US20070044161A1 - RNAi modulation of the Rho-A gene in research models - Google Patents

RNAi modulation of the Rho-A gene in research models Download PDF

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US20070044161A1
US20070044161A1 US11/491,440 US49144006A US2007044161A1 US 20070044161 A1 US20070044161 A1 US 20070044161A1 US 49144006 A US49144006 A US 49144006A US 2007044161 A1 US2007044161 A1 US 2007044161A1
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rhoa
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irna agent
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Juergen Soutschek
Pamela Tan
Anke Geick
Stephane Budel
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Yale University
Alnylam Pharmaceuticals Inc
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Definitions

  • the invention relates to compositions and methods for modulating the expression of RhoA, and more particularly to the downregulation of RhoA mRNA and RhoA protein levels by oligonucleotides via RNA interference, e.g., chemically modified oligonucleotides.
  • 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.
  • RhoA is a member of the large family of Rho (Ras homologue) GTPases, itself belonging to the superfamily of Ras GTPases. All eukaryotes contain at least one Rho GTPase. During the process of evolution the number of Rho GTPases increased from 5 to 6 per organism (yeast) to over 20 (mammals) (Karnoub, A. E., et al., Breast Cancer Res. Treat. 2004, 84:61). Like other GTPases, RhoA has intrinsic GTPase activity and shuttles between an inactive GDP-bound state and an active GTP-bound state.
  • GEFs guanine nucleotide exchange factors
  • GAPs GTPase activating proteins
  • Rho GTPases contains the majority of the amino acids involved in GTP binding and hydrolysis, together with the Switch 1 and 2 regions that change conformation between the GTP-bound and GDP-bound states (Bishop, A. L., Hall, A., Biochem. J. 2000, 348 (Pt. 2):241).
  • the C-terminus of Rho family GTPases is essential for correct localization of the proteins. It is post-translationally modified by prenylation of a conserved C-terminal cysteine followed by methylation and proteolytic removal of the last three amino acids (Shao, F., Dixon, J. E., Adv. Exp. Med. Biol. 2003, 529:79).
  • the prenyl group anchors the GTPases into membranes and this modification is essential for cell growth, transformation, and cytoskeleton organization (Allal, C., et al., J. Biol. Chem. 2000, 275:31001).
  • Prenylation of Rho proteins appears to be important for their stability, inhibitors of enzymes that synthesize prenyl groups induce a decrease in Rho protein levels and their function (Stamatakis, K., et al., J. Biol. Chem 2002, 277:49389).
  • prenylation adds a geranylgeranyl group.
  • RhoA is mainly found in the cytoplasm or at the plasma membrane (Adamson, P., et al., J. Cell Biol. 1992, 119:617).
  • RhoA may bind to the intracellular portion of p75NTR and is activated by Nogo-R in a p75NTR-dependent manner (Wang, K. C., et al., Nature 2002, 420:74), which is how MAG, Nogo-66, and oligodendrocyte-myelin glycoprotein achieve RhoA activation.
  • RhoA is part of the growth inhibitory machinery present in the central nervous system (CNS), but not in peripheral nerves, which prevents the regeneration of CNS tissue after injury. Both the expression and the activation of RhoA is induced in brain and spinal cord injury (Mueller, K., et al., Nature Reviews 2005, 4:387). Activation of RhoA leads to neuronal growth cone collapse, retraction bulb formation and neurite withdrawal. Inactivation of RhoA leads to neurite outgrowth in primary neurons on otherwise inhibitory substrates in vitro, and promotes axon regeneration and functional recovery after spinal cord injury in rats and mice in vivo (Lehmann, M. A., et al., J. Neurosci.
  • RhoA is a potential target for therapeutic intervention strategies aimed at diseases and conditions involving, e.g., the destruction and/or impaired regeneration of cells of the CNS.
  • the present invention advances the art by providing methods and medicaments encompassing short dsRNAs leading to the downregulation of RhoA mRNA and protein levels in cells expressing the RhoA gene. These methods and medicaments may be used in the treatment of disorders or pathological processes mediated, at least in part, by RhoA, e.g., by preventing the RhoA inhibition of axonal elongation and regeneration, and consequently stimulating nerve growth and proliferation.
  • the present invention is based, at least in part, on an investigation of the RhoA gene using iRNA agents and further testing of the iRNA agents that target the RhoA site.
  • the present invention provides compositions and methods that are useful in reducing RhoA mRNA levels, RhoA protein levels and the treatment of pathological process mediated, at least in part, by RhoA, e.g. preventing RhoA inhibition of axonal elongation and regeneration, in a subject, e.g., a mammal, such as a human.
  • the invention provides iRNA agents comprising a sense strand, wherein the sense strand comprises at least 15 contiguous nucleotides that differ by no more than 1, 2, or 3 nucleotides from the sense strand sequences of any one agent selected from the group consisting of: agents number 6477 to 6836 as given in Table 1 below, and an antisense strand, wherein the antisense strand comprises at least 15 contiguous nucleotides that differ by no more than 1, 2, or 3 nucleotides from the antisense sequences of any one agent selected from the group consisting of: agents number 6477 to 6836.
  • the invention provides iRNA agents for inhibiting the expression of a rhoA gene in a cell comprising a sense strand, wherein the sense strand comprises at least 15 contiguous nucleotides that differ by no more than 1, 2, or 3 nucleotides from the sense strand sequences of any one agent selected from the group consisting of: agents number 6477 to 6836, and an antisense strand wherein the antisense strand comprises at least 15 contiguous nucleotides of the antisense sequences of any one agent selected from the group consisting of: agents number 6477 to 6836, and wherein the iRNA agent reduces the amount of RhoA MRNA present in cultured human cells after incubation with these agents by 40% or more compared to cells which have not been incubated with the agent.
  • the invention provides iRNA agents for inhibiting the expression of a rhoA gene in a cell comprising a sense strand and an antisense strand each comprising a sequence of at least 16, 17 or 18 nucleotides which is essentially identical to one of the sequences of any one agent selected from the group consisting of: agents number 6477 to 6836, 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 RhoA expression.
  • agents number 6477 to 6836 e.g. adenosine replaced by uracil
  • the sense and/or antisense strand sequence is chosen from the group consisting of: the sense and antisense strand sequences of agent numbers 6523, 6524, 6530, 6614, 6650, 6656, 6657, 6661, 6662, 6703, 6712, 6713, 6732, 6751, 6756, 6767, 6769, 6787, 6789, 6790, 6832.
  • the sense strands and/or antisense strands of the iRNA agents of the invention can also be identical to the sense strands and antisense strands of the agents, agent numbers 6477 to 6836.
  • the iRNA agents of the invention may comprise a modification, e.g a modification that causes the iRNA agent to have increased stability in a biological sample.
  • they may comprise a phosphorothioate, a 2′-modified nucleotide, a locked nucleotide, an abasic nucleotide, morpholino nucleotide, a phosphoramidate, or a non-natural base comprising nucleotide.
  • an iRNA agent is considered to comprise one of the sequences of the agents, agent numbers 6477 to 6836, irrespective of the potential presence of nucleotide modifications, i.e.
  • the invention provides iRNA agents for inhibiting the expression of a rhoA gene in a cell wherein the sense and/or antisense strand sequence is chosen from the group consisting of: the sense and antisense strand sequences of agent numbers AL-DP-5972, AL-DP-5973, AL-DP-5974, AL-DP-5975, AL-DP-5976, AL-DP-5978, AL-DP-5979, AL-DP-5981, AL-DP-5982, AL-DP-5983, AL-DP-5984, AL-DP-5986, AL-DP-5987, AL-DP-5988, AL-DP-5989, AL-DP-5990, AL-DP-5991, AL-DP-5992, AL-DP-5993, AL-DP-5994, AL-DP-5995,
  • the antisense RNA strand may be 30 or fewer nucleotides in length, and the duplex region of the iRNA agent may be 15-30 nucleotide pairs in length.
