# Patent

## Title
Oligoribonucleotides and methods of use thereof for treatment of fibrotic conditions and other diseases

## Abstract

The invention relates to a double-stranded compound, preferably an oligoribonucleotide (siRNA), which down-regulates the expression of a human TGaseII gene at the post-transcriptional level. The invention also relates to a pharmaceutical composition comprising the compound, or a vector capable of expressing the oligoribonucleotide compound, and a pharmaceutically acceptable carrier. The present invention also contemplates a method of treating a patient suffering from a fibrotic disease such as pulmonary, kidney and liver fibrosis or ocular, scarring comprising administering to the patient the pharmaceutical composition in a therapeutically effective dose so as to thereby treat the patient. The invention also relates to treatment of fibrotic and other diseases by use of antibodies to TGaseII polypeptide.

## Background
This application claims priority of U.S. Ser. No. 11/045,780, filed Jan. 27, 2005 now abandoned, which claims benefit of U.S. Provisional patent applications No. 60/540,687, filed Jan. 30, 2004 and No. 60/641,522 filed Jan. 4, 2005, the contents of all of which are hereby incorporated by reference into this application.
Throughout this application various patent and scientific publications are cited. The disclosures of these publications in their entireties are hereby incorporated by reference into this application to more fully describe the state of the art to which this invention pertains.
BACKGROUND OF THE INVENTION
siRNAs and RNA Interference
RNA interference (RNAi) is a phenomenon involving double-stranded (ds) RNA-dependent gene specific posttranscriptional silencing. Originally, attempts to study this phenomenon and to manipulate mammalian cells experimentally were frustrated by an active, non-specific antiviral defense mechanism which was activated in response to long dsRNA molecules; see Gil et al. 2000, Apoptosis, 5:107-114. Later it was discovered that synthetic duplexes of 21 nucleotide RNAs could mediate gene specific RNAi in mammalian cells, without the stimulation of the generic antiviral defence mechanisms see Elbashir et al. Nature 2001, 411:494-498 and Caplen et al. Proc Natl Acad Sci 2001, 98:9742-9747. As a result, small interfering RNAs (siRNAs), which are short double-stranded RNAs, have become powerful tools in attempting to understand gene function.
Thus, RNA interference (RNAi) refers to the process of sequence-specific post-transcriptional gene silencing in mammals mediated by small interfering RNAs (siRNAs) (Fire et al, 1998, Nature 391, 806) or microRNAs (miRNAs) (Ambros V. Nature 431:7006, 350-355 (2004); and Bartel D P. Cell. 2004 Jan. 23; 116(2): 281-97 MicroRNAs: genomics, biogenesis, mechanism, and function). The corresponding process in plants is commonly referred to as specific post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. An siRNA is a double-stranded RNA molecule which down-regulates or silences (prevents) the expression of a gene/mRNA of its endogenous (cellular) counterpart. RNA interference is based on the ability of dsRNA species to enter a specific protein complex, where it is then targeted to the complementary cellular RNA and specifically degrades it. Thus, the RNA interference response features an endonuclease complex containing an siRNA, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having a sequence complementary to the antisense strand of the siRNA duplex. Cleavage of the target RNA may take place in the middle of the region complementary to the antisense strand of the siRNA duplex (Elbashir et al 2001, Genes Dev., 15, 188). In more detail, longer dsRNAs are digested into short (17-29 bp) dsRNA fragments (also referred to as short inhibitory RNAs—“siRNAs”) by type III RNAses (DICER, DROSHA, etc., Bernstein et al., Nature, 2001, v. 409, p. 363-6; Lee et al., Nature, 2003, 425, p. 415-9). The RISC protein complex recognizes these fragments and complementary mRNA. The whole process is culminated by endonuclease cleavage of target mRNA (McManus & Sharp, Nature Rev Genet, 2002, v. 3, p. 737-47; Paddison & Hannon, Curr Opin Mol. Ther. 2003 June; 5(3): 217-24). For information on these terms and proposed mechanisms, see Bernstein E., Denli A M. Hannon G J: 2001The rest is silence. RNA. I; 7(11): 1509-21; Nishikura K.: 2001 A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst. Cell. 116; 107(4): 415-8 and PCT publication WO 01/36646 (Glover et al).
The selection and synthesis of siRNA corresponding to known genes has been widely reported; see for example Chalk A M, Wahlestedt C, Sonnhammer E L. 2004 Improved and automated prediction of effective siRNA Biochem. Biophys. Res. Commun. Jun. 18; 319(1): 264-74; Sioud M, Leirdal M., 2004, Potential design rules and enzymatic synthesis of siRNAs, Methods Mol. Biol.; 252:457-69; Levenkova N, Gu Q, Rux J J. 2004, Gene specific siRNA selector Bioinformatics. I 12; 20(3): 430-2. and Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K., Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference Nucleic Acids Res. 2004 I 9; 32(3):936-48. See also Liu Y, Braasch D A, Nulf C J, Corey D R. Efficient and isoform-selective inhibition of cellular gene expression by peptide nucleic acids, Biochemistry, 2004 I 24; 43(7):1921-7. See also PCT publications WO 2004/015107 (Atugen) and WO 02/44321 (Tuschl et al), and also Chiu Y L, Rana T M. siRNA function in RNAi: a chemical modification analysis, RNA 2003 September; 9(9):1034-48 and I U.S. Pat. Nos. 5,898,031 and 6,107,094 (Crooke) for production of modified/more stable siRNAs.
Several groups have described the development of DNA-based vectors capable of generating siRNA within cells. The method generally involves transcription of short hairpin RNAs that are efficiently processed to form siRNAs within cells. Paddison et al. PNAS 2002, 99:1443-1448; Paddison et al. Genes & Dev 2002, 16:948-958; Sui et al. PNAS 2002, 8:5515-5520; and Brummelkamp et al. Science 2002, 296:550-553. These reports describe methods to generate siRNAs capable of specifically targeting numerous endogenously and exogenously expressed genes.
siRNA has recently been successfully used for inhibition in primates; for further details see Tolentino et al., Retina 24(1) February 2004 I 132-138.
Transglutaminase (TGase) Family
Transglutaminases (EC 2.3.2.13) are a family of enzymes that catalyze the crosslinking of proteins by epsilon-gamma glutamyl lysine isopeptide bonds. The family comprises 9 different enzymes among which are the factor XIIIa (plasma transglutaminase), keratinocyte transglutaminase (TGaseI), epidermal transglutaminase (TGaseIII), prostate transglutaminase (TGaseIV), and tissue-type transglutaminase (TGaseII). Although the overall primary structure of these enzymes is different, they all share a common amino acid sequence at the active site (Y-G-Q-C-W) and a strict calcium dependence for their activity (Lesort M, Tucholski J, Miller M L, Johnson G V, Tissue transglutaminase: a possible role in neurodegenerative diseases. Prog Neurobiol. 2000 August; 61(5):439-63).
Transglutaminase II. Transglutaminase II (TGaseII) also known as Protein-glutamine gamma-glutamyltransferase, TGase C, TGC, TG(C), and tissue-type transglutaminase, is a unique multifunctional enzyme with dual enzymatic activity:

    1) The enzyme acts as a TGase protein (Ca2+ activated, GTP-inactivated) with crosslinking activities (i.e. it catalyzes reactions resulting in protein cross-links and/or covalent incorporation of biogenic amines). TGase further catalyzes the formation of a covalent glutamyl-lysyl bond, a unique isopeptide bond that is highly resistant to proteolysis and denaturants and that cannot be disrupted by any known vertebrate endopeptidase.
    2) The enzyme also acts as a GTP-binding protein that transduces the activating signal from alpha1B and alpha 1D adrenergic receptors, from TP alpha thromboxane A2 receptor and from oxytocin receptor to phospholipase C delta 1 (i.e. it activates inositol phosphate production, Ca2+ mobilization etc.). It has been shown that both alpha 1D adrenergic receptor and PLC act as guanine nucleotide exchanging factor for transglutaminase II (Baek K J, Kang S, Damron D, Im M, Phospholipase C-delta1 is a guanine nucleotide exchanging factor for transglutaminase II (G alpha h) and promotes alpha IB-adrenoreceptor-mediated GTP binding and intracellular calcium release. J Biol. Chem. 2001 Feb. 23; 276(8):5591-7).


