RNAi Modulation Of TGF-BETA And Therapeutic Uses Thereof

Abstract

The present invention concerns methods of treatment using transforming growth factor beta (TGF-beta) modulators. More specifically, the invention concerns methods of treating disorders associated with undesirable TGF-beta signaling, by administering short interfering RNA which down-regulate the expression of TGF-beta, and agents useful therein.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No. 60/782,829, filed Mar. 16, 2006, and U.S. Ser. No. 11/724,790, filed Mar. 15, 2007, which are hereby incorporated by reference in their entirety.

TECHNICAL FIELD

The present invention concerns methods of treatment using transforming growth factor beta (TGF-beta) modulators. More specifically, the invention concerns methods of treating disorders associated with undesirable TGF-beta signaling, by administering short interfering RNA which down-regulate the expression of TGF-beta, and agents useful therein.

BACKGROUND

RNA interference or “RNAi” is a term initially coined by Fire and co-workers to describe the observation that double-stranded RNA (dsRNA) can block gene expression when it is introduced into worms (Fire et al., Nature 391:806-811, 1998). Short dsRNA directs gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and has provided a new tool for studying gene function. RNAi has been suggested as a method of developing a new class of therapeutic agents. However, to date, these have remained mostly as suggestions with no demonstrate proof that RNAi can be used therapeutically.

Transforming growth factor-beta (TGF-beta) isoforms (−1, −2, & −3) are potent cytokines that act in autocrine and paracrine fashion to effect a broad spectrum of biological processes, including proliferation, differentiation, apoptosis, and extracellular matrix production. TGF-beta exerts its biological effects via binding to TGF-beta receptors (types I, II, & III). The local over-expression of TGF-beta in the kidney, liver, or lung mediates the pathophysiology observed in diabetic nephropathy, chronic liver disease, and pulmonary fibrosis, respectively. TGF-beta1 is up-regulated in patients with diabetic nephropathy (for both type 1 or type 2 diabetes) and in animal models of the disease. Antibodies to TGF-beta have been shown to prevent disease in a mouse genetic model of type 2 diabetes (db/db mouse) and antisense targeting a conserved sequence in TGF-beta RNA has been shown to prevent disease in a streptozotocin-diabetic mouse model.

About 100,000 diabetic patients per year are treated for kidney disease in U.S. with health costs of $5.1 billion per year in the U.S. Diabetic nephropathy is the leading cause of end-stage renal disease in the industrialized world. Almost 40% of all new patients with renal failure admitted to renal replacement programs in the U.S have diabetic kidney disease. Albuminuria, proteinuria, serum creatinine, as well as circulating TGF-beta1 plasma levels, can be used as markers for efficacy determination in therapeutic evaluation.

Liver disease affects all age groups and both genders. The condition can be acute or chronic. The major causes of liver diseases in the United States are viruses (hepatitis A, B, C) and alcohol abuse. However, congenital, autoimmune and drug-induced causes are also significant contributors to the origin of liver diseases. Liver diseases disturb hepatic functions as a result of destruction of functional liver tissue and development of fibrosis (scarring), which blocks blood flow through the liver and causes portal hypertension (pressure in the portal vein). Blood flow then seeks an alternative route, leading to dilated swollen veins (varices) in the esophagus that may hemorrhage. Liver disease and portal hypertension also alter kidney function by causing retention of salt and water (ascites), and can induce renal failure (hepatorenal syndrome) and altered mental state (coma). The primary cytokine involved in tissue scaring in chronic liver disease is TGF-beta1. Recently it has been shown in a rat model of liver fibrosis that blocking TGF-beta1 can lead to improvement in liver histology. Further, in chronic Hepatitis C patients who have responded to interferon alpha, decreased levels of TGF-beta1 are associated with improvements in liver fibrosis.

TGF-beta1 has also been implicated in Idiopathic Pulmonary Fibrosis. Similar to liver disease, the mechanisms of action of TGF-beta1 in pulmonary fibrosis involves both induction and inhibition of the degradation of extracellular matrix proteins, leading to the formation of scar tissue. TGF-beta1 mediated cell signaling, primarily at the local site of connective tissue, is anabolic and leads to pulmonary fibrosis and angiogenesis, strongly indicating that TGF-beta1 may be involved in the repair of tissue injury caused by burns, trauma, or surgery. Pulmonary fibrosis, also called Interstitial Lung Disease (ILD), is a broad category of lung diseases that includes more than 130 disorders which are characterized by scarring of the lungs. ILD accounts for 15% of the cases seen by pulmonologists. Some of the interstitial lung disorders include: Idiopathic pulmonary fibrosis, Hypersensitivity pneumonitis, Sarcoidosis, Eosinophilic granuloma, Wegener's granulomatosis, Idiopathic pulmonary hemosiderosis, and Bronchiolitis obliterans. In ILD, scarring or fibrosis occurs as a result of either an injury or an autoimmune process. Approximately 70% of ILD have no identifiable cause and are therefore termed “idiopathic pulmonary fibrosis.” Some of the known causes include occupational and environmental exposure, dust (silica, hard metal dusts), organic dust (bacteria, animal proteins), gases and fumes, drugs, poisons, chemotherapy medications, radiation therapy, infections, connective tissue disease, systemic lupus erythematosus, and rheumatoid arthritis. In its severest form, ILD can lead to death, which is often caused by respiratory failure due to hypoxemic, right-heart failure, heart attack, stroke, blood clot (embolism) in the lungs, or lung infection brought on by the disease.

The use of small interfering nucleic acid molecules targeting transforming growth factor beta (TGF-beta) genes provides a class of novel therapeutic agents that can be used in the treatment of various diseases and conditions associated with undesired TGF-beta signaling, including diabetic nephropathy, chronic liver disease, pulmonary fibrosis, hematopoietic reconstitution, and any other inflammatory, respiratory, autoimmune, and/or proliferative disease, condition, or trait that responds to the level of TGF-beta in a cell, subject or organism, and particularly idiopathic pulmonary fibrosis.

SUMMARY

The present invention is based on the in vitro demonstration that TGF-beta expression can be inhibited by iRNA agents, and the identification of potent iRNA agents from the TGF-beta gene that can reduce RNA levels and protein levels of TGF-beta in cells, and particularly in an organism. Based on these findings, the present invention provides specific compositions and methods that are useful in reducing TGF-beta mRNA levels and TGF-beta protein levels in cells in vitro as well as in a subject in vivo, e.g., a mammal, such as a human. These compositions are particularly useful in the manufacturing of pharmaceutical compositions for the treatment of, and ultimately in methods to treat, subjects having or at risk of developing a disease or disorder associated with undesired TGF-beta signaling such as, for example, idiopathic pulmonary fibrosis.

The present invention specifically provides methods of reducing the levels of a TGF-beta mRNA in a cell of a subject, or of TGF-beta protein secreted by a cell of a subject, comprising the step of administering an iRNA agent to said subject, wherein the iRNA agent comprises an antisense strand consisting of 15 to 30 nucleotides and having at least 15 or more contiguous nucleotides complementary to a mammalian TGF-beta mRNA, and a sense strand consisting of 15 to 30 nucleotides and having at least 15 or more contiguous nucleotides complementary to said antisense strand. Said iRNA agent may mediate the cleavage of a TGF-beta mRNA within the target sequence of an iRNA agent selected from the group of: AL-DP-6837 to AL-DP-6864 and AD-14419 to AD-14638. In one embodiment, said iRNA agent comprises 15 or more contiguous nucleotides from an iRNA agent selected from the group of: AL-DP-6837 to AL-DP-6864, AL-DP-6140 to AL-DP-6151, AL-DP-6262 to AL-DP-6277 and AD-14419 to AD-14638. In a further embodiment, said iRNA agent is one of the iRNA agents selected from the group of: AL-DP-6837 to AL-DP-6864, AL-DP-6140 to AL-DP-6151, AL-DP-6262 to AL-DP-6277 and AD-14419 to AD-14638. In further embodiments, the iRNA agents mediates the cleavage of a TGF-beta mRNA within the target sequence of an iRNA agent, comprises 15 or more contiguous nucleotides from an iRNA agent, or is an iRNA agent, selected from one of the following groups: the 20%-group, the 30%-group, the 40%-group, the 50%-group, the 60%-group, the 70%-group, the 80%-group, or the 90%-group, as defined below. Said iRNA agent may be administered to a subject, wherein administration may comprise pulmonary administration. As a result of the inventive method, the level of TGF-beta protein and/or TGF-beta mRNA may be reduced by at least 20%.

In another aspect, the invention provides isolated iRNA agents, comprising an antisense strand consisting of 15 to 30 nucleotides and having at least 15 or more contiguous nucleotides complementary to a mammalian TGF-beta mRNA, and a sense strand consisting of 15 to 30 nucleotides and having at least 15 or more contiguous nucleotides complementary to said antisense strand. In one embodiment, said iRNA agent mediates the cleavage of a TGF-beta mRNA within the target sequence of an iRNA agent selected from one of the following groups: the group of AL-DP-6837 to AL-DP-6864 and AD-14419 to AD-14638, the 20%-group, the 30%-group, the 40%-group, the 50%-group, the 60%-group, the 70%-group, the 80%-group, or the 90%-group, as defined below. In a further embodiment, said iRNA agent comprises 15 or more contiguous nucleotides from an iRNA agent selected from one of the following groups: the group of AL-DP-6837 to AL-DP-6864, AL-DP-6140 to AL-DP-6151, AL-DP-6262 to AL-DP-6277 and AD-14419 to AD-14638 the 20%-group, the 30%-group, the 40%-group, the 50%-group, the 60%-group, the 70%-group, the 80%-group, or the 90%-group, as defined below. More specifically, said iRNA agent may be an iRNA agent selected from one of the following groups of: AL-DP-6837 to AL-DP-6864, AL-DP-6140 to AL-DP-6151, AL-DP-6262 to AL-DP-6277 and AD-14419 to AD-14638; the 20%-group, the 30%-group, the 40%-group, the 50%-group, the 60%-group, the 70%-group, the 80%-group, or the 90%-group, as defined below. The iRNA agent may further comprise a non-nucleotide moiety. Furthermore, the sense and/or antisense strand may be stabilized against nucleolytic degradation. The iRNA agent may further comprise at least one 3′-overhang, wherein said 3′-overhang comprises from 1 to 6 nucleotides. Also, the iRNA agent may comprise a phosphorothioate at the first internucleotide linkage at the 5′ end of the antisense and/or sense sequence, and optionally a further phosphorothioate at the first internucleotide linkage at the 3′ end of the antisense and/or sense sequence. The iRNA agent may comprise a 2′-modified nucleotide, preferably selected from the group consisting of: 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP), 2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl (2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), and 2′-O—N-methylacetamido (2′-O-NMA).

In another aspect, the instant invention features a method of reducing the levels of a TGF-beta mRNA in a cell, or of TGF-beta protein secreted by a cell, comprising contacting the cell with an iRNA agent of the invention.

In yet another aspect, the instant invention provides a vector encoding an iRNA agent of the invention.

In yet another aspect, the instant invention provides a cell comprising an iRNA agent or a vector of the invention.

In yet another aspect, the a method of making an iRNA agent of the invention is provided, the method comprising the synthesis of the iRNA agent, wherein the sense and antisense strands comprise at least one modification that stabilizes the iRNA agent against nucleolytic degradation.

In yet another aspect, the instant invention provides a pharmaceutical composition comprising an iRNA agent of the invention and a pharmaceutically acceptable carrier.

In yet another aspect, the instant invention provides a method of treating a human diagnosed as having or at risk for developing a disease or disorder associated with undesired TGF-beta signaling, comprising administering to a subject in need of such treatment a therapeutically effective amount of an iRNA agent of the invention. In one embodiment, the human is diagnosed as having or at risk for having idiopathic pulmonary fibrosis, diabetic nephropathy or chronic liver disease.

Table 1 provides exemplary iRNA agents of the invention.

TABLE 1
Oligonucleotide sequences of siRNAs specific for TGF-beta
Position of
target			SEQ		SEQ
sequence in	Duplex		ID	antisense	ID
NM_000660.3	identifier	sense strand sequence1	NO:	strand sequence1	NO:
1186-1208	AL-DP-6837	ggucacccgcgugcuaaugTT	1	cauuagcacgcgggugaccTT	2
1186-1208	AL-DP-6140	ggumcmacmcmcmgcmgumgcmumaaumgTT	3	cmauumagcmacgcgggugaccTT	4
1184-1206	AL-DP-6838	gaggucacccgcgugcuaaTT	5	uuagcacgcgggugaccucTT	6
1184-1206	AL-DP-6141	gaggumcmacmcmcmgcmgumgcmumaaTT	7	uumagcmacgcgggugaccucTT	8
1112-1134	AL-DP-6839	agcacccgcgaccggguggTT	9	ccacccggucgcgggugcuTT	10
1112-1134	AL-DP-6142	agcmacmcmcmgcmgacmcmgggumggTT	11	ccmacccggucgcgggugcuTT	12
1797-1819	AL-DP-6840	uccacgagcccaagggcuaTT	13	uagcccuugggcucguggaTT	14
1797-1819	AL-DP-6143	umcmcmacmgagcmcmcmaagggcmumaTT	15	umagcccuugggcucguggaTT	16
444-466	AL-DP-6841	auuccggaccagcccucggTT	17	ccgagggcugguccggaauTT	18
444-466	AL-DP-6144	aumumcmcmggacmcmagcmcmcmumcmggTT	19	ccgagggcugguccggaauTT	20
1185-1207	AL-DP-6842	aggucacccgcgugcuaauTT	21	auuagcacgcgggugaccuTT	22
1185-1207	AL-DP-6145	aggumcmacmcmcmgcmgumgcmumaaumTT	23	auumagcmacgcgggugaccuTT	24
445-467	AL-DP-6843	uuccggaccagcccucgggTT	25	cccgagggcugguccggaaTT	26
445-467	AL-DP-6146	umumcmcmggacmcmagcmcmcmumcmgggTT	27	cccgagggcugguccggaaTT	28
1104-1126	AL-DP-6844	uguacaacagcacccgcgaTT	29	ucgcgggugcuguuguacaTT	30
1104-1126	AL-DP-6147	umgumacmaacmagcmacmcmcmgcmgaTT	31	ucgcgggugcuguugumacmaTT	32
1189-1211	AL-DP-6845	cacccgcgugcuaauggugTT	33	caccauuagcacgcgggugTT	34
1189-1211	AL-DP-6148	cmacmcmcmgcmgcmgcmumaaumggumgTT	35	cmaccmauumagcmacgcgggugTT	36
446-468	AL-DP-6846	uccggaccagcccucgggaTT	37	ucccgagggcugguccggaTT	38
446-468	AL-DP-6149	umcmcmggacmcmagcmcmcmumcmgggaTT	39	ucccgagggcugguccggaTT	40
1787-1809	AL-DP-6847	uggaaguggauccacgagcTT	41	gcucguggauccacuuccaTT	42
1787-1809	AL-DP-6150	umggaagumggaumcmcmacmgagcmTT	43	gcucguggauccmacuuccmaTT	44
1806-1828	AL-DP-6848	ccaagggcuaccaugccaaTT	45	uuggcaugguagcccuuggTT	46
1806-1828	AL-DP-6151	cmcmaagggcmumacmcmaumgcmcmaaTT	47	uuggcmauggumagcccuuggTT	48
1187-1209	AL-DP-6849	gucacccgcgugcuaauggTT	49	ccauuagcacgcgggugacTT	50
1187-1209	AL-DP-6262	gumcmacmcmcmgcmgumgcmumaaumggTT	51	ccmauumagcmacgcgggugacTT	52
1106-1128	AL-DP-6850	uacaacagcacccgcgaccTT	53	ggucgcgggugcuguuguaTT	54
1106-1128	AL-DP-6263	umacmaacmagcmacmcmcmgcmgacmcmTT	55	ggucgcgggugcuguugumaTT	56
1804-1826	AL-DP-6851	gcccaagggcuaccaugccTT	57	ggcaugguagcccuugggcTT	58
1804-1826	AL-DP-6264	gcmcmcmaagggcmumacmcmaumgcmcmTT	59	ggcmauggumagcccuugggcTT	60
1790-1812	AL-DP-6852	aaguggauccacgagcccaTT	61	ugggcucguggauccacuuTT	62
1790-1812	AL-DP-6265	aagumggaumcmcmacmgagcmcmcmaTT	63	ugggcucguggauccmacuuTT	64
239-261	AL-DP-6853	gggaggagggacgagcuggTT	65	ccagcucgucccuccucccTT	66
239-261	AL-DP-6266	gggaggagggacmgagcmumggTT	67	ccmagcucgucccuccucccTT	68
1107-1129	AL-DP-6854	acaacagcacccgcgaccgTT	69	cggucgcgggugcuguuguTT	70
1107-1129	AL-DP-6267	acmaacmagcmacmcmcmgcmgacmcmgTT	71	cggucgcgggugcuguuguTT	72
1807-1829	AL-DP-6855	caagggcuaccaugccaacTT	73	guuggcaugguagcccuugTT	74
1807-1829	AL-DP-6268	cmaagggcmumacmcmaumgcmcmaacmTT	75	guuggcmauggumagcccuugTT	76
447-469	AL-DP-6356	ccggaccagcccucgggagTT	77	cucccgagggcugguccggTT	78
447-469	AL-DP-6269	cmcmggacmcmagcmcmcmumcmgggagTT	79	cucccgagggcugguccggTT	80
1711-1733	AL-DP-6857	caacuauugcuucagcuccTT	81	ggagcugaagcaauaguugTT	82
1711-1733	AL-DP-6270	cmaacmumaumumgcmumumcmagcmumcmcmTT	83	ggagcugaagcmaaumaguugTT	84
l748-1770	AL-DP-6858	gugcggcagcuguacauugTT	85	caauguacagcugccgcacTT	86
1748-1770	AL-DP-6271	gumgcmggcmagcmumgumacmaumumgTT	87	cmaaugumacmagcugccgcmacTT	88
1788-1810	AL-DP-6859	ggaaguggauccacgagccTT	89	ggcucguggauccacuuccTT	90
1788-1810	AL-DP-6272	ggaagumggaumcmcmacmgagcmcmTT	91	ggcucguggauccmacuuccTT	92
1789-1811	AL-DP-6860	gaaguggauccacgagcccTT	93	gggcucguggauccacuucTT	94
1789-1811	AL-DP-6273	gaagumggaumcmcmacmgagcmcmcmTT	95	gggcucguggauccmacuucTT	96
1798-1820	Al-DP-6861	ccacgagcccaagggcuacTT	97	guagcccuugggcucguggTT	98
1798-1820	AL-DP-6274	cmcmacmgagcmcmcmaagggcmumacmTT	99	gumagcccuugggcucguggTT	100
1802-1824	AL-DP-6862	gagcccaagggcuaccaugTT	101	caugguagcccuugggcucTT	102
1802-1824	AL-DP-6275	gagcmcmcmaagggcmumacmcmaumgTT	103	cmauggumagcccuugggcucTT	104
1803-1825	AL-DP-6863	agcccaagggcuaccaugcTT	105	gcaugguagcccuugggcuTT	106
1803-1825	AL-DP-6276	agcmcmcmaagggcmumacmcmaumgcmTT	107	gcmauggumagcccuugggcuTT	108
1926-1948	AL-DP-6864	cgugcugcgugccgcaggcTT	109	gccugcggcacgcagcacgTT	110
1926-1948	AL-DP-6277	cmgumgcmumgcmgumgcmcmgcmaggcmTT	111	gccugcggcmacgcmagcmacgTT	112
1a, g, c, u: ribonucleotide 5′-monophosphates (except where in 5′-most position, see below);
cm: 2′-O-methyl-cytidine-5′-monophosphate (except where in 5′-most position, see below);
um: 2′-O-methyl-uridine-5′-monophosphate (except where in 5′-most position, see below);
T: deoxythymidine 5′-monophosphate;
T: deoxythymidine 5′-monothiophosphate;
all sequences given 5′ → 3′; due to synthesis procedures, the 5′-most nucleic acid is a nucleoside, i.e. does not bear a 5′-monophosphate group

The iRNA agents of the invention can either contain only naturally occurring ribonucleotide subunits, or can be synthesized so as to contain one or more modifications to the base, the sugar or the phosphate group of one or more of the ribonucleotide 5′-monophosphate subunits that is included in the agent. The iRNA agent can be further modified so as to be attached to a ligand that is selected to improve stability, distribution or cellular uptake of the agent, e.g. cholesterol. The iRNA agents can further be in isolated form or can be part of a pharmaceutical composition used for the methods described herein, particularly as a pharmaceutical composition formulated for delivery to the lung or formulated for parenteral administration. The pharmaceutical compositions can contain one or more iRNA agents, and in some embodiments, will contain two or more iRNA agents, each one directed to a different segment of a TGF-beta gene or a different TGF-beta gene.