  • a 2′-modified nucleotide according to the instant invention may comprise at least one 5′-uridine-adenine-3′ (5′-ua-3′) dinucleotide wherein the uridine 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′-cytidine-adenine-3′ (5′-ca-3′) dinucleotide, wherein the 5′-cytidine is a 2′-modified nucleotide; or at least one 5′-uridine-uridine-3′ (5′-uu-3′) dinucleotide, wherein the 5′-uridine is a 2′-modified nucleotide.
  • the iRNA agents of the invention may be designed such that
  • every 5′-nucleotide in 5′-ua-3′, 5′-uu-3′, 5′-ca-3′, and 5′-ug-3′ motifs is a 2′-modified in sense strand, and every 5′-nucleotide in 5′-ua-3′ and 5′-ca-3′ motifs is 2′-modified in antisense strand, or
  • every 5′-nucleotide in 5′-ua-3′, 5′-uu-3′, 5′-ca-3′, and 5′-ug-3′ motifs is 2′-modified in the sense and antisense strand, or
  • every pyrimidine nucleotide is 2′-modified in the sense strand, and every 5′-nucleotide in 5′-ua-3′ and 5′-ca-3′ motifs is 2′-modified in the antisense strand, or
  • every pyrimidine nucleotide is 2′-modified in sense strand, and every 5′-nucleotide in 5′-ua-3′, 5′-uu-3′, 5′-ca-3′, and 5′-ug-3′ motifs is 2′-modified in the antisense strand, or
  • every pyrimidine nucleotide in the sense strand is 2′-modified, and no nucleotide is 2′-modified in the antisense strand.
  • the 2′-modification in the iRNA agents of the invention may be 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).
  • the iRNA agents of the invention may comprise a nucleotide overhang having 1 to 4 unpaired nucleotides, preferably 2 or 3 unpaired nucleotides.
  • the nucleotide overhang may be at the 3′-end of the antisense strand of the iRNA agent.
  • the iRNA agents may comprise a cholesterol moiety, which is preferably conjugated to the 3′-end of the sense strand of the iRNA agent.
  • the iRNA agent is targeted for uptake by nerve cells or nerve sheath cells.
  • the present invention further provides methods for reducing the level of RhoA mRNA in a cell.
  • the present methods utilize the cellular mechanisms involved in RNA interference to selectively degrade RhoA mRNA in a cell and are comprised of the step of contacting a cell with one of the 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 of the present invention.
  • Reduction of RhoA mRNA in a cell results in a reduction in the amount of RhoA protein produced, and in an organism, may result in a decrease in RhoA specific pathological/disease effects, e.g. preventing RhoA inhibition of axonal elongation and regeneration.
  • a method of treating a human subject having a pathological process mediated in part by RhoA comprising administering an iRNA agent of the invention, e.g. wherein the iRNA agent comprises a sense strand wherein the sense strand comprises at least 15 contiguous nucleotides that differ by no more than 1, 2, or 3 nucleotides from the sense strand sequences any one of the agents, agent numbers 6477 to 6836, and an antisense strand, wherein the antisense strand comprises at least 15 contiguous nucleotides that differ by no more than 1, 2, or 3 nucleotides from the antisense strand sequences of any one of the agents, agent numbers 6477 to 6836.
  • the pathological process is the inhibition of nerve growth or elongation, preferably as a result of nerve injury or damage.
  • the iRNA agent is administered in an amount sufficient to reduce the expression of RhoA in a cell or tissue of the subject.
  • the subject is a human.
  • compositions comprising:
  • the invention provides a cell comprising an iRNA agent of the invention.
  • the invention provides a method for inhibiting the expression of a RhoA gene in a cell, the method comprising:
  • the invention provides a vector for inhibiting the expression of a RhoA gene in a cell, said vector comprising a regulatory sequence operably linked to a nucleotide sequence that encodes at least one strand of an an iRNA agent of the invention.
  • the invention provides a cell comprising the above vector.
  • compositions of the invention e.g., the methods and iRNA compositions can be used with any dosage and/or formulation described herein, as well as with any route of administration described herein.
  • FIG. 1 is a schematic illustrating the synthesis and structure of cholesterol conjugated RNA strands.
  • the sphere represents the solid phase (controlled pore glass, CPG).
  • FIG. 2 shows the effect of administration of iRNA agents of the invention, and of a control agent, respectively, to the site of injury in rats that have undergone partial dissection of the spinal cord; shown is the improvement in BBB locomotor score from day 10 after spinal cord injury, taking the BBB locomotor score of individual rats on day 10 as 0.
  • 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.
  • RNA agent is an unmodified RNA, modified RNA, or nucleoside surrogate, each of which is described herein or is 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. Preferred examples include those that have a 2′ sugar modification, a modification in a single strand overhang, preferably 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.
  • RNA agent (abbreviation for “interfering RNA agent”) as used herein, is an RNA agent, which can downregulate the expression of a target gene, e.g., RhoA. 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 RNAi, or pre-transcriptional or pre-translational mechanisms.
  • RNAi post-transcriptional cleavage of a target mRNA sometimes referred to in the art as RNAi, or pre-transcriptional or pre-translational mechanisms.
  • An iRNA agent can be a double stranded 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 interstrand hybridization can form a region of duplex structure.
  • a “strand” herein refers to a contigouous 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 polyethyleneglycol linker, to form one molecule. At least one strand can include a region which is sufficiently complementary to a target RNA.
  • strand is termed the “antisense strand.”
  • a second strand of the dsRNA agent which comprises a region complementary to the antisense strand, is termed the “sense strand.”
  • 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.
  • the term “strand” refers to one of the regions of the RNA molecule that is complementary to another region of the same RNA molecule.
  • 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 non-specific interferon response in normal mammalian cells.
  • a composition including an iRNA agent e.g., formulated as described herein
  • siRNA agents or siRNAs are termed herein.
  • siRNA agent 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 can mediate the decreased expression of a RhoA nucleic acid, e.g., by RNA degradation.
  • a RhoA nucleic acid e.g., by RNA degradation.
  • RNA is also referred to herein as the RNA to be silenced.
  • a nucleic acid is also referred to as a target gene.
  • the RNA to be silenced is a gene product of an endogenous RhoA gene.
  • RNAi refers to the ability of an agent to silence, in a sequence specific manner, a target gene.
  • “Silencing a target gene” means the process whereby a cell containing and/or expressing a certain product of the target gene when not in contact with the agent, will contain and/or express at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% less of such gene product when contacted with the agent, as compared to a similar cell which has not been contacted with the agent.
  • Such product of the target gene can, for example, be a messenger RNA (mRNA), a protein, or a regulatory element.
  • the term “complementary” is used to indicate a sufficient degree of complementarity such that stable and specific binding occurs between a compound of the invention and a target RNA molecule, e.g., a RhoA mRNA.
  • Specific binding requires a sufficient degree of complementarity to avoid non-specific binding of the oligomeric compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, or in the case of in vitro assays, under conditions in which the assays are performed.
  • the non-target sequences typically differ from the target sequences by at least 4 nucleotides.
  • an iRNA agent is “sufficiently complementary” to a target RNA, e.g., a target mRNA (e.g., a target RhoA mRNA) if the iRNA agent reduces the production of a protein encoded by the target RNA in a cell.
  • the iRNA agent may also be “exactly complementary” to the target RNA, e.g., the target RNA and the iRNA agent anneal, preferably to form a hybrid made exclusively of Watson-Crick basepairs in the region of exact complementarity.
  • a “sufficiently complementary” iRNA agent can include an internal region (e.g., of at least 10 nucleotides) that is exactly complementary to a target RhoA RNA.
  • the iRNA agent specifically discriminates a single-nucleotide difference.
  • the iRNA agent only mediates RNAi if exact complementarity is found in the region (e.g., within 7 nucleotides of) the single-nucleotide difference.