The dual function of this enzyme is separate and the active sites are located at different positions (Im M J, Russell M A, Feng J F, Transglutaminase II: a new class of GTP-binding protein with new biological junctions. Cell Signal. 1997 November; 9(7):477-82), and inhibition of crosslinking activity of TGaseII may be achieved without the interference with its G-protein function.
TGaseII: Subcellular Localization and Fibrosis Related Intracellular Signaling Activity
TGaseII is ubiquitously expressed and can be found in association with ECM and intracellularly, both as membrane bound and as cytosolic protein. The GTP-binding activity is higher in the membrane fraction of TGase and the cross-linking activity is higher in the cytosolic and extracellular fraction. On the cell surface, TGase binds to fibronectin via its 42 kDa gelatin-binding domain. The cross-linking of fibronectin with collagen contributes to structural stabilization of the ECM rendering the matrix resistant to proteolysis by matrix mettaloproteinases. Thus TGaseII, by favoring deposition of extracellular proteins and inhibiting breakdown of said proteins, contributes to ECM accumulation, a phenomenon that is central to the formation of tissue fibrosis.
In addition, TGase mediates the binding of latent TGF-beta to the ECM, a required step for a proper subsequent processing of this pro-fibrotic factor, which finally results in the release of active TGF-beta (Le et al., Connect Tissue Res. 2001; 42(4):245-53. Rosenthal et al., Arthritis Rheum. 2000 August; 43(8):1729-33).
In the cytoplasm, TGaseII may activate RhoA, a small G protein of the ras family known to have an important role in cytoskeletal rearrangement, regulation of cell morphology and differentiation. Activation of TGaseII results in an increased transamidation of RhoA, which then functions as a constitutively active G-protein showing increased binding to and activation of its downstream target ROCK-2 (Rho-associated kinase) (Singh et al. EMBO J. 2001 May 15; 20(10):2413-23). The specific ROCK kinase inhibitor, Y-27632, showed anti-fibrotic effect in UUO model of renal fibrosis as well as in the models of liver or lung fibrosis (Nagatoya K, Moriyama T, Kawada N, Takeji M, Oseto S, Murozono T, Ando A, Imai E, Hori M. Y-27632 was found to prevent tubulointerstitial fibrosis in mouse kidneys with unilateral urethral obstruction. Kidney Int. 2002 May; 61(5):1684-95; Murata T, Arii S, Nakamura T, Mori A, Kaido T, Furuyama H, Furumoto K, Nakao T, Isobe N, Imamura M, Inhibitory effect of Y-27632, a ROCK inhibitor, on progression of rat liver fibrosis in association with inactivation of hepatic stellate cells. J Hepatol. 2001 October; 35(4):474-81; Shimizu Y, Dobashi K, Iizuka K, Horie T, Suzuki K, Tukagoshi H, Nakazawa T, Nakazato Y, Mori M, Contribution of small GTPase Rho and its target protein ROCK in a murine model of lung fibrosis. Am J Respir Crit. Care Med. 2001 January; 163(1):210-7). Recently, a unique function of TGaseII contributing to activation of NFκB, a transcription factor with a well-documented pro-fibrotic activity was described (Baud et al., J Soc Biol. 2002; 196(4):269-73, Lee at al. J Biol. Chem. 2004 Dec. 17; 279(51): δ3725-35).
Fibrotic Diseases
Fibrotic diseases are all characterized by the excess deposition of a fibrous material within the extracellular matrix, which contributes to abnormal changes in tissue architecture and interferes with normal organ function. Unfortunately, although fibrosis is widely prevalent, debilitating and often life threatening, there is no effective treatment currently available.
All tissues damaged by trauma respond by the initiation of a wound-healing program. Fibrosis, a type of disorder characterized by excessive scarring, occurs when the normal self-limiting process of wound healing response is disturbed, and causes excessive production and deposition of collagen. As a result, normal organ tissue is replaced with scar tissue, which eventually leads to the functional failure of the organ.
Fibrosis may be initiated by diverse causes and in various organs. Liver cirrhosis, pulmonary fibrosis, sarcoidosis, keloids and kidney fibrosis are all chronic conditions associated with progressive fibrosis, thereby causing a continuous loss of normal tissue function.
Acute fibrosis (usually with a sudden and severe onset and of short duration) occurs as a common response to various forms of trauma including accidental injuries (particularly injuries to the spine and central nervous system), infections, surgery, ischemic illness (e.g. cardiac scarring following heart attack), burns, environmental pollutants, alcohol and other types of toxins, acute respiratory distress syndrome, radiation and chemotherapy treatments).
For further information on different types of fibrosis see: Molina V, Blank M, Shoenfeld Y. (2002), “Fibrotic diseases”, Harefuah, 141(11): 973-8, 1009; Yu L, Noble N A, Border W A (2002), “Therapeutic strategies to halt renal fibrosis”, Curr Opin Pharmacol. 2(2):177-81; Keane W F, Lyle P A. (2003), “Recent advances in management of type 2 diabetes and nephropathy: lessons from the RENAAL study”, Am J Kidney Dis. 41(3 Suppl 2): S22-5; Bohle A, Kressel G, Muller C A, Muller G A. (1989), “The pathogenesis of chronic renal failure”, Pathol Res Pract. 185(4):421-40; Kikkawa R, Togawa M, Isono M, Isshiki K, Haneda M. (1997), “Mechanism of the progression of diabetic nephropathy to renal failure”, Kidney Int Suppl. 62:S39-40; Bataller R, Brenner D A. (2001), “Hepatic stellate cells as a target for the treatment of liver fibrosis”, Semin Liver Dis. 21(3):437-51; Gross T J, Hunninghake G W, (2001) “Idiopathic pulmonary fibrosis”, N Engl J. Med. 345(7):517-25; Frohlich E D. (2001) “Fibrosis and ischemia: the real risks in hypertensive heart disease”, Am J Hypertens; 14(6 Pt 2): 194S-199S.
Liver Fibrosis
Liver fibrosis (LF) is a generally irreversible consequence of hepatic damage of several etiologies. In the Western world, the main etiologic categories are: alcoholic liver disease (30-50%), viral hepatitis (30%), biliary disease (5-10%), primary hemochromatosis (5%), and drug-related and cryptogenic cirrhosis of unknown etiology (10-15%). Wilson's disease, α1-antitrypsin deficiency and other rare diseases also have liver fibrosis as one of the symptoms Scheinberg I H, Sternlieb I., Wilson disease and idiopathic copper toxicosis. Am J Clin Nutr 1996 May; 63(5):842S-5S; Parfrey H, Mahadeva R, Lomas D A., Alpha(1)-antitrypsin deficiency, liver disease and emphysema. Int J Biochem Cell Biol. 2003 July; 35(7):1009-14.
Liver cirrhosis, the end stage of liver fibrosis, frequently requires liver transplantation and is among the top ten causes of death in the Western world.
Anti-inflammatory agents, which cause inhibition of activation of hepatic stellate cells, stimulation of growth of hepatocytes and inhibition of post translational modification of collagen have all been used to treat liver fibrosis. However, due to the lack of selective targeting, these treatments suffer from, inter alia, the drawbacks of severe side effects.
For more information see Friedman S L. (2003), “Liver fibrosis—from bench to bedside”, J Hepatol. 38 Suppl 1:S38-53; Albanis E, Safadi R, Friedman S L. (2003), “Treatment of hepatic fibrosis: almost there”, Curr Gastroenterol Rep. 5(1):48-56. See also Grenard P, Bresson-Hadni S, El Alaoui S, Chevallier M, Vuitton D A, Ricard-Blum S., Transglutaminase-mediated cross-linking is involved in the stabilization of extracellular matrix in human liver fibrosis. J Hepatol. 2001 September; 35(3):367-75; Mirza A, Liu S L, Frizell E, Zhu J, Maddukuri S, Martinez J, Davies P, Schwarting R, Norton P, Zern M A., A role for tissue transglutaminase in hepatic injury and fibrogenesis, and its regulation by NF-kappaB. Am J. Physiol. 1997 February; 272(2 Pt 1):G281-8).
Kidney Fibrosis and Related Conditions
Chronic Renal Failure (CRF)
Chronic renal failure is a gradual and progressive loss of the ability of the kidneys to excrete wastes, concentrate urine, and conserve electrolytes. CRF is slowly progressive. It most often results from any disease that causes gradual loss of kidney function, and fibrosis is the main pathology that produces CRF.
Diabetic Nephropathy
Diabetic nephropathy, hallmarks of which are glomerulosclerosis and tubulointerstitial fibrosis, is the single most prevalent cause of end-stage renal disease in the modern world, and diabetic patients constitute the largest population on dialysis. Such therapy is costly and far from optimal. Transplantation offers a better outcome but suffers from a severe shortage of donors. More targeted therapies against diabetic nephropathy (as well as against other types of kidney pathologies) are not developed, since molecular mechanisms underlying these pathologies are largely unknown. Identification of an essential functional target gene that is modulated in the disease and affects the severity of the outcome of diabetes nephropathy has a high diagnostic as well as therapeutic value.
Origins of Kidney Pathology
Many pathological processes in the kidney (e.g., glomerular nephritis, physical obstructions, toxic injuries, metabolic and immunological diseases) eventually culminate in similar or identical morphological changes, namely glomerulosclerosis and tubulointerstitial fibrosis. Thus, different types of insults converge on the same single genetic program resulting in two hallmarks of fibrosis: the proliferation of fibroblasts and overproduction by them of various protein components of connective tissue. In addition, thickening of the basal membrane in the glomeruli accompanies interstitial fibrosis and culminates in glomerulosclerosis. See also Johnson T S, Skill N J, El Nahas A M, Oldroyd S D, Thomas G L, Douthwaite J A, Haylor J L, Griffin M, Transglutaminase transcription and antigen translocation in experimental renal scarring. J Am Soc Nephrol. 1999 October; 10(10):2146-57; Johnson T S, Griffin M, Thomas G L, Skill J, Cox A, Yang B, Nicholas B, Birckbichler P J, Muchaneta-Kubara C, Meguid El Nahas A, The role of transglutaminase in the rat subtotal nephrectomy model of renal fibrosis. J Clin Invest. 1997 Jun. 15; 99(12):2950-60).
Pulmonary Fibrosis
Interstitial pulmonary fibrosis (IPF) is scarring of the lung caused by a variety of inhaled agents including mineral particles, organic dusts, and oxidant gases, or by unknown reasons (idiopathic lung fibrosis). The disease afflicts millions of individuals worldwide, and there are no effective therapeutic approaches. A major reason for the lack of useful treatments is that few of the molecular mechanisms of disease have been defined sufficiently to design appropriate targets for therapy (Lasky J A., Brody A R. (2000), “Interstitial fibrosis and growth factors”, Environ Health Perspect.; 108 Suppl 4:751-62).
The cellular substrate of pathogenesis of pulmonary fibrosis includes endothelial and epithelial cell injury, production of inflammatory cells and their mediators, and fibroblast activation., Fibrosis is believed to be related to a dysregulation in cross-talk between inflammatory and structural cells, mediated by various cytokines, chemokines and growth factors, which are responsible for the maintenance of tissue homeostasis and which coordinate the response to injury (Kelly M, Kolb M, Bonniaud P, Gauldie J. (2003), “Re-evaluation of fibrogenic cytokines in lung fibrosis”, Curr Pharm Des. 9(1):39-49).
Conventional therapy consisting of glucocorticoids or cytotoxic drugs is usually ineffective in preventing progression of the disease. It is believed that further understanding of the molecular mechanisms of endothelial and epithelial cell injury, inflammatory reaction, fibroblast proliferation, collagen deposition and lung repair, is necessary for the development of effective treatments against pulmonary fibrosis (Kuwano K, Hagimoto N, Hara N. (2001), “Molecular mechanisms of pulmonary fibrosis and current treatment”, Curr Mol. Med. 1(5):551-73). See also Griffin M, Smith L L, Wynne J., Changes in transglutaminase activity in an experimental model of pulmonary fibrosis induced by Paraquat. Br. J. Exp. Pathol. 1979 December; 60(6):653-61).
Cardiac Fibrosis
Heart failure is unique among the major cardiovascular disorders in that it alone is increasing in prevalence while there has been a striking decrease in other conditions. Some of this can be attributed to the aging of the populations of the United States and Europe. The ability to salvage patients with myocardial damage is also a major factor, as these patients may develop progression of left ventricular dysfunction due to deleterious remodelling of the heart.
The normal myocardium is composed of a variety of cells, cardiac myocytes and noncardiomyocytes, which include endothelial and vascular smooth muscle cells and fibroblasts. (Weber K T. (2000), “Fibrosis and hypertensive heart disease”, Curr Opin Cardiol. 15(4):264-72).
Structural remodeling of the ventricular wall is a key determinant of clinical outcome in heart disease. Such remodeling involves the production and destruction of extracellular matrix proteins, cell proliferation and migration, and apoptotic and necrotic cell death. Cardiac fibroblasts are crucially involved in these processes, producing growth factors and cytokines that act as autocrine and paracrine factors, as well as extracellular matrix proteins and proteinases. Recent studies have shown that the interactions between cardiac fibroblasts and cardiomyocytes are essential for the progression of cardiac remodeling of which the net effect is deterioration in cardiac function and the onset of heart failure (Manabe I, Shindo T, Nagai R. (2002), “Gene expression in fibroblasts and fibrosis: involvement in cardiac hypertrophy”, Circ Res. 13; 91(12):1103-13).
The use of agents to block the renin-angiotensin-aldosterone and sympathetic nervous systems has been shown to inhibit (and sometimes even reverse) cardiac remodelling and to improve the clinical course of patients with cardiac dysfunction. However, drugs aiming at direct inhibition or reduction of fibrosis are not yet available. See also Greenberg B. (2001), “Treatment of heart failure: state of the art and prospectives”, J Cardiovasc Pharmacol. 38 Suppl 2:S59-63, Zhang Z, Vezza R, Plappert T, McNamara P, Lawson J A, Austin S, Pratico D, Sutton M S, FitzGerald G A, COX-2-dependent cardiac failure in Gh/tTG transgenic mice. Circ Res. 2003 May 30; 92(10):1153-61. Epub 2003 Apr. 17; Hwang K C, Gray C D, Sweet W E, Moravec C S, Im M J., Alpha 1-adrenergic receptor coupling with Gh in the failing human heart. Circulation. 1996 Aug. 15; 94(4):718-26.
Neurological Diseases
Polyglutamine diseases are a group of neurological diseases that are caused by expansion of CAG trinucleotide repeats coding for polyglutamine insert. Polyglutamine diseases include Huntington's disease (HD), spinobulbar muscular atrophy, dentatorubral-pallidoluysian atrophy and spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 7 and 17. All these diseases are characterized by the presence of expansion of polyglutamine stretches (exceeding 35-40 glutamines), thus forming intranuclear aggregates, which leads to neuronal death. Alzheimer's disease (AD) is the most common cause of cognitive impairment in older patients and is expected to increase greatly in prevalence. Neurofibrillary degeneration, associated with the formation of paired helical filaments (PHF), is one of the critical neuropathological hallmarks of Alzheimer's disease (AD). Parkinson disease is a neurodegenerative disorder of aging characterized by a selective and progressive loss of dopaminergic neurons within the substantia nigra. See also Mastroberardino P G, Iannicola C, Nardacci R, Bernassola F, De Laurenzi V, Melino G, Moreno S, Pavone F, Oliverio S, Fesus L, Piacentini M. Tissue transglutaminase ablation reduces neuronal death and prolongs survival in a mouse model of Huntington's disease. Cell Death Differ. 2002 September; 9(9):873-80; Karpuj M V, Becher M W, Springer J E, Chabas D, Youssef S, Pedotti R, Mitchell D, Steinman L., Prolonged survival and decreased abnormal movements in transgenic model of Huntington disease, with administration of the transglutaminase inhibitor cystamine. Nat. Med. 2002 February; 8(2): 143-9; Citron B A, Suo Z, SantaCruz K, Davies P J, Qin F, Festoff B W., Protein crosslinking, tissue transglutaminase, alternative splicing and neurodegeneration. Neurochem Int. 2002 January; 40(1):69-78; Chen J S, Mehta K., Tissue transglutaminase: an enzyme with a split personality. Int J Biochem Cell Biol. 1999 August; 31(8):817-36.
Osteoarthritis
Among the main characteristics of osteoarthritis are the degradation of articular cartilage and the formation of new bone at the joint edges, so-called osteophytes. See Van den Berg W B., Growth factors in experimental osteoarthritis: transforming growth factor beta pathogenic? J Rheumatol Suppl. 1995 February; 43:143-5; Scharstuhl A, Glansbeek H L, Van Beuningen H M, Vitters E L, Van der Kraan P M, Van den Berg W B., Inhibition of endogenous TGF-beta during experimental osteoarthritis prevents osteophyte formation and impairs cartilage repair. J. Immunol. 2002 Jul. 1; 169(1):507-14; Karpouzas G A, Terkeltaub R A., New developments in the pathogenesis of articular cartilage calcification. Curr Rheumatol Rep. 1999 December; 1(2):121-7.
Ocular Diseases
Age-related cataracts: Cataracts are characterized by aggregation and covalent cross-linking of the crystallins, the major structural proteins of the eye lens, resulting in increase light scattering, opacification and cataract. Disturbance of calcium homeostasis in the tissue is one of the factors implicated in cataractogenesis, see Shridas et al., FEBS Lett. 2001 Jun. 22; 499(3):245-50; Shin et al, J Biol. Chem. 2004 Apr. 9; 279(15):15032-9; Wan et al., Br J Opthalmol. 2002 November; 86(11):1293-8. and Takeuchi N, Kamei A. Biol Pharm Bull. 2000 March; 23(3):283-90.
Proliferative vitreoretinopathy Proliferative vitreoretinopathy (PVR) is the most common complication following retinal detachment and associated with a retinal hole or break. PVR refers to the growth of cellular membranes within the vitreous cavity and on the front and back surfaces of the retina containing retinal pigment epithelial (RPE) cells. These membranes, which are essentially scar tissues, exert traction on the retina and may result in recurrences of retinal detachment, even after an initially successful retinal detachment procedure.
Migration and adhesion of dislocated retinal pigment epithelial (RPE) cells to a fibronectin-rich extracellular matrix is an initial step in proliferative vitreoretinopathy (PVR). See also Casaroli-Marano R P et al Invest Opthalmol V is Sci. 1999 August; 40(9):2062-72), and Priglinger S et al, Invest Opthalmol V is Sci. 2004 March; 45(3):955-63; Priglinger et al., Invest Opthalmol V is Sci. 2003 January; 44(1):355-64.
Fibrosis following glaucoma filtering operation. The goal of the glaucoma filtration procedure is to create a new passageway by which aqueous fluid inside the eye can escape, thereby lowering the pressure. The filter, therefore, allows the drainage of fluid from inside the anterior chamber of the eye to a “pocket” created between the conjuctiva, which is the outermost covering of the eye, and the sclera, which is the underlying white anatomical structure of the eye. The fluid is eventually absorbed by blood vessels. Unfortunately, due to postoperational scarring, the generated drainage system may be blocked requiring additional surgical intervention(s).
Current anti-scarring regimens (Mitomycin C or 5FU) are limited due to the complications involved (e.g. blindness) e.g. see Cordeiro M Y, Gay J A, Khaw P T., Human anti-transforming growth factor-beta2 antibody: a new glaucoma anti-scarring agent Invest Opthalmol V is Sci. 1999 September; 40(10):2225-34.
In conclusion, there are no effective modes of therapy for the diseases described above, and there is a need, therefore, to develop novel effective compounds and methods of treatment for these purposes.
SUMMARY OF THE INVENTION
The invention provides novel double stranded oligoribonucleotides. These oligoribonucleotides inhibit human TGaseII via the mechanism of RNA interference. The invention also provides a pharmaceutical composition comprising such an oligoribonucleotide, and a vector capable of expressing the oligoribonucleotide. The present invention also provides a method of treating a patient suffering from a fibrosis-related pathology comprising administering to the patient the oligoribonucleotide typically as a pharmaceutical composition, in a therapeutically effective dose so as to thereby treat the patient. The present invention also contemplates treating other diseases and conditions. The invention also relates to treatment of fibrotic and other diseases by use of an antibody to TGaseII polypeptide.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. This figure sets forth the nucleotide sequence of the human TGaseII cDNA-(gi|13653650|ref|XM—009482.3|—ORF_)—SEQ ID NO:1.
FIG. 2. This figure sets forth the amino acid sequence of the human TGaseII corresponding polypeptide—SEQ ID NO:2.
FIG. 3. Western Blot results demonstrating the effect of various TGaseII siRNAs on human TGaseII polypeptide expression.

    
    
        The figure demonstrates the activity of various siRNAs in reducing expression of human TGase polypeptide in HeLa cells, 72 hr following siRNA transfection. GAPDH expression serves as control for protein loading. The numbers 15 and 30 represent concentration of the oligonucleotide in nM. “Cells” (first lane in each panel) stands for nontransfected control cells. The last lane in each panel contains protein extracts from HeLa cells transfected with non-relevant (NR) siRNA, to ensure that the decrease in TGaseII expression is specific to the anti TGase siRNAs activity.
    
    





DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a method for treatment of various pathologies, as recited below, in a subject in need of such treatment which comprises: administering to the subject an amount of an inhibitor of TGaseII polypeptide sufficient to effect a substantial inhibition of the TGaseII activity so as to thereby treat the subject. The TGaseII inhibitor may be L683685, an antibody to TGaseII polypeptide or an siRNA to TGaseII RNA or any of the TGaseII inhibitors known in the art (for further information on such inhibitors see for example: U.S. Pat. Nos. 5,021,440; 4,968,713 and 5098707). In particular the present invention relates to specific siRNAs targeting TGaseII RNA and the use thereof. The use of neutralizing antibodies against TGaseII is also disclosed.
The present invention relates generally to compounds which down-regulate expression of the human TGaseII gene particularly to novel small interfering RNAs (siRNAs), and to the use of these novel siRNAs in the treatment of various diseases and medical conditions in particular fibrotic diseases, diseases related to fibrotic scarring and other diseases related to aberrant expression of Transglutaminase II.
The present invention provides methods and compositions for inhibiting expression of the target TGaseII gene in vivo. In general, the method includes administering oligoribonucleotides, such as small interfering RNAs (i.e., siRNAs) that are targeted to a particular mRNA and hybridize to, or interact with, it under biological conditions (within the cell), or a nucleic acid material that can produce siRNA in a cell, in an amount sufficient to down-regulate expression of a target gene by an RNA interference mechanism. In particular, the subject method can be used to inhibit expression of the TGaseII gene for treatment of disease.
Thus, the inhibitor of TGaseII expression (transcription or translation) or polypeptide activity may be inter alia siRNA, antibodies, preferably neutralizing antibodies or fragments thereof, including single chain antibodies, antisense oligonucleotides, antisense DNA or RNA molecules, proteins, polypeptides and peptides including peptido-mimetics and dominant negatives, and also expression vectors expressing all the above. Additional inhibitors may be small chemical molecules, which generally have a molecular weight of less than 2000 daltons, more preferably less than 1000 daltons, even more preferably less than 500 daltons. These inhibitors may act as follows: small molecules may affect expression and/or activity; antibodies may affect activity; all kinds of antisense may affect TGaseII expression; and dominant negative polypeptides and peptidomimetics may affect activity; expression vectors may be used inter alia for delivery of antisense or dominant-negative polypeptides or antibodies.
In accordance with the present invention, the siRNA molecules or inhibitors of Transglutaminase II, such as antibodies, may be used as drugs to treat various pathologies including fibrosis related pathologies (as defined below) and also to treat ocular diseases including cataract, cardiovascular diseases, neurological diseases, polyglutamine diseases (including Huntington's disease (HD), spinobulbar muscular atrophy, dentatorubral-pallidoluysian atrophy and spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 7 and 17), Alzheimer's and Parkinson's disease and osteoarthritis.
As used herein, the term “Transglutaminase II gene”, or “TGaseII gene”, or “TGase gene” is defined as any homolog of TGaseII gene having preferably 90% homology, more preferably 95% homology, and even more preferably 98% homology to the amino acid encoding region of SEQ ID NO:1, or nucleic acid sequences which bind to the TGaseII gene under conditions of highly stringent hybridization, which are well-known in the art (for example, see Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1988), updated in 1995 and 1998).
As used herein, the term “Transglutaminase II polypeptide”, or “TGaseII polypeptide”, or “TGase” is defined as any homolog of TGaseII polypeptide having preferably 90% homology, more preferably 95% homology, and even more preferably 98% homology to SEQ ID NO:2, as either to full-length or fragments or a domain thereof, as a mutant of the polypeptide encoded by a spliced variant nucleic acid sequence, as a chimera with other polypeptides, provided that any of the above has the same or substantially the same biological function as the TGaseII polypeptide. TGaseII polypeptide, or a TGaseII polypeptide homolog, may be present in different forms, including but not limited to soluble protein, membrane-bound (either in purified membrane preparations or on a cell surface), bead-bound, or any other form presenting TGaseII protein or fragments and polypeptides derived thereof.
As used herein, an “interactor” is a molecule with which TGaseII binds or interacts or activates in nature; for example, a molecule on the surface of a TGaseII polypeptide expressing cell, a molecule on the surface of a second cell or a cytoplasmic molecule. An interactor may be a ligand that is activated by TGaseII alone or by TGaseII as part of a complex with other components. An interactor may be a component of a signal transduction pathway that facilitates transduction of an extracellular signal from TGaseII through the cell membrane and into the cell. An interactor, for example, can be a second intercellular protein that mediates downstream signaling from TGaseII. The interactor is a molecule with which TGase binds in competition with a known TGase substrate (e.g. fibronectin).
As used herein, the term “lysyl donor” or “K donor” is defined as any polypeptide having the ability to donate a lysyl side chain to allow the formation of gamma-glutamyl-lysine bonds during transglutamination process.
As used herein, the term “glutamyl donor” or “Q donor” is defined as any polypeptide having the ability to donate glutamine side chain to allow the formation of gamma-glutamyl-lysine bonds during transglutamination process.
The present invention provides double-stranded oligoribonucleotides (siRNAs), which down-regulate the expression of TGaseII. The downregulation of the expression of transglutminase II can be measured by e.g., measuring the amount of the lysyl-glutamyl crosslinked material produced in the presence of the siRNAs or by direct assessment of the amounts of TGaseII mRNA or polypeptide. The amount of TGaseII mRNA may be measured by e.g., by Northern blotting, RNase protection, RT-PCR or real-time PCR. The amount of TGaseII polypeptide may be measured by immunoblotting or by immunoprecipitation or by ELISA with TGaseII-specific antibodies.
An siRNA of the invention is a duplex oligoribonucleotide in which the sense strand is derived from the mRNA sequence of gene TGaseII, and the antisense strand is complementary to the sense strand. In general, some deviation from the target mRNA sequence is tolerated without compromising the siRNA activity (see e.g. Czauderna et al 2003 Nucleic Acids Research 31(11), 2705-2716). An siRNA of the invention inhibits gene expression on a post-transcriptional level with or without destroying the mRNA. Without being bound by theory, siRNA may target the mRNA for specific cleavage and degradation and/or may inhibit translation from the targeted message.
There are at least two variant TGaseII polypeptides, for which the GeneBank references are variant 2 NM—198951.1 GI:39777598 and variant 1NM—004613.2 GI:39777596. The sequence given in FIG. 1 is the nucleotide sequence of variant 2 (GI:39777598). Both variants and any other similar minor variants are included in the definition of TGaseII polypeptide and in the definition of the TGaseII genes encoding them.
As used herein, the term “TGaseII gene” is defined as the naturally-occurring human gene including any allelic variant thereof as well as any homolog of the TGaseII gene having preferably 90% homology, more preferably 95% homology, and even more preferably 98% homology to the amino acid encoding region of SEQ ID NO:1 or nucleic acid sequences which bind to the TGaseII gene under conditions of highly stringent hybridization, which are well-known in the art (for example, see Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1988), updated in 1995 and 1998.
As used herein, the term “TGaseII”, or “TGaseII polypeptide” is defined as the naturally-occurring polypeptide product of the gene including any allelic variant thereof as well as any homolog of the TGaseII polypeptide having preferably 90% homology, more preferably 95% homology, and even more preferably 98% homology to SEQ ID NO:2, as either full-length or a fragment or a domain thereof, as a mutant or the polypeptide encoded by a spliced variant nucleic acid sequence, as a chimera with other polypeptides, provided that any of the above has the same or substantially the same biological function as the TGaseII polypeptide.
More particularly, the invention provides a compound having the structure:

5′(N)x—Z3′ (antisense strand)

3′Z′—(N′)y5′ (sense strand)

    
    
        wherein each N and N′ is a ribonucleotide which may be modified or unmodified in its sugar residue and (N)x and (N′)y is oligomer in which each consecutive N or N′ is joined to the next N or N′ by a covalent bond;
        wherein each of x and y is an integer between 19 and 40;
        wherein each of Z and Z′ may be present or absent, but if present is dTdT and is covalently attached at the 3′ terminus of the strand in which it is present;
        and wherein the sequence of (N)x comprises any one of the antisense sequences present in Tables A, B and C
    
    


It will be readily understood by those skilled in the art that the compounds of the present invention consist of a plurality of nucleotides which are linked through covalent linkages. Each such covalent linkage may be a phosphodiester linkage, a phosphothioate linkage, or a combination of both, along the length of the nucleotide sequence of the individual strand. Other possible backbone modifications are described inter alia in U.S. Pat. Nos. 5,587,361; 6,242,589; 6,277,967; 6,326,358; 5,399,676; 5,489,677; and 5,596,086.
In particular embodiments, x and y are preferably an integer between about 19 to about 27, most preferably from about 19 to about 23. In a particular embodiment of the compound of the invention, x may be equal to y (viz., x=y) and in preferred embodiments x=y=19 or x=y=21. In a particularly preferred embodiment x=y=19.
In one embodiment of the compound of the invention, Z and Z′ are both absent; in another embodiment one of Z or Z′ is present.
In one embodiment of the compound of the invention, all of the ribonucleotides of the compound are unmodified in their sugar residues.
In some embodiments of the compound of the invention, at least one ribonucleotide is modified in its sugar residue, preferably a modification at the 2′ position. The modification at the 2′ position results in the presence of a moiety which is preferably selected from the group comprising amino, fluoro, methoxy, alkoxy and alkyl groups. In a presently most preferred embodiment the moiety at the 2′ position is methoxy (2′-0-methyl).
In some embodiments of the invention, alternating ribonucleotides are modified in both the antisense and the sense strands of the compound.
In particularly preferred embodiments of the invention, the antisense strand is phosphorylated at the 5′terminus, and may or may not be phosphorylated at the 3′terminus; and the sense strand may or may not be phosphorylated at the 5′terminus and at the 3′terminus.
In another embodiment of the compound of the invention, the ribonucleotides at the 5′ and 3′ termini of the antisense strand are modified in their sugar residues, and the ribonucleotides at the 5′ and 3′ termini of the sense strand are unmodified in their sugar residues.
The invention further provides a vector capable of expressing any of the aforementioned oligoribonucleotides in unmodified form in a cell after which appropriate modification may be made.
The invention also provides a composition comprising one or more of the compounds of the invention in a carrier, preferably a pharmaceutically acceptable carrier.
The invention also provides a composition comprising a carrier and one or more of the compounds of the invention in an amount effective to down-regulate expression in a cell of a human TGaseII gene, which compound comprises a sequence substantially complementary to the sequence of (N)x.
The invention also provides a method of down-regulating the expression of a human TGaseII gene by at least 50% as compared to a control comprising contacting an mRNA transcript of the gene with one or more of the compounds of the invention.
In one embodiment the compound is down-regulating TGaseII, whereby the down-regulation of TGaseII is selected from the group comprising down-regulation of TGaseII function (which may be examined by an enzymatic assay or a binding assay with a known interactor of the native gene/polypeptide, inter alia), down-regulation of TGaseII protein (which may be examined by Western blotting, ELISA or immuno-precipitation, inter alia) and down-regulation of TGaseII mRNA expression (which may be examined by Northern blotting, quantitative RT-PCR, in-situ hybridisation or microarray hybridisation, inter alia).
The invention also provides a method of treating a patient suffering from fibrosis or a fibrosis-related pathology, comprising administering to the patient a composition of the invention in a therapeutically effective dose so as to thereby treat the patient.
The invention also provides a method of treating a patient suffering from a pathology related to aberrant cross-linking of cellular proteins via Transglutaminase II comprising administering to the patient a composition of the invention in a therapeutically effective dose so as to thereby treat the patient.
The invention also provides a use of a therapeutically effective dose of one or more compounds of the invention for the preparation of a composition for promoting recovery in a patient suffering from fibrosis or a fibrosis-related pathology or a pathology related to aberrant crosslinking of cellular proteins via Transglutaminase II.
Fibrotic diseases or diseases in which fibrosis is evident (fibrosis-related pathology) include both acute and chronic forms of fibrosis of organs, including all etiological variants of the following: pulmonary fibrosis, including interstitial lung disease and fibrotic lung disease, liver fibrosis, cardiac fibrosis including myocardial fibrosis, kidney fibrosis including chronic renal failure, skin fibrosis including scleroderma, keloids and hypertrophic scars; myelofibrosis (bone marrow fibrosis); all types of ocular scarring including proliferative vitreoretinopathy (PVR) and scarring resulting from surgery to treat cataract or glaucoma; inflammatory bowel disease of variable etiology, macular degeneration, Grave's ophthalmopathy, drug induced ergotism, psoriasis, glioblastoma in Li-Fraumeni syndrome, sporadic glioblastoma, myleoid leukemia, acute myelogenous leukemia, myelodysplastic syndrome, myeloproferative syndrome, gynecological cancer, Kaposi's sarcoma, Hansen's disease, and collagenous colitis.
The compounds of the invention may be used to treat many other diseases and conditions apart from fibrotic diseases. Other indications may be ocular diseases including cataract, cardiovascular diseases especially cardiac hypertrophy, atherosclerosis/restenosis, neurological diseases, including polyglutamine diseases (such as Huntington's disease), spinobulbar muscular atrophy, dentatorubral-pallidoluysian atrophy and spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 7 and 17, Alzheimer's disease and Parkinson's disease.
The compound may have homologs wherein up to two of the ribonucleotides in each terminal region a base is altered; the terminal region refers to the four terminal ribonucleotides e.g. refers to bases 1-4 and/or 16-19 in a 19-mer sequence and to bases 1-4 and/or 18-21 in a 21-mer sequence.
The preferred oligonucleotides of the invention are the oligonucleotides listed in Tables A, B and C, preferably the oligonucleotides targeting human cDNA. The most preferred oligonucleotides of the invention are the oligonucleotides having inhibitory activity as demonstrated in Table D, preferably oligonucleotides targeting human TGaseII cDNA.
The presently most preferred compound of the invention is a blunt-ended 19-mer oligonucleotide, i.e. x=y=19 and Z and Z′ are both absent; the oligonucleotide is phosphorylated at the 5′position of the antisense strand and at the 3′ position of the sense strand wherein alternating ribonucleotides are modified at the 2′ position in both the antisense and the sense strands, wherein the moiety at the 2′ position is methoxy (2′-0-methyl) and wherein the ribonucleotides at the 5′ and 3′ termini of the antisense strand are modified in their sugar residues, and the ribonucleotides at the 5′ and 3′ termini of the sense strand are unmodified in their sugar residues. The presently most preferred such compound is TG_HMRG1. The antisense strand of TG_HFMRG1 has SEQ ID NO: 22 and the sense strand has SEQ ID NO: 4. Other preferred compounds are TG_HMG1 and TG_HM1, which have the antisense strand represented by SEQ ID NOS: 23 and 25 respectively and the sense strand represented by SEQ ID NO: 5 and 7 respectively.
In one aspect of the invention the oligonucleotide comprises a double-stranded structure, whereby such double-stranded structure comprises

    
    
        a first strand and a second strand, whereby
        the first strand comprises a first stretch of contiguous nucleotides and the second strand comprises a second stretch of contiguous nucleotides, whereby
        the first stretch is either complementary or identical to a nucleic acid sequence coding for TGaseII and whereby the second stretch is either identical or complementary to a nucleic acid sequence coding for TGaseII.
    
    


In an embodiment the first stretch and/or the second stretch comprises from about 14 to 40 nucleotides, preferably about 18 to 30 nucleotides, more preferably from about 19 to 27 nucleotides and most preferably from about 19 to 23 nucleotides, in particular from about 19 to 21 nucleotides. In such an aspect the oligonucleotide may be from 17-40 nucleotides in length. Additionally, further nucleic acids according to the present invention comprise at least 14 contiguous nucleotides of any one of the SEQ. ID. NO.3 to SEQ ID NO: 416 and more preferably 14 contiguous nucleotide base pairs at any end of the double-stranded structure comprised of the first stretch and second stretch as described above.
The term “treatment” as used herein refers to administration of a therapeutic substance effective to ameliorate symptoms associated with a disease or condition, to lessen the severity or cure the disease or condition, or to prevent the disease or condition from occurring.
In a particular embodiment, the administration comprises intravenous administration. In another particular embodiment the administration comprises topical or local administration.
Additionally, the present invention provides a method of regulating a pathology or disease (as recited above) in a patient in need of such treatment by administering to a patient a therapeutically effective dose of at least one antisense (AS) oligonucleotide or at least one siRNA against the nucleic acid sequences or a dominant negative peptide directed against the TGaseII sequences or TGaseII proteins or an antibody directed against the TGaseII polypeptide.
Delivery: Delivery systems aimed specifically at the enhanced and improved delivery of siRNA into mammalian cells have been developed, see, for example, Shen et al (FEBS letters 539: 111-114 (2003)), Xia et al., Nature Biotechnology 20: 1006-1010 (2002), Reich et al., Molecular Vision 9: 210-216 (2003), Sorensen et al. (J. Mol. Biol. 327: 761-766 (2003), Lewis et al., Nature Genetics 32: 107-108 (2002) and Simeoni et al., Nucleic Acids Research 31, 11: 2717-2724 (2003). siRNA has recently been successfully used for inhibition in primates; for further details see Tolentino et al., Retina 24(1) February 2004 I 132-138 Respiratory formulations for siRNA are described in U.S. patent application No. 2004/0063654 of Davis et al. Cholesterol-conjugated siRNAs (and other steroid and lipid conjugated siRNAs) can been used for delivery (see Soutschek et al Nature 432: 173-177 (2004) Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs; and Lorenz et al. Bioorg. Med. Chemistry. Lett. 14:4975-4977 (2004) Steroid and lipid conjugates of siRNAs to enhance cellular uptake and gene silencing in liver cells. 
The siRNAs or pharmaceutical compositions of the present invention are administered and dosed in accordance with good medical practice, taking into account the clinical condition of the individual patient, the disease to be treated, the site and method of administration, scheduling of administration, patient age, sex, body weight and other factors known to medical practitioners.
The “therapeutically effective dose” for purposes herein is thus determined by such considerations as are known in the art. The dose must be effective to achieve improvement including but not limited to improved survival rate or more rapid recovery, or improvement or elimination of symptoms and other indicators as are selected as appropriate measures by those skilled in the art. The compounds of the present invention can be administered by any of the conventional routes of administration. It should be noted that the compound can be administered as the compound or as pharmaceutically acceptable salt and can be administered alone or as an active ingredient in combination with pharmaceutically acceptable carriers, solvents, diluents, excipients, adjuvants and vehicles. The compounds can be administered orally, subcutaneously or parenterally including intravenous, intraarterial, intramuscular, intraperitoneally, and intranasal administration as well as intrathecal and infusion techniques. Implants of the compounds are also useful. Liquid forms may be prepared for injection, the term including subcutaneous, transdermal, intravenous, intramuscular, intrathecal, and other parental routes of administration. The liquid compositions include aqueous solutions, with and without organic cosolvents, aqueous or oil suspensions, emulsions with edible oils, as well as similar pharmaceutical vehicles. In addition, under certain circumstances the compositions for use in the novel treatments of the present invention may be formed as aerosols, for intranasal and like administration. The patient being treated is a warm-blooded animal and, in particular, mammals including man. The pharmaceutically acceptable carriers, solvents, diluents, excipients, adjuvants and vehicles as well as implant carriers generally refer to inert, non-toxic solid or liquid fillers, diluents or encapsulating material not reacting with the active ingredients of the invention and they include liposomes and microspheres. Examples of delivery systems useful in the present invention include U.S. Pat. Nos. 5,225,182; 5,169,383; 5,167,616; 4,959,217; 4,925,678; 4,487,603; 4,486,194; 4,447,233; 4,447,224; 4,439,196; and 4,475,196. Many other such implants, delivery systems, and modules are well known to those skilled in the art. In one specific embodiment of this invention topical and transdermal formulations are particularly preferred.
In general, the active dose of compound for humans is in the range of from 1 ng/kg to about 20-100 mg/kg body weight per day, preferably about 0.01 mg to about 2-10 mg/kg body weight per day, in a regimen of one dose per day or twice or three or more times per day for a period of 1-4 weeks or longer. Treatment for many years or even lifetime treatment is also envisaged for some of the indications disclosed herein.
The present invention also provides for a process of preparing a pharmaceutical composition, which comprises:

    
    
        obtaining at least one double stranded siRNA compound of the invention; and
        admixing said compound with a pharmaceutically acceptable carrier.
    
