and at least 1.4-fold change in a second dosing group comparison. The 26 genes listed represent a panel of psoriasis-related genes, subdivided into 6 functional categories, which undergo expression modulation indicative of the resolution of psoriasis and improvement towards normal skin structure and function. Only the genes identified at week 1 are reported; the genes meeting the same criteria but from the day 0 samples have been excluded.
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Though many Th1 cytokines, such as TNF-α and IFN-γ, were known to be up regulated in psoriatic lesional skin (2,3), anti-IL-12p40 treatment selectively down regulated three lesser known IL-1 family members: IL1F5 (IL-1 delta) and IL1F9 (IL-1 epsilon), and IL1RN (IL-1 receptor antagonist which is highly homologous to IL1F5) at week 1. Although all of these IL-1 cytokines had been reported to be substantially up-regulated in psoriatic skin (Debets, et al. 2001. J. Immunol. 167(3)1440-6; Zhou et al, Physiol Genomics, 2003. 13(1). 69-78), the present invention shows them to be among the first wave of cytokines down-regulated as result of therapy, weeks ahead of visible clinical improvement. The fact that IL1F5 and IL1F9 are known to be preferably expressed in epithelial cells, in particular by keratinocytes, indicates that these two cytokines may play a larger and more specific role in psoriasis pathogenesis.
Similarly, among many chemokines found to be over-expressed in psoriatic lesions (Zhou et al., 2003, supra), anti-IL-12p40 treatment selectively down-regulated IL-8 and CXCL1 (GRO1), both potential chemotractants of neutrophils. Since neutrophil chemokine over-production and the result of neutrophil infiltration are molecular and cellular hallmarks of psoriasis, it is expected that effective treatment would reduce the production of these chemokines. Surprisingly, macrophages chemokine CCL3 was also down regulated by anti-IL-12p40. The involvement of CCL3 in psoriasis has not been reported, though it was found to be up regulated in the PBMCs of patients with atopic dermatitis (AD) (Hatano, et al., 1999. Clin Exp Immunol, 117(2). 237-43), a disease that shares many clinical features with psoriasis.
Some serine proteases and their inhibitors have been reported to be associated with psoriasis. We have observed down regulation of these groups of genes. For example, two members of the kallikrein (KLK) family of serine proteases, KLK6 and KLK 13, were down regulated by the anti-IL-12p40 treatment. The KLKs, which are encoded by clusters of 15 genes on chromosome 19q13, are involved in the differentiated to terminal differentiation of keratinocytes into corneocytes (Lu, J. et al., 2005. J Invest Dermatol. 124(4). 778-85). At least some KLKs are negatively regulated by members of the serine proteinase inhibitor (SERPINs) family. Interestingly, four SERPINs members, SERPINB3, B4, B5 and B13 of the SERPINs were down regulated by anti-IL-12p40. Taken together, the KLK-SERPIN network is intimately involved in the pathogenesis of psoriasis.
Another example of a skin protease is tissue plasminogen activator (PLAT), which was a marker common to psoriatic epidermis, epidermis during wound repair, and keratinocytes in culture (Jensen, P J et al., 1990. J Invest Dermatol 95(5). 13S-14S). PLAT was down regulated by anti-IL-12p40 treatment.
Another example of a skin specific protease inhibitor is PI3, or skin-derived protease inhibitor 3, or elafin precursor. PI3 is an epithelial host-defense protein that is absent in normal skin but highly induced in keratinocytes of inflamed skin, such as psoriasis (Pol A, et al., 2003 J Invest Dermatol 120(2). 301-7). It was known that PI3 expression could be induced by serum or TNF-α, and suppressed by retinoids, dithranol, and p38 MAP kinase inhibitors. The present invention discloses that its expression can also be down regulated by anti-IL-12p40.
Among the genes that were up regulated as the result of ani-IL-12p40 treatment, the most consistent one is bleomycin hydrolase (BLMH). It is a cytoplasmic cysteine peptidase. Polymorphism of this gene was associated with neurodegenerative diseases, notably Alzheimer disease (Montoya, S E et al., 1998. Nat Genet. 18(3). 211-2). No role of BLMH in psoriasis has ever been reported.
Clearing of psoriatic lesions involves many structural changes, and indeed many gene alterations of molecules integral to the dermal and epidermal components were detected. For example, GJB2 (Connexin26), a gap junction component during both early and later stages of keratinocyte differentiation, was down-regulated by anti-IL12p40 treatment. GJB2 was consistently detected between keratinocytes of the basal and granular layers at the periphery of psoriatic plaques and in all layers of fully developed psoriatic epidermis. However, none or a minimal amount of GJB2 had previously been observed in both control and nonlesional regions of psoriatic epidermis (Labarthe, M P et al., 1998. J Invest Dermatol 111(1). 72-6).