  • Preferred iRNA agents will be based on or consist of or comprise the sense and antisense sequences provided in Table 1.
  • “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).
  • an iRNA agent derived from an iRNA agent of Table 1 which lowers the amount of RhoA mRNA present in cultured human Rho-A expressing cells by 70% may itself lower the amount of RhoA mRNA present in cultured human RhoA expressing cells by at least 50% in order to be considered as essentially retaining the ability to inhibit RhoA expression in cultured human RhoA expressing cells.
  • an iRNA agent of the invention may lower the amount of RhoA mRNA present in cultured human RhoA expressing cells by at least 50%, or at least 40%.
  • a “subject” refers to a mammalian organism undergoing treatment for a disorder mediated by RhoA protein expression.
  • the subject can be any mammal, such as a cow, horse, mouse, rat, dog, pig, goat, or a primate. In the preferred embodiment, the subject is a human.
  • disorders associated with RhoA expression refers to any biological or pathological state that (1) is mediated in part by the presence of RhoA mRNA and/or protein and (2) whose outcome can be affected by reducing the level of RhoA mRNA and/or protein present. Specific disorders associated with RhoA expression are noted below and are primarily based on the responsibility of RhoA action in inhibiting axonal elongation and regeneration.
  • the present invention is based on the design, synthesis and generation of iRNA agents that target RhoA and the demonstration of silencing of a RhoA gene in vitro in cultured cells after incubation with an iRNA agent, and the resulting RhoA-specific effect.
  • An iRNA agent can be rationally designed based on sequence information and desired characteristics.
  • an iRNA agent can be designed according to the relative melting temperature of the candidate duplex.
  • 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.
  • Candidate iRNA agents can also be designed by performing, for example, a gene walk analysis of the genes that will serve as the target gene. 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”).
  • iRNA agents targeting RhoA were designed using the known sequences of RhoA for human, rat and mouse and other known RhoA sequences.
  • the target sequences shown in Table 1 hereinabove were selected from those regions of the human RhoA mRNA sequences that show complete homology with the corresponding sequences in rat and mouse. Therefore, the siRNA agents, agent numbers 6477-6836 should show cross reactivity between these three species.
  • the present invention provides iRNA agents that silence RhoA in cultured human RhoA expressing cells and in a subject.
  • Table 1 provides exemplary iRNA agents targeting RhoA TABLE 1 Exemplary iRNA agents for targeting RhoA mRNA Start duplex sense strand antisense strand pos.
  • SEQ design SEQ SEQ Agent in ID (over- ID ID number RNA b NO. target sequence (5′-3′) hang) a NO. sequence (5′-3′) NO.
  • NM_001664 mRNA to which the 5′-most nucleotide of the sense strand corresponds for single overhang designs; for double overhang designs, the 5′-most ribonucleotide of the sense strand corresponds to (Start position + 2)
  • the invention specifically provides an iRNA agent that includes a sense strand having at least 15 contiguous nucleotides of the sense strand sequences of the agents provided in Table 1 under agent numbers 6477-6836, and an antisense strand having at least 15 contiguous nucleotides of the antisense sequences of the agents provided in Table 1 under agent numbers 6477 to 6836.
  • the iRNA agents shown in Table 1 are composed of two strands of 19 nucleotides in length which are complementary or identical to the target sequence, plus a 3′-TT overhang.
  • the present invention provides agents that comprise 15 contiguous nucleotides from these agents. However, while these lengths may potentially be optimal, the iRNA agents are not meant to be limited to these lengths.
  • the skilled person is well aware that shorter or longer iRNA agents may be similarly effective, since, within certain length ranges, the efficacy is rather a finction of the nucleotide sequence than strand length. For example, Yang, et al., PNAS 99:9942-9947 (2002), demonstrated similar efficacies for iRNA agents of lengths between 21 and 30 base pairs.
  • the first 15 nucleotides from one of the agents can be combined with the 8 nucleotides found 5′ to these sequence in the RhoA mRNA to obtain an agent with 23 nucleotides in the sense and antisense strands.
  • All such derived iRNA agents are included in the iRNA agents of the present invention, provided they essentially retain the ability to inhibit RhoA expression in cultured human RhoA expressing cells.
  • the antisense strand of an iRNA agent should be equal to or at least, 14, 15, 16 17, 18, 19, 25, 29, 40, or 50 nucleotides in length. It should be equal to or less than 60, 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.
  • the sense strand of an iRNA agent should be equal to or at least 14, 15, 16 17, 18, 19, 25, 29, 40, or 50 nucleotides in length. It should be equal to or less than 60, 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.
  • the iRNA agents of the instant invention include a region of sufficient complementarity to the respective RhoA gene, and are of sufficient length in terms of nucleotides, that the iRNA agent, or a fragment thereof, can mediate down regulation of the RhoA gene.
  • ribonucleotide portions of the antisense strands of the iRNA agents of Table 1 under agent numbers 6477 to 6836 are fully complementary to the mRNA sequences of the RhoA gene, respectively, and ribonucleotide portion of their sense strands are fully complementary to the ribonucleotide portions of the respective antisense strands, except for the two 3′-terminal nucleotides on the antisense strand in single overhang design iRNA agents.
  • RNAi cleavage of a RhoA mRNA 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 a RhoA mRNA.
  • 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 Table 1 under agent numbers 6477 to 6836, 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 RhoA expression in cultured human RhoA expressing cells, respectively.
  • 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 Table 1 under agent numbers 6477 to 6836, except that not more than 1, 2 or 3 nucleotides per strand, respectively, have been substituted by other nucleotides (e.g. adenosine replaced by
  • agents will therefore possess at least 15 nucleotides identical to one of the sequences of Table 1 under agent numbers 6477 to 6836, but 1, 2 or 3 base mismatches with respect to either the target RhoA mRNA sequence or between the sense and antisense strand are introduced.
  • Mismatches to the target RhoA 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.
  • 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.
  • 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 4, or preferably 2 or 3 nucleotides, in length, at 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.
  • the unpaired nucleotides forming the overhang can be ribonucleotides, or they can be deoxyribonucleotides, preferably thymidine. 5′-ends are preferably phosphorylated.
  • Preferred lengths for the duplexed region are 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.
  • siRNA agents can resemble in length and structure the natural Dicer processed products from long dsRNAs.
  • 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.
  • a candidate iRNA agent can be evaluated for its ability to downregulate target gene expression.
  • a candidate iRNA agent can be provided, and contacted with a cell, that expresses the target gene, e.g., the RhoA gene, either endogenously or because it has been transfected with a construct from which a RhoA protein can be expressed.
  • 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 downregulates target gene expression.
  • the level of target RhoA RNA or RhoA protein in the cell can be determined by any method desired.
  • the level of target RNA can be determined by Northern blot analysis, reverse transcription coupled with polymerase chain reaction (RT-PCR), or RNAse protection assay.
  • the level of protein can be determined, for example, by Western blot analysis or immuno-fluorescence.
  • the assay also tests the ability of the iRNA agent to inhibit RhoA expression on a functional level, e.g. by assessing the ability of the iRNA agent to facilitate neuronal growth, e.g. the restoration of neurite outgrowth on an otherwise inhibitory substrate, e.g a substrate comprising myelin.
  • 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.
  • 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.
  • An iRNA agent identified as being capable of inhibiting RhoA gene expression can be tested for functionality in vivo in an animal model (e.g., in a mammal, such as in mouse or rat).
  • 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 RhoA gene expression or reduce a biological or pathological process mediated at least in part by RhoA.
  • the iRNA agent can be administered directly to the target tissue, e.g. the spinal cord, and, in the case of a spinal cord injury model, to the site of spinal cord injury, such as by injection.
  • the iRNA agent is administered to the animal model in the same manner that it would be administered to a human.