In a preferred embodiment, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 20% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, AD-14635, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, AL-DP-6837, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, AD-14637, AL-DP-6840, AL-DP-6860, AL-DP-6861, AL-DP-6849, AL-DP-6272, AL-DP-6271, AL-DP-6847, AL-DP-6863, AD-14447, AD-14451, AD-14471, AD-14484, AD-14487, AD-14498, AD-14523, AD-14527, AD-14529, AD-14539, AD-14541, AD-14558, AD-14561, AD-14573, AD-14589, AD-14596, AD-14605, AD-14615, AD-14626, AD-14630, AL-DP-6846, AL-DP-6853, AL-DP-6856, AL-DP-6864, AL-DP-6844, AL-DP-6143, AD-14432, AD-14480, AD-14485, AD-14488, AD-14499, AD-14504, AD-14516, AD-14518, AD-14520, AD-14547, AD-14572, AD-14577, AD-14580, AD-14583, AD-14584, AD-14618, AD-14621, AD-14625, AL-DP-6276, AD-14435, AD-14445, AD-14450, AD-14456, AD-14466, AD-14475, AD-14489, AD-14492, AD-14511, AD-14535, AD-14536, AD-14538, AD-14553, AD-14560, AD-14562, AD-14576, AD-14581, AD-14586, AD-14627, AL-DP-6150 AL-DP-6850, AD-14433, AD-14472, AD-14478, AD-14493, AD-14510, AD-14544, AD-14566, AD-14570, AD-14575, AD-14593, AD-14613, AL-DP-6269, AL-DP-6270, AL-DP-6147, AL-DP-6262, AL-DP-6841, AL-DP-6274, AL-DP-6843, AL-DP-6145, AD-14424, AD-14442, AD-14444, AD-14446, AD-14454, AD-14525, AD-14543, AD-14571, AD-14606, AD-14611, AD-14616, AD-14617, AD-14619, and AD-14638 (the “20% group”).

More preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 30% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, AD-14635, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, AL-DP-6837, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, AD-14637, AL-DP-6840, AL-DP-6860, AL-DP-6861, AL-DP-6849, AL-DP-6272, AL-DP-6271, AL-DP-6847, AL-DP-6863, AD-14447, AD-14451, AD-14471, AD-14484, AD-14487, AD-14498, AD-14523, AD-14527, AD-14529, AD-14539, AD-14541, AD-14558, AD-14561, AD-14573, AD-14589, AD-14596, AD-14605, AD-14615, AD-14626, AD-14630, AL-DP-6846, AL-DP-6853, AL-DP-6856, AL-DP-6864, AL-DP-6844, AL-DP-6143, AD-14432, AD-14480, AD-14485, AD-14488, AD-14499, AD-14504, AD-14516, AD-14518, AD-14520, AD-14547, AD-14572, AD-14577, AD-14580, AD-14583, AD-14584, AD-14618, AD-14621, AD-14625, AL-DP-6276, AD-14435, AD-14445, AD-14450, AD-14456, AD-14466, AD-14475, AD-14489, AD-14492, AD-14511, AD-14535, AD-14536, AD-14538, AD-14553, AD-14560, AD-14562, AD-14576, AD-14581, AD-14586, AD-14627, AL-DP-6150 AL-DP-6850, AD-14433, AD-14472, AD-14478, AD-14493, AD-14510, AD-14544, AD-14566, AD-14570, AD-14575, AD-14593, and AD-14613 (the “30% group”).

More preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 40% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, AD-14635, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, AL-DP-6837, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, AD-14637, AL-DP-6840, AL-DP-6860, AL-DP-6861, AL-DP-6849, AL-DP-6272, AL-DP-6271, AL-DP-6847, AL-DP-6863, AD-14447, AD-14451, AD-14471, AD-14484, AD-14487, AD-14498, AD-14523, AD-14527, AD-14529, AD-14539, AD-14541, AD-14558, AD-14561, AD-14573, AD-14589, AD-14596, AD-14605, AD-14615, AD-14626, AD-14630, AL-DP-6846, AL-DP-6853, AL-DP-6856, AL-DP-6864, AL-DP-6844, AL-DP-6143, AD-14432, AD-14480, AD-14485, AD-14488, AD-14499, AD-14504, AD-14516, AD-14518, AD-14520, AD-14547, AD-14572, AD-14577, AD-14580, AD-14583, AD-14584, AD-14618, AD-14621, AD-14625, AL-DP-6276, AD-14435, AD-14445, AD-14450, AD-14456, AD-14466, AD-14475, AD-14489, AD-14492, AD-14511, AD-14535, AD-14536, AD-14538, AD-14553, AD-14560, AD-14562, AD-14576, AD-14581, AD-14586, and AD-14627 (the “40% group”).

More preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 50% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, AD-14635, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, AL-DP-6837, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, AD-14637, AL-DP-6840, AL-DP-6860, AL-DP-6861, AL-DP-6849, AL-DP-6272, AL-DP-6271, AL-DP-6847, AL-DP-6863, AD-14447, AD-14451, AD-14471, AD-14484, AD-14487, AD-14498, AD-14523, AD-14527, AD-14529, AD-14539, AD-14541, AD-14558, AD-14561, AD-14573, AD-14589, AD-14596, AD-14605, AD-14615, AD-14626, AD-14630, AL-DP-6846, AL-DP-6853, AL-DP-6856, AL-DP-6864, AL-DP-6844, AL-DP-6143, AD-14432, AD-14480, AD-14485, AD-14488, AD-14499, AD-14504, AD-14516, AD-14518, AD-14520, AD-14547, AD-14572, AD-14577, AD-14580, AD-14583, AD-14584, AD-14618, AD-14621, and AD-14625 (the “50% group”).

Yet more preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 60% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, AD-14635, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, AL-DP-6837, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, AD-14637, AL-DP-6840, AL-DP-6860, AL-DP-6861, AL-DP-6849, AL-DP-6272, AL-DP-6271, AL-DP-6847, AL-DP-6863, AD-14447, AD-14451, AD-14471, AD-14484, AD-14487, AD-14498, AD-14523, AD-14527, AD-14529, AD-14539, AD-14541, AD-14558, AD-14561, AD-14573, AD-14589, AD-14596, AD-14605, AD-14615, AD-14626, and AD-14630 (the “60% group”).

Yet more preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 70% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, AD-14635, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, AL-DP-6837, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, and AD-14637 (the “70% group”).

Yet more preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 80% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, AD-14633, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, AL-DP-6862, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, and AD-14635 (the “80% group”).

Yet more preferably, an iRNA agent of the invention reduces the level of TGF-beta protein secreted by, and/or TGF-beta mRNA found inside, a cell by at least 90% or more. Thus, the iRNA agent may preferably be chosen from the group of AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, and AD-14633 (the “90% group”).

The present invention provides methods for reducing the level of TGF-beta protein and TGF-beta mRNA in a cell. Such methods optionally comprise the step of administering one of the iRNA agents of the present invention to a subject as further described below. The present methods utilize the cellular mechanisms involved in RNA interference to selectively degrade the TGF-beta mRNA in a cell and are comprised of the step of contacting a cell with one of the TGF-beta iRNA agents of the present invention. Such methods can be performed directly on a cell or can be performed on a mammalian subject by administering to a subject one of the iRNA agents/pharmaceutical compositions of the present invention. Reduction of TGF-beta mRNA in a cell results in a reduction in the amount of TGF-beta protein produced, and in an organism (as shown in the Examples).

The methods and compositions of the invention, e.g., the methods and iRNA agent compositions can be used with any dosage and/or formulation described herein, as well as with any route of administration described herein.

In another aspect, the invention features a method for treating or preventing a disease or condition associated with undesired TGF-beta signaling in a subject. The method can include administering to the subject a composition of the invention under conditions suitable for the treatment or prevention of the disease or condition associated with undesired TGF-beta signaling in the subject, alone or in conjunction with one or more other therapeutic compounds.

In one embodiment, the iRNA agent is administered at or near the site of undesired TGF-beta signaling, e.g., direct injection at the site, or by a catheter or other placement device (e.g., an implant including a porous, non-porous, or gelatinous material). In another embodiment the iRNA agent is administered via pulmonary delivery, e.g. by inhalation, which may be nasal and/or oral.

In one embodiment, an iRNA agent is administered repeatedly. Administration of an iRNA agent can be carried out over a range of time periods. It can be administered hourly, daily, once every few days, weekly, or monthly. The timing of administration can vary from patient to patient, depending upon such factors as the severity of a patient's symptoms. For example, an effective dose of an iRNA agent can be administered to a patient once a month for an indefinite period of time, or until the patient no longer requires therapy. In addition, sustained release compositions containing an iRNA agent can be used to maintain a relatively constant dosage in the area of the target TGF-beta nucleotide sequences.

In another embodiment, an iRNA agent is delivered at a dosage on the order of about 0.00001 mg to about 3 mg per kg body weight of the subject to be treated, or preferably about 0.0001-0.001 mg per kg body weight, about 0.03-3.0 mg per kg body weight, about 0.1-3.0 mg per kg body weight or about 0.3-3.0 mg per kg body weight.

In another embodiment, an iRNA agent is administered prophylactically such as to prevent or slow the onset of a disease or disorder or condition associated with undesired TGF-beta signaling. For example, an iRNA can be administered to a patient who is susceptible to or otherwise at risk for such a disease or disorder.

In another aspect, a method of inhibiting TGF-beta expression is provided. One such method includes administering an effective amount of an iRNA agent including sense and antisense sequences capable of forming an RNA duplex. The sense sequence of the iRNA agent can include a nucleotide sequence substantially identical to a target sequence of about 19 to 23 nucleotides of TGF-beta mRNA, and the antisense sequence can include a nucleotide sequence complementary to a target sequence of about 19-23 nucleotides of TGF-beta mRNA.

In one aspect, methods of treating any disease or disorder associated with undesired TGF-beta signaling are provided.

In another aspect, a method of treating idiopathic pulmonary fibrosis is provided. One such method includes administering a therapeutically effective amount of an iRNA agent that includes sense and antisense sequences capable of forming an RNA duplex. The sense sequence can include a nucleotide sequence substantially identical to a target sequence of about 19 to 23 nucleotides of TGF-beta mRNA. The antisense sequence can include a nucleotide sequence complementary to a target sequence of about 19 to 23 nucleotides of TGF-beta mRNA.

In one embodiment, a human has been diagnosed with a disease or disorder associated with undesired TGF-beta signaling. In one embodiment, said disease or disorder is Interstitial Lung Disease (ILD). In a preferred embodiment, the human has been diagnosed with one of: Idiopathic pulmonary fibrosis, Hypersensitivity pneumonitis, Sarcoidosis, Eosinophilic granuloma, Wegener's granulomatosis, Idiopathic pulmonary hemosiderosis, and Bronchiolitis obliterans. In a particularly preferred embodiment, the human has been diagnosed with idiopathic pulmonary fibrosis.

In another aspect, the invention features a kit containing an iRNA agent of the invention. The iRNA agent of the kit can be chemically modified and can be useful for modulating the expression of a TGF-beta target gene in a cell, tissue or organism. In one embodiment, the kit contains more than one iRNA agent of the invention.

The details of one or more embodiments of the invention are set forth in the description below. Other features, objects, and advantages of the invention will be apparent from this description and from the claims. This application incorporates all cited references, patents, and patent applications by references in their entirety for all purposes.

DETAILED DESCRIPTION

For ease of exposition the term “nucleotide” or “ribonucleotide” is sometimes used herein in reference to one or more monomeric subunits of an RNA agent. It will be understood that the usage of the term “ribonucleotide” or “nucleotide” herein can, in the case of a modified RNA or nucleotide surrogate, also refer to a modified nucleotide, or surrogate replacement moiety, as further described below, at one or more positions.

An “RNA agent” as used herein, is an unmodified RNA, modified RNA, or nucleoside surrogate, all of which are described herein or are well known in the RNA synthetic art. While numerous modified RNAs and nucleoside surrogates are described, preferred examples include those which have greater resistance to nuclease degradation than do unmodified RNAs. Examples include those that have a 2′ sugar modification, a modification in a single strand overhang, such as a 3′ single strand overhang, or, particularly if single stranded, a 5′-modification which includes one or more phosphate groups or one or more analogs of a phosphate group.

An “iRNA agent” (abbreviation for “interfering RNA agent”) as used herein, is an RNA agent, which can down-regulate the expression of a target gene, e.g., a TGF-beta gene, and preferably a human TGF-beta gene. While not wishing to be bound by theory, an iRNA agent may act by one or more of a number of mechanisms, including post-transcriptional cleavage of a target mRNA sometimes referred to in the art as RNA interference or RNAi, or pre-transcriptional or pre-translational mechanisms. An iRNA agent can be a double stranded (ds) iRNA agent.

A “ds iRNA agent” (abbreviation for “double stranded iRNA agent”), as used herein, is an iRNA agent which includes more than one, and preferably two, strands in which interchain hybridization can form a region of duplex structure. A “strand” herein refers to a contiguous sequence of nucleotides (including non-naturally occurring or modified nucleotides). The two or more strands may be, or each form a part of, separate molecules, or they may be covalently interconnected, e.g. by a linker, e.g. a polyethylene glycol linker, to form but one molecule. At least one strand can include a region which is sufficiently complementary to a target RNA. Such strand is termed the “antisense strand”. A second strand comprised in the dsRNA agent that comprises a region complementary to the antisense strand is termed the “sense strand”. However, a ds iRNA agent can also be formed from a single RNA molecule which is, at least partly; self-complementary, forming, e.g., a hairpin or panhandle structure, including a duplex region. In such case, the term “strand” refers to one of the regions of the RNA molecule that is complementary to another region of the same RNA molecule.

Although, in mammalian cells, long ds iRNA agents can induce the interferon response which is frequently deleterious, short ds iRNA agents do not trigger the interferon response, at least not to an extent that is deleterious to the cell and/or host. The iRNA agents of the present invention include molecules which are sufficiently short that they do not trigger a deleterious interferon response in mammalian cells. Thus, the administration of a composition of an iRNA agent (e.g., formulated as described herein) to a mammalian cell can be used to silence expression of an TGF-beta gene while circumventing a deleterious interferon response. Molecules that are short enough that they do not trigger a deleterious interferon response are termed siRNA agents or siRNAs herein. “siRNA agent” or “siRNA” as used herein, refers to an iRNA agent, e.g., a ds iRNA agent, that is sufficiently short that it does not induce a deleterious interferon response in a human cell, e.g., it has a duplexed region of less than 60 but preferably less than 50, 40, or 30 nucleotide pairs.

The isolated iRNA agents described herein, including ds iRNA agents and siRNA agents, can mediate silencing of a gene, e.g., by RNA degradation. For convenience, such RNA is also referred to herein as the RNA to be silenced, or target RNA. Such a gene is also referred to as a target gene. Preferably, the RNA to be silenced is a gene product of a TGF-beta gene.

As used herein, the phrases “mediate RNAi”, “silence a TGF-beta gene”, “reducing the level of TGF-beta mRNA” and/or “reducing the level of TGF-beta protein” all refer to the at least partial suppression of the expression of the TGF-beta gene, as manifested, e.g., by a reduction of the amount of mRNA transcribed from the TGF-beta gene which may be isolated from a first cell or group of cells in which the TGF-beta gene is transcribed and which has or have been treated such that the expression of the TGF-beta gene is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has or have not been so treated (control cells). Alternatively, the degree of inhibition may be given in terms of a reduction of a parameter that is functionally linked to TGF-beta gene transcription, e.g. the amount of protein encoded by the TGF-beta gene which is secreted by a cell, or the number of cells displaying a certain phenotype associated with TGF-beta signalling. The degree of inhibition is usually expressed in terms of

$\frac{\left(\mathrm{mRNA}\mathrm{in}\mathrm{control}\mathrm{cells}\right)-\left(\mathrm{mRNA}\mathrm{in}\mathrm{treated}\mathrm{cells}\right)}{\left(\mathrm{mRNA}\mathrm{in}\mathrm{control}\mathrm{cells}\right)}·100\%$

(“mRNA” may be replaced by another parameter used to assess TGF-beta gene expression, where applicable)

For example, in certain instances, expression of the TGF-beta gene is suppressed by at least about 20%, 25%, 35%, or 50% by administration of the double-stranded oligonucleotide of the invention. In a preferred embodiment, the TGF-beta gene is suppressed by at least about 60%, 70%, or 80% by administration of the double-stranded oligonucleotide of the invention. In a more preferred embodiment, the TGF-beta gene is suppressed by at least about 85%, 90%, or 95% by administration of the double-stranded oligonucleotide of the invention. In a most preferred embodiment, the TGF-beta gene is suppressed by at least about 98%, 99% or more by administration of the double-stranded oligonucleotide of the invention.

In principle, TGF-beta gene silencing may be determined in any cell expressing the target, either constitutively or by genomic engineering, and by any appropriate assay. However, when a reference is needed in order to determine whether a given siRNA inhibits the expression of the TGF-beta gene by a certain degree and therefore is encompassed by the instant invention, the assay provided in the Examples below shall serve as such reference.

As used herein, and unless otherwise indicated, the term “complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for example, be stringent conditions, where stringent conditions may include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50° C. or 70° C. for 12-16 hours followed by washing. Other conditions, such as physiologically relevant conditions as may be encountered inside an organism, can apply. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides.

This includes base-pairing of the oligonucleotide or polynucleotide comprising the first nucleotide sequence to the oligonucleotide or polynucleotide comprising the second nucleotide sequence over the entire length of the first and second nucleotide sequence. Such sequences can be referred to as “fully complementary” with respect to each other herein. However, where a first sequence is referred to as “substantially complementary” with respect to a second sequence herein, the two sequences can be fully complementary, or they may form one or more, but preferably not more than 4, 3 or 2 mismatched base pairs upon hybridization, while retaining the ability to hybridize under the conditions most relevant to their ultimate application. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, a dsRNA comprising one oligonucleotide 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, may yet be referred to as “fully complementary” for the purposes of the invention.

“Complementary” sequences, as used herein, may also include, or be formed entirely from, non-Watson-Crick base pairs and/or base pairs formed from non-natural and modified nucleotides, in as far as the above requirements with respect to their ability to hybridize are fulfilled.

The terms “complementary”, “fully complementary” and “substantially complementary” herein may be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between the antisense strand of a dsRNA and a target sequence, as will be understood from the context of their use.

As used herein, “essentially identical” when used referring to a first nucleotide sequence in comparison to a second nucleotide sequence means that the first nucleotide sequence is identical to the second nucleotide sequence except for up to one, two or three nucleotide substitutions (e.g. adenosine replaced by uracil).

As used herein, a “subject” refers to a mammalian organism undergoing treatment for a disorder associated with undesired TGF-beta signaling, such as undergoing treatment prophylactically or therapeutically to prevent TGF-beta production. The subject can be any mammal, such as a primate, cow, horse, mouse, rat, dog, pig, goat. In the preferred embodiment, the subject is a human.

As used herein, “target sequence” refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a TGF-beta gene, including mRNA that is a product of RNA processing of a primary transcription product.

As used herein, treating a disorder associated with undesired TGF-beta signaling refers to the amelioration of any biological or pathological endpoints that 1) is mediated in part by the unwanted expression or over expression of TGF-beta in the subject and 2) whose outcome can be affected by reducing the level of TGF-beta gene products present.

As used herein, the phrases “therapeutically effective amount” and “prophylactically effective amount” refer to an amount that provides a therapeutic benefit in the treatment, prevention, or management of pain or an overt symptom of pain. The specific amount that is therapeutically effective can be readily determined by ordinary medical practitioner, and may vary depending on factors known in the art, such as, e.g. the type of pain, the patient's history and age, the stage of pain, and the administration of other anti-pain agents.

As used herein, a “pharmaceutical composition” comprises a pharmacologically effective amount of a dsRNA and a pharmaceutically acceptable carrier. As used herein, “pharmacologically effective amount,” “therapeutically effective amount” or simply “effective amount” refers to that amount of an RNA effective to produce the intended pharmacological, therapeutic or preventive result. For example, if a given clinical treatment is considered effective when there is at least a 25% reduction in a measurable parameter associated with a disease or disorder, a therapeutically effective amount of a drug for the treatment of that disease or disorder is the amount necessary to effect at least a 25% reduction in that parameter.

The term “pharmaceutically acceptable carrier” refers to a carrier for administration of a therapeutic agent. Such carriers include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. The term specifically excludes cell culture medium. For drugs administered orally, pharmaceutically acceptable carriers include, but are not limited to pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavoring agents, coloring agents and preservatives. Suitable inert diluents include sodium and calcium carbonate, sodium and calcium phosphate, and lactose, while corn starch and alginic acid are suitable disintegrating agents. Binding agents may include starch and gelatin, while the lubricating agent, if present, will generally be magnesium stearate, stearic acid or talc. If desired, the tablets may be coated with a material such as glyceryl monostearate or glyceryl distearate, to delay absorption in the gastrointestinal tract.

As used herein, a “transformed cell” is a cell into which a vector has been introduced from which a dsRNA molecule may be expressed.

Design and Selection of iRNA Agents

The present invention is based on the demonstration of target gene silencing of the TGF-beta gene in vitro following administration of an iRNA agent results in reducing TGF-beta signaling.

Based on these results, the invention specifically provides an iRNA agent that can be used in reducing TGF-beta levels in a cell or organism, particularly for use in reducing undesired TGF-beta signaling, in isolated form and as a pharmaceutical composition described below. Such agents will include a sense strand having at least 15 or more contiguous nucleotides that are complementary to a TGF-beta gene and an antisense strand having at least 15 or more contiguous nucleotides that are complementary to the sense strand sequence. Particularly useful are iRNA agents that comprise a nucleotide sequence from the TGF-beta gene as provided in Table 1 and Table 5.

Other candidate iRNA agents can be designed by performing, for example, a gene walk analysis of the TGF-beta gene that will serve as the iRNA target. Overlapping, adjacent, or closely spaced candidate agents corresponding to all or some of the transcribed region can be generated and tested. Each of the iRNA agents can be tested and evaluated for the ability to down regulate the target gene expression (see below, “Evaluation of Candidate iRNA agents”).