Because of the abnormal differentiation of keratinocytes in psoriasis lesions, early differentiation markers, such as proline-rich proteins (SPRR1A), are over-expressed, while late differentiation markers, such as loricrin (LOR), are abolished (lizuka, H et al., 2004. J Dermatol 31(4). 271-6). The reverse of this trend was detected only one week after the anti-IL-12p40 treatment, a strong indication of clinical improvement.
One of the best known and possibly the most reliable marker of clinical resolution was the reduction in keratin 16 (KRT16) (Holland, D B et al., 1989. Br J Dermatol 120(1). 9-19). Both KRT16 and keratin 14 were detected to be suppressed in the early stage of treatment by anti-IL-12p40.
Annexin I (lipocortin I), which is a calcium- and phospholipid-binding protein that is involved in the regulation of differentiation and proliferation of epidermal keratinocytes and has higher expression in psoriatic epidermis than in normal epidermis (lizuka, H. 2004, supra), was detected to be down regulated by anti-IL-12p40.
Another important immune mediator that was detected to be down regulated by anti-IL12p40 is Neutrophil gelatinase-associated lipocalin (NGAL, Lipocalin-2, LCN2). LCN2 protein is believed to bind small lipophilic substances, such as bacteria-derived lipopolysaccharide (LPS) and formylpeptides, and may function as a modulator of inflammation (Flo, T H S et al, 2004. Nature 432: 917-921). In addition, LCN is also a marker for dysregulated keratinocyte differentiation in human skin (Mallbris, L et al., 2002. Exp Dermatol 11(6). 584-91).
Psoriasis-associated fatty acid-binding protein (FABP5 or PA-FABP) is another marker that is highly up regulated in psoriatic skin (Madsen, P. et al., 1992. J Invest Dermatol 99(3). 299-305), but down regulated by anti-IL-12p40 treatment. It has been previously reported that when treating lesional psoriatic skin with topical steroids, the changes in expression patterns of PI3 and FABP5 alter in a manner consistent with known cellular biological events during regression of the psoriatic lesion (Kuijpers, A I et al, 1997. Acta Derm Venereol 77(1). 14-9).
With limited RNA samples left after microarray analysis, Taqman analysis was performed on a few of the genes in Table 2. One microgram of total RNA in the volume of 50 ul was converted to cDNA in the presence of MultiScribe Reverse Transcriptase. The reaction was carried out by incubating for 10 minutes at 25° C. followed by 30 minutes at 48° C. Reverse Transcriptase was inactivated at 95° C. for 5 minutes. Twenty nanograms of cDNA per reaction was used in real time PCR with the ABI 7900 system (Foster City, Calif.). In the presence of AmpliTaq Gold DNA polymerase (ABI biosystem, Foster City, Calif.), the reaction was incubated for 2 minutes at 50° C. followed by 10 minutes at 95° C. Then, the reaction ran for 40 cycles at 15 seconds, 95° C. and 1 minute, 60° C. per cycle.
The housekeeping gene GAPDH (glyceraldehydes-3-phosphate dehydrogenase) was used to normalize gene expression.
The study (C0379T04) was a phase II, randomized, double-blind, placebo-controlled, parallel study of single and multiple dose regimens with subcutaneous (SC) administration of CNTO 1275 in subjects with moderate to severe psoriasis. CNTO1275 is a fully human monoclonal antibody specific for the p40 subunit of human IL-12 and IL-23. This study consists of 5 groups of subjects that received single or multiple doses of subcutaneous (SC) administrations of CNTO 1275 or placebo as described below:
A representative target lesion, located on the trunk or extremities with adequate dermis and SC tissue was identified by the study investigator for biopsy analyses. A 4-mm punch biopsy was obtained from the pre-identified target lesion at baseline and 12 weeks after administration of the study agent. Total RNA was obtained from the biopsy samples using an RNeasy mini kit (Qiagen Inc, Valencia, Calif.). RNA quality was verified with the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, Calif.). In total, 39 RNA samples (as listed in Table 3) were used for DNA microarray.
Total RNA was isolated from these skin biopsies using RNeasy kit (Qiagen, Valencia, Calif.). RNA quality was assessed using the BioAnalyzer (Agilent, South Plainfield, N.J.). Only high quality RNA is used for microarray analysis that contains 8160 unique human cDNA clones collected from IMAGE consortium and Incyte Genomices (Santa Clara, Calif.). RNA amplification, probe synthesis and labeling, cDNA chip hybridization and washing were performed as described previously (Salunga, et a1.1999. In: M. Schena (Ed.), DNA microarrays a practical approach, Oxford University Press, Oxford, pp. 121-137). An Agilent Image Scanner was used to scan the cDNA chips (Palo Alto, Calif.). Fluorescence intensity for each feature of the array was obtained by using ImaGene software (BioDiscovery, Los Angeles, Calif.).