  • 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 35 S, 32 P, 33 P, or 3 H; gold particles; or antigen particles for immunohistochemistry).
  • a traceable marker e.g., a fluorescent marker such as fluorescein; a radioactive label, such as 35 S, 32 P, 33 P, or 3 H; gold particles; or antigen particles for immunohistochemistry.
  • the iRNA agent can be evaluated with respect to its ability to down regulate RhoA gene expression.
  • Levels of RhoA 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.
  • RhoA 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, RhoA gene expression can be monitored by performing Western blot analysis on tissue extracts treated with the iRNA agent.
  • Animal models may be used to establish the concentration necessary to achieve a certain desired effect (e.g., EC 50 or ED 50 ). Such animal models may include transgenic animals that express a human gene, e.g., a gene that produces a target human RhoA RNA.
  • the composition for testing includes an iRNA agent that is complementary, at least in an internal region, to a sequence that is conserved between the target RhoA RNA in the animal model and the target RhoA RNA in a human.
  • iRNA agents e.g., ds RNA agents that mediate RNAi to inhibit expression of a RhoA gene.
  • RNA agents discussed herein include otherwise unmodified RNA as well as RNA which has 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. Nucleic Acids Res. 22: 2183-2196, 1994.
  • modified RNA 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 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.
  • 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.
  • 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.
  • 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.
  • a modification may occur on the sense strand, antisense strand, or both.
  • 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.
  • iRNA agents 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.
  • an iRNA agent can include a ribose mimic for increased nuclease resistance. Exemplary intemucleotide 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.
  • 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.
  • pyrimidine nucleotides and specifically the 5′ nucleotide in a 5′-ua-3′ sequence context, a 5′-ug-3′ sequence context, a 5′-ca-3′ sequence context, a 5′-uu-3′ sequence context, or a 5′-cc-3′ sequence context are particularly prone to degradative attack, in that approximate order.
  • 2′-modifying all pyrimidine nucleotides in the sense strand and the 5′-most pyrimidines in all occurrences of the sequence contexts 5′-ua-3′ and 5′-ca-3′ in the antisense strand has given good results in terms of activity and stability.
  • the iRNA agent can include at least 2, at least 3, at least 4 or at least 5 of such dinucleotides.
  • the 2′-modified nucleotides include, for example, a 2′-modified ribose unit, e.g., the 2′-hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents.
  • a 2′-modified ribose unit e.g., the 2′-hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents.
  • MOE methoxyethyl group
  • Preferred substitutents are 2′-methoxyethyl, 2′-OCH 3 , 2′-O-allyl, 2′-C-allyl, and 2′-fluoro.
  • 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.
  • 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.
  • a 3′ conjugate such as naproxen or ibuprofen
  • Even small alkyl chains, aryl groups, or heterocyclic conjugates or modified sugars can block 3′-5′-exonucleases.
  • Nucleolytic cleavage can also be inhibited by the introduction of phosphate linker modifications, e.g., phosphorothioate linkages.
  • preferred iRNA agents include nucleotide dimers enriched or pure for a particular chiral form of a modified phosphate group containing a heteroatom at a nonbridging position normally occupied by oxygen.
  • the heteroatom can be S, Se, Nr 2 , or Br 3 .
  • When the heteroatom is S enriched or chirally pure Sp linkage is preferred.
  • Enriched means at least 70, 80, 90, 95, or 99% of the preferred form.
  • Modified phosphate linkages are particularly efficient in inhibiting exonucleolytic cleavage when introduced near the 5′- or 3′-terminal positions, and preferably the 5′-terminal positions, of an iRNA agent.
  • 5′ conjugates can also 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.
  • a 5′ conjugate such as naproxen or ibuprofen
  • 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.
  • the nucleotide overhang includes 1 to 4, preferably 2 to 3, unpaired nucleotides.
  • 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.
  • 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.
  • 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.
  • nucleases e.g., endonucleases or exonucleases
  • NRMs Nuclease Resistance promoting Monomers
  • 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.
  • a protein e.g., a transport protein, e.g., serum albumin, or a member of the RISC
  • 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.
  • 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 can inhibit hybridization so it is preferable to use them only in terminal regions, and preferable to not use them 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.
  • 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.
  • cleavage site refers to the nucleotides on either side of the cleavage site, on the target or on the iRNA agent strand which hybridizes to it.
  • Cleavage region means the nucleotides within 1, 2, or 3 nucleotides of the cleavagee 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 sense or antisense strand.
  • a wide variety of entities 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.
  • 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.
  • 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.
  • a monomer having, e.g., an amino-terminated tether, e.g., TAP-(CH 2 ) n NH 2 may be incorporated into a growing sense or antisense 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.
  • a ligand alters the distribution, targeting or lifetime of an iRNA agent into which it is incorporated.
  • 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.
  • the ligand may be a naturally occurring or recombinant or synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid.
  • polyamino acids include 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.
  • PLL polylysine
  • poly L-aspartic acid poly L-glutamic acid
  • styrene-maleic acid anhydride copolymer poly(L-l
  • 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.
  • 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.
  • the ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF- ⁇ B.
  • 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, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.
  • the ligand is a lipid or lipid-based molecule.
  • a lipid or lipid-based molecule preferably binds a serum protein, e.g., human serum albumin (HSA).
  • 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, neproxin or aspirin can be used.
  • a lipid based ligand can be used to modulate, e.g., control the binding of the conjugate to a target tissue.
  • 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.
  • the lipid based ligand binds HSA.
  • it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non-kidney tissue.
  • the affinity it is preferred that the affinity not be so strong that the HSA-ligand binding cannot be reversed.
  • the ligand is a moiety, e.g., a vitamin or nutrient, which is taken up by a target cell, e.g., a proliferating cell.
  • a target cell e.g., a proliferating cell.
  • 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.
  • iRNA agents are 5′ phosphorylated or include a phosphoryl analog at the 5′ prime terminus.
  • 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 ((HO)2(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 (N—O-5′-(HO)(HO)
  • 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 Nyhimnen 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.
  • a large bulky group may be added to the 5′-phosphate turning it into a phosphodiester linkage.
  • the chemical similarity between cholesterol-conjugated iRNA agents and certain constituents of lipoproteins may lead to the association of iRNA agents with lipoproteins (e.g. LDL, HDL) in blood and/or the interaction of the iRNA agent with cellular components having an affinity for cholesterol, e.g. components of the cholesterol transport pathway.
  • lipoproteins e.g. LDL, HDL
  • Lipoproteins as well as their constituents are taken up and processed by cells by various active and passive transport mechanisms, for example, without limitation, endocytosis of LDL-receptor bound LDL, endocytosis of oxidized or otherwise modified LDLs through interaction with Scavenger receptor A, Scavenger receptor B1-mediated uptake of HDL cholesterol in the liver, pinocytosis, or transport of cholesterol across membranes by ABC (ATP-binding cassette) transporter proteins, e.g. ABC-A1, ABC-G1 or ABC-G4.
  • ABC ATP-binding cassette
  • cholesterol-conjugated iRNA agents could enjoy facilitated uptake by cells possessing such transport mechanisms, e.g. cells of the liver.
  • the present invention provides evidence and general methods for targeting iRNA agents to cells expressing certain cell surface components, e.g. receptors, by conjugating a natural ligand for such component (e.g. cholesterol) to the iRNA agent, or by conjugating a chemical moiety (e.g. cholesterol) to the iRNA agent which associates with or binds to a natural ligand for the component (e.g. LDL, HDL).
  • a natural ligand for such component e.g. cholesterol
  • a chemical moiety e.g. cholesterol
  • the DNA templates can include two transcription units, one that produces a transcript that includes the top strand of an iRNA agent and one that produces a transcript that includes the bottom strand of an iRNA agent.
  • the iRNA agent is produced, and processed into siRNA agent fragments that mediate gene silencing.
  • iRNA agents described herein can be formulated for administration to a subject.