Preferably, the iRNA agents of the present invention are based on and comprise at least 15 or more contiguous nucleotides from one of the iRNA agents shown to be active in Table 1 and Table 5. In such agents, the agent can comprise the entire sequence provided in the table or can comprise 15 or more contiguous residues along with additional nucleotides from contiguous regions of the target gene. Alternatively, an iRNA agent of the instant invention may effect the cleavage of a TGF-beta mRNA within a sequence on the TGF-beta mRNA that is the target sequence of one of the iRNA agents provided in Table 1 and Table 5. The target sequences of the iRNA agents in Table 5 is expressly provided therein, the target sequence of the iRNA agents provided in Table 1 is equal to the sense strand sequence of these agents, minus the 5′-terminal deoxythymidines (and, where applicable, replacing 2′-β-methyl ribonucleotides by ribonucleotides). The skilled person is well aware of how an iRNA agent that cleaves a target mRNA within a given mRNA sequence may be designed. Cleavage of a target mRNA occurs between the two nucleotides hybridized to those in positions 10 and 11, counting 5′ to 3′, of the iRNA agent's antisense strand (Elbashir, S., et al., EMBO J. 2001, 23:6877). Therefore, an iRNA agent may be designed to cleave at a given site by including a sequence in its antisense strand sufficiently complementary to the target mRNA to hybridize to the target mRNA such that 10 nucleotides of the antisense strand are hybridized 3′ to the intended cleavage site on the mRNA, the remainder being hybridized to a sequence 5′ on the target mRNA.

An iRNA agent can be rationally designed based on sequence information and desired characteristics and the information provided in Table 1 and Table 5. For example, an iRNA agent can be designed according to the relative melting temperature of the candidate duplex. Generally, the duplex should have a lower melting temperature at the 5′ end of the antisense strand than at the 3′ end of the antisense strand.

The skilled person is well aware that dsRNAs comprising a duplex structure of between 20 and 23, but specifically 21, base pairs have been hailed as particularly effective in inducing RNA interference (Elbashir et al., EMBO 2001, 20:6877-6888). However, others have found that shorter or longer dsRNAs can be effective as well. In the embodiments described above, by virtue of the nature of the oligonucleotide sequences provided in Table 1 and Table 5, the dsRNAs of the invention can comprise at least one strand of a length of minimally 21 nt. It can be reasonably expected that shorter dsRNAs comprising one of the sequences of Table 1 and Table 5 minus only a few nucleotides on one or both ends may be similarly effective as compared to the dsRNAs described above. Hence, dsRNAs comprising a partial sequence from one of the sequences of Table 1 and Table 5, and differing in their ability to inhibit the expression of a TGF-beta gene in an assay as described herein below by not more than 5, 10, 15, 20, 25, or 30% inhibition from a dsRNA comprising the full sequence, are contemplated by the invention.

Accordingly, the present invention provides iRNA agents comprising a sense strand and antisense strand each comprising a sequence of at least 15, 16, 17, 18, 19, 20, 21 or 23 nucleotides which is essentially identical to, as defined above, a portion of the TGF-beta gene. Exemplified iRNA agents include those that comprise 15 or more contiguous nucleotides from one of the agents provided in Table 1 and Table 5.

The antisense strand of an iRNA agent should be equal to or at least, 15, 16, 17, 18, 19, 25, 29, 40, or 50 nucleotides in length. It should be equal to or less than 50, 40, or 30, nucleotides in length. Preferred ranges are 15-30, 17 to 25, 19 to 23, and 19 to 21 nucleotides in length. Exemplified iRNA agents include those that comprise 15 or more nucleotides from one of the agents in Table 1 and Table 5.

The sense strand of an iRNA agent should be equal to or at least 15, 16 17, 18, 19, 25, 29, 40, or 50 nucleotides in length. It should be equal to or less than 50, 40, or 30 nucleotides in length. Preferred ranges are 15-30, 17 to 25, 19 to 23, and 19 to 21 nucleotides in length. Exemplified iRNA agents include those that comprise 15 or more nucleotides from one of the agents Table 1 and Table 5.

The double stranded portion of an iRNA agent should be equal to or at least, 15, 16 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 40, or 50 nucleotide pairs in length. It should be equal to or less than 50, 40, or 30 nucleotides pairs in length. Preferred ranges are 15-30, 17 to 25, 19 to 23, and 19 to 21 nucleotides pairs in length.

The agents provided in Table 1 and Table 5 are 21 nucleotides in length for each strand. The iRNA agents contain a 19 nucleotide double stranded region with a 2 nucleotide overhang on each of the 3′ ends of the agent. These agents can be modified as described herein to obtain equivalent agents comprising at least a portion of these sequences (15 or more contiguous nucleotides) and or modifications to the oligonucleotide bases and linkages.

Generally, the iRNA agents of the instant invention include a region of sufficient complementarity to the TGF-beta gene, and are of sufficient length in terms of nucleotides, that the iRNA agent, or a fragment thereof, can mediate down regulation of the specific TGF-beta gene. The antisense strands of the iRNA agents of the present invention are preferably fully complementary to the mRNA sequences of TGF-beta gene. However, it is not necessary that there be perfect complementarity between the iRNA agent and the target, but the correspondence must be sufficient to enable the iRNA agent, or a cleavage product thereof, to direct sequence specific silencing, e.g., by RNAi cleavage of an TGF-beta mRNA.

Therefore, the iRNA agents of the instant invention include agents comprising a sense strand and antisense strand each comprising a sequence of at least 16, 17 or 18 nucleotides which is essentially identical, as defined below, to one of the sequences of a TGF-beta gene such as those agent provided in Table 1 and Table 5, except that not more than 1, 2 or 3 nucleotides per strand, respectively, have been substituted by other nucleotides (e.g. adenosine replaced by uracil), while essentially retaining the ability to inhibit TGF-beta expression in cultured human cells, as defined below. These agents will therefore possess at least 15 or more nucleotides identical to one of the sequences of a TGF-beta gene but 1, 2 or 3 base mismatches with respect to either the target TGF-beta mRNA sequence or between the sense and antisense strand are introduced. Mismatches to the target TGF-beta mRNA sequence, particularly in the antisense strand, are most tolerated in the terminal regions and if present are preferably in a terminal region or regions, e.g., within 6, 5, 4, or 3 nucleotides of a 5′ and/or 3′ terminus, most preferably within 6, 5, 4, or 3 nucleotides of the 5′-terminus of the sense strand or the 3′-terminus of the antisense strand. The sense strand need only be sufficiently complementary with the antisense strand to maintain the overall double stranded character of the molecule.

It is preferred that the sense and antisense strands be chosen such that the iRNA agent includes a single strand or unpaired region at one or both ends of the molecule, such as those exemplified in Table 1 and Table 5. Thus, an iRNA agent contains sense and antisense strands, preferably paired to contain an overhang, e.g., one or two 5′ or 3′ overhangs but preferably a 3′ overhang of 2-3 nucleotides. Most embodiments will have a 3′ overhang. Preferred siRNA agents will have single-stranded overhangs, preferably 3′ overhangs, of 1 to 6, preferably 1 to 4, or more preferably 2 or 3 nucleotides, in length, on one or both ends of the iRNA agent. The overhangs can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered. 5′-ends are preferably phosphorylated.

Moreover, the present inventors have discovered that the presence of only one nucleotide overhang strengthens the interference activity of the dsRNA, without affecting its overall stability. dsRNA having only one overhang has proven particularly stable and effective in vivo, as well as in a variety of cells, cell culture mediums, blood, and serum. Preferably, the single-stranded overhang is located at the 3′-terminal end of the antisense strand or, alternatively, at the 3′-terminal end of the sense strand. The dsRNA may also have a blunt end, preferably located at the 5′-end of the antisense strand. Such dsRNAs have improved stability and inhibitory activity, thus allowing administration at low dosages, i.e., less than 5 mg/kg body weight of the recipient per day. Preferably, the antisense strand of the dsRNA has a nucleotide overhang at the 3′-end, and the 5′-end is blunt. In another embodiment, one or more of the nucleotides in the overhang is replaced with a nucleoside thiophosphate.

Preferred lengths for the duplexed region is between 15 and 30, most preferably 18, 19, 20, 21, 22, and 23 nucleotides in length, e.g., in the siRNA agent range discussed above. Embodiments in which the two strands of the siRNA agent are linked, e.g., covalently linked are also included. Hairpin, or other single strand structures which provide the required double stranded region, and preferably a 3′ overhang are also within the invention.

Evaluation of Candidate iRNA Agents

A candidate iRNA agent can be evaluated for its ability to down regulate target gene expression. For example, a candidate iRNA agent can be provided, and contacted with a cell, e.g. a human cell that expresses TGF-beta. Alternatively, the cell can be transfected with a construct from which a target TGF-beta gene is expressed, thus preventing the need for endogenous TGF-beta expression. The level of target gene expression prior to and following contact with the candidate iRNA agent can be compared, e.g. on an mRNA or protein level. If it is determined that the amount of RNA or protein expressed from the target gene is lower following contact with the iRNA agent, then it can be concluded that the iRNA agent down-regulates target gene expression. The level of target TGF-beta mRNA or TGF-beta protein in the cell or tissue can be determined by any method desired. For example, the level of target RNA can be determined by Northern blot analysis, reverse transcription coupled with polymerase chain reaction (RT-PCR), bDNA analysis, or RNAse protection assay. The level of protein can be determined, for example, by Western blot analysis or immunofluorescence.

Stability Testing, Modification, and Retesting of iRNA Agents

A candidate iRNA agent can be evaluated with respect to stability, e.g., its susceptibility to cleavage by an endonuclease or exonuclease, such as when the iRNA agent is introduced into the body of a subject. Methods can be employed to identify sites that are susceptible to modification, particularly cleavage, e.g., cleavage by a component found in the body of a subject.

When sites susceptible to cleavage are identified, a further iRNA agent can be designed and/or synthesized wherein the potential cleavage site is made resistant to cleavage, e.g. by introduction of a 2′-modification on the site of cleavage, e.g. a 2′-O-methyl group. This further iRNA agent can be retested for stability, and this process may be iterated until an iRNA agent is found exhibiting the desired stability. Table 1 provides a variety of sequence modifications as exemplars, which are nevertheless not to be understood as limiting.

In Vivo Testing

An iRNA agent identified as being capable of inhibiting TGF-beta gene expression can be tested for functionality in vivo in an animal model (e.g., in a mammal, such as in mouse or rat) as shown in the examples. For example, the iRNA agent can be administered to an animal, and the iRNA agent evaluated with respect to its biodistribution, stability, and its ability to inhibit TGF-beta, e.g. lower TGF-beta protein or gene expression.

The iRNA agent can be administered directly to the target tissue, such as by injection, or the iRNA agent can be administered to the animal model in the same manner that it would be administered to a human, e.g. by inhalation, injection or infusion.

The iRNA agent can also be evaluated for its intracellular distribution. The evaluation can include determining whether the iRNA agent was taken up into the cell. The evaluation can also include determining the stability (e.g., the half-life) of the iRNA agent. Evaluation of an iRNA agent in vivo can be facilitated by use of an iRNA agent conjugated to a traceable marker (e.g., a fluorescent marker such as fluorescein; a radioactive label, such as ³⁵S, ³²P, ³³P or ³H; gold particles; or antigen particles for immunohistochemistry).

The iRNA agent can be evaluated with respect to its ability to down regulate TGF-beta gene expression. Levels of TGF-beta gene expression in vivo can be measured, for example, by in situ hybridization, or by the isolation of RNA from tissue prior to and following exposure to the iRNA agent. Where the animal needs to be sacrificed in order to harvest the tissue, an untreated control animal will serve for comparison. Target TGF-beta mRNA can be detected by any desired method, including but not limited to RT-PCR, Northern blot, branched-DNA assay, or RNAase protection assay. Alternatively, or additionally, TGF-beta gene expression can be monitored by performing Western blot analysis on tissue extracts treated with the iRNA agent.

iRNA Chemistry

Described herein are isolated iRNA agents, e.g., ds RNA agents, that mediate RNAi to inhibit expression of a TGF-beta gene.

RNA agents discussed herein include otherwise unmodified RNA as well as RNA which have been modified, e.g., to improve efficacy, and polymers of nucleoside surrogates. Unmodified RNA refers to a molecule in which the components of the nucleic acid, namely sugars, bases, and phosphate moieties, are the same or essentially the same as that which occur in nature, preferably as occur naturally in the human body. The art has referred to rare or unusual, but naturally occurring, RNAs as modified RNAs, see, e.g., Limbach et al., (1994) Nucleic Acids Res. 22: 2183-2196. Such rare or unusual RNAs, often termed modified RNAs (apparently because these are typically the result of a post-transcriptional modification) are within the term unmodified RNA, as used herein. Modified RNA as used herein refers to a molecule in which one or more of the components of the nucleic acid, namely sugars, bases, and phosphate moieties, are different from that which occurs in nature, preferably different from that which occurs in the human body. While they are referred to as modified “RNAs,” they will of course, because of the modification, include molecules which are not RNAs. Nucleoside surrogates are molecules in which the ribophosphate backbone is replaced with a non-ribophosphate construct that allows the bases to the presented in the correct spatial relationship such that hybridization is substantially similar to what is seen with a ribophosphate backbone, e.g., non-charged mimics of the ribophosphate backbone. Examples of each of the above are discussed herein.

Modifications described herein can be incorporated into any double-stranded RNA and RNA-like molecule described herein, e.g., an iRNA agent. It may be desirable to modify one or both of the antisense and sense strands of an iRNA agent. As nucleic acids are polymers of subunits or monomers, many of the modifications described below occur at a position which is repeated within a nucleic acid, e.g., a modification of a base, or a phosphate moiety, or the non-linking O of a phosphate moiety. In some cases the modification will occur at all of the subject positions in the nucleic acid but in many, and in fact in most, cases it will not. By way of example, a modification may only occur at a 3′ or 5′ terminal position, may only occur in a terminal region, e.g. at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand. A modification may occur in a double strand region, a single strand region, or in both. E.g., a phosphorothioate modification at a non-linking O position may only occur at one or both termini, may only occur in a terminal regions, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand, or may occur in double strand and single strand regions, particularly at termini. Similarly, a modification may occur on the sense strand, antisense strand, or both. In some cases, the sense and antisense strand will have the same modifications or the same class of modifications, but in other cases the sense and antisense strand will have different modifications, e.g., in some cases it may be desirable to modify only one strand, e.g. the sense strand.

Two prime objectives for the introduction of modifications into iRNA agents is their stabilization towards degradation in biological environments and the improvement of pharmacological properties, e.g. pharmacodynamic properties, which are further discussed below. Other suitable modifications to a sugar, base, or backbone of an iRNA agent are described in co-owned PCT Application No. PCT/US2004/01193, filed Jan. 16, 2004. An iRNA agent can include a non-naturally occurring base, such as the bases described in co-owned PCT Application No. PCT/US2004/011822, filed Apr. 16, 2004. An iRNA agent can include a non-naturally occurring sugar, such as a non-carbohydrate cyclic carrier molecule. Exemplary features of non-naturally occurring sugars for use in iRNA agents are described in co-owned PCT Application No. PCT/US2004/11829 filed Apr. 16, 2003.

An iRNA agent can include an internucleotide linkage (e.g., the chiral phosphorothioate linkage) useful for increasing nuclease resistance. In addition, or in the alternative, an iRNA agent can include a ribose mimic for increased nuclease resistance. Exemplary internucleotide linkages and ribose mimics for increased nuclease resistance are described in co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8, 2004.

An iRNA agent can include ligand-conjugated monomer subunits and monomers for oligonucleotide synthesis. Exemplary monomers are described in co-owned U.S. application Ser. No. 10/916,185, filed on Aug. 10, 2004.

An iRNA agent can have a ZXY structure, such as is described in co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8, 2004.

An iRNA agent can be complexed with an amphipathic moiety. Exemplary amphipathic moieties for use with iRNA agents are described in co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8, 2004.

In another embodiment, the iRNA agent can be complexed to a delivery agent that features a modular complex. The complex can include a carrier agent linked to one or more of (preferably two or more, more preferably all three of): (a) a condensing agent (e.g., an agent capable of attracting, e.g., binding, a nucleic acid, e.g., through ionic or electrostatic interactions); (b) a fusogenic agent (e.g., an agent capable of fusing and/or being transported through a cell membrane); and (c) a targeting group, e.g., a cell or tissue targeting agent, e.g., a lectin, glycoprotein, lipid or protein, e.g., an antibody, that binds to a specified cell type. iRNA agents complexed to a delivery agent are described in co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8, 2004.

An iRNA agent can have non-canonical pairings, such as between the sense and antisense sequences of the iRNA duplex. Exemplary features of non-canonical iRNA agents are described in co-owned PCT Application No. PCT/US2004/07070 filed on Mar. 8, 2004.

Enhanced Nuclease Resistance

An iRNA agent, e.g., an iRNA agent that targets TGF-beta, can have enhanced resistance to nucleases.

For increased nuclease resistance and/or binding affinity to the target, an iRNA agent, e.g., the sense and/or antisense strands of the iRNA agent, can include, for example, 2′-modified ribose units and/or phosphorothioate linkages. E.g., the 2′ hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents.

Examples of “oxy”-2′ hydroxyl group modifications include alkoxy or aryloxy (OR, e.g., R═H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar); polyethyleneglycols (PEG), O(CH₂CH₂O)_nCH₂CH₂OR; “locked” nucleic acids (LNA) in which the 2′ hydroxyl is connected, e.g., by a methylene bridge, to the 4′ carbon of the same ribose sugar; O-AMINE and aminoalkoxy, O(CH₂)_nAMINE, (e.g., AMINE=NH₂; alkylamino, dialkylamino, heterocyclyl amino, arylamino, diaryl amino, heteroaryl amino, or diheteroaryl amino, ethylene diamine, polyamino). It is noteworthy that oligonucleotides containing only the methoxyethyl group (MOE), (OCH₂CH₂OCH₃, a PEG derivative), exhibit nuclease stabilities comparable to those modified with the robust phosphorothioate modification.

“Deoxy” modifications include hydrogen (i.e. deoxyribose sugars, which are of particular relevance to the overhang portions of partially ds RNA); halo (e.g., fluoro); amino (e.g. NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl amino, diheteroaryl amino, or amino acid); NH(CH₂CH₂NH)_nCH₂CH₂-AMINE (AMINE=NH₂; alkylamino, dialkylamino, heterocyclyl amino, arylamino, diaryl amino, heteroaryl amino, or diheteroaryl amino), —NHC(O)R(R=alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl; thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which may be optionally substituted with e.g., an amino functionality.

Preferred substituents are 2′-methoxyethyl, 2′-OCH3,2′-O-allyl, 2′-C-allyl, and 2′-fluoro.

One way to increase resistance is to identify cleavage sites and modify such sites to inhibit cleavage, as described in co-owned U.S. Application No. 60/559,917, filed on May 4, 2004. For example, the dinucleotides 5′-ua-3′,5′-ug-3′,5′-ug-3′,5′-uu-3′, or 5′-cc-3′ can serve as cleavage sites. In certain embodiments, all the pyrimidines of an iRNA agent carry a 2′-modification in either the sense strand, the antisense strand, or both strands, and the iRNA agent therefore has enhanced resistance to endonucleases. Enhanced nuclease resistance can also be achieved by modifying the 5′ nucleotide, resulting, for example, in at least one 5′-uridine-adenine-3′ (5′-ua-3′) dinucleotide wherein the uridine is a 2′-modified nucleotide; at least one 5′-cytidine-adenine-3′ (5′-ug-3′) dinucleotide, wherein the 5′-cytidine is a 2′-modified nucleotide; at least one 5′-uridine-guanine-3′ (5′-ug-3′) dinucleotide, wherein the 5′-uridine is a 2′-modified nucleotide; at least one 5′-uridine-uridine-3′ (5′-uu-3′) dinucleotide, wherein the 5′-uridine is a 2′-modified nucleotide; or at least one 5′-cytidine-cytidine-3′ (5′-cc-3′) dinucleotide, wherein the 5′-cytidine is a 2′-modified nucleotide, as described in co-owned International Application No. PCT/US2005/018931, filed on May 27, 2005. The iRNA agent can include at least 2, at least 3, at least 4 or at least 5 of such dinucleotides. In a particularly preferred embodiment, the 5′ nucleotide in all occurrences of the sequence motifs 5′-ua-3′ and 5′-ug-3′ in either the sense strand, the antisense strand, or both strands is a modified nucleotide. Preferably, the 5′ nucleotide in all occurrences of the sequence motifs 5′-ua-3′,5′-ca-3′ and 5′-ug-3′ in either the sense strand, the antisense strand, or both strands is a modified nucleotide. More preferably, all pyrimidine nucleotides in the sense strand are modified nucleotides, and the 5′ nucleotide in all occurrences of the sequence motifs 5′-ua-3′ and 5′-ca-3′ in the antisense strand are modified nucleotides, or where the antisense strand does comprise neither of a 5′-ua-3′ and a 5′-ca-3′ motif, in all occurrences of the sequence motif 5′-ug-3′. Preferably, sites particularly prone to nuclease degradation are first determined, e.g. by mass spectrometry of degradation products, and only those sites are sequentially modified until a desired level of stability is attained.