    


The present invention also provides for a process of preparing a pharmaceutical composition, which comprises admixing a compound of the present invention with a pharmaceutically acceptable carrier.
In a preferred embodiment, the compound used in the preparation of a pharmaceutical composition is admixed with a carrier in a pharmaceutically effective dose. In a particular embodiment the compound of the present invention is conjugated to a steroid or to a lipid or to another suitable molecule e.g. to cholesterol.
Modifications or analogs of nucleotides can be introduced to improve the therapeutic properties of the nucleotides. Improved properties include increased nuclease resistance and/or increased ability to permeate cell membranes.
Accordingly, the present invention also includes all analogs of, or modifications to, a oligonucleotide of the invention that does not substantially affect the function of the polynucleotide or oligonucleotide. In a preferred embodiment such modification is related to the base moiety of the nucleotide, to the sugar moiety of the nucleotide and/or to the phosphate moiety of the nucleotide.
In embodiments of the invention, the nucleotides can be selected from naturally occurring or synthetically modified bases. Naturally occurring bases include adenine, guanine, cytosine, thymine and uracil. Modified bases of the oligonucleotides include inosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl-, 2-propyl- and other alkyl-adenines, 5-halo uracil, 5-halo cytosine, 6-aza cytosine and 6-aza thymine, pseudo uracil, 4-thiuracil, 8-halo adenine, 8-aminoadenine, 8-thiol adenine, 8-thiolalkyl adenines, 8-hydroxyl adenine and other 8-substituted adenines, 8-halo guanines, 8-amino guanine, 8-thiol guanine, 8-thioalkyl guanines, 8-hydroxyl guanine and other substituted guanines, other aza and deaza adenines, other aza and deaza guanines, 5-trifluoromethyl uracil and 5-trifluoro cytosine.
In addition, analogs of nucleotides can be prepared wherein the structures of the nucleotides are fundamentally altered and are better suited as therapeutic or experimental reagents. An example of a nucleotide analog is a peptide nucleic acid (PNA) wherein the deoxyribose (or ribose) phosphate backbone in DNA (or RNA) is replaced with a polyamide backbone similar to that found in peptides. PNA analogs have been shown to be resistant to degradation by enzymes and to have extended lives in vivo and in vitro. Further, PNAs have been shown to bind more strongly to a complementary DNA sequence than to a DNA molecule. This observation is attributed to the lack of charge repulsion between the PNA strand and the DNA strand. Other modifications that can be made to oligonucleotides include polymer backbones, cyclic backbones, or acyclic backbones.
In one embodiment the modification is a modification of the phosphate moiety, whereby the modified phosphate moiety is selected from the group comprising phosphothioate.
The compounds of the present invention can be synthesized by any of the methods that are well-known in the art for synthesis of ribonucleic (or deoxyribonucleic) oligonucleotides. Such synthesis is, among others, described in Beaucage S. L. and Iyer R. P., Tetrahedron 1992; 48: 2223-2311, Beaucage S. L. and Iyer R. P., Tetrahedron 1993; 49: 6123-6194 and Caruthers M. H. et. al., Methods Enzymol. 1987; 154: 287-313, the synthesis of thioates is, among others, described in Eckstein F., Annu. Rev. Biochem. 1985; 54: 367-402, the synthesis of RNA molecules is described in Sproat B., in Humana Press 2005 Edited by Herdewijn P.; Kap. 2: 17-31 and respective downstream processes are, among others, described in Pingoud A. et. al., in IRL Press 1989 Edited by Oliver R. W. A.; Kap. 7: 183-208 and Sproat B., in Humana Press 2005 Edited by Herdewijn P.; Kap. 2: 17-31 (supra).
Other synthetic procedures are known in the art e.g. the procedures as described in Usman et al., 1987, J. Am. Chem. Soc., 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433; Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684; and Wincott et al., 1997, Methods Mol. Bio., 74, 59, and these procedures may make use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. The modified (e.g. 2′-O-methylated) nucleotides and unmodified nucleotides are incorporated as desired.
The oligonucleotides of the present invention can be synthesized separately and joined together post-synthetically, for example, by ligation (Moore et al., 1992, Science 256, 9923; Draper et al., International PCT publication No. WO93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides & Nucleotides, 16, 951; Bellon et al., 1997, Bioconjugate Chem. 8, 204), or by hybridization following synthesis and/or deprotection.
It is noted that a commercially available machine (available, inter alia, from Applied Biosystems) can be used; the oligonucleotides are prepared according to the sequences disclosed herein. Overlapping pairs of chemically synthesized fragments can be ligated using methods well known in the art (e.g., see U.S. Pat. No. 6,121,426). The strands are synthesized separately and then are annealed to each other in the tube. Then, the double-stranded siRNAs are separated from the single-stranded oligonucleotides that were not annealed (e.g. because of the excess of one of them) by HPLC. In relation to the siRNAs or siRNA fragments of the present invention, two or more such sequences can be synthesized and linked together for use in the present invention.
The compounds of the invention can also be synthesized via a tandem synthesis methodology, as described in US patent application publication No. US2004/0019001 (McSwiggen), wherein both siRNA strands are synthesized as a single contiguous oligonucleotide fragment or strand separated by a cleavable linker which is subsequently cleaved to provide separate siRNA fragments or strands that hybridize and permit purification of the siRNA duplex. The linker can be a polynucleotide linker or a non-nucleotide linker.
The compounds of the present invention can be delivered either directly or with viral or non-viral vectors. When delivered directly the sequences are generally rendered nuclease resistant. Alternatively the sequences can be incorporated into expression cassettes or constructs such that the sequence is expressed in the cell as discussed herein below. Generally the construct contains the proper regulatory sequence or promoter to allow the sequence to be expressed in the targeted cell. Vectors optionally used for delivery of the compounds of the present invention are commercially available, and may be modified for the purpose of delivery of the compounds of the present invention by methods known to one of skill in the art.
It is also envisaged that a long double stranded oligonucleotide (typically 25-500 nucleotides in length) comprising one or more of the sequences of the oligonucleotides of the invention may be delivered and may be processed intracellularly by endogenous cellular complexes (e.g. by DICER as described above) to produce smaller double stranded oligonucleotides which are oligonucleotides of the invention.
As used herein, the term “polypeptide” refers to, in addition to a polypeptide, an oligopeptide, peptide and a full protein.
Animal model systems: Testing the active siRNAs of the invention may be done in predictive animal models. Several models for kidney fibrosis are described in Example 3.
Two models of liver fibrosis in rats are the Bile Duct Ligation (BDL) with sham operation as controls, and CCl4 poisoning, with olive oil fed animals as controls, as described in the following references: Lotersztajn S, Julien B, Teixeira-Clerc F, Grenard P, Mallat A, Hepatic Fibrosis: Molecular Mechanisms and Drug Targets. Annu Rev Pharmacol Toxicol. 2004 Oct. 7; Uchio K, Graham M, Dean N M, Rosenbaum J, Desmouliere A., Down-regulation of connective tissue growth factor and type I collagen mRNA expression by connective tissue growth factor antisense oligonucleotide during experimental liver fibrosis. Wound Repair Regen. 2004 January-February; 12(1):60-6; and. Xu X Q, Leow C K, Lu X, Zhang X, Liu J S, Wong W H, Asperger A, Deininger S, Eastwood Leung H C., Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics Proteomics. 2004 October; 4(10):3235-45.
Models for ocular scarring are well known in the art e.g. Sherwood M B et al., J Glaucoma. 2004 October; 13(5):407-12. A new model of glaucoma filtering surgery in the rat; Miller M H et al., Ophthalmic Surg. 1989 May; 20(5):350-7. Wound healing in an animal model of glaucoma fistulizing surgery in the rabbit; vanBockxmeer F M et al., Retina. 1985 Fall-Winter; 5(4): 239-52. Models for assessing scar tissue inhibitors; Wiedemann P et al., J Pharmacol Methods. 1984 August; 12(1): 69-78. Proliferative vitreoretinopathy: the rabbit cell injection model for screening of antiproliferative drugs. 
Models of cataract are described in the following publications: The role of Src family kinases in cortical cataract formation. Zhou J, Menko A S. Invest Opthalmol V is Sci. 2002 July; 43(7):2293-300; Bioavailability and anticataract effects of a topical ocular drug delivery system containing disulfuram and hydroxypropyl-beta-cyclodextrin on selenite-treated rats. Wang S, Li D, Ito Y, Nabekura T, Wang S, Zhang J, Wu C. Curr Eye Res. 2004 July; 29(1):51-8; and Long-term organ culture system to study the effects of UV-Airradiation on lens transglutaminase. Weinreb O, Dovrat A.; Curr Eye Res. 2004 July; 29(1):51-8.
Antibody Production
By the term “antibody” as used in the present invention is meant both poly- and mono-clonal complete antibodies as well as fragments thereof, such as Fab, F(ab′)2, and Fv, which are capable of binding the epitopic determinant. These antibody fragments retain the ability to selectively bind with its antigen or receptor and are exemplified as follows, inter alia:

    (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule can be produced by digestion of whole antibody with the enzyme papain to yield a light chain and a portion of the heavy chain;
    (2) (Fab′)2, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′2) is a dimer of two Fab fragments held together by two disulfide bonds;
    (3) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and
    (4) Single chain antibody (SCA), defined as a genetically engineered molecule containing the variable region of the light chain and the variable region of the heavy chain linked by a suitable polypeptide linker as a genetically fused single chain molecule.


Such fragments having antibody functional activity can be prepared by methods known to those skilled in the art (e.g. Bird et al. (1988) Science 242:423-426)
Conveniently, antibodies may be prepared against the immunogen or portion thereof, for example, a synthetic peptide based on the sequence, or prepared recombinantly by cloning techniques or the natural gene product and/or portions thereof may be isolated and used as the immunogen. Immunogens can be used to produce antibodies by standard antibody production technology well known to those skilled in the art, as described generally in Harlow and Lane (1988), Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., and Borrebaeck (1992), Antibody Engineering—A Practical Guide, W.H. Freeman and Co., NY.
For producing polyclonal antibodies a host, such as a rabbit or goat, is immunized with the immunogen or immunogen fragment, generally with an adjuvant and, if necessary, coupled to a carrier; antibodies to the immunogen are collected from the sera. Further, the polyclonal antibody can be absorbed such that it is monospecific; that is, the sera can be absorbed against related immunogens so that no cross-reactive antibodies remain in the sera, rendering it monospecific.
For producing monoclonal antibodies the technique involves hyperimmunization of an appropriate donor with the immunogen, generally a mouse, and isolation of splenic antibody-producing cells. These cells are fused to an immortal cell, such as a myeloma cell, to provide a fused cell hybrid that is immortal and secretes the required antibody. The cells are then cultured, in bulk, and the monoclonal antibodies harvested from the culture media for use.
For producing recombinant antibody see generally Huston et al. (1991) “Protein engineering of single-chain Fv analogs and fusion proteins” in Methods in Enzymology (J J Langone, ed., Academic Press, New York, N.Y.) 203:46-88; Johnson and Bird (1991) “Construction of single-chain Fvb derivatives of monoclonal antibodies and their production in Escherichia coli in Methods in Enzymology (J J Langone, ed.; Academic Press, New York, N.Y.) 203:88-99; Mernaugh and Mernaugh (1995) “An overview of phage-displayed recombinant antibodies” in Molecular Methods In Plant Pathology (RP Singh and US Singh, eds.; CRC Press Inc., Boca Raton, Fla.: 359-365). In particular scFv antibodies are described in WO 2004/007553 (Tedesco and Marzari). Additionally, messenger RNAs from antibody-producing B-lymphocytes of animals, or hybridoma can be reverse-transcribed to obtain complementary DNAs (cDNAs). Antibody cDNA, which can be full or partial length, is amplified and cloned into a phage or a plasmid. The cDNA can be a partial length of heavy and light chain cDNA, separated or connected by a linker. The antibody, or antibody fragment, is expressed using a suitable expression system to obtain recombinant antibody. Antibody cDNA can also be obtained by screening pertinent expression libraries.
The antibody can be bound to a solid support substrate or conjugated with a detectable moiety or be both bound and conjugated as is well known in the art. (For a general discussion of conjugation of fluorescent or enzymatic moieties see Johnstone & Thorpe (1982), Immunochemistry in Practice, Blackwell Scientific Publications, Oxford). The binding of antibodies to a solid support substrate is also well known in the art (for a general discussion, see Harlow & Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Publications, New York; and Borrebaeck (1992), Antibody Engineering—A Practical Guide, W.H. Freeman and Co.). The detectable moieties contemplated with the present invention can include, but are not limited to, fluorescent, metallic, enzymatic and radioactive markers such as biotin, gold, ferritin, alkaline phosphatase, β-galactosidase, peroxidase, urease, fluorescein, rhodamine, tritium, 14C and iodination.
Additional compounds which are also considered to be useful in the treatment of the diseases and disorders discussed herein may be antisense DNA molecules (which can be generated using the sequence in FIG. 1 by methods known in the art), catalytic RNAs such as ribozymes, polypeptides such as dominant negative peptides (which can be generated using the sequence in FIG. 2 by methods known in the art) or other polypeptide inhibitors. Antisense DNA molecules which comprise the siRNA sequences disclosed herein (with the appropriate nucleic acid modifications stemming from the differences between DNA and RNA) are particularly desirable and may be used in the same capacity as their corresponding siRNAs for all uses and methods disclosed herein.
Screening of TGase Inactivating Compounds
Some of the compounds and compositions of the present invention may be used in a screening assay for identifying and isolating compounds that modulate the activity of TGaseII, in particular compounds that modulate fibrotic disease or fibrosis-related pathology. The compounds to be screened comprise inter alia substances such as small chemical molecules, antibodies especially neutralizing antibodies, inhibitory polypeptides and dominant negative peptides.
The inhibitory activity of the compounds of the present invention on TGaseII polypeptide enzymatic activity or binding of the compounds of the present invention to TGaseII may be used to determine the interaction of an additional compound with the TGaseII polypeptide, e.g., if the additional compound competes with the antibodies or dominant-negative peptides of the present invention for TGaseII inhibition, or if the additional compound rescues said inhibition. The inhibition or activation can be tested by various means, such as, inter alia, assaying for the product of the activity of the TGaseII polypeptide or displacement of binding compound from the TGaseII polypeptide in radioactive or fluorescent competition assays.
The present invention additionally provides for a process of obtaining a compound capable of inhibiting the enzymatic activity of a TGaseII polypeptide, preferably a human TGaseII polypeptide, that comprises the steps of:

    
    
        (i) contacting the TGaseII polypeptide or cells expressing the TGaseII polypeptide with the compound, a lysyl donor and with a glutamyl donor which is a biological molecule;
        (ii) removing excess lysyl donor from the mixture of step (i);
        (iii) measuring the amount of the lysyl-glutamyl crosslinked material produced in the presence of the compound;
        (iv) comparing the amount of lysyl-glutamyl crosslinked material measured in step (iii) to that measured in the absence of the compound under controlled conditions, wherein a decrease in the amount of lysyl-glutamyl crosslinked material is indicative of inhibition of the TGaseII polypeptide activity by the compound; and
        (v) identifying the compound as an inhibitor of TGaseII polypeptide activity.
    