  • 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.
  • a formulated iRNA agent composition can assume a variety of states.
  • the composition is at least partially crystalline, uniformly crystalline, and/or anhydrous (e.g., less than 80, 50, 30, 20, or 10% water).
  • the iRNA agent is in an aqueous phase, e.g., in a solution that includes water.
  • the aqueous phase or the crystalline compositions can, e.g., 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).
  • 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).
  • the iRNA agent composition is formulated in a manner that is compatible with the intended method of administration.
  • 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.
  • 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 Mg 2+ ), salts, RNAse inhibitors (e.g., a broad specificity RNAse inhibitor such as RNAsin) and so forth.
  • the iRNA agent preparation includes two or more iRNA agent(s), e.g., two or more iRNA agents that can mediate RNAi with respect to the same gene, or different alleles of the gene, or with respect to different genes.
  • Such preparations can include at least three, five, ten, twenty, fifty, or a hundred or more different iRNA agent species.
  • Such iRNA agents can mediate RNAi with respect to a similar number of different genes.
  • the two or more iRNA agents in such preparation target the same gene, they can have target sequences that are non-overlapping and non-adjacent, or the target sequences may be overlapping or adjacent.
  • Such a treatment is useful in treating injuries to the nervous system such as spinal cord injury or peripheral nerve death (caused by, e.g., Metastatic cancers of the CNS, e.g., gliomas (such as glioblastomas, astrocytomas, oligodendrogliomas, ependymomas), meningiomas, medulloblastomas, neuroblastomas, choroid plexus papillomas, sarcomas can also be treated by the iRNA agents described herein.
  • gliomas such as glioblastomas, astrocytomas, oligodendrogliomas, ependymomas
  • meningiomas medulloblastomas
  • neuroblastomas choroid plexus papillomas
  • sarcomas can also be treated by the iRNA agents described herein.
  • an iRNA agent that targets RhoA mRNA can be used to treat a subject with a spinal cord injury or a subject having another pathological state which can be ameliorated, at least in part, by nerve growth and elongation.
  • an iRNA agent of the present invention is administered preferably locally at the site of nerve damage or the site at which the inhibitory effects of RhoA is desired to be reversed.
  • Administration of the iRNA agent leads to decrease in RhoA protein resulting in reversing Nogo mediated inhibition of axonal elongation and growth.
  • a composition that includes an iRNA agent can be delivered to a subject by a variety of routes to achieve either local delivery to the site of action of systemic delivery to the subject.
  • routes include direct injection to the site of treatment, intrathecal, parenchymal, intravenous, nasal, oral, and ocular delivery.
  • the preferred means of administering the iRNA agents of the present invention is through direct injection or infusion to the site of treatment.
  • compositions can include one or more species of an iRNA agent and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. 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.
  • compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic, intranasal, transdermal), oral or parenteral. Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, or intrathecal or intraventricular administration.
  • the route of delivery can be dependent on the disorder of the patient.
  • the delivery of the iRNA agents of the present invention is done to achieve systemic delivery into the subject.
  • One preferred means of achieving this is through parenteral administration.
  • the application is achieved by direct application of the pharmaceutical composition to the site of nerve injury, such as the the site of spinal cord injury.
  • Formulations for parenteral administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives.
  • the total concentration of solutes should be controlled to render the preparation isotonic.
  • the invention also provides devices, systems, and methods for delivery of small interfering RNA to target locations in the nervous system and or/the brain.
  • the envisioned route of delivery is through the use of implanted, indwelling, intrathecal or intraparenchymal catheters that provide a means for injecting small volumes of fluid containing the dsRNA of the invention directly into local nerves or local brain tissue.
  • the proximal end of these catheters may be connected to an implanted, intrathecal or intracerebral access port surgically affixed to the patient's body or cranium, or to an implanted drug pump located in the patient's torso.
  • implantable delivery devices such as an implantable pump may be employed.
  • the delivery devices within the scope of the invention include the Model 8506 investigational device (by Medtronic, Inc. of Minneapolis, Minn.), which can be implanted subcutaneously in the body or on the cranium, and provides an access port through which therapeutic agents may be delivered to the nerves or brain. Delivery occurs through a stereotactically implanted polyurethane catheter.
  • Two models of catheters that can finction with the Model 8506 access port include the Model 8770 ventricular catheter by Medtronic, Inc., for delivery to the intracerebral ventricles, which is disclosed in U.S. Pat. No.
  • the IPA1 catheter by Medtronic, Inc. for delivery to the brain tissue itself (i.e., intraparenchymal delivery), disclosed in U.S. Ser. Nos. 09/540,444 and 09/625,751, which are incorporated herein by reference.
  • the latter catheter has multiple outlets on its distal end to deliver the therapeutic agent to multiple sites along the catheter path.
  • the delivery of the small interfering RNA vectors in accordance with the invention can be accomplished with a wide variety of devices, including but not limited to U.S. Pat. Nos. 5,735,814, 5,814,014, and 6,042,579, all of which are incorporated herein by reference. Using the teachings of the invention and those of skill in the art will recognize that these and other devices and systems may be suitable for delivery of small interfering RNA vectors for the treatment of pain in accordance with the invention.
  • the method further comprises the steps of implanting a pump outside the body or brain, the pump coupled to a proximal end of the catheter, and operating the pump to deliver the predetermined dosage of the at least one small interfering RNA or small interfering RNA vector through the discharge portion of the catheter.
  • a further embodiment comprises the further step of periodically refreshing a supply of the at least one small interfering RNA or small interfering RNA vector to the pump outside said body or brain.
  • the invention includes the delivery of small interfering RNA vectors using an implantable pump and catheter, like that taught in U.S. Pat. Nos. 5,735,814 and 6,042,579, and further using a sensor as part of the infusion system to regulate the amount of small interfering RNA vectors delivered to the nerves or brain, like that taught in U.S. Pat. No. 5,814,014.
  • Other devices and systems can be used in accordance with the method of the invention, for example, the devices and systems disclosed in U.S. Ser. No. 09/872,698 (filed Jun. 1, 2001) and Ser. No. 09/864,646 (filed May 23, 2001), which are incorporated herein by reference.
  • the outlet of the pump or catheter is placed in close proximity of the desired site of action of the pharmaceutical composition, such as near the site of spinal cord, or other nerve, injury.
  • Administration can be provided by the subject or by another person, e.g., a caregiver.
  • a caregiver can be any entity involved with providing care to the human: for example, a hospital, hospice, doctor's office, outpatient clinic; a healthcare worker such as a doctor, nurse, or other practitioner; or a spouse or guardian, such as a parent.
  • the medication can be provided in measured doses or in a dispenser which delivers a metered dose.
  • terapéuticaally 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.
  • physiologically effective amount is that amount delivered to a subject to give the desired palliative or curative effect.
  • 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.
  • both Nogo-L, RhoA, and Nogo-R iRNA agents are co-administered.
  • 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.
  • HSA human serum albumin
  • bulking agents such as carbohydrates, amino acids and polypeptides
  • pH adjusters or buffers such as sodium chloride
  • salts such as sodium chloride
  • 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 raffmose, maltodextrins, dextrans, and the like; alditols, such as mannitol, xylitol, and the like.
  • a preferred group of carbohydrates includes lactose, threhalose, 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.
  • 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 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 eye or about 0.3-3.0 mg per organ.
  • the dosage can be an amount effective to treat or prevent a disease or disorder.
  • the unit dose is administered less frequently than once a day, e.g., less than every 2, 4, 8 or 30 days.
  • the unit dose is not administered with a frequency (e.g., not a regular frequency).
  • the unit dose may be administered a single time. 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.
  • 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 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 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 body weight per day.
  • the maintenance doses are preferably administered no more than once every 5, 10, or 30 days.
  • 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.
  • 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.
  • 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.
  • a delivery device e.g., a pump, semi-permanent stent (e.g., intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable.