To maximize nuclease resistance, the 2′ modifications can be used in combination with one or more phosphate linker modifications (e.g., phosphorothioate), as further described below. The so-called “chimeric” oligonucleotides are those that contain two or more different modifications. Preferably, phosphate linker modifications are located near the 3′- and/or 5′-end of either or both strands, or at or near sites particularly prone to degradative attack.

The inclusion of furanose sugars in the oligonucleotide backbone can also decrease endonucleolytic cleavage. An iRNA agent can be further modified by including a 3′ cationic group, or by inverting the nucleoside at the 3′-terminus with a 3′-3′ linkage. In another alternative, the 3′-terminus can be blocked with an aminoalkyl group, e.g., a 3′ C5-aminoalkyl dT. Other 3′ conjugates can inhibit 3′-5′ exonucleolytic cleavage. While not being bound by theory, a 3′ conjugate, such as naproxen or ibuprofen, may inhibit exonucleolytic cleavage by sterically blocking the exonuclease from binding to the 3′-end of oligonucleotide. Even small alkyl chains, aryl groups, or heterocyclic conjugates or modified sugars (D-ribose, deoxyribose, glucose etc.) can block 3′-5′-exonucleases.

Similarly, 5′ conjugates can inhibit 5′-3′ exonucleolytic cleavage. While not being bound by theory, a 5′ conjugate, such as naproxen or ibuprofen, may inhibit exonucleolytic cleavage by sterically blocking the exonuclease from binding to the 5′-end of oligonucleotide. Even small alkyl chains, aryl groups, or heterocyclic conjugates or modified sugars (D-ribose, deoxyribose, glucose etc.) can block 3′-5′-exonucleases.

An iRNA agent can have increased resistance to nucleases when a duplexed iRNA agent includes a single-stranded nucleotide overhang on at least one end. In preferred embodiments, the nucleotide overhang includes 1 to 4, preferably 2 to 3, unpaired nucleotides. In a preferred embodiment, the unpaired nucleotide of the single-stranded overhang that is directly adjacent to the terminal nucleotide pair contains a purine base, and the terminal nucleotide pair is a G-C pair, or at least two of the last four complementary nucleotide pairs are G-C pairs. In further embodiments, the nucleotide overhang may have 1 or 2 unpaired nucleotides, and in an exemplary embodiment the nucleotide overhang is 5′-GC-3′. In preferred embodiments, the nucleotide overhang is on the 3′-end of the antisense strand. In one embodiment, the iRNA agent includes the motif 5′-CGC-3′ on the 3′-end of the antisense strand, such that a 2-nt overhang 5′-GC-3′ is formed.

Thus, an iRNA agent can include modifications so as to inhibit degradation, e.g., by nucleases, e.g., endonucleases or exonucleases, found in the body of a subject. These monomers are referred to herein as NRMs, or Nuclease Resistance promoting Monomers, the corresponding modifications as NRM modifications. In many cases these modifications will modulate other properties of the iRNA agent as well, e.g., the ability to interact with a protein, e.g., a transport protein, e.g., serum albumin, or a member of the RISC, or the ability of the first and second sequences to form a duplex with one another or to form a duplex with another sequence, e.g., a target molecule.

One or more different NRM modifications can be introduced into an iRNA agent or into a sequence of an iRNA agent. An NRM modification can be used more than once in a sequence or in an iRNA agent.

NRM modifications include some which can be placed only at the terminus and others which can go at any position. Some NRM modifications that can inhibit hybridization are preferably used only in terminal regions, and more preferably not at the cleavage site or in the cleavage region of a sequence which targets a subject sequence or gene, particularly on the antisense strand. They can be used anywhere in a sense strand, provided that sufficient hybridization between the two strands of the ds iRNA agent is maintained. In some embodiments it is desirable to put the NRM at the cleavage site or in the cleavage region of a sense strand, as it can minimize off-target silencing.

In most cases, the NRM modifications will be distributed differently depending on whether they are comprised on a sense or antisense strand. If on an antisense strand, modifications which interfere with or inhibit endonuclease cleavage should not be inserted in the region which is subject to RISC mediated cleavage, e.g., the cleavage site or the cleavage region (As described in Elbashir et al., 2001, Genes and Dev. 15: 188, hereby incorporated by reference). Cleavage of the target occurs about in the middle of a 20 or 21 nt antisense strand, or about 10 or 11 nucleotides upstream of the first nucleotide on the target mRNA which is complementary to the antisense strand. As used herein cleavage site refers to the nucleotides on either side of the site of cleavage, on the target mRNA or on the iRNA agent strand which hybridizes to it. Cleavage region means the nucleotides within 1, 2, or 3 nucleotides of the cleavage site, in either direction.

Such modifications can be introduced into the terminal regions, e.g., at the terminal position or with 2, 3, 4, or 5 positions of the terminus, of a sequence which targets or a sequence which does not target a sequence in the subject.

In a particular embodiment, the 5′-end of the antisense strand and the 3′-end of the sense strand are chemically linked via a hexaethylene glycol linker. In another embodiment, at least one nucleotide of the dsRNA comprises a phosphorothioate or phosphorodithioate groups. The chemical bond at the ends of the dsRNA is preferably formed by triple-helix bonds.

In certain embodiments, a chemical bond may be formed by means of one or several bonding groups, wherein such bonding groups are preferably poly-(oxyphosphinicooxy-1,3-propandiol)- and/or polyethylene glycol chains. In other embodiments, a chemical bond may also be formed by means of purine analogs introduced into the double-stranded structure instead of purines. In further embodiments, a chemical bond may be formed by azabenzene units introduced into the double-stranded structure. In still further embodiments, a chemical bond may be formed by branched nucleotide analogs instead of nucleotides introduced into the double-stranded structure. In certain embodiments, a chemical bond may be induced by ultraviolet light.

Teachings regarding the synthesis of particular modified oligonucleotides may be found in the following U.S. patents: U.S. Pat. Nos. 5,138,045 and 5,218,105, drawn to polyamine conjugated oligonucleotides; U.S. Pat. No. 5,212,295, drawn to monomers for the preparation of oligonucleotides having chiral phosphorus linkages; U.S. Pat. Nos. 5,378,825 and 5,541,307, drawn to oligonucleotides having modified backbones; U.S. Pat. No. 5,386,023, drawn to backbone-modified oligonucleotides and the preparation thereof through reductive coupling; U.S. Pat. No. 5,457,191, drawn to modified nucleobases based on the 3-deazapurine ring system and methods of synthesis thereof; U.S. Pat. No. 5,459,255, drawn to modified nucleobases based on N-2 substituted purines; U.S. Pat. No. 5,521,302, drawn to processes for preparing oligonucleotides having chiral phosphorus linkages; U.S. Pat. No. 5,539,082, drawn to peptide nucleic acids; U.S. Pat. No. 5,554,746, drawn to oligonucleotides having β-lactam backbones; U.S. Pat. No. 5,571,902, drawn to methods and materials for the synthesis of oligonucleotides; U.S. Pat. No. 5,578,718, drawn to nucleosides having alkylthio groups, wherein such groups may be used as linkers to other moieties attached at any of a variety of positions of the nucleoside; U.S. Pat. Nos. 5,587,361 and 5,599,797, drawn to oligonucleotides having phosphorothioate linkages of high chiral purity; U.S. Pat. No. 5,506,351, drawn to processes for the preparation of 2′-O-alkyl guanosine and related compounds, including 2,6-diaminopurine compounds; U.S. Pat. No. 5,587,469, drawn to oligonucleotides having N-2 substituted purines; U.S. Pat. No. 5,587,470, drawn to oligonucleotides having 3-deazapurines; U.S. Pat. No. 5,223,168, and U.S. Pat. No. 5,608,046, both drawn to conjugated 4′-desmethyl nucleoside analogs; U.S. Pat. Nos. 5,602,240, and 5,610,289, drawn to backbone-modified oligonucleotide analogs; U.S. Pat. Nos. 6,262,241, and 5,459,255, drawn to, inter alia, methods of synthesizing 2′-fluoro-oligonucleotides.

In some preferred embodiments, functionalized nucleoside sequences of the invention possessing an amino group at the 5′-terminus are prepared using a DNA synthesizer, and then reacted with an active ester derivative of a selected ligand. Active ester derivatives are well known to those skilled in the art. Representative active esters include N-hydroxsuccinimide esters, tetrafluorophenolic esters, pentafluorophenolic esters and pentachlorophenolic esters. The reaction of the amino group and the active ester produces an oligonucleotide in which the selected ligand is attached to the 5′-position through a linking group. The amino group at the 5′-terminus can be prepared utilizing a 5′-Amino-Modifier C6 reagent. In a preferred embodiment, ligand molecules may be conjugated to oligonucleotides at the 5′-position by the use of a ligand-nucleoside phosphoramidite wherein the ligand is linked to the 5′-hydroxy group directly or indirectly via a linker. Such ligand-nucleoside phosphoramidites are typically used at the end of an automated synthesis procedure to provide a ligand-conjugated oligonucleotide bearing the ligand at the 5′-terminus

In many cases, protecting groups are used during the preparation of the compounds of the invention. As used herein, the term “protected” means that the indicated moiety has a protecting group appended thereon. In some preferred embodiments of the invention, compounds contain one or more protecting groups. A wide variety of protecting groups can be employed in the methods of the invention. In general, protecting groups render chemical functionalities inert to specific reaction conditions, and can be appended to and removed from such functionalities in a molecule without substantially damaging the remainder of the molecule.

Representative hydroxyl protecting groups, for example, are disclosed by Beaucage et al. (Tetrahedron, 1992, 48:2223-2311). Further hydroxyl protecting groups, as well as other representative protecting groups, are disclosed in Greene and Wuts, Protective Groups in Organic Synthesis, Chapter 2, 2d ed., John Wiley & Sons, New York, 1991, and Oligonucleotides And Analogues A Practical Approach, Ekstein, F. Ed., IRL Press, N.Y, 1991.

Examples of hydroxyl protecting groups include, but are not limited to, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,4-dinitrophenyl, benzyl, 2,6-dichlorobenzyl, diphenylmethyl, p,p′-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, acetate, chloroacetate, trichloroacetate, trifluoroacetate, pivaloate, benzoate, p-phenylbenzoate, 9-fluorenylmethyl carbonate, mesylate and tosylate.

Amino-protecting groups stable to acid treatment are selectively removed with base treatment, and are used to make reactive amino groups selectively available for substitution. Examples of such groups are the Fmoc (E. Atherton and R. C. Sheppard in The Peptides, S. Udenfriend, J. Meienhofer, Eds., Academic Press, Orlando, 1987, volume 9, p. 1) and various substituted sulfonylethyl carbamates exemplified by the Nsc group (Samukov et al., Tetrahedron Lett., 1994, 35:7821; Verhart and Tesser, Rec. Tray. Chim. Pays-Bas, 1987, 107:621).

Additional amino-protecting groups include, but are not limited to, carbamate protecting groups, such as 2-trimethylsilylethoxycarbonyl (Teoc), 1-methyl-1-(4-biphenylyl)ethoxycarbonyl (Bpoc), t-butoxycarbonyl (BOC), allyloxycarbonyl (Alloc), 9-fluorenylmethyloxycarbonyl (Fmoc), and benzyloxycarbonyl (Cbz); amide protecting groups, such as formyl, acetyl, trihaloacetyl, benzoyl, and nitrophenylacetyl; sulfonamide protecting groups, such as 2-nitrobenzenesulfonyl; and imine and cyclic imide protecting groups, such as phthalimido and dithiasuccinoyl. Equivalents of these amino-protecting groups are also encompassed by the compounds and methods of the invention.

Many solid supports are commercially available and one of ordinary skill in the art can readily select a solid support to be used in the solid-phase synthesis steps. In certain embodiments, a universal support is used. A universal support allows for preparation of oligonucleotides having unusual or modified nucleotides located at the 3′-terminus of the oligonucleotide. Universal Support 500 and Universal Support II are universal supports that are commercially available from Glen Research, 22825 Davis Drive, Sterling, Va. For further details about universal supports see Scott et al., Innovations and Perspectives in solid-phase Synthesis, 3rd International Symposium, 1994, Ed. Roger Epton, Mayflower Worldwide, 115-124]; Azhayev, A. V. Tetrahedron 1999, 55, 787-800; and Azhayev and Antopolsky Tetrahedron 2001, 57, 4977-4986. In addition, it has been reported that the oligonucleotide can be cleaved from the universal support under milder reaction conditions when oligonucleotide is bonded to the solid support via a syn-1,2-acetoxyphosphate group which more readily undergoes basic hydrolysis. See Guzaev, A. I.; Manoharan, M. J. Am. Chem. Soc. 2003, 125, 2380.

Ligand Conjugates

The properties of an iRNA agent, including its pharmacological properties, can be influenced and tailored, for example, by the introduction of ligands, e.g. tethered ligands.

A wide variety of entities, e.g., ligands, can be tethered to an iRNA agent, e.g., to the carrier of a ligand-conjugated monomer subunit. Examples are described below in the context of a ligand-conjugated monomer subunit but that is only preferred, entities can be coupled at other points to an iRNA agent.

Preferred moieties are ligands, which are coupled, preferably covalently, either directly or indirectly via an intervening tether, to the carrier. In preferred embodiments, the ligand is attached to the carrier via an intervening tether. The ligand or tethered ligand may be present on the ligand-conjugated monomer when the ligand-conjugated monomer is incorporated into the growing strand. In some embodiments, the ligand may be incorporated into a “precursor” ligand-conjugated monomer subunit after a “precursor” ligand-conjugated monomer subunit has been incorporated into the growing strand. For example, a monomer having, e.g., an amino-terminated tether, e.g., TAP-(CH₂)_nNH₂ may be incorporated into a growing sense or antisense strand. In a subsequent operation, i.e., after incorporation of the precursor monomer subunit into the strand, a ligand having an electrophilic group, e.g., a pentafluorophenyl ester or aldehyde group, can subsequently be attached to the precursor ligand-conjugated monomer by coupling the electrophilic group of the ligand with the terminal nucleophilic group of the precursor ligand-conjugated monomer subunit tether.

In preferred embodiments, a ligand alters the distribution, targeting or lifetime of an iRNA agent into which it is incorporated. In preferred embodiments a ligand provides an enhanced affinity for a selected target, e.g., molecule, cell or cell type, compartment, e.g., a cellular or organ compartment, tissue, organ or region of the body, as, e.g., compared to a species absent such a ligand.

Preferred ligands can improve transport, hybridization, and specificity properties and may also improve nuclease resistance of the resultant natural or modified oligoribonucleotide, or a polymeric molecule comprising any combination of monomers described herein and/or natural or modified ribonucleotides.

Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake; diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking agents; nuclease-resistance conferring moieties; and natural or unusual nucleobases. General examples include lipophilic molecules, lipids, lectins, steroids (e.g., uvaol, hecigenin, diosgenin), terpenes (e.g., triterpenes, e.g., sarsasapogenin, Friedelin, epifriedelanol derivatized lithocholic acid), vitamins, carbohydrates (e.g., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin or hyaluronic acid), proteins, protein binding agents, integrin targeting molecules, polycationics, peptides, polyamines, and peptide mimics

The ligand may be a naturally occurring or recombinant or synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid. Examples of polyamino acids include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacrylic acid), N-isopropylacrylamide polymers, or polyphosphazine. Example of polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic moieties, e.g., cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or an alpha helical peptide.

Ligands can also include targeting groups, e.g., a cell or tissue targeting agent, e.g., a thyrotropin, melanotropin, surfactant protein A, Mucin carbohydrate, a glycosylated polyaminoacid, transferrin, bisphosphonate, polyglutamate, polyaspartate, or an RGD peptide or RGD peptide mimetic.

Ligands can be proteins, e.g., glycoproteins, lipoproteins, e.g. low density lipoprotein (LDL), or albumins, e.g. human serum albumin (HSA), or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell. Ligands may also include hormones and hormone receptors. They can also include non-peptidic species, such as cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-glucosamine, multivalent mannose, or multivalent fucose. The ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-KB.

The ligand can be a substance, e.g, a drug, which can increase the uptake of the iRNA agent into the cell, for example, by disrupting the cell's cytoskeleton, e.g., by disrupting the cell's microtubules, microfilaments, and/or intermediate filaments. The drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, jasplakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.

In one aspect, the ligand is a lipid or lipid-based molecule. Such a lipid or lipid-based molecule preferably binds a serum protein, e.g., human serum albumin (HSA). An HSA binding ligand allows for distribution of the conjugate to a target tissue, e.g., liver tissue, including parenchymal cells of the liver. Other molecules that can bind HSA can also be used as ligands. For example, neproxen or aspirin can be used. A lipid or lipid-based ligand can (a) increase resistance to degradation of the conjugate, (b) increase targeting or transport into a target cell or cell membrane, and/or (c) can be used to adjust binding to a serum protein, e.g., HSA.

A lipid based ligand can be used to modulate, e.g., control the binding of the conjugate to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA more strongly will be less likely to be targeted to the kidney and therefore less likely to be cleared from the body. A lipid or lipid-based ligand that binds to HSA less strongly can be used to target the conjugate to the kidney.

In a preferred embodiment, the lipid based ligand binds HSA. Preferably, it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non-kidney tissue. However, it is preferred that the affinity not be so strong that the HSA-ligand binding cannot be reversed.

In another aspect, the ligand is a moiety, e.g., a vitamin or nutrient, which is taken up by a target cell, e.g., a proliferating cell. These are particularly useful for treating disorders characterized by unwanted cell proliferation, e.g., of the malignant or non-malignant type, e.g., cancer cells. Exemplary vitamins include vitamin A, E, and K. Other exemplary vitamins include the B vitamins, e.g., folic acid, B12, riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up by cancer cells.

In another aspect, the ligand is a cell-permeation agent, preferably a helical cell-permeation agent. Preferably, the agent is amphipathic. An exemplary agent is a peptide such as tat or antennapedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, inverters, non-peptide or pseudo-peptide linkages, and use of D-amino acids. The helical agent is preferably an alpha-helical agent, which preferably has a lipophilic and a lipophobic phase.

Backbone Modifications

Specific examples of preferred modified oligonucleotides envisioned for use in the ligand-conjugated oligonucleotides of the invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. As defined here, oligonucleotides having modified backbones or internucleoside linkages include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of the invention, modified oligonucleotides that do not have a phosphorus atom in their intersugar backbone can also be considered to be oligonucleosides.

Specific oligonucleotide chemical modifications are described below. It is not necessary for all positions in a given compound to be uniformly modified. Conversely, more than one modifications may be incorporated in a single dsRNA compound or even in a single nucleotide thereof.

Preferred modified internucleoside linkages or backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free-acid forms are also included.

Representative United States Patents relating to the preparation of the above phosphorus-atom-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,625,050; and 5,697,248, each of which is herein incorporated by reference.

Preferred modified internucleoside linkages or backbones that do not include a phosphorus atom therein (i.e., oligonucleosides) have backbones that are formed by short chain alkyl or cycloalkyl intersugar linkages, mixed heteroatom and alkyl or cycloalkyl intersugar linkages, or one or more short chain heteroatomic or heterocyclic intersugar linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts.

Representative United States patents relating to the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference.

5′-Terminal Modifications

In preferred embodiments, iRNA agents are 5′ phosphorylated or include a phosphoryl analog at the 5′ prime terminus, e.g. 5′ prime terminus of the antisense strand. 5′-phosphate modifications of the antisense strand include those which are compatible with RISC mediated gene silencing. Suitable modifications include: 5′-monophosphate ((HO)2(O)P—O-5′); 5′-diphosphate ((HO2(O)P—O—P(HO)(O)—O-5′); 5′-triphosphate ((HO)₂(O)P—O—(HO)(O)P—O—P(HO)(O)—O-5′); 5′-guanosine cap (7-methylated or non-methylated) (7m-G-O-5′-(HO)(O)P—O—(HO)(O)P—O—P(HO)(O)—O-5′); 5′-adenosine cap (Appp), and any modified or unmodified nucleotide cap structure. Other suitable 5′-phosphate modifications will be known to the skilled person.

The sense strand can be modified in order to inactivate the sense strand and prevent formation of an active RISC, thereby potentially reducing off-target effects. This can be accomplished by a modification which prevents 5′-phosphorylation of the sense strand, e.g., by modification with a 5′-O-methyl ribonucleotide (see Nykänen et al., (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321.) Other modifications which prevent phosphorylation can also be used, e.g., simply substituting the 5′-OH by H rather than O-Me. Alternatively, a large bulky group may be added to the 5′-phosphate turning it into a phosphodiester linkage.