    


In one embodiment of all the processes described herein, the TGaseII polypeptide used in such process comprises consecutive amino acids, the sequence of which is set forth in SEQ ID NO: 2.
In another embodiment, the lysyl donor of step (i) is tagged and the measurement in step (iii) is of the tag related read-out, and wherein, a decrease in the read-out level is indicative of inhibition of the TGaseII polypeptide activity by the compound.
The glutamyl donor which is a biological molecule may be e.g. fibronectin. or collagen.
In another embodiment, the lysyl donor used in such process is cadaverin tagged with a dansyl fluorescent tag.
In another embodiment the lysyl donor used in such process is tagged with biotin, and in a specific embodiment, the lysyl donor is biotin cadaverine. Biotin is detected by streptavidin (or a modified streptavidin such as nutravidin) conjugated to readouts known in the art (e.g. conjugated to horseradish peroxidase, wherein the amount of horseradish peroxidase is quantified using tetramethylbenzidine as a substrate).
In yet another embodiment of the invention, the glutamyl donor in the provided process may be an extra-cellular matrix protein or a cellular protein. The extra cellular matrix protein is selected from the group consisting of: fibronectin, collagen, osteonectin, ECM-gel (e.g. Sigma E-1270), and the intracellular protein is selected inter alia from the group consisting of: RhoA, fialmin, spectrin, vimentin, HSP90, HSP60, (see Orru S, Caputo I, D'Amato A, Ruoppolo M, Esposito C Proteomics identification of acyl-acceptor and acyl-donor substrates for transglutaminase in a human intestinal epithelial cell line. Implications for celiac disease. J Biol. Chem. 2003 Aug. 22; 278(34):31766-73).
In a different embodiment, the compound is contacted with cells expressing the TGaseII polypeptide. The cells that may be used in such process may either be separated or present in a tissue. The cells may express the TGaseII polypeptide naturally or as a result of having been transfected with TGaseII gene, either transiently or stably or may over-express the TGaseII gene and the activity of TGaseII will be compared between over-expressors to normal TGaseII expressing cells. In a further embodiment, the glutamyl donor is either a natural product of the cells or it is added from outside.
In a different embodiment, the TGaseII polypeptide is contacted with the compound. The TGaseII polypeptide can be either immobilized or free in a solution. In an embodiment of the provided screening process the glutamyl donor is immobilized.
In a further embodiment, the processes provided for obtaining a compound capable of inhibiting the activity of human TGaseII may comprise a further step in which prior to step (i) TGaseII is contacted with a second compound known to bind TGaseII.
In one embodiment of the invention, the tag read-out in the provided processes described herein is the interaction of biotin with neutravidin conjugated to horseradish peroxidase, wherein the amount of cell-bound horseradish peroxidase is quantified using TMB (tetramethylbenzidine) as a substrate.
In yet a further embodiment, the compound obtained by the provided process inhibits the activity of the TGaseII polypeptide at least 2-fold more effectively than it inhibits the activity of at least one other member of the TGase family, and more preferably the inhibition is at least 10-fold, 50-fold and even 100-fold more effective. In such process, either the TGaseII polypeptide or the second compound may be immobilized.
In one another embodiment, the compound obtained by any of the provided processes is an antibody.
The invention further provides a process of obtaining a compound which modulates the activity of a TGaseII polypeptide, preferably a human TGaseII polypeptide, which comprises the steps of:

    
    
        (i) contacting the TGaseII polypeptide with an interactor with which the TGaseII polypeptide interacts specifically in vivo;
        (ii) contacting the TGaseII polypeptide or the interactor with said compound; and
        (iii) measuring the effect of the compound on the interaction between TGaseII polypeptide and the interactor by measuring a parameter related to fibrosis; and
        (iv) comparing the effect measured in step (iii) with the effect measured in the absence of the compound, a change in the effect measured indicating that the compound modulates the activity of the human TGaseII polypeptide.
    
    


In one embodiment of the invention the compound obtained by the provided process inhibits the activity of a human TGaseII polypeptide.
In another embodiment of the invention the TGaseII polypeptide in such process comprises consecutive amino acids, the sequence of which is set forth in SEQ ID NO: 2. In a further embodiment either the TGaseII polypeptide or the interactor are immobilized.
In a further embodiment of the invention, the parameter measured in any of the provided processes is related to a pathology characterized by TGaseII up-regulation in general and to fibrosis related pathologies as defined above, and also to cataract, cardiovascular diseases, neurological disorders, polyglutamine diseases including Huntington's disease (HD), spinobulbar muscular atrophy, dentatorubral-pallidoluysian atrophy and spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 7 and 17), Alzheimer's and Parkinson's disease, coeliac disease and osteoarthritis. It is another object of the present invention to provide a process of obtaining a compound capable of inhibiting the activity of a human TGaseII polypeptide that comprises the steps of:

    
    
        (i) contacting the TGaseII polypeptide or cells expressing the TGaseII polypeptide with a plurality of compounds, a tagged lysyl donor and with a glutamyl donor which is a biological molecule;
        (ii) washing excess tagged lysyl donor from the mixture of step (i); and
        (iii) measuring the tag related read-out in the presence of the plurality of compounds;
        (iv) comparing the tag read-out measured in step (iii) to that measured in the absence of the plurality of compounds under controlled conditions, wherein a decrease in the read-out level is indicative of inhibition of the TGaseII polypeptide activity by the plurality of compounds;
        (v) separately determining which compound or compounds present in the plurality inhibit the activity of a human TGaseII.
    
    


It is another aspect of the present invention to provide a cell-based process of obtaining a compound capable of inhibiting the activity of a TGaseII polypeptide, preferably human TGaseII polypeptide, that comprises the steps of:

    
    
        (i) contacting cells expressing active TGaseII polypeptide with the compound and with a lysyl donor;
        (ii) removing excess lysyl donor from the mixture of step (i);
        (iii) measuring the amount of lysyl-glutamyl crosslinked material produced in the presence of the compound;
        (iv) comparing the amount of lysyl-glutamyl crosslinked material measured in step (iii) to that measured in the absence of the compound under controlled conditions, wherein a decrease in the amount of lysyl-glutamyl crosslinked material is indicative of inhibition of the TGaseII polypeptide activity by the compound; and
        (v) identifying the compound as an inhibitor of TGaseII polypeptide
    
    


It is another aspect of the present invention to provide a cell-based process of obtaining a compound capable of inhibiting the activity of a human TGaseII polypeptide that comprises the steps of:

    
    
        a. contacting cells expressing the TGaseII polypeptide with a plurality of compounds and with a lysyl donor;
        b. removing excess lysyl donor from the mixture of step (i); and
        c. measuring the amount of the lysyl-glutamyl crosslinked material produced in the presence of the plurality of compounds;
        d. comparing the amount of lysyl-glutamyl crosslinked material measured in step (iii) to that measured in the absence of the plurality of compounds under controlled conditions, wherein a decrease in the amount of lysyl-glutamyl crosslinked material is indicative of inhibition of the TGaseII polypeptide activity by the plurality of compounds; and
        (e) separately determining which compound or compounds present in the plurality inhibit the activity of a human TGaseII.

Methods

General Methods in Molecular Biology

    
    


Standard molecular biology techniques known in the art and not specifically described were generally followed as in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York (1989), and as in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989) and as in Perbal, A Practical Guide to Molecular Cloning, John Wiley & Sons, New York (1988), and as in Watson et al., Recombinant DNA, Scientific American Books, New York and in Birren et al (eds) Genome Analysis: A Laboratory Manual Series, Vols. 1-4 Cold Spring Harbor Laboratory Press, New York (1998) and methodology as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057 and incorporated herein by reference. Polymerase chain reaction (PCR) was carried out generally as in PCR Protocols: A Guide To Methods And Applications, Academic Press, San Diego, Calif. (1990). In situ (in cell) PCR in combination with Flow Cytometry can be used for detection of cells containing specific DNA and mRNA sequences (e.g. Testoni et al., 1996, Blood 87:3822.) Methods of performing RT-PCR are also well known in the art.
The present invention is illustrated in detail below with reference to Examples, but is not to be construed as being limited thereto.
EXAMPLES
Example 1
Design of Active siRNA Compounds
Using proprietary algorithms and the known sequence of cDNA of TGaseII (SEQ ID NO:1), the sequences of many potential siRNAs were generated. These are shown in the Tables below. Note that the abbreviations for species are: H: human; M: mouse; R: rat; G: guinea pig; C: cow.
Table A shows 18 siRNAs that have so far been chemically synthesized and tested for activity (see Example 2). All these siRNAs are 19-mers. In Table A the sense strands of siRNAs 1-18 have SEQ ID NOS: 3-20 respectively, and the antisense strands of siRNAs 1-18 have SEQ ID NOS: 21-38 respectively.
Table B below shows 153 additional 19-mer siRNAs, which have been generated by the proprietary algorithms but not yet tested for activity. In Table B, the sense strands of siRNAs 1-153 have SEQ ID NOS: 39-191, respectively, and the antisense strands of siRNAs 1-153 have SEQ ID NOS: 192-344 respectively.
Table C below shows 36 additional 21-mer siRNAs that have been generated by the proprietary algorithms. In Table C, the sense strands of siRNAs 1-36 have SEQ ID NOS: 345-380 respectively, and the antisense strands of siRNAs 1-36 have SEQ ID NOS: 381-416, respectively.










TABLE A







No.
name
Sense strand
Antisense strand





1
TG_HMR1
ACAAGAGCGAGAUGAUCUG
CAGAUCAUCUCGCUCUUGU


2
TG_HMRG1
AGAGCGAGAUGAUCUGGAA
UUCCAGAUCAUCUCGCUCU


3
TG_HMG1
ACCCCAAGUUCCUGAAGAA
UUCUUCAGGAACUUGGGGU


4
TG_HMG2
GCGAGAUGAUCUGGAACUU
AAGUUCCAGAUCAUCUCGC


5
TG_HM1
CAAAUCCAUCAACCGUUCC
GGAACGGUUGAUGGAUUUG


6
TG_M1
GAACAUCCAUGAGAAACUU
AAGUUUCUCAUGGAUGUUC


7
TG_M2
CGACCUAUGCCAAGAGAAA
UUUCUCUUGGCAUAGGUCG


8
TG_M3
GGUGUGAUUUGGAGAUUCA
UGAAUCUCCAAAUCACACC


9
TG_M4
CCAACCACCUGAACAAACU
AGUUUGUUCAGGUGGUUGG


10
TG_M5
GAACAAACUGGCAGAGAAA
UUUCUCUGCCAGUUUGUUC


11
TG_M6
GCUCUGUCAAGUUCAUCAA
UUGAUGAACUUGACAGAGC


12
TG_M7
GAUCCCUACUCUGAGAACA
UGUUCUCAGAGUAGGGAUC


13
TG_M8
CCAGAGUGGUGACCAACUA
UAGUUGGUCACCACUCUGG


14
TG_M9
GCAACAAGAGCGAGAUGAU
AUCAUCUCGCUCUUGUUGC


15
TG_M10
GCAACCUGCUCAUCGAGUA
UACUCGAUGAGCAGGUUGC


16
TG_H1
GUGACCUAACCACUUAGCA
UGCUAAGUGGUUAGGUCAC


17
TG_H2
GUAGUGACCUAACCACUUA
UAAGUGGUUAGGUCACUAC


18
TG_HG1
GACGCUGGGACAACAACUA
UAGUUGUUGUCCCAGCGUC



















NM_198951
NM_009373
NM_198851
M19646.1



No.
Species
(human)
(mouse)
(RAT)
(GP)






5
hum_mus_rat
[1077-1095]
[1069-1087]
[1033-1051]




2
hum_mus_rat_GP
[1080-1098]
[1072-1090]
[1036-1054]
[1048-1066]



3
hum_mus_GP
[699-717]
[691-709]

[667-685]



4
hum_mus_GP
[1083-1101]
[1075-1093]

[1051-1069]



5
hum_mus
[1339-1357]
[1331-1349]





6
mus

2599-2617





7
mus

164-182





8
mus

118-136





9
mus_rat

[1468-1486]
[1432-1450]




10
mus_rat

[1478-1496]
[1442-1460]




11
mus_rat

601-619





12
mus_rat

1692-1637





13
mus_rat

[976-994]
[940-958]




14
mus_rat

[1066-1084]
[1030-1048]




15
mus_rat

[1018-1036]
[982-1000]




16
hum
1773-1791






17
hum
1770-1788






18
hum_GP
[816-834]


[784-802]



