  • the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the compound of the invention is administered in maintenance doses, ranging from 0.001 g to 100 g per kg of body weight (see U.S. Pat. No. 6,107,094).
  • 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.
  • concentration or amount of iRNA agent administered will depend on the parameters determined for the agent and the method of administration, e.g. nasal, buccal, pulmonary, or topical, such as intrathecal or at the site of nerve injury.
  • topical formulations tend to require much lower concentrations of some ingredients in order to avoid irritation or burning.
  • Certain factors may influence the dosage required to effectively treat a subject, including but not limited to the severity 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 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.
  • Dosing is dependent on severity and responsiveness of the disease condition to be treated, with the course of treatment lasting 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, or of drug accumulation at the site of application when delivering locally, e.g. at the site of nerve injusry, e.g. at the site of spinal cord injury. 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 as described above.
  • nucleic acid sequences are represented below using standard nomenclature, and specifically the abbreviations of Table 2. TABLE 2 Abbreviations of nucleotide monomers used in nucleic acid sequence representation. It will be understood that these monomers, when present in an oligonucleotide, are mutually linked by 5′-3′-phosphodiester bonds.
  • nucleotide(s) A a 2′-deoxy-adenosine-5′-phosphate, adenosine-5′-phosphate C, c 2′-deoxy-cytidine-5′-phosphate, cytidine-5′-phosphate G, g 2′-deoxy-guanosine-5′-phosphate, guanosine-5′-phosphate T, t 2′-deoxy-thymidine-5′-phosphate, thymidine-5′-phosphate U, u 2′-deoxy-uridine-5′-phosphate, uridine-5′-phosphate N, n any 2′-deoxy-nucleotide/nucleotide (G, A, C, or T, g, a, c or u) am 2′-O-methyladenosine-5′-phosphate cm 2′-O-methylcytidine-5′-phosphate gm 2′-O-methylguanosine-5
  • such reagent may be obtained from any supplier of reagents for molecular biology at a quality/purity standard for application in molecular biology.
  • the siRNAs were synthesized such that in the sense strands, all cytidine and uridine nucleotides comprise a 2′-O-methyl group, and in the antisense strand, all cytidines and uridines appearing in a sequence context of 5′-ca-3′ or 5′-ua-3′ comprise a 2′-O-methyl group.
  • the sense strand may be protected in a similar fashion, and/or it may be 3′-conjugated to a tethered ligand via a phosphodiester or a phosphorothioate diester.
  • RNAs Single-stranded RNAs were produced by solid phase synthesis on a scale of 1 ⁇ mole using an Expedite 8909 synthesizer (Applied Biosystems, Appleratechnik GmbH, Darmstadt, Germany) and controlled pore glass (CPG, 500 ⁇ , Glen Research, Sterling Va.) as solid support.
  • RNA and RNA containing 2′-O-methyl nucleotides were 30 generated by solid phase synthesis employing the corresponding phosphoramidites and 2′-O-methyl phosphoramidites, respectively (Proligo Biochemie GmbH, Hamburg, Germany).
  • the purified RNA solution was stored at ⁇ 20° C. until use.
  • Cholesterol was 3′-conjugated to siRNA as illustrated in FIG. 1 .
  • an appropriately modified solid support was used for RNA synthesis.
  • the modified solid support was prepared as follows: Diethyl-2-azabutane-1,4-dicarboxylate AA
  • Fmoc-6-amino-hexanoic acid (9.12 g, 25.83 mmol) was dissolved in dichloromethane (50 mL) and cooled with ice.
  • Diisopropylcarbodiimde (3.25 g, 3.99 mL, 25.83 mmol) was added to the solution at 0° C. It was then followed by the addition of Diethyl-azabutane-1,4-dicarboxylate (5 g, 24.6 mmol) and dimethylamino pyridine (0.305 g, 2.5 mmol). The solution was brought to room temperature and stirred further for 6 h. the completion of the reaction was ascertained by TLC.
  • Potassium t-butoxide (1.1 g, 9.8 mmol) was slurried in 30 mL of dry toluene. The mixture was cooled to 0° C. on ice and 5 g (6.6 mmol) of diester AD was added slowly with stirring within 20 mins. The temperature was kept below 5° C. during the addition. The stirring was continued for 30 mins at 0° C.
  • Diol AF (1.25 gm 1.994 mmol) was dried by evaporating with pyridine (2 ⁇ 5 mL) in vacuo.
  • the reaction was carried out at room temperature overnight.
  • the reaction was quenched by the addition of methanol.
  • the reaction mixture was concentrated in vacuum and to the residue dichloromethane (50 mL) was added.
  • the organic layer was washed with IM aqueous sodium bicarbonate.
  • the organic layer was dried over anhydrous sodium sulfate, filtered and concentrated.
  • FIG. 1 The synthesis and structure of cholesterol conjugated RNA strands is illustrated in FIG. 1 .
  • siRNAs listed Table 3 were synthesized for activity screening. TABLE 3 siRNAs specific for RhoA SEQ SEQ Agent ID ID C. a. number Sense strand NO. Antisense strand NO. # 1 AL-DP-5850 gauuaugaccgucugaggcTT 1081 gccucagucggucauaaucT T 1082 n.a. AL-DP-5851 ggaucuucggaaugaugagTT 1083 cucaucauuccgaagauccT T 1084 n.a. AL-DP-5852 agaccaaagacggagugagTT 1085 cucacuccgucuuuggucuT T 1086 na.
  • agent # corresponding agent # in Table 2.
  • the agent given under this agent number in Table 3 possesses the same core nucleotide sequence when nucleotide modifications, e.g. 2′-O-methyl modifications and phosphorothioate linkages, are disregarded
  • the ability of the iRNA agents represented in Table 3 to inhibit the expression of human RhoA was tested in human cell lines expressing the respective gene product from an expression construct, or in cell lines constitutively expressing the respective gene product.
  • the iRNA agent is transfected into the cells, e.g., by transfection or electroporation, allowed to act on the cells for a certain time, e.g., 24 hours, and levels of RhoA expression were determined by measurement of RhoA mRNA concentrations in cell lysates. These expression levels were then compared to RhoA expression levels in cells treated equivalently but without addition of the iRNA agent, or to expression levels of housekeeping genes (e.g. GAPDH), and the ability of the iRNA agents representend in Table 3 to inhibit the expression of human RhoA thereby assessed.
  • housekeeping genes e.g. GAPDH
  • Neuroscreen-1 cells (Cellomics Inc., Pittsburgh, USA) were seeded at 1.5 ⁇ 10 4 cells/well on 96-well collagen-coated plates (Greiner Bio-One GmbH, Frickenhausen, Germany) in 100 ⁇ l of growth medium (RPMI 1640, 10% horse serum, 5% fetal calf serum, 100 u penicillin/100 ⁇ g/ml streptomycin, 2 mM L-glutamine, Biochrom AG, Berlin, Germany). Transfections were performed in triplicates. For each well 0.5 ⁇ l Lipofectamine2000 (Invitrogen GmbH, Düsseldorf, Germany) were mixed with 12 ⁇ l Opti-MEM (Invitrogen) and incubated for 15 min at room temperature.
  • RPMI 1640 10% horse serum, 5% fetal calf serum, 100 u penicillin/100 ⁇ g/ml streptomycin, 2 mM L-glutamine, Biochrom AG, Berlin, Germany.
  • mRNA levels in cell lysates were quantitated by a commercially available branched DNA hybridization assay (QuantiGene bDNA-kit, Genospectra, Fremont, USA).
  • Cells were harvested by applying 50 ⁇ l additional growth medium and 75 ⁇ l of Lysis Mixture (from QuantiGene bDNA-kit) to each well and were lysed at 53° C. for 30 min.
  • 50 ⁇ l of the lysates were incubated with probes specific to rat RhoA and rGAPDH (sequence of probes given in Table 4 and Table 5) according to the manufacturer's protocol for the QuantiGene bDNA kit assay.