Disorders and Diseases Associated with Undesired TGF-Beta Signaling

Diseases that can be treated in accordance with the present invention include, without limitation, kidney disorders associated with undesired TGF-beta signaling and excessive fibrosis and/or sclerosis, such as glomerulonephritis (GN) of all etiologies, e.g., mesangial proliferative GN, immune GN, and crescentic GN; diabetic nephropathy; renal interstitial fibrosis and all causes of renal interstitial fibrosis, including hypertension; renal fibrosis resulting from complications of drug exposure, including cyclosporin treatment of transplant recipients, e.g. cyclosporin treatment; HIV-associated nephropathy, transplant necropathy. The invention further includes the treatment of hepatic diseases associated with excessive scarring and progressive sclerosis, including cirrhosis due to all etiologies, disorders of the biliary tree, and hepatic dysfunction attributable to infections such as infection with hepatitis virus or parasites; pulmonary fibrosis and symptoms associates with pulmonary fibrosis with consequential loss of gas exchange or ability to efficiently move air into and out of the lungs, including adult respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD); idiopathic pulmonary fibrosis (IPF), acute lung injury (ALI), or pulmonary fibrosis due to infectious or toxic agents such as smoke, chemicals, allergens, or autoimmune diseases, such as systemic lupus erythematosus and scleroderma, chemical contact, or allergies. Fibroproliferative diseases targeted by the agents, pharmaceutical compositions, and treatment methods herein further include cardiovascular diseases, such as congestive heart failure, dilated cardiomyopathy, myocarditis, or vascular stenosis associated with atherosclerosis, angioplasty treatment, or surgical incisions or mechanical trauma. The invention also includes the treatment of all collagen vascular disorders of a chronic or persistent nature including progressive systemic sclerosis, polymyositis, scleroderma, dermatomyositis, fascists, or Raynaud's syndrome, or arthritic conditions such as rheumatoid arthritis; eye diseases associated with fibroproliferative states, including proliferative vitreoretinopathy of any etiology or fibrosis associated with ocular surgery such as treatment of glaucoma, retinal reattachment, cataract extraction, or drainage procedures of any kind; excessive or hypertrophic scar formation in the dermis occurring during wound healing resulting from trauma or surgical wounds.

While the above list is not meant in any way limiting, the treatment of all the above disorders and diseases are contemplated by the invention.

Delivery of iRNA Agents to Tissues and Cells

Formulation

For ease of exposition, the formulations, compositions, and methods in this section are discussed largely with regard to unmodified iRNA agents. It should be understood, however, that these formulations, compositions, and methods can be practiced with other iRNA agents, e.g., modified iRNA agents, and such practice is within the invention.

The term “therapeutically effective amount” is the amount present in the composition that is needed to provide the desired level of drug in the subject to be treated to give the anticipated physiological response.

The term “physiologically effective amount” is that amount delivered to a subject to give the desired palliative or curative effect.

The term “co-administration” refers to administering to a subject two or more agents, and in particular two or more iRNA agents. The agents can be contained in a single pharmaceutical composition and be administered at the same time, or the agents can be contained in separate formulation and administered serially to a subject. So long as the two agents can be detected in the subject at the same time, the two agents are said to be co-administered.

In the present methods, the iRNA agent can be administered to the subject either as naked iRNA agent, in conjunction with a delivery reagent, or as a recombinant plasmid or viral vector which expresses the iRNA agent. Preferably, the iRNA agent is administered as naked iRNA.

The iRNA agents described herein can be formulated for administration to a subject, preferably for administration locally to a site of fibrosis or sclerosis, or parenterally, e.g. via injection.

A formulated iRNA agent composition can assume a variety of states. In some examples, the composition is at least partially crystalline, uniformly crystalline, and/or anhydrous (e.g., less than 80, 50, 30, 20, or 10% water). In other examples, the composition is amorphous, such as a wax. In another example, the iRNA agent is in an aqueous phase, e.g., in a solution that includes water, this form being the preferred form for administration via inhalation. The aqueous phase may contain other solvents or excipients, e.g. ethanol.

The aqueous phase or the crystalline compositions can be incorporated into a delivery vehicle, e.g., a liposome (particularly for the aqueous phase), or a particle (e.g., a microparticle as can be appropriate for a crystalline composition). Generally, the iRNA agent composition is formulated in a manner that is compatible with the intended method of administration.

Formulations for direct injection and parenteral administration are well known in the art. Such formulation may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives. For intravenous use, the total concentration of solutes should be controlled to render the preparation isotonic.

The nucleic acid molecules of the present invention can also be co-administered to a subject in combination with other therapeutic compounds to increase the overall therapeutic effect. The use of multiple compounds to treat an indication can increase the beneficial effects while reducing the presence of side effects.

An iRNA agent preparation can be formulated in combination with another agent, e.g., another therapeutic agent or an agent that stabilizes an iRNA agent, e.g., a protein that complexes with the iRNA agent to form an iRNP. Still other agents include chelators, e.g., EDTA (e.g., to remove divalent cations such as Mg²⁺), salts, RNAse inhibitors (e.g., a broad specificity RNAse inhibitor such as RNAsin) and so forth.

In one embodiment, the iRNA agent preparation includes another iRNA agent, e.g., a second iRNA agent that can mediate RNAi with respect to a second gene. Still other preparations can include at least three, five, ten, twenty, fifty, or a hundred or more different iRNA species. In some embodiments, the agents are directed to the same gene but different target sequences. In another embodiment, each iRNA agent is directed to a different gene, e.g. TGF-beta.

An iRNA agent can be incorporated into pharmaceutical compositions suitable for administration. For example, compositions can include one or more iRNA agents and a pharmaceutically acceptable carrier.

The iRNA agents featured by the invention are preferably formulated as pharmaceutical compositions prior to administering to a subject, according to techniques known in the art. Pharmaceutical compositions of the present invention are characterized as being at least sterile and pyrogen-free. As used herein, “pharmaceutical formulations” include formulations for human and veterinary use. Methods for preparing pharmaceutical compositions of the invention are within the skill in the art, for example as described in Remington's Pharmaceutical Science, 18th ed., Mack Publishing Company, Easton, Pa. (1990), and The Science and Practice of Pharmacy, 2003, Gennaro et al., the entire disclosures of which are herein incorporated by reference.

The present pharmaceutical formulations comprise an iRNA agent of the invention (e.g., 0.1 to 90% by weight), or a physiologically acceptable salt thereof, mixed with a physiologically acceptable carrier medium. Preferred physiologically acceptable carrier media are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid and the like.

Pharmaceutical compositions of the invention can also comprise conventional pharmaceutical excipients and/or additives. Suitable pharmaceutical excipients include stabilizers, antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents. Suitable additives include physiologically biocompatible buffers (e.g., tromethamine hydrochloride), additions of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (as for example calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate). Pharmaceutical compositions of the invention can be packaged for use in liquid form, or can be lyophilized.

For solid compositions, conventional non-toxic solid carriers can be used; for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.

For example, a solid pharmaceutical composition for oral administration can comprise any of the carriers and excipients listed above and 10-95%, preferably 25%-75%, of one or more iRNA agents of the invention.

By “pharmaceutically acceptable formulation” is meant a composition or formulation that allows for the effective distribution of the nucleic acid molecules of the instant invention in the physical location most suitable for their desired activity. Non-limiting examples of agents suitable for formulation with the nucleic acid molecules of the instant invention include: P-glycoprotein inhibitors (such as PluronicP85), which can enhance entry of drugs into the CNS (Jolliet-Riant and Tillement, Fundam. Clin. Pharmacol. 13:16, 1999); biodegradable polymers, such as poly (DL-lactide-coglycolide) microspheres for sustained release delivery. Other non-limiting examples of delivery strategies for the nucleic acid molecules of the instant invention include material described in Boado et al., J. Pharm. Sci. 87:1308, 1998; Tyler et al., FEBS Lett. 421:280, 1999; Pardridge et al., PNAS USA. 92:5592, 1995; Boado, Adv. Drug Delivery Rev. 15:73, 1995; Aldrian-Herrada et al., Nucleic Acids Res. 26:4910, 1998; and Tyler et al., PNAS USA 96:7053, 1999.

The invention also features the use of the composition comprising surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al., Chem. Rev. 95:2601, 1995; Ishiwata et al., Chem. Phare. Bull. 43:1005, 1995).

Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., Science 267:1275, 1995; Oku et al., Biochim. Biophys. Acta 1238:86, 1995). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, particularly compared to conventional cationic liposomes which are known to accumulate in tissues of the MPS (Liu et al., J. Biol. Chem. 42:24864, 1995; Choi et al., International PCT Publication No. WO 96/10391; Ansell et al., International PCT Publication No. WO 96/10390; Holland et al., International PCT Publication No. WO 96/10392). Long-circulating liposomes are also likely to protect drugs from nuclease degradation to a greater extent compared to cationic liposomes, based on their ability to avoid accumulation in metabolically aggressive MPS tissues such as the liver and spleen.

Alternatively, certain iRNA agents of the instant invention can be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, Science 229:345, 1985; McGarry and Lindquist, Proc. Natl. Acad. Sci. USA 83:399, 1986; Scanlon et al., Proc. Natl. Acad. Sci. USA 88:10591, 1991; Kashani-Sabet et al., Antisense Res. Dev. 2:3, 1992; Dropulic et al., J. Virol. 66:1432, 1992; Weerasinghe et al., J. Virol. 65:5531, 1991; Ojwanget al., Proc. Natl. Acad. Sci. USA 89:10802, 1992; Chen et al., Nucleic Acids Res. 20:4581, 1992; Sarver et al., Science 247:1222, 1990; Thompson et al., Nucleic Acids Res. 23:2259, 1995; Good et al., Gene Therapy 4:45, 1997). Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by a enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595; Ohkawa et al., Nucleic Acids Symp. Ser. 27:156, 1992; Taira et al., Nucleic Acids Res. 19:5125, 1991; Ventura et al., Nucleic Acids Res. 21:3249, 1993; Chowrira et al., J. Biol. Chem. 269:25856, 1994).

In another aspect of the invention, RNA molecules of the present invention can be expressed from transcription units (see for example Couture et al., Trends in Genetics 12:510, 1996) inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. iRNA agent-expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. In another embodiment, pol III based constructs are used to express nucleic acid molecules of the invention (see for example Thompson, U.S. Pats. Nos. 5,902,880 and 6,146,886). The recombinant vectors capable of expressing the iRNA agents can be delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the iRNA agent interacts with the target mRNA and generates an RNAi response. Delivery of iRNA agent-expressing vectors can be systemic, such as by intravenous or intra-muscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al., Trends in Genetics 12:510, 1996).

The present invention also includes compositions prepared for storage or administration that include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” means that the carrier can be taken into the subject with no significant adverse toxicological effects on the subject. Acceptable carriers for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985), hereby incorporated by reference herein. The term is intended to include any and all solvents, dispersion media, coatings, preservatives, e.g. antibacterial and antifungal agents, isotonic and absorption delaying agents, stabilizers, antioxidants, suspending agents, dyes, flavoring agents, and the like, compatible with pharmaceutical administration. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.

The types of pharmaceutical excipients that are useful as carrier include stabilizers such as human serum albumin (HSA), bulking agents such as carbohydrates, amino acids and polypeptides; pH adjusters or buffers; salts such as sodium chloride; and the like. These carriers may be in a crystalline or amorphous form or may be a mixture of the two.

Preservatives include, for example, without limitation, sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid.

Bulking agents that are particularly valuable include compatible carbohydrates, polypeptides, amino acids or combinations thereof. Suitable carbohydrates include monosaccharides such as galactose, D-mannose, sorbose, and the like; disaccharides, such as lactose, trehalose, and the like; cyclodextrins, such as 2-hydroxypropyl-beta-cyclodextrin; and polysaccharides, such as raffinose, maltodextrins, dextrans, and the like; alditols, such as mannitol, xylitol, and the like. A preferred group of carbohydrates includes lactose, trehalose, raffinose maltodextrins, and mannitol. Suitable polypeptides include aspartame. Amino acids include alanine and glycine, with glycine being preferred.

Suitable pH adjusters or buffers include organic salts prepared from organic acids and bases, such as sodium citrate, sodium ascorbate, and the like; sodium citrate is preferred.

Treatment Methods and Delivery

Administration of the iRNA Agents A patient who has been diagnosed with a disorder characterized by undesired TGF-beta signaling can be treated by administration of an iRNA agent described herein to block the negative effects of TGF-beta, thereby alleviating the symptoms associated with undesired TGF-beta signaling. For example, the iRNA agent can alleviate symptoms associated with a disease of the lung, such as a fibrotic disorder. In other examples, the iRNA agent can be administered to treat a patient who has a fibrotic or sclerotic disease of the kidney or liver; a fibroproliferative cardiovascular disease; a collagen vascular disorder; or any other fibroproliferative disorder associated with undesired TGF-beta signaling.

A composition that includes an iRNA agent of the present invention, e.g., an iRNA agent that targets TGF-beta, can be delivered to a subject by a variety of routes, depending upon whether local or systemic treatment is desired and upon the area to be treated. In general, the delivery of the iRNA agents of the present invention is done to achieve delivery into the subject to the site of undesired TGF-beta signaling. The preferred means of administering the iRNA agents of the present invention is through either a local administration to the site of fibrosis or sclerosis, such as the lung, e.g. by inhalation, or systemically through enteral or parenteral administration.

Suitable enteral administration routes include oral delivery.

Suitable parenteral administration routes include intravascular administration (e.g., intravenous bolus injection, intravenous infusion, intra-arterial bolus injection, intra-arterial infusion and catheter instillation into the vasculature); peri- and intra-tissue injection; subcutaneous injection, deposition including subcutaneous infusion (such as by osmotic pumps), or transdermal application; intraperitoneal or intramuscular injection; intrathecal or intraventricular administration; intraocular, intraotic, intranasal, or intrapulmonary administration; or direct application to the area at or near the site of undesired TGF-beta signaling, for example by a catheter or other placement device (e.g., a pellet or implant comprising a porous, non-porous, or gelatinous material). It is preferred that injections or infusions of the iRNA agent be given at or near the site of undesired TGF-beta signaling.

The anti-TGF-beta iRNA agents can be administered systemically, e.g., orally or by intramuscular injection or by intravenous injection, in admixture with a pharmaceutically acceptable carrier adapted for the route of administration. Methods for the delivery of nucleic acid molecules are described in Akhtar et al., Trends in Cell Bio. 2:139, 1992; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995; Maurer et al., Mol. Membr. Biol., 16:129, 1999; Hofland and Huang, Handb. Exp. Pharmacol. 137:165, 1999; and Lee et al., ACS Symp. Ser. 752:184, 2000, all of which are incorporated herein by reference. Beigelman et al., U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595 further describe the general methods for delivery of nucleic acid molecules. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins (see for example Gonzalez et al., Bioconjugate Chem. 10:1068, 1999), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722).

Another aspect of the invention provides for the delivery of IRNA agents to the respiratory tract. The respiratory tract includes the upper airways, including the oropharynx and larynx, followed by the lower airways, which include the trachea followed by bifurcations into the bronchi and bronchioli. The upper and lower airways are called the conductive airways. The terminal bronchioli then divide into respiratory bronchioli which then lead to the ultimate respiratory zone, the alveoli, or deep lung. The deep lung, or alveoli, are the primary target of inhaled therapeutic aerosols for systemic delivery of iRNA agents.

Pulmonary delivery compositions can be delivered by inhalation by the patient of a dispersion so that the composition, preferably the iRNA agent, within the dispersion can reach the lung where it can, for example, be readily absorbed through the alveolar region directly into blood circulation. Pulmonary delivery can be effective both for systemic delivery and for localized delivery to treat diseases of the lungs.

Pulmonary delivery can be achieved by different approaches, including the use of nebulized, aerosolized, micellular and dry powder-based formulations; administration by inhalation may be oral and/or nasal. Delivery can be achieved with liquid nebulizers, aerosol-based inhalers, and dry powder dispersion devices. Metered-dose devices are preferred. One of the benefits of using an atomizer or inhaler is that the potential for contamination is minimized because the devices are self contained. Dry powder dispersion devices, for example, deliver drugs that may be readily formulated as dry powders. An iRNA composition may be stably stored as lyophilized or spray-dried powders by itself or in combination with suitable powder carriers. The delivery of a composition for inhalation can be mediated by a dosing timing element which can include a timer, a dose counter, time measuring device, or a time indicator which when incorporated into the device enables dose tracking, compliance monitoring, and/or dose triggering to a patient during administration of the aerosol medicament.

Examples of pharmaceutical devices for aerosol delivery include metered dose inhalers (MDIs), dry powder inhalers (DPIs), and air-jet nebulizers. Exemplary delivery systems by inhalation which can be readily adapted for delivery of the subject iRNA agents are described in, for example, U.S. Pat. Nos. 5,756,353; 5,858,784; and PCT applications WO98/31346; WO98/10796; WO00/27359; WO01/54664; WO02/060412. Other aerosol formulations that may be used for delivering the iRNA agents are described in U.S. Pat. Nos. 6,294,153; 6,344,194; 6,071,497, and PCT applications WO02/066078; WO02/053190; WO01/60420; WO00/66206. Further, methods for delivering iRNA agents can be adapted from those used in delivering other oligonucleotides (e.g., an antisense oligonucleotide) by inhalation, such as described in Templin et al., Antisense Nucleic Acid Drug Dev, 2000, 10:359-68; Sandrasagra et al., Expert Opin Biol Ther, 2001, 1:979-83; Sandrasagra et al., Antisense Nucleic Acid Drug Dev, 2002, 12:177-81.

The delivery of the inventive agents may also involve the administration of so called “pro-drugs”, i.e. formulations or chemical modifications of a therapeutic substance that require some form of processing or transport by systems innate to the subject organism to release the therapeutic substance, preferably at the site where its action is desired. For example, the human lungs can remove or rapidly degrade hydrolytically cleavable deposited aerosols over periods ranging from minutes to hours. In the upper airways, ciliated epithelia contribute to the “mucociliary excalator” by which particles are swept from the airways toward the mouth. Pavia, D., “Lung Mucociliary Clearance,” in Aerosols and the Lung: Clinical and Experimental Aspects, Clarke, S. W. and Pavia, D., Eds., Butterworths, London, 1984. In the deep lungs, alveolar macrophages are capable of phagocytosing particles soon after their deposition. Warheit et al. Microscopy Res. Tech., 26: 412-422 (1993); and Brain, J. D., “Physiology and Pathophysiology of Pulmonary Macrophages,” in The Reticuloendothelial System, S. M. Reichard and J. Filkins, Eds., Plenum, New. York., pp. 315-327, 1985.

In preferred embodiments, particularly where systemic dosing with the iRNA agent is desired, the aerosoled iRNA agents are formulated as microparticles. Microparticles having a diameter of between 0.5 and ten microns can penetrate the lungs, passing through most of the natural barriers. A diameter of less than ten microns is required to bypass the throat; a diameter of 0.5 microns or greater is required to avoid being exhaled.

The iRNA agent of the invention can be delivered using an implant. Such implants can be biodegradable and/or biocompatible implants, or may be non-biodegradable implants. The implants may be permeable or impermeable to the active agent.

The iRNA agent of the invention can also be administered topically, e.g. to the skin, for example by patch or by direct application to the dermis, or by iontophoresis. Ointments, sprays, or droppable liquids can be delivered by delivery systems known in the art such as applicators or droppers.

The iRNA agent of the invention may be provided in sustained release compositions, such as those described in, for example, U.S. Pat. Nos. 5,672,659 and 5,595,760. The use of immediate or sustained release compositions depends on the nature of the condition being treated. If the condition consists of an acute or over-acute disorder, treatment with an immediate release form will be preferred over a prolonged release composition. Alternatively, for certain preventative or long-term treatments, a sustained release composition may be appropriate.

In addition to treating pre-existing disorders or diseases associated with undesired TGF-beta signaling, iRNA agents of the invention can be administered prophylactically in order to prevent or slow the onset of these and related disorders or diseases. In prophylactic applications, an iRNA of the invention is administered to a patient susceptible to or otherwise at risk of a particular disorder or disease associated with undesired TGF-beta signaling.

The iRNA agent of the invention can be administered in a single dose or in multiple doses. Where the administration of the iRNA agent of the invention is by infusion, the infusion can be a single sustained dose or can be delivered by multiple infusions. Injection of the agent directly into the tissue is at or near the site of undesired TGF-beta signaling is preferred. Multiple injections of the agent into the tissue at or near the site of undesired TGF-beta signaling are also preferred.

Dosage. The dosage can be an amount effective to treat or prevent a disorder or disease associated with undesired TGF-beta signaling.

One skilled in the art can readily determine an appropriate dosage regimen for administering the iRNA agent of the invention to a given subject. For example, the iRNA agent can be administered to the subject once, e.g., as a single injection or deposition at or near the site of undesired TGF-beta signaling. Alternatively, the unit dose is administered less frequently than once a day, e.g., less than every 2, 4, 8 or 30 days. In another embodiment, the unit dose is not administered with a frequency (e.g., not a regular frequency). Because iRNA agent mediated silencing can persist for several days after administering the iRNA agent composition, in many instances, it is possible to administer the composition with a frequency of less than once per day, or, for some instances, only once for the entire therapeutic regimen, or only upon the reoccurrence of a symptom or disease state. Alternatively, the iRNA agent can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more preferably from about seven to about ten days. In a preferred dosage regimen, the iRNA agent is injected at or near a site of unwanted TGF-beta expression (such as near a site of fibrosis or sclerosis) once a day for seven days. Where a dosage regimen comprises multiple administrations, it is understood that the effective amount of iRNA agent administered to the subject can comprise the total amount of iRNA agent administered over the entire dosage regimen.

In one embodiment, a subject is administered an initial dose, and one or more maintenance doses of an iRNA agent, e.g., a double-stranded iRNA agent, or siRNA agent, (e.g., a precursor, e.g., a larger iRNA agent which can be processed into an siRNA agent, or a DNA which encodes an iRNA agent, e.g., a double-stranded iRNA agent, or siRNA agent, or precursor thereof). The maintenance doses are preferably administered no more than once every 5, 10, or 30 days. Further, the treatment regimen may last for a period of time which will vary depending upon the nature of the particular disease, its severity and the overall condition of the patient. In preferred embodiments the dosage may be delivered no more than once per day, e.g., no more than once per 24, 36, 48, or more hours, e.g., no more than once every 5 or 8 days. Following treatment, the patient can be monitored for changes in his condition and for alleviation of the symptoms of the disease state. The dosage of the compound may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disease state is observed, if the disease state has been ablated, or if undesired side-effects are observed.