TABLE B







No.
Method
Sense siRNA
AntiSense siRNA





1
Cross Sp
UUCCACUGCUGGGUGGAGU
ACUCCACCCAGCAGUGGAA


2
Cross Sp
AAGAGCGAGAUGAUCUGGA
UCCAGAUCAUCUCGCUCUU


3
Cross Sp
CAAGAGCGAGAUGAUCUGG
CCAGAUCAUCUCGCUCUUG


4
Cross Sp
AACCACCUGAACAAACUGG
CCAGUUUGUUCAGGUGGUU


5
Cross Sp
ACCACCUGAACAAACUGGC
GCCAGUUUGUUCAGGUGGU


6
Cross Sp
CUGGAACUUCCACUGCUGG
CCAGCAGUGGAAGUUCCAG


7
Cross Sp
AACUUCCACUGCUGGGUGG
CCACCCAGCAGUGGAAGUU


8
Cross Sp
AGGAGAAGAGCGAAGGGAC
GUCCCUUCGCUCUUCUCCU


9
Cross Sp
UGAUCUGGAACUUCCACUG
CAGUGGAAGUUCCAGAUCA


10
Cross Sp
GAGCGAGAUGAUCUGGAAC
GUUCCAGAUCAUCUCGCUC


11
Cross Sp
UCUGGAACUUCCACUGCUG
CAGCAGUGGAAGUUCCAGA


12
Cross Sp
GAUCUGGAACUUCCACUGC
GCAGUGGAAGUUCCAGAUC


13
Cross Sp
GAGAUGAUCUGGAACUUCC
GGAAGUUCCAGAUCAUCUC


14
Cross Sp
AGCGAGAUGAUCUGGAACU
AGUUCCAGAUCAUCUCGCU


15
Cross Sp
AGAUGAUCUGGAACUUCCA
UGGAAGUUCCAGAUCAUCU


16
Cross Sp
CCCCAAGUUCCUGAAGAAC
GUUCUUCAGGAACUUGGGG


17
Cross Sp
AUCUGGAACUUCCACUGCU
AGCAGUGGAAGUUCCAGAU


18
Cross Sp
AGCUUUGUGCUGGGCCACU
AGUGGCCCAGCACAAAGCU


19
Cross Sp
AACCCCAAGUUCCUGAAGA
UCUUCAGGAACUUGGGGUU


20
Cross Sp
CAGGAGAAGAGCGAAGGGA
UCCCUUCGCUCUUCUCCUG


21
Cross Sp
UUGUGCUGGGCCACUUCAU
AUGAAGUGGCCCAGCACAA


22
Cross Sp
GAACUUCCACUGCUGGGUG
CACCCAGCAGUGGAAGUUC


23
Cross Sp
GGAACUUCCACUGCUGGGU
ACCCAGCAGUGGAAGUUCC


24
Cross Sp
ACUUCCACUGCUGGGUGGA
UCCACCCAGCAGUGGAAGU


25
Cross Sp
CGAGAUGAUCUGGAACUUC
GAAGUUCCAGAUCAUCUCG


26
Cross Sp
AUGAUCUGGAACUUCCACU
AGUGGAAGUUCCAGAUCAU


27
Cross Sp
UUUGUGCUGGGCCACUUCA
UGAAGUGGCCCAGCACAAA


28
Cross Sp
GAUGAUCUGGAACUUCCAC
GUGGAAGUUCCAGAUCAUC


29
Cross Sp
UGGAACUUCCACUGCUGGG
CCCAGCAGUGGAAGUUCCA


30
Cross Sp
CUUUGUGCUGGGCCACUUC
GAAGUGGCCCAGCACAAAG


31
Cross Sp
GCUUUGUGCUGGGCCACUU
AAGUGGCCCAGCACAAAGC


32
Cross Sp
UCAGCACUAAGAGCGUGGG
CCCACGCUCUUAGUGCUGA


33
Cross Sp
AGAUCAGCACUAAGAGCGU
ACGCUCUUAGUGCUGAUCU


34
Cross Sp
GAAGAUCAGCACUAAGAGC
GCUCUUAGUGCUGAUCUUC


35
Cross Sp
GAUCAGCACUAAGAGCGUG
CACGCUCUUAGUGCUGAUC


36
Cross Sp
AGUAUGGCCAGUGCUGGGU
ACCCAGCACUGGCCAUACU


37
Cross Sp
AAGUAUGGCCAGUGCUGGG
CCCAGCACUGGCCAUACUU


38
Cross Sp
AUCAGCACUAAGAGCGUGG
CCACGCUCUUAGUGCUGAU


39
Cross Sp
AAGAUCAGCACUAAGAGCG
CGCUCUUAGUGCUGAUCUU


40
Cross Sp
GGAUCCUAGACAUCUGCCU
AGGCAGAUGUCUAGGAUCC


41
Cross Sp
CGCUGGGACAACAACUACG
CGUAGUUGUUGUCCCAGCG


42
Cross Sp
CUUGGAAUUUUGGGCAGUU
AACUGCCCAAAAUUCCAAG


43
Cross Sp
GUCAACUGCAACGAUGACC
GGUCAUCGUUGCAGUUGAC


44
Cross Sp
CAAGAACAUACCUUGGAAU
AUUCCAAGGUAUGUUCUUG


45
Cross Sp
CUCAUCGAGUACUUCCGCA
UGCGGAAGUACUCGAUGAG


46
Cross Sp
GCAUGGUCAACUGCAACGA
UCGUUGCAGUUGACCAUGC


47
Cross Sp
CGGAUGCUGUGUACCUGGA
UCCAGGUACACAGCAUCCG


48
Cross Sp
CCAUGACCAGAACAGCAAC
GUUGCUGUUCUGGUCAUGG


49
Cross Sp
ACAUACCUUGGAAUUUUGG
CCAAAAUUCCAAGGUAUGU


50
Cross Sp
UCGAGUACUUCCGCAAUGA
UCAUUGCGGAAGUACUCGA


51
Cross Sp
AUGGUCAACUGCAACGAUG
CAUCGUUGCAGUUGACCAU


52
Cross Sp
ACCUUGGAAUUUUGGGCAG
CUGCCCAAAAUUCCAAGGU


53
Cross Sp
CAAGUUCAUCAAGAACAUA
UAUGUUCUUGAUGAACUUG


54
Cross Sp
UUCAUCAAGAACAUACCUU
AAGGUAUGUUCUUGAUGAA


55
Cross Sp
AUACCUUGGAAUUUUGGGC
GCCCAAAAUUCCAAGGUAU


56
Cross Sp
AGUACUUCCGCAAUGAGUU
AACUCAUUGCGGAAGUACU


57
Cross Sp
UGGGUGGAGUCGUGGAUGA
UCAUCCACGACUCCACCCA


58
Cross Sp
CCCAUGACCAGAACAGCAA
UUGCUGUUCUGGUCAUGGG


59
Cross Sp
CCAAGUUCAUCAAGAACAU
AUGUUCUUGAUGAACUUGG


60
Cross Sp
GUCAACCCCAAGUUCCUGA
UCAGGAACUUGGGGUUGAC


61
Cross Sp
AUCAAGAACAUACCUUGGA
UCCAAGGUAUGUUCUUGAU


62
Cross Sp
UGGUCAACUGCAACGAUGA
UCAUCGUUGCAGUUGACCA


63
Cross Sp
CAUGGUCAACUGCAACGAU
AUCGUUGCAGUUGACCAUG


64
Cross Sp
UGGAAUUUUGGGCAGUUUG
CAAACUGCCCAAAAUUCCA


65
Cross Sp
ACUGCAACGAUGACCAGGG
CCCUGGUCAUCGUUGCAGU


66
Cross Sp
AUCCUAGACAUCUGCCUGA
UCAGGCAGAUGUCUAGGAU


67
Cross Sp
CAACUGCAACGAUGACCAG
CUGGUCAUCGUUGCAGUUG


68
Cross Sp
GGAAUUUUGGGCAGUUUGA
UCAAACUGCCCAAAAUUCC


69
Cross Sp
AGCGGAUGCUGUGUACCUG
CAGGUACACAGCAUCCGCU


70
Cross Sp
UUUGCCCACAUCACCAACA
UGUUGGUGAUGUGGGCAAA


71
Cross Sp
AAGAACAUACCUUGGAAUU
AAUUCCAAGGUAUGUUCUU


72
Cross Sp
UCCUAGACAUCUGCCUGAU
AUCAGGCAGAUGUCUAGGA


73
Cross Sp
CGAGUACUUCCGCAAUGAG
CUCAUUGCGGAAGUACUCG


74
Cross Sp
UGUCAACCCCAAGUUCCUG
CAGGAACUUGGGGUUGACA


75
Cross Sp
GACGUCUUUGCCCACAUCA
UGAUGUGGGCAAAGACGUC


76
Cross Sp
GAUGCUGUGUACCUGGACU
AGUCCAGGUACACAGCAUC


77
Cross Sp
AGAACAUACCUUGGAAUUU
AAAUUCCAAGGUAUGUUCU


78
Cross Sp
ACGUCUUUGCCCACAUCAC
GUGAUGUGGGCAAAGACGU


79
Cross Sp
AUCGAGUACUUCCGCAAUG
CAUUGCGGAAGUACUCGAU


80
Cross Sp
AAGUUCAUCAAGAACAUAC
GUAUGUUCUUGAUGAACUU


81
Cross Sp
UGGAGUCGUGGAUGACCAG
CUGGUCAUCCACGACUCCA


82
Cross Sp
GUGACAAGAGCGAGAUGAU
AUCAUCUCGCUCUUGUCAC


83
Cross Sp
UCAUCGAGUACUUCCGCAA
UUGCGGAAGUACUCGAUGA


84
Cross Sp
GUUCGUGCCAUCAAGGAGG
CCUCCUUGAUGGCACGAAC


85
Cross Sp
CAUCAAGAACAUACCUUGG
CCAAGGUAUGUUCUUGAUG


86
Cross Sp
UACCUUGGAAUUUUGGGCA
UGCCCAAAAUUCCAAGGUA


87
Cross Sp
GACAAGAGCGAGAUGAUCU
AGAUCAUCUCGCUCUUGUC


88
Cross Sp
CGUCUUUGCCCACAUCACC
GGUGAUGUGGGCAAAGACG


89
Cross Sp
AUGCUGUGUACCUGGACUC
GAGUCCAGGUACACAGCAU


90
Cross Sp
UUGGAAUUUUGGGCAGUUU
AAACUGCCCAAAAUUCCAA


91
Cross Sp
GCCAAGUUCAUCAAGAACA
UGUUCUUGAUGAACUUGGC


92
Cross Sp
AGUUCAUCAAGAACAUACC
GGUAUGUUCUUGAUGAACU


93
Cross Sp
GUCUUUGCCCACAUCACCA
UGGUGAUGUGGGCAAAGAC


94
Cross Sp
GGGAUCCUAGACAUCUGCC
GGCAGAUGUCUAGGAUCCC


95
Cross Sp
GAUCCUAGACAUCUGCCUG
CAGGCAGAUGUCUAGGAUC


96
Cross Sp
AUGUCAACCCCAAGUUCCU
AGGAACUUGGGGUUGACAU


97
Cross Sp
UCAUCAAGAACAUACCUUG
CAAGGUAUGUUCUUGAUGA


98
Cross Sp
UCAAGAACAUACCUUGGAA
UUCCAAGGUAUGUUCUUGA


99
Cross Sp
CAUCGAGUACUUCCGCAAU
AUUGCGGAAGUACUCGAUG


100
Cross Sp
GGAUGCUGUGUACCUGGAC
GUCCAGGUACACAGCAUCC


101
Cross Sp
GAUGUCAACCCCAAGUUCC
GGAACUUGGGGUUGACAUC


102
Cross Sp
CAUGACCAGAACAGCAACC
GGUUGCUGUUCUGGUCAUG


103
Cross Sp
GCCCAUGACCAGAACAGCA
UGCUGUUCUGGUCAUGGGC


104
Cross Sp
GAACAUACCUUGGAAUUUU
AAAAUUCCAAGGUAUGUUC


105
Cross Sp
GUGGAGUCGUGGAUGACCA
UGGUCAUCCACGACUCCAC


106
Cross Sp
UCAACUGCAACGAUGACCA
UGGUCAUCGUUGCAGUUGA


107
Cross Sp
AUUUUGGGCAGUUUGAAGA
UCUUCAAACUGCCCAAAAU


108
Cross Sp
AACAUACCUUGGAAUUUUG
CAAAAUUCCAAGGUAUGUU


109
Cross Sp
UGACAAGAGCGAGAUGAUC
GAUCAUCUCGCUCUUGUCA


110
Cross Sp
UUCGUGCCAUCAAGGAGGG
CCCUCCUUGAUGGCACGAA


111
Cross Sp
UCAGCCCCAUGUCCUGGAU
AUCCAGGACAUGGGGCUGA


112
Cross Sp
GGUCAACUGCAACGAUGAC
GUCAUCGUUGCAGUUGACC


113
Cross Sp
AAUUUUGGGCAGUUUGAAG
CUUCAAACUGCCCAAAAUU


114
Cross Sp
CAGCGGAUGCUGUGUACCU
AGGUACACAGCAUCCGCUG


115
Cross Sp
AACUGCAACGAUGACCAGG
CCUGGUCAUCGUUGCAGUU


116
Cross Sp
AUGACCAGAACAGCAACCU
AGGUUGCUGUUCUGGUCAU


117
Cross Sp
CAUACCUUGGAAUUUUGGG
CCCAAAAUUCCAAGGUAUG


118
Cross Sp
CUUUGCCCACAUCACCAAC
GUUGGUGAUGUGGGCAAAG


119
Cross Sp
GAGUACUUCCGCAAUGAGU
ACUCAUUGCGGAAGUACUC


120
Cross Sp
GGCAUGGUCAACUGCAACG
CGUUGCAGUUGACCAUGCC


121
Cross Sp
UCUUUGCCCACAUCACCAA
UUGGUGAUGUGGGCAAAGA


122
Cross Sp
GAAUUUUGGGCAGUUUGAA
UUCAAACUGCCCAAAAUUC


123
Cross Sp
CCUUGGAAUUUUGGGCAGU
ACUGCCCAAAAUUCCAAGG


124
Cross Sp
GUUCAUCAAGAACAUACCU
AGGUAUGUUCUUGAUGAAC


125
Cross Sp
UGUAUCGCCUCAGCCUGGA
UCCAGGCUGAGGCGAUACA


126
Cross Sp
GCUCGGCCAAGUUCAUCAA
UUGAUGAACUUGGCCGAGC


127
Cross Sp
GGCUCGGCCAAGUUCAUCA
UGAUGAACUUGGCCGAGCC


128
Cross Sp
GGACGCUGGGACAACAACU
AGUUGUUGUCCCAGCGUCC


129
Cross Sp
GGCAGUUUGAAGAUGGGAU
AUCCCAUCUUCAAACUGCC


130
Cross Sp
AGUUUGAAGAUGGGAUCCU
AGGAUCCCAUCUUCAAACU


131
Cross Sp
CAGUUUGAAGAUGGGAUCC
GGAUCCCAUCUUCAAACUG


132
Cross Sp
AGGGCUCGGCCAAGUUCAU
AUGAACUUGGCCGAGCCCU


133
Cross Sp
GCAGUUUGAAGAUGGGAUC
GAUCCCAUCUUCAAACUGC


134
Cross Sp
CAACCCCAAGUUCCUGAAG
CUUCAGGAACUUGGGGUUG


135
Cross Sp
GGGCAGUUUGAAGAUGGGA
UCCCAUCUUCAAACUGCCC


136
Cross Sp
ACGCUGGGACAACAACUAC
GUAGUUGUUGUCCCAGCGU


137
Cross Sp
UACUGCUGUGGCCCAGUUC
GAACUGGGCCACAGCAGUA


138
Single Sp
UUGCCCACAUCACCAACAA
UUGUUGGUGAUGUGGGCAA


139
Single Sp
CCAAGUACCUGCUCAACCU
AGGUUGAGCAGGUACUUGG


140
Single Sp
CGGCCAAGUUCAUCAAGAA
UUCUUGAUGAACUUGGCCG


141
Single Sp
CGAUGGGUCUGUGCACAAA
UUUGUGCACAGACCCAUCG


142
Single Sp
CAGUGACUUUGACGUCUUU
AAAGACGUCAAAGUCACUG


143
Single Sp
GCAUGAACAUGGGCAGUGA
UCACUGCCCAUGUUCAUGC


144
Single Sp
CAACUACGAGGCCAGUGUA
UACACUGGCCUCGUAGUUG


145
Single Sp
CAUGGGCAGUGACUUUGAC
GUCAAAGUCACUGCCCAUG


146
Single Sp
GCCCACAUCACCAACAACA
UGUUGUUGGUGAUGUGGGC


147
Single Sp
CGAACCACCUGAACAAACU
AGUUUGUUCAGGUGGUUCG


148
Single Sp
GGCCCGUUUUCCACUAAGA
UCUUAGUGGAAAACGGGCC


149
Single Sp
UGACGUCUUUGCCCACAUC
GAUGUGGGCAAAGACGUCA


150
Single Sp
GAACAUGGGCAGUGACUUU
AAAGUCACUGCCCAUGUUC


151
Single Sp
GCAGUGACUUUGACGUCUU
AAGACGUCAAAGUCACUGC


152
Single Sp
CUGUGUUCCUGGAGCAUUU
AAAUGCUCCAGGAACACAG


153
Single Sp
CAACCUGGAGCCUUUCUCU
AGAGAAAGGCUCCAGGUUG



















human GI
Mouse GI
Rat GI
Guinea-pig
Cow GI




No.
39777598
31543859
42476286
GI 387604
31343554
species






1
1100-1118
1092-1110
1056-1074
1068-1086
1046-1064
hmrgc



2
1079-1097
1071-1089
1035-1053
1047-1065
1025-1043
hmrgc



3
1078-1096
1070-1088
1034-1052
1046-1064
1024-1042
hmrgc



4
1478-1496
1470-1488
1434-1452
—
1424-1442
hmr



5
1479-1497
1471-1489
1435-1453
—
1425-1442
hmr



6
1093-1111
1085-1103
1049-1067
1061-1079
1039-1057
hm



7
1097-1115
1089-1107
1056-1071
1065-1083
1043-1061
hm



8
1185-1203
1177-1195
1141-1156
—
1131-1149
hm



9
1089-1107
1081-1099
—
1057-1075
1035-1053
hm



10
1081-1099
1073-1091
1037-1054
1049-1067
1027-1045
hm



11
1092-1110
1084-1102
1048-1066
1060-1078
1038-1056
hm



12
1090-1108
1082-1100
—
1058-1076
1036-1054
hm



13
1085-1103
1077-1095
1041-1059
1053-1071
1031-1049
hm



14
1082-1100
1074-1092
1038-1054
1050-1068
1028-1046
hm



15
1086-1104
1078-1096
1042-1060
1054-1072
1032-1050
hm



16
700-718
692-710
656-671
668-685
646-659
hm



17
1091-1109
1083-1101
—
1059-1077
1037-1055
hm



18
485-503
477-495
—
—
—
hm



19
698-716
690-708
654-671
666-684
644-659
hm



20
1184-1202
1176-1194
1140-1156
1152-1170
1130-1148
hm



21
489-507
481-499
—
462-475
—
hm



22
1096-1114
1088-1106
1056-1070
1064-1082
1042-1060
hm



23
1095-1113
1087-1105
1051-1069
1063-1081
1041-1059
hm



24
1098-1116
1090-1108
1056-1072
1066-1084
1044-1062
hm



25
1084-1102
1076-1094
1040-1054
1052-1070
1030-1048
hm



26
1088-1106
1080-1098
1044-1062
1056-1074
1034-1052
hm



27
488-506
480-498
—
462-474
—
hm



28
1087-1105
1079-1097
1043-1061
1055-1073
1033-1051
hm



29
1094-1112
1086-1104
1050-1068
1062-1080
1040-1058
hm



30
487-505
479-497
—
462-473
—
hm



31
486-504
478-496
—
462-472
—
hm



32
1377-1395
1369-1387
1333-1351
—
—
hr



33
1374-1392
1366-1381
1330-1348
—
—
hr



34
1372-1390
1364-1381
1328-1346
—
1318-1329
hr



35
1375-1393
1367-1381
1331-1349
—
—
hr



36
918-936
918-928
874-892
886-904
864-882
hr



37
917-935
—
873-891
885-903
863-881
hr



38
1376-1394
1368-1386
1332-1350
—
—
hr



39
1373-1391
1365-1381
1329-1347
—
1319-1329
hr



40
663-681
—
—
—
609-627
hc



41
818-836
810-826
774-787
786-803
764-782
hc



42
636-654
628-646
592-610
—
582-600
hc



43
782-800
774-792
738-756
750-760
728-746
hc



44
625-643
—
—
599-610
571-589
hc



45
1034-1052
1026-1042
 990-1006
1002-1018
980-998
hc



46
777-795
770-784
733-748
746-760
723-741
hc



47
534-552
—
—
—
480-498
hc



48
1012-1030
1008-1022
972-986
984-998
958-976
hc



49
630-648
—
—
599-610
576-594
hc



50
1038-1056
1030-1048
 994-1006
1006-1018
 984-1002
hc



51
779-797
771-789
735-753
747-760
725-743
hc



52
634-652
—
—
—
580-598
hc



53
616-634
608-621
572-585
584-595
562-580
hc



54
620-638
—
—
—
566-584
hc



55
632-650
—
—
600-610
578-596
hc



56
1041-1059
—
—
—
 987-1005
hc



57
1109-1127
1101-1119
1065-1083
1077-1095
1055-1073
hc



58
1011-1029
1003-1021
967-985
979-997
957-975
hc



59
615-633
608-621
572-585
583-595
561-579
hc



60
695-713
690-705
654-669
665-681
641-659
hc



61
623-641
—
—
599-609
569-587
hc



62
780-798
772-790
736-754
748-760
726-744
hc



63
778-796
770-784
734-748
746-760
724-742
hc



64
638-656
630-646
594-612
—
584-602
hc



65
786-804
778-796
742-760
—