  • chemoluminescence was measured in a Victor2-Light (Perkin Elmer, Wiesbaden, Germany) as RLUs (relative light units) and values obtained with RhoA probes were normalized to the respective GAPDH values for each well.
  • Mock transfected cells (following the same protocol except that no siRNA was added) served as controls and forcomparison of mRNA levels.
  • Effective siRNAs from the screen were further characterized by establishment of dose response curves and calculation of IC 50 concentrations (the concentration at which 50% inhibition of gene expression would be observed).
  • transfections were performed at the following concentrations: 100 nM, 33.3 nM, 11.1 nM, 3.7 nM, 1.2 nM, 0.4 nM, 137 pM, 46 pM, 15 pM, 5 pM and mock (no siRNA) by serially diluting the 5 ⁇ M siRNA stock solution with annealing buffer and using 2 ⁇ l of the diluted stock according to the above protocol.
  • TABLE 4 Rat RhoA probes SEQ Probe ID type 1 Nucleotide sequence NO.
  • Table 6 lists the agent number, the position of the nucleotide within the human RhoA mRNA sequence (Genbank accession number NM — 001664) corresponding to the 5′-most nucleotide of the sense strand of the agent, the amount of total RhoA mRNA remaining in cells treated with the agent at 100 nM concentration in % of controls, and the IC 50 value for selected agents. TABLE 6 Ability of siRNAs specific for RhoA to reduce RhoA mRNA levels in cultured cells Rem. RhoA mRNA at Rem. RhoA 100 nM mRNA at 100 nM Agent Pos.
  • agents AL-DP-5979, AL-DP-5990, AL-DP-5988, AL-DP-5981, AL-DP-5982, AL-DP-5986, AL-DP-5989 AL-DP-6176, and AL-DP-6177 were able to reduce the expression of RhoA mRNA by 80% or more
  • AL-DP-5973, AL-DP-5987, AL-DP-5994, AL-DP-5995, AL-DP-5976, AL-DP-5984, and AL-DP-5972 were able to reduce the expression of RhoA mRNA by 70% or more
  • AL-DP-5993, AL-DP-5975, and AL-DP-5983 were able to reduce the expression of RhoA mRNA by 60% or more
  • AL-DP-5974 was able to reduce the expression of RhoA mRNA by 50% or more
  • AL-DP-5991, AL-DP-5992, and AL-DP-5978 were able to reduce the expression of RhoA mRNA by 40% or
  • AL-DP-6176 and AL-DP-6177 shwos that a cholesteryl moiety may be conjugated to the 3′-end of the sense strand of an siRNA without significant loss of activity.
  • AL-DP-6176 and AL-DP-6177 are identical to AL-DP-5973 and AL-DP-5987, respectively, except for the 3′-conjugated cholesteryl moiety on the sense strand.
  • cerebrospinal fluid CSF
  • This method comprises the incubation of siRNAs with CSF followed by Proteinase K treatment of the CSF sample and the separation of CSF sample constituents on an HPLC.
  • Bovine CSF was obtained from a calf (Bos bovis), age 6 months (Prof. Dr. J. Rehage, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany). Porcine CSF was pooled from 3 healthy weaner pigs (Sus scrofa domesticus), age 3-4 months (Prof. Dr. M. Wendt, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany). Rat CSF was pooled from 20 male Sprague Dawley rats (Rattus norvegicus), 175-200 g in weight (Charles River Laboratories, L'Arbresle Cedex, France). Proteinase K (20 mg/ml) was obtained from peQLab (Er Weg, Germany; Cat.-No.
  • Proteinase K Buffer (4.0 ml TRIS-HCl 1M pH 7.5, 1.0 ml EDTA 0.5M, 1.2 ml NaCl 5M, 4.0 ml SDS 10%) was prepared fresh and kept at 50° C. until use to avoid precipitation.
  • a 40 mer of poly(L-dT), (L-dT) 40 was obtained from Noxxon Pharma AG (Berlin, Germany) and used as an internal standard.
  • Polymers of the L-enantiomers of nucleic acids show an extraordinary stability towards nucleolytic degradation (Klussman S, et al., Nature Biotechn. 1996, 14:1112) but otherwise very similar properties when compared to naturally occuring nucleic acids consisting of R-enantiomers.
  • the incubation wells were washed with 47.5 ⁇ l deionized water (18.2 m ⁇ ), the wash filtered through the Captiva Filter Unit at 21900 rcf for 15 min, and the wash step repeated. Approximately 180 ⁇ l of the theoretical total volume of 200 ⁇ l are on average recovered after the second washing step.
  • the chromatographic parameters were adjusted by changing temperature, pH, replacement of NaClO 4 by NaBr, the concentration of acetonitrile, and/or adjusting the slope of the eluent gradient until separation was achieved which allowed separate quantitation of the peaks from sense and antisense strand.
  • Peak areas for full length strands were obtained by integration of the UV detector signal using software supplied by the manufacturer of the instrument (Chromeleon 6.6; Dionex GmbH, Idstein, Germany).
  • Integrated sense strand, antisense strand, and internal standard peak areas were obtained for all samples and the normalization control.
  • a correction factor CF accounting for liquid losses in the filtration and washing steps, was determined for every sample by calculating the ratio of experimental to theoretical internal standard peak area.
  • the theoretical internal standard peak area is obtained, e.g. from a calibration curve of the internal standard obtained by injecting 50 ⁇ l each of a serial dilution of the 50 ⁇ M solution of (L-dT) 40 onto the HPLC column, and calculation of the theoretical peak area corresponding to 25 pmole (L-dT) 40 with the equation obtained by linear least square fit to the peak areas from the dilution series.
  • NPA sense,t (Peak Area sense or antisense,t ) ⁇ CF
  • % FLP Full Length Product
  • the value obtained from the control sample, where the siRNA was incubated with annealing buffer only, may serve as a control of the accuracy of the method.
  • the % FLP for both strands should lie near 100%, within error margins, regardless of time of incubation.
  • Table 7 shows the results for select siRNAs of the determination of the relative amount of full length dsRNA present in porcine, rat, and bovine CSF, and PBS, after 48 h of incubation in the respective medium. In addition, the degradation half life was determined for the sense and antisense strands separately for some siRNAs. TABLE 7 Stability of various siRNAs specific for NogoL and RhoA in rat, bovine and porcine CSF % full length duplex present after 48 h in Agent Porcine Rat Bovine Specific Modifi- C.a.
  • agent # corresponding agent # in Table 2.
  • the agent given under this agent number in Table 2 possesses the same core nucleotide sequence when nucleotide modifications, e.g. 2′-O-methyl modifications and phosphorothioate linkages, are disregarded
  • DRG cells were isolated from Sprague-Dawley rats at postnatal day 3 to 6. Rats were dissected and cells dissociated into single cells by addition of 1.3 ml (0.28 Wunsch units/ml) Liberase Blendzyme (Roche) in S-MEM (Invitrogen Gibco, Carlsbad Calif., USA) and incubated for 35 min at 37° C. The cell suspension was pre-plated on tissue-culture plates to remove non-neuronal cells.
  • Neurons were then plated onto tissue-culture BiocoatTM PDL Poly-D-Lysine/Laminin 96 well plates (BD Biosciences, Bedford Mass., USA) in F12-HAM's Medium containing glutamine (Invitrogen Gibco, Carlsbad Calif., USA) with 5% fetal bovine serum (FBS, heat inactivated) and 5% horse serum (heat inactivated) (both Invitrogen Gibco, Carlsbad Calif., USA) supplemented with 50 ng/ml mouse nerve growth factor 2.5S (NGF; Promega Corp., Madison Wis., USA) and kept at 37° C., 5% CO 2 in a humidified incubator until transfection.