The effective dose can be administered in a single dose or in two or more doses, as desired or considered appropriate under the specific circumstances. If desired to facilitate repeated or frequent infusions, implantation of a delivery device, e.g., a pump, semi-permanent stent (e.g., intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable.

The concentration of the iRNA agent composition is an amount sufficient to be effective in treating or preventing a disorder or to regulate a physiological condition in humans. The concentration or amount of iRNA agent administered will depend on the parameters determined for the agent and the method of administration, e.g. administration to the lung. For example, inhalable formulations may require lower concentrations of some ingredients in order to avoid irritation or discomfort compared to oral formulations. It is sometimes desirable to dilute an oral formulation up to 10-100 times in order to provide a suitable inhalable formulation.

Certain factors may influence the dosage required to effectively treat a subject, including but not limited to the severity and responsiveness of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. It will also be appreciated that the effective dosage of an iRNA agent such as an siRNA agent used for treatment may increase or decrease over the course of a particular treatment. Changes in dosage may result and become apparent from the results of diagnostic assays. For example, the subject can be monitored after administering an iRNA agent composition. Based on information from the monitoring, an additional amount of the iRNA agent composition can be administered.

Moreover, depending on the above factors, the course of treatment may last from several days to several months, or until a cure is effected or a diminution of disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual compounds, and can generally be estimated based on EC50s found to be effective in in vitro and in vivo animal models.

Dosage levels on the order of about 1 μg/kg to 100 mg/kg of body weight per administration are useful in the treatment of the disorders or diseases associated with undesired TGF-beta signaling. The preferred dosage range is about 0.00001 mg to about 3 mg per kg body weight of the subject to be treated, or preferably about 0.0001-0.001 mg per kg body weight, about 0.03-3.0 mg per kg body weight, about 0.1-3.0 mg per kg body weight or about 0.3-3.0 mg per kg body weight.

An iRNA agent can be administered at a unit dose less than about 75 mg per kg of bodyweight, or less than about 70, 60, 50, 40, 30, 20, 10, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.005, 0.001, or 0.0005 mg per kg of bodyweight, and less than 200 nmol of iRNA agent (e.g., about 4.4×10¹⁶ copies) per kg of bodyweight, or less than 1500, 750, 300, 150, 75, 15, 7.5, 1.5, 0.75, 0.15, 0.075, 0.015, 0.0075, 0.0015, 0.00075, 0.00015 nmol of iRNA agent per kg of bodyweight. The unit dose, for example, can be administered by injection (e.g., intravenous or intramuscular, intrathecally, or directly into an organ), an inhaled dose, or a topical application.

Delivery of an iRNA agent directly to an organ (e.g., directly to the liver or lung) can be at a dosage on the order of about 0.00001 mg to about 3 mg per organ, or preferably about 0.0001-0.001 mg per organ, about 0.03-3.0 mg per organ, about 0.1-3.0 mg per kg body weight or about 0.3-3.0 mg per organ.

Where an initial dose/maintenance dose regimen is followed, the maintenance dose or doses are generally lower than the initial dose, e.g., one-half less of the initial dose. A maintenance regimen can include treating the subject with a dose or doses ranging from 0.01 μg to 75 mg/kg of body weight per day, e.g., 70, 60, 50, 40, 30, 20, 10, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.005, 0.001, or 0.0005 mg per kg of bodyweight per day.

The invention is further illustrated by the following examples, which should not be construed as further limiting.

EXAMPLES

Example 1

Selection for the Targeting of TGF-Beta by Short Interfering siRNAs

siRNA design was carried out to identify siRNAs targeting human and mouse TGF-beta 1 genes. The siRNA in silicon selection resulted in 28 siRNAs satisfying our selection criteria.

Human (NM_—000660.3; May 4, 2005) and mouse (NM_—011577.1; Dec. 17, 2003) mRNA sequences to TGF-beta were downloaded from NCBI resource http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=nucleotide.

To setup an environment for sequence analysis, BioEdit Sequence Alignment Editor software (Version 7.0.4.1; Hall, T. A., Nucl. Acids. Symp. Ser., 1999, 41:95-98) was downloaded from http://www.mbio.ncsu.edu/BioEdit/bioedit.html and installed on a windows 2000 computer.

The siRNA selection process was run as follows: ClustalW multiple alignment (Thompson J D, et al., Nucleic Acids Res. 1994, 22:4673-80) function of the software was used to generate a global alignment of human and mouse mRNA sequences. Conserved regions were identified by embedded sequence analysis function of the software. For this, conserved regions were defined as sequence stretches with a minimum length of 19 bases for all aligned sequences containing no internal gaps. In order to have a reference sequence available for positions of conserved stretches and finally siRNA target region coordination, a mapping file with positions of consensus sequence relative to human mRNA sequence was generated by the software and analyzed by a perl script.

The siRNA design web interface at Whitehead Institute for Biomedical Research (http://jura.wi.mit.edu/siRNAext/) was used to identify all candidate siRNAs targeting the conserved regions as well as their predicted off-target hits to human and mouse sequences. For this purpose, candidate siRNAs proposed by the tool were subjected to the software embedded off-target analysis by running the NCBI blast algorithm against the NCBI human and mouse RefSeq database.

Blast results were downloaded and analyzed by a perl script in order to extract an off-target score for each candidate siRNA that was used for siRNA ranking. Final goal for ranking and selection was to prefer siRNAs with high specificity. We defined an off-target score to express off-target potential of each siRNA based on the following assumptions:

1) high specificity can be predicted by weak identity to off-target hits

2) positions 2 to 9 (counting 5′ to 3′) of a strand (seed region) may contribute more to off-target potential than rest of sequence (non-seed region)

Thus, the identity score of the antisense strand calculated by blast was considered as well as the positions of occurring mismatches. The off-target score was defined as the highest score out of all scores for an siRNA calculated for each off-target hit obtained by blast.

The off-target score was calculated as follows: identity score—0.2 * mismatches in seed region.

siRNAs were sorted according to off-target score (ascending). The top 28 siRNAs according to the above criteria were selected and synthesized.

Designing siRNAs Against TGF-Beta mRNA

siRNA against TGF-beta mRNA were synthesized chemically using procedures established in the art. Two different designs of siRNAs were synthesized and tested for each base sequence obtained in the selection step described above, for a total of 56 siRNAs. The first group consisted of unmodified ribonucleotides, except that the unpaired 3′-overhangs on both strands consisted of 2′-deoxy thymidines. The second group further included a phosphorothioate linkage between the two unpaired 2′-deoxy thymidines at the end of each strand, 2′O-methyl modifications at every pyrimidine base in the sense strand, and 2′O-methyl modifications at every uridine occurring in a sequence context of 5′-ua-3′ and every cytidine occurring in a sequence context of 5′-ca-3′. Modifications in the oligonucleotide strands were accomplished by using the appropriate modified monomer phosphoramidite. The siRNA sequences of those siRNAs synthesized are listed in Table 1, together with the position of the target sequence for each siRNA in NM_—000660.3.

Example 2

TGF-Beta siRNA in Vitro Screening Protocol

Human lung epithelial A549 carcinoma cells were transfected with unstabilized and phosphorothioate/O-methyl exo-/endonuclease stabilized siRNAs to select a set of most active siRNAs for further development as potential drug candidates in preclinical and clinical studies.

For transfections, A549 cells (ATCC, Manassas, USA, ATCC #: CCL-185) were seeded at 1.5×10⁴ cells/well on 96-well cell culture plates (Greiner Bio-One GmbH, Frickenhausen, Germany) in 100 μl growth medium (RPMI 1640, 10% fetal calf serum, 100 u/ml penicillin 100 μg/ml streptomycin, 2 mM L-glutamine; Biochrom AG, Berlin, Germany) Transfection of each siRNA was performed 24 h post-seeding at 100 nM and 10 nM final concentration of siRNA duplex in quadruplets using Lipofectamine 2000 (Invitrogen GmbH, Karlsruhe, Germany). For each well, 0.5 μl Lipofectamine 2000 were mixed with 12.5 μl Opti-MEM (Invitrogen) and incubated for 5 min at room temperature. To achieve a final siRNA concentration of 100 nM in the incubation mixture, 2.5 μl of a 5 μM solution of siRNA in annealing buffer per well were mixed with 10 μl Opti-MEM, per well. To achieve a final siRNA concentration of 10 nM, 2.5 μl of a 0.5 μM solution of siRNA in annealing buffer were mixed with 10 μl Opti-MEM, per well. The siRNA solution was combined with the diluted Lipofectamine 2000 solution, gently mixed and incubated for 20 minutes at room temperature to allow complex formation. In the meantime, growth medium was removed from cells and replaced by 100 μl/well of fresh medium. 25 μl of the siRNA-Lipofectamine-2000-complex solution were applied to the cells to a final volume of 125 μl per well and cells were incubated for 24 h at 37° C. and 5% CO₂ in a humidified incubator (Heraeus GmbH, Hanau).

Following incubation, TGF-beta mRNA levels were determined by QuantiGene bDNA-kit (Genospectra, Fremont, USA). The incubation mixture was replaced by 100 μl fresh growth medium and cells were lysed by applying 50 μl of lysis mixture from the QuantiGene bDNA-kit and incubation for 30 min at 53° C. Cell lysates were incubated in parallel with bDNA probes specific to hGAPDH (10 μl lysate) and hTGF-beta (40 μl lysate) on QuantiGene Capture Plates and processed according to the manufacturer's protocol for the QuantiGene bDNA kit. The nucleotide sequences of the bDNA probes used for hTGF-beta and hGAPDH are given in Table 2 and Table 3 below, respectively. Finally, chemoluminescence was measured in a Victor2-Light (Perkin Elmer, Wiesbaden, Germany) as relative light units (RLU) and values obtained with hGAPDH and hTGF-beta probesets were normalized to the respective GAPDH values for each well. TGF-beta/GAPDH ratios obtained with siRNAs directed against TGF-beta finally were related to the value obtained with the same concentration (100 nM or 10 nM) of an unspecific siRNA (directed against ApoB) which was set to 100%.

Effective siRNAs from the screen were further characterized by dose response curves (DRC). Transfections for dose response curves were performed at the following concentrations: 100 nM, 25 nM, 6.3 nM, 1.6 nM, 0.4 nM, 0.1 nM, 25 pM according to the above protocol. The % TGF-beta mRNA knockdown again was related to a 100% value obtained from a control siRNA transfection. The dsRNA concentrations at which 50% of their maximal activity was achieved (Inhibitory concentration 50%, IC50) were calculated by curve fitting with the computer software Xlfit, (ID Business Solutions Ltd., Guildford, Surrey, UK) using the following parameters: Dose Response One Site, 4 Parameter Logistic Model, fit=(A+((B−A)/(1+(((10̂C)/x)̂D)))), inv=((10̂C)/((((B−A)/(y−A))−1)̂(1/D))), res=(y−fit).

bDNA probes used in bDNA assay for TGF-β (generated with Bayer QuantiGene Probeset Software):

TABLE 2
TGF-β-specific probes detecting hsTGF-β1 (Genbank accession no.
NM_000660.3)
			SEQ ID
FPL Name	Function	Sequence	NO
hsTGFb 001	CE	GGGCTCCGGTTCTGCACTCTTTTTTCTCTTGGAAAGAAAGT	113
hsTGFb 002	CE	CGCGGGTGACCTCCTTGGTTTTTCTCTTGGAAAGAAAGT	114
hsTGFb 003	CE	GCAGCTCTGCCCGGGAGATTTTTCTCTTGGAAAGAAAGT	115
hsTGFb 004	CE	TTTTAACTTGAGCCTCAGCAGACTTTTTCTCTTGGAAAGAAAGT	116
hsTGFb 005	CE	GGTTGCTGAGGTATCGCCAGTTTTTCTCTTGGAAAGAAAGT	117
hsTGFb 006	CE	GCTGGGTGCCAGCAGCCTTTTTCTCTTGGAAAGAAAGT	118
hsTGFb 007	LE	CGTAGTAGTCGGCCTCAGGCTCTTTTTAGGCATAGGACCCGTGTCT	119
hsTGFb 008	LE	TGTGGGTTTCCACCATTAGCATTTTTAGGCATAGGACCCGTGTCT	120
hsTGFb 009	LE	GCTTCTCGGAGCTCTGATGTGTTTTTTAGGCATAGGACCCGTGTCT	121
hsTGFb 010	LE	GCAACACGGGTTCAGGTACCTTTTTAGGCATAGGACCCGTGTCT	122
hsTGFb 011	LE	GAATTGTTGCTGTATTTCTGGTACATTTTTAGGCATAGGACCCGTGTCT	123
hsTGFb 012	BL	TGCTTGAACTTGTCATAGATTTCGT	124
hsTGFb 013	BL	TGAAGAACATATATATGCTGTGTGTACTC	125
hsTGFb 014	BL	GCTCCACGTGCTGCTCCAC	126

TABLE 3
GAPDH-specific probes detecting hsGAPDH (Genbank accession no.
NM_002046.2):
			SEQ ID
FPL Name	Function	Sequence	NO
hGAP001	CE	GAATTTGCCATGGGTGGAATTTTTTCTCTTGGAAAGAAAGT	127
hGAP002	CE	GGAGGGATCTCGCTCCTGGATTTTTCTCTTGGAAAGAAAGT	128
hGAP003	CE	CCCCAGCCTTCTCCATGGTTTTTTCTCTTGGAAAGAAAGT	129
hGAP004	CE	GCTCCCCCCTGCAAATGAGTTTTTCTCTTGGAAAGAAAGT	130
hGAP005	LE	AGCCTTGACGGTGCCATGTTTTTAGGCATAGGACCCGTGTCT	131
hGAP006	LE	GATGACAAGCTTCCCGTTCTCTTTTTAGGCATAGGACCCGTGTCT	132
hGAP007	LE	AGATGGTGATGGGATTTCCATTTTTTTAGGCATAGGACCCGTGTCT 133
hGAP008	LE	GCATCGCCCCACTTGATTTTTTTTTAGGCATAGGACCCGTGTCT	134
hGAP009	LE	CACGACGTACTCAGCGCCATTTTTAGGCATAGGACCCGTGTCT	135
hGAP010	LE	GGCAGAGATGATGACCCTTTTGTTTTTAGGCATAGGACCCGTGTCT	136
hGAP011	BL	GGTGAAGACGCCAGTGGACTC	137

Table 4 shows the relative activity of the dsRNA duplexes of Table 1 towards reducing TGF-beta mRNA in A549 cells after incubation with the respective dsRNA at 100 nM or 10 nM concentration, expressed as % of the TGF-beta mRNA concentration found in A549 cells that were similarly treated except for incubation with the same concentration of a dsRNA specific for ApoB. In addition, IC50 are given for select duplexes.

TABLE 4
Activity of siRNAs in lowering TGF-beta mRNA
in A549 cells compared to A549 cells treated
with a control siRNA specific for ApoB
	remaining TGF-beta
	RNA in % of control
Duplex	at 100 nM	at 10 nM	IC(50)
identifier	duplex conc.	duplex conc.	[nM]
AL-DP-6837	29 ± 5%	47 ± 19%
AL-DP-6140	84 ± 7%	88 ± 9%
AL-DP-6838	22 ± 12%	34 ± 8%	0, 67
AL-DP-6141	81 ± 16%	118 ± 13%
AL-DP-6839	99 ± 10%	105 ± 5%
AL-DP-6142	87 ± 3%	115 ± 18%
AL-DP-6840	31 ± 6%	37 ± 1%
AL-DP-6143	48 ± 3%	86 ± 7%	23
AL-DP-6841	75 ± 13%	65 ± 29%
AL-DP-6144	80 ± 7%	94 ± 12%
AL-DP-6842	28 ± 10%	27 ± 4%	0, 12
AL-DP-6145	78 ± 9%	100 ± 22%
AL-DP-6843	77 ± 9%	69 ± 13%
AL-DP-6146	81 ± 3%	102 ± 4%
AL-DP-6844	48 ± 7%	45 ± 20%
AL-DP-6147	71 ± 18%	99 ± 12%
AL-DP-6845	20 ± 17%	29 ± 5%	0, 16
AL-DP-6148	87 ± 20%	98 ± 11%
AL-DP-6846	40 ± 14%	49 ± 29%
AL-DP-6149	90 ± 13%	96 ± 13%
AL-DP-6847	36 ± 22%	46 ± 27%
AL-DP-6150	66 ± 22%	75 ± 9%
AL-DP-6848	14 ± 5%	20 ± 6%	0, 31
AL-DP-6151	95 ± 5%	122 ± 20%
AL-DP-6849	33 ± 12%	31 ± 9%
AL-DP-6262	75 ± 5%	113 ± 4%
AL-DP-6850	68 ± 30%	74 ± 6%
AL-DP-6263	102 ± 27%	142 ± 19%
AL-DP-6851	26 ± 11%	52 ± 11%
AL-DP-6264	23 ± 3%	59 ± 9%	4, 4
AL-DP-6852	21 ± 9%	32 ± 18%
AL-DP-6265	86 ± 15%	79 ± 16%
AL-DP-6853	41 ± 12%	52 ± 14%
AL-DP-6266	83 ± 3%	97 ± 32%
AL-DP-6854	92 ± 12%	118 ± 33%
AL-DP-6267	79 ± 12%	83 ± 11%
AL-DP-6855	22 ± 2%	28 ± 6%
AL-DP-6268	88 ± 15%	107 ± 46%
AL-DP-6856	43 ± 4%	54 ± 3%
AL-DP-6269	70 ± 11%	92 ± 24%
AL-DP-6857	13 ± 5%	35 ± 24%	0, 04
AL-DP-6270	71 ± 15%	89 ± 30%
AL-DP-6858	11 ± 3%	28 ± 17%	0, 13
AL-DP-6271	34 ± 12%	51 ± 15%	0, 68
AL-DP-6859	14 ± 2%	26 ± 11%	0, 15
AL-DP-6272	33 ± 5%	56 ± 6%	2, 2
AL-DP-6860	31 ± 1%	45 ± 11%
AL-DP-6273	118 ± 29%	161 ± 17%
AL-DP-6861	32 ± 7%	65 ± 37%
AL-DP-6274	76 ± 4%	111 ± 11%
AL-DP-6862	16 ± 3%	27 ± 14%	0, 19
AL-DP-6275	93 ± 41%	96 ± 20%
AL-DP-6863	36 ± 17%	37 ± 15%
AL-DP-6276	56 ± 12%	74 ± 32%
AL-DP-6864	46 ± 26%	62 ± 19%
AL-DP-6277	110 ± 18%	83 ± 40%

From Table 4, it can be seen that, at 100 nM concentration, AL-DP-6858, AL-DP-6857, AL-DP-6859, AL-DP-6848, and AL-DP-6862 reduced TGF-beta mRNA in A549 cells by more than 80%. Additionally, under these circumstances, AL-DP-6845, AL-DP-6852, AL-DP-6838, AL-DP-6855, AL-DP-6264, AL-DP-6851, AL-DP-6842, and AL-DP-6837 reduced TGF-beta mRNA in A549 cells by more than 70%. Additionally, AL-DP-6840, AL-DP-6860, AL-DP-6861, AL-DP-6849, AL-DP-6272, AL-DP-6271, AL-DP-6847, AL-DP-6863 reduced TGF-beta mRNA in A549 cells by more than 60%. Additionally, AL-DP-6846, AL-DP-6853, AL-DP-6856, AL-DP-6864, AL-DP-6844, AL-DP-6143 reduced TGF-beta mRNA in A549 cells by more than 50%. Additionally, AL-DP-6276 reduced TGF-beta mRNA in A549 cells by more than 40%. Additionally, AL-DP-6150 and AL-DP-6850 reduced TGF-beta mRNA in A549 cells by more than 30%. Finally, AL-DP-6269, AL-DP-6270, AL-DP-6147, AL-DP-6262, AL-DP-6841, AL-DP-6274, AL-DP-6843, AL-DP-6145, and AL-DP-6267 reduced TGF-beta mRNA in A549 cells by more than 20%.

Example 3

Screening of Additional siRNA for Activity in Inhibiting TGF-Beta Expression

In order to identify as many RNAi agents with suitable activity as possible, the above screen was extended to further target sequences. For the selection of an expanded screening set we re-calculated the predicted specificity based on the newly available human RefSeq database (Human mRNA sequences in RefSeq release version 21 (downloaded Jan. 12, 2007)) and selected only those 220 non-poly-G siRNAs (no occurrence of 3 or more consecutive guanines) targeting 19mer target sequences in NM_—000660.3 with off-target scores of 3 or more for the antisense strand. These agents were then screened for their activity in lowering the amount of TGF-beta mRNA present in A549 cells treated with the agents as described above, except that transfection with the agents was performed directly after seeding, rather than 24 h after seeding, and that the concentration of the agents in the transfection mixture was 30 nM.