732-750
hc



66
665-683
—
—
—
611-629
hc



67
784-802
—
—
—
730-748
hc



68
639-657
631-646
595-613
615-625
585-603
hc



69
532-550
—
—
500-511
478-496
hc



70
1574-1592
1566-1577
1530-1541
—
1520-1538
hc



71
626-644
—
—
599-610
572-590
hc



72
666-684
—
—
—
612-630
hc



73
1039-1057
1031-1049
 995-1006
1007-1018
 985-1003
hc



74
694-712
690-704
654-668
665-680
640-658
hc



75
1568-1586
1560-1577
1524-1541
—
1514-1532
hc



76
536-554
—
—
—
482-500
hc



77
627-645
—
—
599-610
573-591
hc



78
1569-1587
1561-1577
1525-1541
—
1515-1533
hc



79
1037-1055
1029-1047
 993-1006
1005-1018
 983-1001
hc



80
617-635
609-621
573-585
585-595
563-581
hc



81
1113-1131
1105-1123
1069-1087
1081-1099
1059-1077
hc



82
1074-1092
1069-1084
1033-1048
1045-1060
1020-1038
hc



83
1035-1053
1027-1042
 991-1006
1003-1018
981-999
hc



84
1226-1244
1224-1236
1188-1200
1194-1212
1172-1190
hc



85
622-640
—
—
—
568-586
hc



86
633-651
—
—
—
579-597
hc



87
1076-1094
1069-1086
1033-1050
1045-1062
1022-1040
hc



88
1570-1588
1566-1577
1530-1541
—
1516-1534
hc



89
537-555
—
—
—
483-501
hc



90
637-655
629-646
593-611
—
583-601
hc



91
614-632
608-621
572-585
582-595
560-578
hc



92
618-636
610-621
574-585
—
564-582
hc



93
1571-1589
1566-1577
1530-1541
—
1517-1535
hc



94
662-680
—
—
—
608-626
hc



95
664-682
—
—
—
610-628
hc



96
693-711
690-703
649-667
665-679
639-657
hc



97
621-639
—
—
—
567-585
hc



98
624-642
—
—
599-610
570-588
hc



99
1036-1054
1028-1042
 992-1006
1004-1018
 982-1000
hc



100
535-553
—
—
—
481-499
hc



101
692-710
690-702
648-666
665-678
638-656
hc



102
1013-1031
1008-1023
972-987
984-999
959-977
hc



103
1010-1028
1002-1020
966-984
978-996
956-974
hc



104
628-646
—
—
599-610
574-592
hc



105
1112-1130
—
—
1080-1098
1058-1076
hc



106
783-801
—
—
—
729-747
hc



107
642-660
636-646
600-613
615-628
588-606
hc



108
629-647
—
—
599-610
575-593
hc



109
1075-1093
1069-1085
1033-1049
1045-1061
1021-1039
hc



110
1227-1245
1224-1237
1188-1201
1195-1213
1173-1191
hc



111
846-864
—
—
814-832
792-810
hc



112
781-799
773-791
737-755
749-760
727-745
hc



113
641-659
636-646
600-613
615-627
587-605
hc



114
531-549
—
—
499-511
477-495
hc



115
785-803
—
—
—
731-749
hc



116
1014-1032
1008-1024
972-988
 984-1000
960-978
hc



117
631-649
—
—
599-610
577-595
hc



118
1573-1591
1566-1577
1530-1541
—
1519-1537
hc



119
1040-1058
1032-1050
 996-1006
1008-1018
 986-1004
hc



120
776-794
770-784
732-748
746-760
722-740
hc



121
1572-1590
1566-1577
1530-1541
—
1518-1536
hc



122
640-658
636-646
600-613
615-626
586-604
hc



123
635-653
—
—
—
581-599
hc



124
619-637
611-621
575-585
—
565-583
hc



125
441-459
—
402-415
409-427
3571-3582
hg



126
609-627
608-619
572-583
577-595
555-573
hg



127
608-626
608-618
572-582
576-594
554-572
hg



128
815-833
810-825
774-787
783-801
764-779
hg



129
648-666
—
—
616-634
594-612
hg



130
651-669
—
607-625
619-637
—
hg



131
650-668
—
—
618-636
596-614
hg



132
606-624
—
—
574-592
552-570
hg



133
649-667
—
—
617-635
595-613
hg



134
697-715
690-707
654-671
665-683
643-659
hg



135
647-665
—
603-621
615-633
593-611
hg



136
817-835
810-826
774-787
785-803
764-781
hg



137
1205-1223
1197-1213
1161-1177
1173-1191
1151-1169
hg



138
1575-1593
1567-1577
1531-1541
—
1521-1538
h



139
1677-1695
—
—
1660-1672
—
h



140
612-630
608-621
572-585
580-595
560-576
h



141
1324-1342
1317-1334
1281-1298
—
—
h



142
1558-1576
—
1517-1528
1535-1553
—
h



143
1545-1563
—
—
1530-1540
—
h



144
244-262
239-250
—
—
—
h



145
1552-1570
—
—
1530-1547
—
h



146
1577-1595
—
—
—
1523-1538
h



147
1476-1494
1470-1486
1434-1450
—
1424-1440
h



148
322-340
—
—
—
—
h



149
1567-1585
1560-1577
1523-1541
—
1514-1531
h



150
1549-1567
—
—
1530-1544
—
h



151
1557-1575
—
1517-1528
1534-1552
—
h



152
1724-1742
—
—
—
—
h



153
1696-1714
—
—
1105-1115
—
h



















TABLE C







No.
Method
Sense siRNA
AntiSense siRNA





1
Single Sp
CUAGACAUCUGCCUGAUCCUU
AAGGAUCAGGCAGAUGUCUAG


2
Single Sp
CAACUGACAACAUGCUAGGUA
UACCUAGCAUGUUGUCAGUUG


3
Single Sp
CCAAGUUCAUCAAGAACAUAC
GUAUGUUCUUGAUGAACUUGG


4
Single Sp
CCUGAUCCUUCUAGAUGUCAA
UUGACAUCUAGAAGGAUCAGG


5
Cross Sp
ACAAGAGCGAGAUGAUCUGGA
UCCAGAUCAUCUCGCUCUUGU


6
Single Sp
CAAGAACAUACCUUGGAAUUU
AAAUUCCAAGGUAUGUUCUUG


7
Single Sp
CGGCCAAGUUCAUCAAGAACA
UGUUCUUGAUGAACUUGGCCG


8
Single Sp
CUGUGUUCCUGGAGCAUUUGU
ACAAAUGCUCCAGGAACACAG


9
Cross Sp
CAAGAGCGAGAUGAUCUGGAA
UUCCAGAUCAUCUCGCUCUUG


10
Single Sp
CAACUACGAGGCCAGUGUAGA
UCUACACUGGCCUCGUAGUUG


11
Single Sp
GGCCCGUUUUCCACUAAGAGA
UCUCUUAGUGGAAAACGGGCC


12
Single Sp
GCAACCUUCUCAUCGAGUACU
AGUACUCGAUGAGAAGGUUGC


13
Cross Sp
CGAGAUGAUCUGGAACUUCCA
UGGAAGUUCCAGAUCAUCUCG


14
Cross Sp
ACUUCCACUGCUGGGUGGAGU
ACUCCACCCAGCAGUGGAAGU


15
Cross Sp
AACCCCAAGUUCCUGAAGAAC
GUUCUUCAGGAACUUGGGGUU


16
Cross Sp
AUGAUCUGGAACUUCCACUGC
GCAGUGGAAGUUCCAGAUCAU


17
Cross Sp
GAACUUCCACUGCUGGGUGGA
UCCACCCAGCAGUGGAAGUUC


18
Cross Sp
UGGAACUUCCACUGCUGGGUG
CACCCAGCAGUGGAAGUUCCA


19
Cross Sp
AGCGAGAUGAUCUGGAACUUC
GAAGUUCCAGAUCAUCUCGCU


20
Cross Sp
GAUGAUCUGGAACUUCCACUG
CAGUGGAAGUUCCAGAUCAUC


21
Cross Sp
AGAGCGAGAUGAUCUGGAACU
AGUUCCAGAUCAUCUCGCUCU


22
Cross Sp
CUGGAACUUCCACUGCUGGGU
ACCCAGCAGUGGAAGUUCCAG


23
Cross Sp
UGAUCUGGAACUUCCACUGCU
AGCAGUGGAAGUUCCAGAUCA


24
Cross Sp
AAGAGCGAGAUGAUCUGGAAC
GUUCCAGAUCAUCUCGCUCUU


25
Cross Sp
CAGCUUUGUGCUGGGCCACUU
AAGUGGCCCAGCACAAAGCUG


26
Cross Sp
GCUUUGUGCUGGGCCACUUCA
UGAAGUGGCCCAGCACAAAGC


27
Cross Sp
AGAUGAUCUGGAACUUCCACU
AGUGGAAGUUCCAGAUCAUCU


28
Cross Sp
CUUUGUGCUGGGCCACUUCAU
AUGAAGUGGCCCAGCACAAAG


29
Cross Sp
GCGAGAUGAUCUGGAACUUCC
GGAAGUUCCAGAUCAUCUCGC


30
Cross Sp
AUCUGGAACUUCCACUGCUGG
CCAGCAGUGGAAGUUCCAGAU


31
Cross Sp
UCUGGAACUUCCACUGCUGGG
CCCAGCAGUGGAAGUUCCAGA


32
Cross Sp
GAUCUGGAACUUCCACUGCUG
CAGCAGUGGAAGUUCCAGAUC


33
Cross Sp
GAGAUGAUCUGGAACUUCCAC
GUGGAAGUUCCAGAUCAUCUC


34
Cross Sp
AGCUUUGUGCUGGGCCACUUC
GAAGUGGCCCAGCACAAAGCU


35
Cross Sp
GAGCGAGAUGAUCUGGAACUU
AAGUUCCAGAUCAUCUCGCUC


36
Cross Sp
AACUUCCACUGCUGGGUGGAG
CUCCACCCAGCAGUGGAAGUU






















Guinea-






human
mouse
rat
pig
Cow




No.
39777598
31543859
42476286
387604
31343554
file






1
668-688
—
—
—
614-630
hmrgc



2
1752-1772
—
—
—
—
hmrgc



3
615-635
608-621
572-585
583-595
561-581
hmrgc



4
679-699
—
—
—
—
hmrgc



5
1077-1097
1069-1089
1033-1053
1045-1065
1023-1043
hmrgc



6
625-645
—
—
599-610
571-591
hmrgc



7
612-632
608-621
572-585
580-595
560-578
hmrgc



8
1724-1744
—
—
—
—
hmrgc



9





hmrgc



10
244-264
239-250
—
—
—
hmrgc



11
322-342
—
—
—
—
hmrgc



12
1026-1046
1018-1038
 982-1002
 994-1014
972-992
hmrgc



13
1084-1104
1076-1096
1040-1060
1052-1072
1030-1050
hm



14
1098-1118
1090-1110
1056-1074
1066-1086
1044-1064
hm



15
698-718
690-710
654-671
666-685
644-659
hm



16
1088-1108
1080-1100
1044-1064
1056-1076
1034-1054
hm



17
1096-1116
1088-1108
1056-1072
1064-1084
1042-1062
hm



18
1094-1114
1086-1106
1050-1070
1062-1082
1040-1060
hm



19
1082-1102
1074-1094
1038-1054
1050-1070
1028-1048
hm



20
1087-1107
1079-1099
1043-1063
1055-1075
1033-1053
hm



21
1080-1100
1072-1092
1036-1054
1048-1068
1026-1046
hm



22
1093-1113
1085-1105
1049-1069
1061-1081
1039-1059
hm



23
1089-1109
1081-1101
—
1057-1077
1035-1055
hm



24
1079-1099
1071-1091
1035-1054
1047-1067
1025-1045
hm



25
484-504
476-496
—
452-472
—
hm



26
486-506
478-498
—
462-474
—
hm



27
1086-1106
1078-1098
1042-1062
1054-1074
1032-1052
hm



28
487-507
479-499
—
462-475
—
hm



29
1083-1103
1075-1095
1039-1059
1051-1071
1029-1049
hm



30
1091-1111
1083-1103
1047-1067
1059-1079
1037-1057
hm



31
1092-1112
1084-1104
1048-1068
1060-1080
1038-1058
hm



32
1090-1110
1082-1102
1046-1066
1058-1078
1036-1056
hm



33
1085-1105
1077-1097
1041-1061
1053-1073
1031-1051
hm



34
485-505
477-497
—
453-473
—
hm



35
1081-1101
1073-1093
1037-1054
1049-1069
1027-1047
hm



36
1097-1117
1089-1109
1056-1073
1065-1085
1043-1063
hm









Example 2
Testing the siRNA Compounds for Anti-TGaseII Activity
I. Preparation of Working Solutions of siRNAs (Double-Stranded Oligonucleotides)
Lyophilized oligonucleotides were dissolved in RNAse-free double-distilled water to produce a final concentration of 100 uM. The diluted oligonucleotides were kept at room temperature for 15 min and immediately frozen in liquid nitrogen. The oligonucleotides were stored at −80° C. and diluted before use with PBS.
II. Establishment of NRK49 Cell Line Stably Overexpressing rat TGaseII
The full length cDNA of rat TGaseII cloned in PLXSN vector (CLONTECH) was used for transfection into a Rat1 fibroblast cell line. Lipofectamine reagent (Invitrogen) was used as the transfection reagent using the protocol described below. 48 hr following transfection, selection of stable clones was performed using G418 antibiotic (neomycin). The stable overexpression of TGaseII in this polyclonal population was verified by Western blotting and TGaseII activity assay. The cells were designated as NRK49-TGaseII (TGASE-OE®).
III. Activity Assay for TGaseII in NRK49
4×103 NRK49-rat TGASE-OE cells were seeded per well in a 96 well plate. TGaseII activity was measured using a cell-based assay for TGaseII activity. Briefly, the growth medium was replaced with cell labeling medium (DMEM in 0.1% BSA, 25 uM BC, 10 uM Calcimycin, 16.2 mM CaCl2) for 45 min at 37° C. 45 min later, the cells were fixed with 4% formaldehyde, treated with 0.6% H2O2 and stained with Netravidin-HRP Ab in order to test the cross-linking of biotin-labeled cadaverin. The absorbance was read at λ=450 nm. For normalization, the cells were stained with Hoechst dye solution. The activity of TGaseII is 75 fold higher in NRK49-TGaseII cells compared to NRK49 control cells.
IV. Transfection by siRNA Oligonucleotides Using Lipofectamine-2000 Reagent
2×105 cells were seeded per well in 6 well-plates. After 24 hrs, the cells were transfected with TGaseII specific siRNA oligonucleotides using Lipofectamine-2000 reagent (Invitrogen) according to the following procedure:

    
    
        1. Before transfection, the cell medium was replaced with 1500 ul of fresh medium without antibiotics.
        2. In a sterile plastic tube, Lipofectamine2000 reagent (the amount is calculated according to 5 ul per well) was added to 250 ul of serum-free medium, and incubated for 5 min at room temperature.
        3. In another tube, the siRNA oligonucleotides (varying amounts to fit the desired final concentration per well) were added to 250 ul of serum-free medium.
        4. Lipofectamine2000 complex was combined with the siRNA solution and incubated for 20 min at room temperature.
        5. The resulting mixture was added dropwise to the cells, and the cells were incubated at 37° C. until analysis of siRNA activity.
    
    


V. Testing the Activity of Anti TGaseII siRNAs in Transfected Human, Mouse and Rat Cells
The activity of TGaseII siRNAs listed in Table A was tested in 3 different cell lines originating from different species:

    
    
        1. Mouse-specific TGaseII siRNAs were tested in mouse cells, which express mouse TGaseII—NMUMG cells.
        2. Human-specific TGaseII siRNA were tested in human HeLa cells which express human TgaseII; see FIG. 3.
        3. Rat-specific TGaseII siRNAs were tested in NRK49 overexpressing rat TGaseII (TGASE-OE® cells).
    
    


48 h to 6 days after transfection of siRNAs, the cells were harvested and expression of TGaseII protein was examined by Western blot analysis with specific antibodies. The decrease in TGaseII polypeptide expression in the cells transfected with siRNA oligonucleotides specific to TGaseII as compared to controls indicated that siRNAs elicited inhibitory effect on TGaseII protein expression, which can be quantified.