  • FBS fetal bovine serum
  • horse serum horse serum
  • TransMessengerTM Transfection reagent Qiagen GmbH, Hilden, Germany, cat. no. 301525) which is based on a lipid formulation, specific RNA-condensing reagent (Enhancer RTM) and an RNA-condensing buffer (Buffer EC-RTM) keeping siRNA:Enhancer RTM ratio ( ⁇ g: ⁇ l) constant at 1:2, and siRNA:
  • DRG neurons were transfected 24 h post-plating.
  • Enhancer RTM were first mixed with 13.68 ⁇ l Buffer EC-RTM.
  • 0.8 ⁇ l of a 25 ⁇ M solution of AL-DP-5987 (0.26 ⁇ g) in annealing buffer (20 mM sodium phosphate, pH 6.8; 100 mM sodium chloride), or 0.8 ⁇ l of annealing buffer (siRNA-free control) were added and the mixture incubated for 5 min at RT.
  • the growth medium was removed from the DRG cells, and 90 ⁇ l of the above transfection complex mixture were added onto the cells. After 8 h of incubation at 37° C., 5% CO 2 in a humidified incubator supernatant was removed from the cells, fresh F12-HAM's medium containing glutamine supplemented with 5% FBS, 5% horse serum (both Invitrogen Gibco, Carlsbad Calif., USA), 50 ng/ml mouse NGF 2.5S (Promega Corp., Madison Wis., USA) and 1:100 Penicillin/Streptomycin (Invitrogen Gibco, Carlsbad Calif., USA) was added, the cells were incubated for another 16 h at 37° C., 5% CO 2 in a humidified incubator, and rhoA mRNA was quantified.
  • RhoA mRNA levels were measured using the QuantiGeneTM bDNA kit (Genospectra, Fremont, USA) according to manufacturer's protocol. Briefly, the supernatant was removed from the DRG cells, and the cells were lysed by addition of 150 ⁇ l of Lysis Working Reagent (1 volume of Lysis Mixture plus 2 volumes of medium) and incubation at 52° C. for 30min. 40 ⁇ l of the lysates were incubated at 52° C. for 40 min with the probe sets specific to rat RhoA and rat GAPDH given above in Table 4 and Table 5.
  • rhoA mRNA was reduced in primary DRG cells treated with AL-DP-5987 in culture consistently to 20-25% of rhoA mRNA levels found in the siRNA free controls.
  • DRG Dorsal root ganglia
  • the suspension was then triturated 15-20 times with a fire-polished pipette until a homogeneous cell suspension was achieved. Cells were spun down three times for 3 minutes at 1500 RPM, and the cell debris aspirated off. Cells were then resuspended in 500 ⁇ l of culture media and passed through a 70 ⁇ m strainer (Falcon, 352350). The cell suspension was pre-plated on a 24 well tissue-culture plate in 300 ⁇ l of culture media for 24 hours at 37° C., 5% CO2 in a humidified incubator. Neurons were then transfected with appropriate siRNA as follows:
  • CSPG Chondroitin sulfate proteoglycan
  • myelin was dried down overnight in 50 ⁇ l in individual wells of a biocoat Poly-D-Lysine plate (BD Biosciences, Bedford Mass., USA). The plate was rinsed once with water to remove salt deposits. laminin (Invitrogen, CA; 1 ⁇ g/ml) was then coated for 1 h at room temperature.
  • Neurons were resuspended from the 24 well plate by gently pipetting up and down, spun down at 1500 RPM for 3 minutes and resuspended in the appropriate volume. Neurons were replated at a concentration of 3000 neurons/well onto the prepared Poly-D-Lysine/Laminin 96-well plates in culture medium. The neurons were allowed to grow for 16-24 hours at 37° C., 5% CO2 in a humidified incubator and subjected to neurite quantification as follows.
  • the cells were fixed in 4% formaldehyde, 20% sucrose in PBS for 15 minutes. The cells were rinsed once with PBS, permeabilized and blocked for an hour at room temperature using 0.1% Triton, 10% Goat serum in PBS. The cells were stained with a beta-III tubulin, polyclonal rabbit antibody (Covance, 1:500) diluted in PBS and incubated overnight at 4° C. After three 5 minutes rinses in PBS, the secondary Alexa-Fluor 488 goat anti-rabbit IgG antibody (Molecular Probes, 1:500 filtered through 0.22 um) was incubated overnight at 4° C. Following 3 rinses in PBS, neurite outgrowth was quantified using an automated cellular imaging and analysis system (Axon Instrument, Union City, Calif.).
  • the iRNA agent of the invention AL-DP-6176 was tested at a concentration of 250 nM at transfection for its effect on neurite outgrowth on growth substrate supplemented with 0, 40, or 200 ng myelin, and compared to the effect of AL-DP-5266.
  • neurite outgrowth is expressed as percent of neurite outgrowth seen without myelin.
  • the green fluorescent protein-specific iRNA agent has no effect on neunte outgrowth of DRG on the inhibitory substrate, while the RhoA-specific iRNA agent strongly counters the growth inhibitory effect of myelin.
  • the iRNA agents of the invention AL-DP 5973, AL-DP 5987, AL-DP 6176, and AL-DP 6177 were tested at a concentration of 250 nM at transfection for its effect on neurite outgrowth on growth substrate supplemented with 30 ng CSPG, and compared to the effect of AL-DP-5549 and AL-DP-5266.
  • neurite outgrowth is expressed as percent of neurite outgrowth seen without CSPG.
  • the green fluorescent protein-specific iRNA agent has no effect on neurite outgrowth of DRG on the inhibitory substrate, while the RhoA-specific iRNA agents counter the growth inhibitory effect of CSPG.
  • iRNA agents were administered in blinded fashion to the three different groups.
  • Group A being administered a first rhoA-specific iRNA agent (AL-DP-6177), group B receiving a second rhoA-specific iRNA agent (AL-DP-6176), group C as a control group getting the unrelated control iRNA agent, directed against Luciferase (AL-DP-1956, for nucleic acid sequence see Table 11).
  • the iRNA agents were delivered through an osmotic minipump (Alzet 2004, 0.25 ⁇ l/hr, 28 day delivery), which was filled with appropriate drug for the groups A, B, C, and pre-incubated overnight at 37° C. before implantation to the animals (described below).
  • the siRNA was released at a dose of 0.4 mg per day for 28 days.
  • the rats were deeply anesthetized with ketamine (60 mg/kg) and xylazine (10 mg/kg).
  • a complete laminectomy was conducted at spinal level T6-7 under a surgical microscope.
  • the dorsal part of spinal cord was transected with the sharp tip of a 30 gauge needle and a pair of microscissors.
  • the depth of transection (1.85 mm) was confirmed by passing the sharp part of number 11 blade across the dorsal spinal cord for several times with the aid of a stereotaxic (David Kopf Instruments, Tujunga, Calif.).
  • the dura over the dorsal spinal cord was gently lifted with a pair of microforceps and a small hole was made in the midline with a pair of microscissors at T7 level.
  • the minipump was sutured to the muscles under the skin on the back of the animals.
  • the outlet of the minipump was connected to one end of an intrathecal catheter (PE-60, MS-0040, Marsil Scientific).
  • the other end of the catheter with a small diameter of PE-5 was inserted into the subdura space of spinal cord at T7 level through the small opening made for drug infusion. After pump and catheter implantation, muscle and connective tissue layers were sutured with 4.0 silk.
  • BBB Bresnahan locomotor rating scale
  • the BBB score was evaluated by two individuals unaware of experimental treatments at several time points (Li, S., et al., J Neurosci 2004, 24:10511-10520). In particular, the locomotion was analyzed on day 3, 10, 17, 24, 31 and 45 post hemisection of the spinal cord.
  • the obtained BBB score data were plotted by normalizing all the single day score data of the animals to the score at day 10.
  • the group averages of those normalized scores were charted including the error representing the calculated standard error.

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