As may be concluded from the results shown in Table 5, AD-14501, AD-14503, AD-14507, AD-14554, AD-14594, AD-14597, and AD-14633 reduced TGF-beta mRNA in A549 cells by more than 90%. Additionally, under these circumstances, AD-14419, AD-14420, AD-14421, AD-14422, AD-14423, AD-14428, AD-14430, AD-14434, AD-14438, AD-14449, AD-14453, AD-14459, AD-14460, AD-14464, AD-14469, AD-14470, AD-14473, AD-14474, AD-14476, AD-14486, AD-14490, AD-14495, AD-14496, AD-14497, AD-14509, AD-14515, AD-14522, AD-14526, AD-14540, AD-14552, AD-14555, AD-14557, AD-14565, AD-14567, AD-14568, AD-14582, AD-14588, AD-14590, AD-14592, AD-14598, AD-14600, AD-14601, AD-14603, AD-14604, AD-14608, AD-14610, AD-14612, AD-14614, AD-14622, AD-14634, and AD-14635 reduced TGF-beta mRNA in A549 cells by more than 80%. Additionally, under these circumstances, AD-14425, AD-14426, AD-14427, AD-14429, AD-14431, AD-14436, AD-14437, AD-14441, AD-14448, AD-14458, AD-14463, AD-14467, AD-14477, AD-14482, AD-14483, AD-14491, AD-14502, AD-14505, AD-14508, AD-14512, AD-14513, AD-14519, AD-14524, AD-14537, AD-14546, AD-14548, AD-14549, AD-14559, AD-14563, AD-14564, AD-14569, AD-14578, AD-14579, AD-14587, AD-14595, AD-14599, AD-14607, AD-14609, AD-14629, AD-14631, and AD-14637 reduced TGF-beta mRNA in A549 cells by more than 70%. Additionally, under these circumstances, AD-14447, AD-14451, AD-14471, AD-14484, AD-14487, AD-14498, AD-14523, AD-14527, AD-14529, AD-14539, AD-14541, AD-14558, AD-14561, AD-14573, AD-14589, AD-14596, AD-14605, AD-14615, AD-14626, and AD-14630 reduced TGF-beta mRNA in A549 cells by more than 60%. Additionally, under these circumstances, AD-14432, AD-14480, AD-14485, AD-14488, AD-14499, AD-14504, AD-14516, AD-14518, AD-14520, AD-14547, AD-14572, AD-14577, AD-14580, AD-14583, AD-14584, AD-14618, AD-14621, and AD-14625 reduced TGF-beta mRNA in A549 cells by more than 50%. Additionally, under these circumstances, AD-14435, AD-14445, AD-14450, AD-14456, AD-14466, AD-14475, AD-14489, AD-14492, AD-14511, AD-14535, AD-14536, AD-14538, AD-14553, AD-14560, AD-14562, AD-14576, AD-14581, AD-14586, and AD-14627 reduced TGF-beta mRNA in A549 cells by more than 40%. Additionally, under these circumstances, AD-14433, AD-14472, AD-14478, AD-14493, AD-14510, AD-14544, AD-14566, AD-14570, AD-14575, AD-14593, and AD-14613 reduced TGF-beta mRNA in A549 cells by more than 30%. Additionally, under these circumstances, AD-14424, AD-14442, AD-14444, AD-14446, AD-14454, AD-14525, AD-14543, AD-14571, AD-14606, AD-14611, AD-14616, AD-14617, AD-14619, and AD-14638 reduced TGF-beta mRNA in A549 cells by more than 20%.

TABLE 5
Additional RNAi agents targeting hTGF-beta
							Remaining
							TGF-beta
		Position of					mRNA in %
		target		SEQ		SEQ	of controls
Duplex	19mer target	sequence in	Sense	ID	Antisense	ID	± stand.
identifer	sequence	NM_000660.3	strand sequence	NO:	strand sequence	NO:	dev.
AD-14419	aauuccuggcgauaccuca	1396-1414	aauuccuggcgauaccucaTT	138	ugagguaucgccaggaauuTT	139	16 ± 1
AD-14420	ucgcgcccaucuagguuau	654-672	ucgcgcccaucuagguuauTT	140	auaaccuagaugggcgcgaTT	141	19 ± 2
AD-14421	ggucacccgcgugcuaaug	1188-1206	ggucacccgcgugcuaaugTT	142	cauuagcacgcgggugaccTT	143	19 ± 2
AD-14422	aggucacccgcgugcuaau	1187-1205	aggucacccgccugcuaauTT	144	auuagcacgcgggugaccuTT	145	10 ± 1
AD-14423	cacccgcgugcuaauggug	1191-1209	cacccgcgugcuaauggugTT	146	caccauuagcacgcgggugTT	147	18 ± 1
AD-14424	uacaaccagcauaacccgg	1894-1912	uacaaccagcauaacccggTT	148	ccggguuaugcugguuguaTT	149	79 ± 5
AD-14425	aucgcgcccaucuagguua	653-671	aucgcgcccaucuagguuaTT	150	uaaccuagaugggcgcgauTT	151	24 ± 1
AD-14426	guaccagaucgcgcccauc	646-664	guaccagaucgcgcccaucTT	152	gaugggcgcgaucugguacTT	153	21 ± 1
AD-14427	agacggaucucucuccgac	589-607	agacggaucucucuccgacTT	154	gucggagagagauccgucuTT	155	26 ± 4
AD-14428	cgcgcccaucuagguuauu	655-673	cgcgcccaucuagguuauuTT	156	aauaaccuagaugggcgcgTT	157	19 ± 1
AD-14429	cccgcgcauccuagacccu	558-576	cccgcgcauccuagacccuTT	158	agggucuaggaugcgcgggTT	159	24 ± 3
AD-14430	gcgcccaucuagguuauuu	656-674	gcgcccaucuagguuauuuTT	160	aaauaaccuagaugggcgcTT	161	18 ± 1
AD-14431	uccgugggauacugagaca	674-692	uccgugggauacugagacaTT	162	ugucucaguaucccacggaTT	163	25 ± 3
AD-14432	cuuucgccuuagcgcccac	1515-1533	cuuucgccuuagcgcccacTT	164	gugggcgcuaaggcgaaagTT	165	41 ± 2
AD-14433	acccgcgugcuaauggugg	1192-1210	acccgcgugcuaaugguggTT	166	ccaccauuagcacgcggguTT	167	60 ± 4
AD-14434	gcaacaauuccuggcgaua	1391-1409	gcaacaauuccuggcgauaTT	168	uaucgccaggaauuguugcTT	169	10 ± 0
AD-14435	aacggguucacuaccggcc	1576-1594	aacggguucacuaccggccTT	170	ggccgguagugaacccguuTT	171	57 ± 4
AD-14436	cggguucacuaccggccgc	1578-1596	cggguucacuaccggccgcTT	l72	gcggccgguagugaacccgTT	173	28 ± 3
AD-14437	cuguauuuaaggacacccg	2117-2135	cuguauuuaaggacacccgTT	174	cggguguccuuaaauacagTT	175	21 ± 1
AD-14438	agguuauuuccgugggaua	666-684	agguuauuuccgugggauaTT	176	uaucccacggaaauaaccuTT	177	19 ± 1
AD-14439	cccucgggagucgccgacc	458-476	cccucgggagucgccgaccTT	178	ggucggcgacucccgagggTT	179	90 ± 4
AD-14440	ugugcggcagugguugagc	1476-1494	ugugcggcagugguugagcTT	180	gcucaaccacugccgcacaTT	181	375 ± 34
AD-14441	caaccagcauaacccgggc	1896-1914	caaccagcauaacccgggcTT	182	gcccggguuaugcugguugTT	183	28 ± 4
AD-14442	uuuugagacuuuuccguug	281-299	uuuugagacuuuuccguugTT	184	caacggaaaagucucaaaaTT	185	75 ± 2
AD-14443	uuugagacuuuuccguugc	282-300	uuugagacuuuuccguugcTT	186	gcaacggaaaagucucaaaTT	187	98 ± 9
AD-14444	cucuuggcgcgacgcugcc	326-344	cucuuggcgcgacgcugccTT	188	ggcagcgucgcgccaagagTT	189	70 ± 4
AD-14445	ucugguaccagaucgcgcc	642-660	ucugguaccagaucgcgccTT	190	ggcgcgaucugguaccagaTT	191	50 ± 2
AD-14446	acaccagcccuguucgcgc	817-835	acaccagcccuguucgcgcTT	192	gcgcgaacagggcugguguTT	193	71 ± 4
AD-14447	cggccggccgcgggacuau	940-958	cggccggccgcgggacuauTT	194	auagucccgcggccggccgTT	195	38 ± 1
AD-14448	gguaccugaacccguguug	1296-1314	gguaccugaacccguguugTT	196	caacacggguucagguaccTT	197	21 ± 1
AD-14449	guaccugaacccguguugc	1297-1315	guaccugaacccguguugcTT	198	gcaacacggguucagguacTT	199	17 ± 1
AD-14450	auuccuggcgauaccucag	1397-1415	auuccuggcgauaccucagTT	200	cugagguaucgccaggaauTT	201	58 ± 6
AD-14451	auugagggcuuucgccuua	1507-1525	auugagggcuuucgccuuaTT	202	uaaggcgaaagcccucaauTT	203	31 ± 3
AD-14452	acaaccagcauaacccggg	1895-1913	acaaccagcauaacccgggTT	204	cccggguuaugcugguuguTT	205	87 ± 8
AD-14453	uguauuuaaggacacccgu	2118-2136	uguauuuaaggacacccguTT	206	acggguguccuuaaauacaTT	207	16 ± 2
AD-14454	gaggacugcggaucucugu	2174-2192	gaggacugcggaucucuguTT	208	acagagauccgcaguccucTT	209	77 ± 5
AD-14455	gggaacacuacuguaguua	2324-2342	gggaacacuacuguaguuaTT	210	uaacuacaguaguguucccTT	211	86 ± 4
AD-14456	accagcccuguucgcgcuc	819-837	accagcccuguucgcgcucTT	212	gagcgcgaacagggcugguTT	213	59 ± 0
AD-14457	agaggacugcggaucucug	2173-2191	agaggacugcggaucucugTT	214	cagagauccgcaguccucuTT	215	91 ± 3
AD-14458	guacuacgugggccgcaag	1968-1986	guacuacgugggccgcaagTT	216	cuugcggcccacguaguacTT	217	24 ± 1
AD-14459	gaucgcgcccaucuagguu	652-670	gaucgcgcccaucuagguuTT	218	aaccuagaugggcgcgaucTT	219	13 ± 1
AD-14460	aacgaaaucuaugacaagu	1219-1237	aacgaaaucuaugacaaguTT	220	acuugucauagauuucguuTT	221	16 ± 2
AD-14461	uucgccuuagcgcccacug	1517-1535	uucgccuuagcgcccacugTT	222	cagugggcgcuaaggcgaaTT	223	107 ± 6
AD-14462	aucaacggguucacuaccg	1573-1591	aucaacggguucacuaccgTT	224	cgguagugaacccguugauTT	225	107 ± 3
AD-14463	ccgcgcauccuagacccuu	559-577	ccgcgcauccuagacccuuTT	226	aagggucuaggaugcgcggTT	227	24 ± 3
AD-14464	gcgcauccuagacccuuuc	561-579	gcgcauccuagacccuuucTT	228	gaaagggucuaggaugcgcTT	229	15 ± 1
AD-14465	uuucgccuuagcgcccacu	1516-1534	uuucgccuuagcgcccacuTT	230	agugggcgcuaaggcgaaaTT	231	85 ± 6
AD-14466	cugguaccagaucgcgccc	641-661	cugguaccagaucgcgcccTT	232	gggcgcgaucugguaccagTT	233	54 ± 3
AD-14467	cagaucgcgcccaucuagg	650-668	cagaucgcgcccaucuaggTT	234	ccuagaugggcgcgaucugTT	235	25 ± 1
AD-14468	uccuaccuuuugccgggag	763-781	uccuaccuuuugccgggagTT	236	cucccggcaaaagguaggaTT	237	93 ± 5
AD-14469	cccuguucgcgcucucggc	824-842	cccuguucgcgcucucggcTT	238	gccgagagcgcgaacagggTT	239	16 ± 2
AD-14470	ccuguucgcgcucucggca	825-843	ccuguucgcgcucucggcaTT	240	ugccgagagcgcgaacaggTT	241	16 ± 3
AD-14471	cuguucgcgcucucggcag	826-844	cuguucgcgcucucggcagTT	242	cugccgagagcgcgaacagTT	243	32 ± 3
AD-14472	aagacuaucgacauggagc	967-985	aagacuaucgacauggagcTT	244	gcuccaugucgauagucuuTT	245	63 ± 9
AD-14473	cccgcgugcuaauggugga	1193-1211	cccgcgugcuaaugguggaTT	246	uccaccauuagcacgcgggTT	247	12 ± 2
AD-14474	cgugcuaaugguggaaacc	1197-1215	cgugcuaaugguggaaaccTT	248	gguuuccaccauuagcacgTT	249	13 ± 1
AD-14475	ccggaguugugcggcagug	1469-1487	ccggaguugugcggcagugTT	250	cacugccgcacaacuccggTT	251	52 ± 6
AD-14476	gcuuucgccuuagcgccca	1514-1532	gcuuucgccuuagcgcccaTT	252	ugggcgcuaaggcgaaagcTT	253	16 ± 0
AD-14477	agggauaacacacugcaag	1549-1567	agggauaacacacugcaagTT	254	cuugcaguguguuaucccuTT	255	22 ± 1
AD-14478	caucaacggguucacuacc	1572-1590	caucaacggguucacuaccTT	256	gguagugaacccguugaugTT	257	68 ± 1
AD-14479	uuuaaggacacccgugccc	2122-2140	uuuaaggacacccgugcccTT	258	gggcacggguguccuuaaaTT	259	92 ± 5
AD-14480	gacuuuuccguugccgcug	287-305	gacuuuuccguugccgcugTT	260	cagcggcaacggaaaagucTT	261	41 ± 5
AD-14481	uuuuccguugccgcuggga	290-308	uuuuccguugccgcugggaTT	262	ucccagcggcaacggaaaaTT	263	81 ± 3
AD-14482	gggaccucuuggcgcgacg	321-339	gggaccucuuggcgcgacgTT	264	cgucgcgccaagaggucccTT	265	26 ± 1
AD-14483	ggaccucuuggcgcgacgc	322-340	ggaccucuuggcgcgacgcTT	266	gcgucgcgccaagagguccTT	267	28 ± 3
AD-14484	gaccucuuggcgcgacgcu	323-341	gaccucuuggcgcgacgcuTT	268	agcgucgcgccaagaggucTT	269	33 ± 1
AD-14485	ccuacacggcgucccucag	419-437	ccuacacggcgucccucagTT	270	cugagggacgccguguaggTT	271	49 ± 1
AD-14486	cgcgcauccuagacccuuu	560-578	cgcgcauccuagacccuuuTT	272	aaagggucuaggaugcgcgTT	273	15 ± 2
AD-14487	cauccuagacccuuucucc	564-582	cauccuagacccuuucuccTT	274	ggagaaagggucuaggaugTT	275	33 ± 7
AD-14488	ugguaccagaucgcgccca	644-662	ugguaccagaucgcgcccaTT	276	ugggcgcgaucugguaccaTT	277	49 ± 5
AD-14489	uaccagaucgcgcccaucu	647-665	uaccagaucgcgcccaucuTT	278	agaugggcgcgaucugguaTT	279	59 ± 6
AD-14490	agaucgcgcccaucuaggu	651-669	agaucgcgcccaucuagguTT	280	accuagaugggcgcgaucuTT	281	19 ± 3
AD-14491	gcccaucuagguuauuucc	658-676	gcccaucuagguuauuuccTT	282	ggaaauaaccuagaugggcTT	283	25 ± 1
AD-14492	cuaccuuuugccgggagac	765-783	cuaccuuuugccgggagacTT	284	gucucccggcaaaagguagTT	285	55 ± 2
AD-14493	guucgcgcucucggcagug	828-846	guucgcgcucucggcagugTT	286	cacugccgagagcgcgaacTT	287	66 ± 9
AD-14494	uucgcgcucucggcagugc	829-847	uucgcgcacucggcagugcTT	288	gcacugccgagagcgcgaaTT	289	102 ± 12
AD-14495	accugcaagacuaucgaca	961-979	accugcaagacuaucgacaTT	290	ugucgauagucuugcagguTT	291	19 ± 1
AD-14496	cugcaagacuaucgacaug	963-981	cugcaagacuaucgacaugTT	292	caugucgauagucuugcagTT	293	14 ± 1
AD-14497	gcaagacuaucgacaugga	965-983	gcaagacuaucgacauggaTT	294	uccaugucgauagucuugcTT	295	15 ± 1
AD-14498	caagacuaucgacauggag	966-984	caagacuaucgacauggagTT	296	cuccaugucgauagucuugTT	297	37 ± 3
AD-14499	uguacaacagcacccgcga	1106-1124	uguacaacagcacccgcgaTT	298	ucgcgggugcuguuguacaTT	299	42 ± 2
AD-14500	ugaggccgacuacuacgcc	1164-1182	ugaggccgacuacuacgccTT	300	ggcguaguagucggccucaTT	301	122 ± 7
AD-14501	aaacccacaacgaaaucua	1211-1229	aaacccacaacgaaaucuaTT	302	uagauuucguuguggguuuTT	303	9 ± 1
AD-14502	ccacaacgaaaucuaugac	1215-1233	ccacaacgaaaucuaugacTT	304	gucauagauuucguuguggTT	305	24 ± 2
AD-14503	aguacacacagcauauaua	1246-1264	aguacacacagcauauauaTT	306	uauauaugcuguguguacuTT	307	8 ± 0
AD-14504	cgguaccugaacccguguu	1295-1313	cgguaccugaacccguguuTT	308	aacacggguucagguaccgTT	309	45 ± 4
AD-14505	uaccugaacccguguugcu	1298-1316	uaccugaacccguguugcuTT	310	agcaacacggguucagguaTT	311	29 ± 2
AD-14506	cccguguugcucucccggg	1336-1324	cccguguugcucucccgggTT	312	cccgggagagcaacacgggTT	313	107 ± 5
AD-14507	cugcgucugcugaggcuca	1330-1348	cugcgucugcugaggcucaTT	314	ugagccucagcagacgcagTT	315	9 ± 1
AD-14508	aggcucaaguuaaaagugg	1342-1360	aggcucaaguuaaaaguggTT	316	ccacuuuuaacuugagccuTT	317	20 ± 1
AD-14509	caacaauuccuggcgauac	1392-1410	caacaauuccuggcgauacTT	318	guaucgccaggaauuguugTT	319	14 ± 1
AD-14510	aacaauuccuggcgauacc	1393-1411	aacaauuccuggcgauaccTT	320	gguaucgccaggaauuguuTT	321	65 ± 3
AD-14511	uggcgauaccucagcaacc	1402-1420	uggcgauaccucagcaaccTT	322	gguugcugagguaucgccaTT	323	58 ± 5
AD-145l2	cgauaccucagcaaccggc	1405-1423	cgauaccucagcaaccggcTT	324	gccgguugcugagguaucgTT	325	20 ± 0
AD-14513	gauaccucagcaaccggcu	1406-1424	gauaccucagcaaccggcuTT	326	agccgguugcugagguaucTT	327	24 ± 1
AD-14514	cuggcacccagcgacucgc	1426-1444	cuggcacccagcgacucgcTT	328	gcgagucgcugggugccagTT	329	86 ± 13
AD-14515	gacucgccagagugguuau	1438-l456	gacucgccagagugguuauTT	330	auaaccacucuggcgagucTT	331	11 ± 1
AD-14516	acucgccagagugguuauc	1439-1457	acucgccagagugguuaucTT	332	gauaaccacucuggcgaguTT	333	47 ± 2
AD-14517	ugucaccggaguugugcgg	1464-1482	ugucaccggaguugugcggTT	334	ccgcacaacuccggugacaTT	335	115 ± 7
AD-14518	caccggaguugugcggcag	1467-1485	caccggaguugugcggcagTT	336	cugccgcacaacuccggugTT	337	44 ± 3
AD-14519	accggaguugugcggcagu	1468-1486	accggaguugugcggcaguTT	338	acugccgcacaacuccgguTT	339	28 ± 2
AD-14520	aaauugagggcuuucgccu	1505-1523	aaauugagggcuuucgccuTT	340	aggcgaaagcccucaauuuTT	341	46 ± 2
AD-14521	uugagggcuuucgccuuag	1508-1526	uugagggcuuucgccuuagTT	342	cuaaggcgaaagcccucaaTT	343	130 ± 15
AD-14522	gggcuuucgccuuagcgcc	1512-1530	gggcuuucgccuuagcgccTT	344	ggcgcuaaggcgaaagcccTT	345	14 ± 1
AD-14523	ccuuagcgcccacugcucc	1521-1539	ccuuagcgcccacugcuccTT	346	ggagcagugggcgcuaaggTT	347	30 ± 1
AD-14524	aaguggacaucaacggguu	1565-1583	aaguggacaucaacggguuTT	348	aacccguugauguccacuuTT	349	20 ± 1
AD-14525	caacggguucacuaccggc	1575-1593	caacggguucacuaccggcTT	350	gccgguagugaacccguugTT	351	73 ± 6
AD-14526	cuaccggccgccgagguga	1586-1604	cuaccggccgccgaggugaTT	352	ucaccucggcggccgguagTT	353	18 ± 1
AD-14527	caucugcaaagcucccggc	1675-1693	caucugcaaagcucccggcTT	354	gccgggagcuuugcagaugTT	355	37 ± 2
AD-14528	cguguacuacgugggccgc	1965-1983	cguguacuacgugggccgcTT	356	gcggcccacguaguacacgTT	357	80 ± 4
AD-14529	caacaugaucgugcgcucc	2007-2025	caacaugaucgugcgcuccTT	358	ggagcgcacgaucauguugTT	359	35 ± 2
AD-14530	cugugucauugggcgccug	2189-2207	cugugucauugggcgccugTT	360	caggcgcccaaugacacagTT	361	89 ± 6
AD-14531	ugccugucugcacuauucc	2273-2291	ugccugucugcacuauuccTT	362	ggaauagugcagacaggcaTT	363	97 ± 4
AD-14532	cacuauuccuuugcccggc	2283-2301	cacuauuccuuugcccggcTT	364	gccgggcaaaggaauagugTT	365	98 ± 8
AD-14533	aacacuacuguaguuagau	2327-2345	aacacuacuguaguuagauTT	366	aucuaacuacaguaguguuTT	367	89 ± 8
AD-14534	acacuacuguaguuagauc	2328-2346	acacuacuguaguuagaucTT	368	gaucuaacuacaguaguguTT	369	80 ± 2
AD-14535	gucugagacgagccgccgc	185-203	gucugagacgagccgccgcTT	370	gcggcggcucgucucagacTT	371	57 ± 4
AD-14536	cccuacacggcgucccuca	418-436	cccuacacggcgucccucaTT	372	ugagggacgccguguagggTT	373	50 ± 4
AC-14537	acggaucucucuccgaccu	591-609	acggaucucucuccgaccuTT	374	aggucggagagagauccguTT	375	23 ± 3
AD-14538	ggccggccgcgggacuauc	941-959	ggccggccgcgggacuaucTT	376	gauagucccgcggccggccTT	377	50 ± 2
aD-14539	cgcggccagauccugucca	1015-1033	cgcggccagauccuguccaTT	378	uggacaggaucuggccgcgTT	379	34 ± 3
AD-14540	ggaaacccacaacgaaauc	1209-1227	ggaaacccacaacgaaaucTT	380	gauuucguuguggguuuccTT	381	11 ± 0
AD-14541	acaauuccuggcgauaccu	1394-1412	acaauuccuggcgauaccuTT	382	agguaucgccaggaauuguTT	383	31 ± 2
AD-14542	agucugagacgagccgccg	184-202	agucugagacgagccgccgTT	384	cggcggcucgucucagacuTT	385	87 ± 1
AD-14543	cacggcgucccucaggcgc	423-441	cacggcgucccucaggcgcTT	386	gcgccugagggacgccgugTT	387	76 ± 3
AD-14544	acggcgucccucaggcgcc	424-442	acggcgucccucaggcgccTT	388	ggcgccugagggacgccguTT	389	68 ± 3
AD-14545	accagcccucgggagucgc	453-471	accagcccucgggagucgcTT	390	gcgacucccgagggcugguTT	391	96 ± 7
AD-14546	gcauccuagacccuuucuc	563-581	gcauccuagacccuuucucTT	392	gagaaagggucuaggaugcTT	393	22 ± 2
AD-14547	gacggaucucucuccgacc	590-608	gacggaucucucuccgaccTT	394	ggucggagagagauccgucTT	395	43 ± 2
AD-14548	gguaccagaucgcgcccau	645-663	gguaccagaucgcgcccauTT	396	augggcgcgaucugguaccTT	397	27 ± 3
AD-14549	uagguuauuuccgugggau	665-683	uagguuauuuccgugggauTT	398	aucccacggaaauaaccuaTT	399	22 ± 1
AD-14550	accuuuugccgggagaccc	767-785	accuuuugccgggagacccTT	400	gggucucccggcaaaagguTT	401	89 ± 2
AD-14551	ucgcgcucucggcagugcc	830-848	ucgcgcucucggcagugccTT	402	ggcacugccgagagcgcgaTT	403	95 ± 3
AD-14552	uauccaccugcaagacuau	956-974	uauccaccugcaagacuauTT	404	auagucuugcagguggauaTT	405	15 ± 1
AD-14553	ccgcggccagauccugucc	1014-1032	ccgcggccagauccuguccTT	406	ggacaggaucuggccgcggTT	407	53 ± 5
AD-14554	aacccacaacgaaaucuau	1212-1230	aacccacaacgaaaucuauTT	408	auagauuucguuguggguuTT	409	8 ± 1
AD-14555	agcgguaccugaacccgug	1293-1311	agcgguaccugaacccgugTT	410	cacggguucagguaccgcuTT	411	14 ± 2
AD-14556	uggcacccagcgacucgcc	1427-1445	uggcacccagcgacucgccTT	412	ggcgagucgcugggugccaTT	413	88 ± 9
AD-14557	cucgccagagugguuaucu	1440-1458	cucgccagagugguuaucuTT	414	agauaaccacucuggcgagTT	415	18 ± 2
AD-14558	cggcagugguugagccgug	1480-1498	cggcagugguugagccgugTT	416	cacggcucaaccacugccgTT	417	32 ± 2
AD-14559	gugguugagccguggaggg	1485-1503	gugguugagccguggagggTT	418	cccuccacggcucaaccacTT	419	24 ± 1
AD-14560	gagggcuuucgccuuagcg	1510-1528	gagggcuuucgccuuagcgTT	420	cgcuaaggcgaaagcccucTT	421	51 ± 2
AD-14561	agggcuuucgccuuagcgc	1511-1529	agggcuuucgccuuagcgcTT	422	gcgcuaaggcgaaagcccuTT	423	37 ± 1
AD-14562	ggugaccuggccaccauuc	1600-1618	ggugaccuggccaccauucTT	424	gaaugguggccaggucaccTT	425	51 ± 5
AD-14563	accauucauggcaugaacc	1612-1630	accauucauggcaugaaccTT	426	gguucaugccaugaaugguTT	427	29 ± 2
AD-14564	cauggcaugaaccggccuu	1618-1636	cauggcaugaaccggccuuTT	428	aaggccgguucaugccaugTT	429	25 ± 2
AD-14565	ccaacuauugcuucagcuc	1712-1730	ccaacuauugcuucagcucTT	430	gagcugaagcaauaguuggTT	431	11 ± 1
AD-14566	gaacugcugcgugcggcag	1740-1758	gaacugcugcgugcggcagTT	432	cugccgcacgcagcaguucTT	433	62 ± 3
AD-14567	gcccuguacaaccagcaua	1888-1906	gcccuguacaaccagcauaTT	434	uaugcugguuguacagggcTT	435	10 ± 0
AD-14568	cuguacaaccagcauaacc	1891-1909	cuguacaaccagcauaaccTT	436	gguuaugcugguuguacagTT	437	19 ± 0
AD-14569	guacaaccagcauaacccg	1893-1911	guacaaccagcauaacccgTT	438	cggguuaugcugguuguacTT	439	21 ± 1
AD-14570	cuauuccuuugcccggcau	2285-2303	cuauuccuuugcccggcauTT	440	augccgggcaaaggaauagTT	441	65 ± 2
AD-14571	agcggaggaaggagucgcc	143-161	agcggaggaaggagucgccTT	442	ggcgacuccuuccuccgcuTT	443	75 ± 2
AD-14572	ggaggaaggagucgccgag	146-164	ggaggaaggagucgccgagTT	444	cucggcgacuccuuccuccTT	445	43 ± 2
AD-14573	acuuuugagacuuuuccgu	279-297	acuuuugagacuuuuccguTT	446	acggaaaagucucaaaaguTT	447	32 ± 2
AD-14574	uugagacuuuuccguugcc	283-301	uugagacuuuuccguugccTT	448	ggcaacggaaaagucucaaTT	449	96 ± 4
AD-14575	accucuuggcgcgacgcug	324-342	accucuuggcgcgacgcugTT	450	cagcgucgcgccaagagguTT	451	67 ± 3
AD-14576	gacccggccucccgcaaag	473-491	gacccggccucccgcaaagTT	452	cuuugcgggaggccgggucTT	453	54 ± 3
AD-14577	cccggccucccgcaaagac	475-493	cccggccucccgcaaagacTT	454	gucuuugcgggaggccgggTT	455	48 ± 4
AD-14578	cuccuccaggagacggauc	579-597	cuccuccaggagacggaucTT	456	gauccgucuccuggaggagTT	457	25 ± 1
AD-14579	caccuucugguaccagauc	637-655	caccuucugguaccagaucTT	458	gaucugguaccagaaggugTT	459	25 ± 1
AD-14580	cuucugguaccagaucgcg	640-658	cuucugguaccagaucgcgTT	460	cgcgaucugguaccagaagTT	461	42 ± 2
AD-14581	uucugguaccagaucgcgc	641-659	uucugguaccagaucgcgcTT	462	gcgcgaucugguaccagaaTT	463	56 ± 2
AD-14582	gguuauuuccgugggauac	667-685	gguuauuuccgugggauacTT	464	guaucccacggaaauaaccTT	465	19 ± 2
AD-14583	accucagcuuucccucgag	740-758	accucagcuuucccucgagTT	466	cucgagggaaagcugagguTT	467	40 ± 4
AD-14584	ccucagcuuucccucgagg	741-759	ccucagcuuucccucgaggTT	468	ccucgagggaaagcugaggTT	469	47 ± 5
AD-14585	uaccuuuugccgggagacc	766-784	uaccuuuugccgggagaccTT	470	ggucucccggcaaaagguaTT	471	102 ± 7
AD-14586	ccaugccgcccuccgggcu	866-884	ccaugccgcccuccgggcuTT	472	agcccggagggcggcauggTT	473	54 ± 3
AD-14587	acuauccaccugcaagacu	954-972	acuauccaccugcaagacuTT	474	agucuugcagguggauaguTT	475	22 ± 2
AD-14588	cuauccaccugcaagacua	955-973	cuauccaccugcaagacuaTT	476	uagucuugcagguggauagTT	477	14 ± 1
AD-14589	guccaagcugcggcucgcc	1029-1047	guccaagcugcggcucgccTT	478	ggcgagccgcagcuuggacTT	479	31 ± 2
AD-14590	cgagccugaggccgacuac	1158-1176	cgagccugaggccgacuacTT	480	guagucggccucaggcucgTT	481	16 ± 1
AD-14591	ugguggaaacccacaacga	1205-1223	ugguggaaacccacaacgaTT	482	ucguuguggguuuccaccaTT	483	98 ± 4
AD-14592	acccacaacgaaaucuaug	1213-1231	acccacaacgaaaucuaugTT	484	cauagauuucguuguggguTT	485	14 ± 1
AD-14593	ucaagcagaguacacacag	1238-1256	ucaagcagaguacacacagTT	486	cuguguguacucugcuugaTT	487	67 ± 8
AD-14594	cagaguacacacagcauau	1243-1261	cagaguacacacagcauauTT	488	auaugcuguguguacucugTT	489	9 ± 1
AD-14595	ucuucaacacaucagagcu	1268-1286	ucuucaacacaucagagcuTT	490	agcucugauguguugaagaTT	491	23 ± 3
AD-14596	gcgguaccugaacccgugu	1294-1312	gcgguaccugaacccguguTT	492	acacggguucagguaccgcTT	493	33 ± 2
AD-14597	cugcugaggcucaaguuaa	1336-1354	cugcugaggcucaaguuaaTT	494	uuaacuugagccucagcagTT	495	8 ± 1
AD-14598	gcgauaccucagcaaccgg	1404-1422	gcgauaccucagcaaccggTT	496	ccgguugcugagguaucgcTT	497	15 ± 0
AD-14599	ggcacccagcgacucgcca	1428-1446	ggcacccagcgacucgccaTT	498	uggcgagucgcugggugccTT	499	20 ± 2
AD-14600	ccagcgacucgccagagug	1433-1451	ccagcgacucgccagagugTT	500	cacucuggcgagucgcuggTT	501	17 ± 2
AD-14601	gagugguuaucuuuugaug	1447-1465	gagugguuaucuuuugaugTT	502	caucaaaagauaaccacucTT	503	13 ± 1
AD-14602	uugugcggcagugguugag	1475-1493	uugugcggcagugguugagTT	504	cucaaccacugccgcacaaTT	505	132 ± 9
AD-14603	ugugacagcagggauaaca	1540-1558	ugugacagcagggauaacaTT	506	uguuaucccugcugucacaTT	507	16 ± 3
AD-14604	acagcagggauaacacacu	1544-1562	acagcagggauaacacacuTT	508	aguguguuaucccugcuguTT	509	19 ± 1
AD-14605	cagcagggauaacacacug	1545-1563	cagcagggauaacacacugTT	510	caguguguuaucccugcugTT	511	34 ± 2
AD-14606	uaacacacugcaaguggac	1554-1572	uaacacacugcaaguggacTT	512	guccacuugcaguguguuaTT	513	76 ± 2
AD-14607	guucacuaccggccgccga	1581-1599	guucacuaccggccgccgaTT	514	ucggcggccgguagugaacTT	515	23 ± 1
AD-14600	uggccaccauucauggcau	1607-1625	uggccaccauucauggcauTT	516	augccaugaaugguggccaTT	517	19 ± 1
AD-14609	cauucauggcaugaaccgg	1614-1632	cauucauggcaugaaccggTT	518	ccgguucaugccaugaaugTT	519	24 ± 2
AD-14610	cagcaucugcaaagcuccc	1672-1690	cagcaucugcaaagcucccTT	520	gggagcuuugcagaugcugTT	521	17 ± 2
AD-14611	gcaaagcucccggcaccgc	1680-1698	gcaaagcucccggcaccgcTT	522	gcggugccgggagcuuugcTT	523	73 ± 5
AD-14612	ggagaagaacugcugcgug	1734-1752	ggagaagaacugcugcgugTT	524	cacgcagcaguucuucuccTT	525	13 ± 0
AD-14613	gaagaacugcugcgugcgg	1737-1755	gaagaacugcugcgugcggTT	526	ccgcacgcagcaguucuucTT	527	62 ± 4
AD 14614	gcuggaaguggauccacga	1787-1805	gcuggaaguggauccacgaTT	528	ucguggauccacuuccagcTT	529	12 ± 1
AD-14615	uuuggagccuggacacgca	1853-1871	uuuggagccuggacacgcaTT	530	ugcguguccaggcuccaaaTT	531	35 ± 1
AD-14616	uuggagccuggacacgcag	1854-1872	uuggagccuggacacgcagTT	532	cugcguguccaggcuccaaTT	533	76 ± 7
AD-14617	gccgugcugcgugccgcag	1926-1944	gccgugcugcgugccgcagTT	534	cugcggcacgcagcacggcTT	535	71 ± 5
AD-14618	uguccaacaugaucgugcg	2003-2021	uguccaacaugaucgugcgTT	536	cgcacgaucauguuggacaTT	537	41 ± 2
AD-14619	cugcggaucucugugucau	2179-2197	cugcggaucucugugucauTT	538	augacacagagauccgcagTT	539	76 ± 7
AD-14620	gcacuauuccuuugcccgg	2282-2300	gcacuauuccuuugcccggTT	540	ccgggcaaaggaauagugcTT	541	89 ± 9
AD-14621	ccggccucccgcaaagacu	476-494	ccggccucccgcaaagacuTT	542	agucuuugcgggaggccggTT	543	48 ± 3
AD-14622	cuacuggugcugacgccug	919-937	cuacuggugcugacgccugTT	544	caggcgucagcaccaguagTT	545	14 ± 1
AD-14623	auucauggcaugaaccggc	1615-1633	auucauggcaugaaccggcTT	546	gccgguucaugccaugaauTT	547	103 ± 6
AD-14624	aacugcugcgugcggcagc	1741-1759	aacugcugcgugcggcagcTT	548	gcugccgcacgcagcaguuTT	549	82 ± 3
AD-14625	cggaggaaggagucgccga	145-163	cggaggaaggagucgccgaTT	550	ucggcgacuccuuccuccgTT	551	47 ± 3
AD-14626	ggagcgggaggagggacga	236-254	ggagcgggaggagggacgaTT	552	ucgucccuccucccgcuccTT	553	31 ± 1
AD-14627	gcccucgggagucgccgac	457-475	gcccucgggagucgccgacTT	554	gucggcgacucccgagggcTT	555	56 ± 6
AD-14628	uuucuccuccaggagacgg	576-594	uuucuccuccaggagacggTT	556	ccgucuccuggaggagaaaTT	557	90 ± 3
AD-14629	ucgaggcccuccuaccuuu	754-772	ucgaggcccuccuaccuuuTT	558	aaagguaggagggccucgaTT	559	25 ± 2
AD-14630	uacuggugcugacgccugg	920-938	uacuggugcugacgccuggTT	560	ccaggcgucagcaccaguaTT	561	34 ± 2
AD-14631	gacuauccaccugcaagac	953-971	gacuauccaccugcaagacTT	562	gucuugcagguggauagucTT	563	24 ± 3
AD-14632	uacaacagcacccgcgacc	1108-1126	uacaacagcacccgcgaccTT	564	ggucgcgggugcuguuguaTT	565	113 ± 4
AD-14633	ugcugaggcucaaguuaaa	1337-1355	ugcugaggcucaaguuaaaTT	566	uuuaacuugagccucagcaTT	567	8 ± 1
AD-14634	ccugugacagcagggauaa	1538-1556	ccugugacagcagggauaaTT	568	uuaucccugcugucacaggTT	569	14 ± 1
AD-14635	auaacacacugcaagugga	1553-1571	auaacacacugcaaguggaTT	570	uccacuugcaguguguuauTT	571	18 ± 1
AD-14636	uauugcuucagcuccacgg	1717-1735	uauugcuucagcuccacggTT	572	ccguggagcugaagcaauaTT	573	109 ± 5
AD-14637	gcuguccaacaugaucgug	2001-2019	gcuguccaacaugaucgugTT	574	cacgaucauguuggacagcTT	575	29 ± 1
AD-14638	gucuccaucccugacguuc	2214-2232	gucuccaucccugacguucTT	576	gaacgucagggauggagacTT	577	75 ± 11
1a, g, c, u: ribonucleotide 5′-monophosphates (except where in 5′-most position, see below);
T: deoxythymidine 5′-monophosphate;
all sequences given 5′ → 3′; due to synthesis procedures, the 5′-most nucleic acid is a nucleoside, i.e. does not bear a 5′-monophosphate group