Using GeneSpring™ software version 6.0 (Silicon Genetics, Redwood City, Calif.), the average intensity for each feature was further normalized across all samples. Chip-to-chip normalization was performed by dividing the average intensity of each clone by the median intensity of a chip. The intensity of each clone was then normalized to the median intensity of that clone in the control group. The baseline values in this study were the average of all day 0 samples before the treatment. The statistical comparison of anti-IL-12p40 treated groups vs. placebo within each dosing group was done by one-way ANOVA (P<0.05) on the log2 transformed normalized intensity.
Subsequently, statistical pairwise analysis also used a p-value of 0.05. These parameters result in the possibility that 350-400 genes could be identified by chance out of the universe of possible genes. However, the genes identified appear credibly related to the disease because their expression patterns are consistent with clinical response; being relatively constant in the pre-treatment samples, down-regulated after treatment, and, finally, many were known immune response genes, e.g., PBEF, S100A11, and IL4R, and have been previously associated with inflammatory conditions. Thus, they are believed to be authentic psoriasis-related gene biomarkers.
Tables 4A-E list the 10 genes that showed significant changes by statistical test in at least one dosing group comparison and at least 1.5-fold change in a second dosing group comparison. The 10 genes listed represent a panel of psoriasis-related genes, subdivided into 5 functional categories, which undergo expression modulation indicative of the resolution of psoriasis and improvement towards normal skin structure and function. Only the genes identified at week 12 are reported; the genes meeting the same criteria but from the day 0 samples have been excluded.
Table 4. List of Significantly Changed Genes from Baseline by Their Function Categories
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On the RNA samples left after microarray analysis, Taqman analysis was performed on a few of the genes in Table 4. One microgram of total RNA in the volume of 50 ul was converted to cDNA in the presence of MultiScribe Reverse Transcriptase. The reaction was carried out by incubating for 10 minutes at 25° C. followed by 30 minutes at 48° C. Reverse Transcriptase was inactivated at 95° C. for 5 minutes. Twenty nanograms of cDNA per reaction was used in real time PCR with the ABI 7900 system (Foster City, Calif.). In the presence of AmpliTaq Gold DNA polymerase (ABI biosystem, Foster City, Calif.), the reaction was incubated for 2 minutes at 50° C. followed by 10 minutes at 95° C. Then, the reaction ran for 40 cycles at 15 seconds, 95° C. and 1 minute, 60° C. per cycle.
The housekeeping gene GAPDH (glyceraldehydes-3-phosphate dehydrogenase) was used to normalize gene expression.
In summary, a panel of potential molecular biomarkers that is indicative of favorable outcome for the treatment of psoriasis has been identified along with the direction in which they are modulated. This panel of biomarkers is particular useful in guiding clinical development, as the change in expression of genes in this panel appears prior to improvement of clinically measurable parameters, such as PASI score (Psoriasis Area and Severity Index), can be achieved and/or detected. Thus, the 36 identified genes represent a psoriasis-related gene panel which can be used as a tool to monitor the efficacy of any psoriasis therapeutic, such as CNTO 1275, and provide valuable information that guides dosing regimens.
A panel of genes identified as psoriasis-related genes herein has demonstrated relevance to psoriasis, skin, and inflammation. As demonstrated by the present analysis, the panel as a whole provides a fingerprint for gauging the efficacy of a treatment of psoriasis that leads to an improvement in the involvement and severity of skin lesions. A number of the genes, which are members of the psoriasis-related gene panel, have been previously shown to be aberrantly expressed in psoriatic skin. For example, increased levels of IL1F5, IL1F9, and IL1RN have been reported to be substantially up-regulated in psoriasis skin. The present study provides evidence that IL1F5, IL1F9, and IL1RN are key cytokines that maintain the inflammatory status in this disorder. Other genes, such as IL-8 and PI3, are common to other inflammatory diseases. Thus, together, monitoring genes in this panel provides a method for evaluating drug candidates and in so far as the modulation of the expression of these genes predicts the clinical outcome of a psoriasis therapy.
Although illustrated and described above with reference to certain specific embodiments, the present invention is nevertheless not intended to be limited to the details shown. Rather, the present invention is directed to the psoriasis related genes and gene products. Polynucleotides, antibodies, apparatus, and kits disclosed herein and uses thereof, and methods for controlling the levels of the psoriasis-related biomarker genes, and various modifications may be made in the details within the scope and range of equivalents of the claims and without departing from the spirit of the invention.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/US06/62670 | 12/28/2006 | WO | 00 | 11/25/2008 |
| Number | Date | Country | |
|---|---|---|---|
| 60754243 | Dec 2005 | US |