Table D below summarizes the information about TGaseII inhibitory activity of each siRNA oligonucleotide. The names of oligonucleotides in Table D correspond to the names used in Table A. Note that the comparison is to the activity in each cell line transfected by different siRNAs, and not between cell lines. The presently most preferred human siRNA is TG_HMRG1, which elicited high TGaseII inhibitory effect and also inhibited mouse, rat and guinea pig to TGaseII. Other preferred human siRNAs are TG_HMG1 and TG_HM1.











TABLE D







Human
Mouse
Rat


name
Species
TGII
TGII
TGII







TG_HMR1
hum_mus_rat
+
−
+


TG_HMRG1
hum_mus_rat_GP
++++
+++
++++


TG_HMG1
hum_mus_GP
++++
+
ND


TG_HMG2
hum_mus_GP
++++
++++
ND




(toxic)
(toxic)


TG_HM1
hum_mus
++++
+
ND


TG_M1
Mus
+
+++
ND


TG_M2
Mus
−
+++
ND


TG_M3
Mus
+++
++++
ND


TG_M4
mus_rat
ND
++
++


TG_M5
mus_rat
+++
+++
+++


TG_M6
mus_rat
ND
++
+++


TG_M7
mus_rat
ND
++
++++


TG_M8
mus_rat
ND
++
++


TG_M9
mus_rat
+++
+++
+++


TG_M10
mus_rat
ND
+
+++


TG_H1
Hum
−
ND
ND


TG_H2
Hum
−
ND
ND


TG_HG1
hum_GP
++
ND
ND









Example 3
Animal Models of Kidney Fibrosis
Testing of the in vivo therapeutic activity of anti-TGaseII siRNAs, or of neutralizing antibodies against TGaseII or of other TGaseII inhibitors may be done in the following animal models of kidney fibrosis in which disease-associated overexpression of TGaseII was found (as detected by in situ hybridization; see below).
A. Rat diabetic and Aging Models of Kidney Fibrosis
A1. ZDF Rats
Kidney samples of 9-month-old ZDF rats (Zucker diabetic fatty rats) presented hydronephrotic changes with dilated calyces. Microscopically these samples displayed the features of glomerulosclerosis and tubulointerstitial fibrosis. In accordance with these morphological changes, the expression of fibrosis marker genes (osteopontin (OPN), transforming growth factor β1 (TGF-β1) and procollagen α1(I) (Col1)), as measured by in situ hybridization, was significantly increased compared to normal kidneys. Strong OPN expression was detectable in all tubular structures in both kidney cortex and medulla. TGF-β1 expression was widespread throughout interstitial cells. Some epithelial cells also showed TGF-β1 expression. Col1 expression was detectable by in situ hybridization in most interstitial cells within the medulla, while cortical expression was “focal”.
A2. Aged fa/fa (Obese Zucker) Rats
Fa/fa rats are genetically deficient for leptin receptor; and, as a result, develop insulin resistant diabetes (type II diabetes) with progressive diabetic nephropathy,
Kidney samples of 12-month-old fa/fa rats presented with high degree glomerulosclerosis and diffuse tubulointerstitial fibrosis throughout both the cortex and the medulla. The pattern of fibrosis marker gene expression corresponded to the morphological changes. OPN was expressed in tubular structures in the cortex and in the medulla. Multiple interstitial cells expressed TGF-β1. Significantly, multiple foci and single interstitial cells showed strong Col1 expression in both cortex and medulla so that the number of Col1-expressing cells appeared to be higher in fa/fa kidney samples than in ZDF samples.
A3. Aged Sprague-Dawley (SD) (Normal) Rats
Kidney samples of aged SD rats also showed increased accumulation of collagen in glomeruli and interstitial space and increased expression of fibrosis marker genes. Significantly, the intensity of fibrotic changes varied among samples. Thus, one of the four samples studied displayed very few changes compared with young animals; in the second sample, fibrotic changes were confined only to “polar” regions, and the remaining two samples displayed uniform accumulation of collagen and elevated expression of marker genes throughout the sections
A4. Goto Kakizaki (GK)48-Week-Old Rats
GK rats are an inbred strain derived from Wistar rats, selected for spontaneous development of NIDDM (diabetes type II). Kidney samples from both GK and control Wistar 48-week-old rats showed accumulation of collagen in glomeruli and interstitial space. This accumulation was more pronounced in the GK samples.
TGaseII Hybridization Pattern
TGaseII-specific hybridization signal was associated with fibrotic phenotype (diffuse or focal) in kidneys of both healthy and diabetic rats. Non-fibrotic kidney samples demonstrate a diffuse, low but detectable TGaseII-specific hybridisation signal over proximal tubules. By 12 months of age, a stronger signal is concentrated over interstitial cells and epithelial lining of distended tubules that show clear signs of atrophy. In chronic renal failure sample (kidney from two years old rat), a strong TGaseII expression is visible in tubular profiles lined by atrophic or proliferating epithelium cells within surrounding interstitium. Similarly, ZDF samples showed intensification of the hybridization signal along with the progression of the fibrosis (or aging).
B. Induced Models of Kidney Fibrosis
B1. Permanent Unilateral Ureteral Obstruction (UUO) Model
Unilateral ureteral obstruction (UUO) is a model of acute interstitial fibrosis occurring in healthy non-diabetic animals. Renal fibrosis develops within days following the obstruction.
To produce the model, rats were anaesthetized with Ketamin/Xylazine and the abdominal cavity was opened. After exposure, the right ureter was ligated with a suture at the level of the lower kidney pole. In sham-operated rats, the ureter was exposed but not ligated. The study was terminated at different timepoints following ureteral obstruction (e.g., at 24 hr, 5 days, 10 days, 15 days, 20 days and 25 days), and the kidneys were removed and examined.
Histological examination revealed that permanent UUO results in a rapid activation of collagen synthesis by interstitial cells in both medulla and cortex. By 20-25 days of UUO, significant amounts of interstitial collagen were deposited in the interstitial space, whereas glomerular accumulation of collagen was confined to the outer capsule.
In situ hybridization analysis of obstructed kidney samples indicated rapid and significant changes in the pattern of TGaseII expression dependent on the duration of UUO. After 24 hours of UUO, a very strong hybridization signal was detected over cortical tubular epithelium, whereas medullar epithelial cells showed much weaker signal. At 5 and 10 days of UUO, the “foci” of strong hybridization signal were associated with the areas of developing tubulointerstitial fibrosis where the signal was located to both epithelial and interstitial cells. Similar results were observed in mice exposed to the same UUO model.
B2. 5/6 Nephrectomy
5/6 nephrectomy is another useful animal model for chronic renal insufficiency (CRI) in which fibrosis is evident.
In summary, the results suggest that an increase in TGaseII expression and activity level accompanies fibrotic changes in the kidneys.
Example 4
Establishment of TGaseII Role in Renal Fibrosis Employing the UUO Model Using TGaseII Knock-Out Mice
TgaseII knock-out mice were obtained from Dr. Melino (De Laurenzi V, Melino G., Gene disruption of tissue transglutaminase, Mol Cell Biol. 2001 January; 21(1):148-55). The mice appeared phenotypically normal. Also no morphological changes were observed in kidneys obtained from these mice.
TGaseII KO mice were then used for the analysis of the development of kidney fibrosis following induction of UUO by assessing kidney collagen accumulation compared to normal mice The results clearly demonstrated that disruption of TGaseII results in statistically significant reduced collagen accumulation following both three (3) and seven (7) days of obstruction, as compared to collagen accumulation in obstructed kidneys of wild type mice, thus implicating TGaseII as a functionally important factor in kidney fibrosis. It is thus suggested that inhibition of TGaseII activity may have an anti-fibrotic therapeutic effect.
Example 5
Inhibition of TGaseII Activity Using Monoclonal Neutralizing Antibodies
Recombinant monoclonal human-anti-human antibodies against TGaseII were obtained by screening of a phage display library. 720 clones were screened for binding human TGaseII. Seven (7) clones were selected which showed intense binding to the enzyme. The activity assay demonstrated that these antibodies inhibited the crosslinking activity of human TGaseII enzyme at a range of concentrations (1-5 nM).

## Claims

1. A double-stranded RNA compound having the structure:


5′(N)x—Z3′ (antisense strand)



3′Z′—(N′)y5′ (sense strand)

wherein each of N and N′ is a ribonucleotide which may independently be modified or unmodified in its sugar residue;
wherein each of (N)x and (N′)y is an oligomer in which each consecutive N or N′ is joined to the next N or N′ by a covalent bond;
wherein each of x and y is an integer from 19 to 40;
wherein each of Z and Z′ may be present or absent, but if present is 1-5 consecutive nucleotides covalently attached at the 3′ terminus of the strand in which it is present;
wherein the sequence of (N)x comprises the sequence 5′ UUCCAGAUCAUCUCGCUCU 3′ (SEQ ID NO: 22)
and wherein the sequence of (N′)y comprises the sequence 5′ AGAGCGAGAUGAUCUGGAA 3′ (SEQ ID NO:4).

2. The compound of claim 1, wherein the covalent bond is a phosphodiester bond.

3. The compound of claim 1, wherein x=y.

4. The compound of claim 1, wherein x=y=19.

5. The compound of claim 1, wherein both Z and Z′ are absent.

6. The compound of claim 1, wherein one of Z or Z′ is present.

7. The compound of claim 1, wherein all of the ribonucleotides in (N)x or (N′)y or both are unmodified in their sugar residues.

8. The compound of claim 1, wherein at least one ribonucleotide is modified in its sugar residue.

9. The compound of claim 8, wherein the modification comprises a modification at the 2′ position of the sugar residue.

10. The compound of claim 9, wherein the modification at the 2′ position of the sugar residue results in the presence of a moiety selected from the group comprising amino, fluoro, alkoxy and alkyl groups.

11. The compound of claim 10, wherein the alkoxy group is a methoxy (2′-O-methyl).

12. The compound of claim 1, wherein in alternating ribonucleotides in both the antisense strand and the sense strand their sugar residues are modified.

13. The compound of claim 12, wherein each of the modified alternating ribonucleotides is modified at the 2′ position of its sugar moiety.

14. A composition comprising a double-stranded siRNA oligoribonucleotide compound of claim 1 and a carrier.

15. The compound of claim 13, wherein each of the ribonucleotides at the 5′ terminus and at the 3′ terminus of the antisense strand is modified in its sugar residue, and each ribonucleotide at the 5′ terminus and at the 3′ terminus of the sense strand is unmodified in its sugar residue.

16. A double-stranded RNA compound having the structure:


5′UUCCAGAUCAUCUCGCUCU3′(SEQ ID NO: 22) antisense strand



3′AAGGUCUAGUAGAGCGAGA5′(SEQ ID NO: 4) sense strand

wherein each of A, C, U and G is an unmodified or 2′-O-Methyl sugar modified ribonucleotide and each consecutive ribonucleotide is joined to the next ribonucleotide by a phosphodiester bond; and
wherein alternating ribonucleotides in both the antisense strand and the sense strand are 2′-O-Methyl sugar modified ribonucleotides, a 2-O-Methyl sugar modified ribonucleotide is present at both the 5′ terminus and the 3′ terminus of the antisense strand and an unmodified ribonucleotide is present at both the 5′ terminus and the 3′ terminus of the sense strand.