Claims

1. An isolated iRNA agent, comprising an antisense strand and a sense strand substantially complementary to said antisense strand, wherein the iRNA agent mediates the cleavage of a TGF-beta mRNA within the target sequence of iRNA agent AL-DP-6857.

2. The iRNA agent of claim 1, wherein the target sequence is nucleotides 1711 to 1733 of NM—000660.3.

3. The iRNA agent of claim 1, wherein the iRNA agent further comprises a non-nucleotide moiety.

4. The iRNA of claim 1, wherein the iRNA agent is stabilized against nucleolytic degradation.

5. The iRNA agent of claim 1, wherein the sense strand and/or the antisense strand further comprises at least one 3′-overhang wherein the 3′-overhang comprises from 1 to 6 nucleotides.

6. The iRNA agent of claim 1, further comprising a phosphorothioate at the first internucleotide linkage at the 5′ end of the sense strand and/or the antisense strand.

7. The iRNA agent of claim 1, further comprising a phosphorothioate at the first internucleotide linkage at the 3′ end of the sense strand and/or the antisense strand.

8. The iRNA agent of claim 1, further comprising a 2′-modified nucleotide in the sense strand and/or the antisense strand.

9. The iRNA agent of claim 8, wherein the 2′-modified nucleotide comprises a modification selected from the group consisting of: 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP), 2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl (2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), and 2′-O—N-methylacetamido (2′-O-NMA).

10. The iRNA agent of claim 1, wherein the sense strand comprises 15 or more contiguous nucleotides of the nucleotide sequence of SEQ ID NO:81.

11. The iRNA agent of claim 1, wherein the iRNA agent is AL-DP-6857.

12. The iRNA agent of claim 1, wherein the antisense strand comprises 15 or more contiguous nucleotides of the nucleotide sequence of SEQ ID NO:82.

13. The iRNA agent of claim 1, wherein the sense strand comprises SEQ ID NO:83.

14. The iRNA agent of claim 1, wherein the antisense strand comprises SEQ ID NO:84.

15. The iRNA agent of claim 1, wherein the iRNA agent is AL-DP-6270.

16. A vector encoding the iRNA agent of claim 1.

17. A cell comprising the iRNA agent of claim 1.

18. A method of making the iRNA agent of claim 1, the method comprising the synthesis of the iRNA agent, wherein the sense and antisense strands comprise at least one modification that stabilizes the iRNA agent against nucleolytic degradation.

19. A pharmaceutical composition comprising the iRNA agent of claim 1 and a pharmaceutically acceptable carrier.

20. A method of treating a human diagnosed as having a disease or disorder associated with undesired TGF-beta signaling, comprising administering to a subject in need of such treatment a therapeutically effective amount of the iRNA agent of claim 1.

21. The method of claim 20, wherein the human is diagnosed as having idiopathic pulmonary fibrosis, diabetic nephropathy or chronic liver disease.

22. A method of reducing the levels of a TGF-beta mRNA in a cell of a subject, or of TGF-beta protein secreted by a cell of a subject, comprising the step of administering the iRNA agent of claim 1 to said subject.

23. The method of claim 22, wherein said iRNA agent mediates the cleavage of a TGF-beta mRNA within the target sequence of iRNA agent AL-DP-6857.

24. The method of claim 22, wherein said administration comprises pulmonary administration.