WO2017136399A1 - POTENTIATION OF mmRNA THERAPEUTICS - Google Patents

Abstract

The present invention relates to the use of immune regulatory oligonucleotide (IRO) compounds as antagonists of toll-like receptors (TLRs) to inhibit and/or suppress a TLR-mediated immune response induced by endogenous and/or exogenous nucleic acids such as modified messenger RNA (mmRNA) therapeutics or DNA used in gene therapy.

Description

POTENTIATION OF mmRNA THERAPEUTICS

(Attorney Docket No. 4204.3005 WO)

RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Patent

Application Serial No. 62/290,223, filed on February 2, 2016, the contents of which are incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

[0002] Exogenous nucleic acids (e.g., RNA or DNA) have been proposed for use in therapeutic applications to treat or prevent disease. However, to date there have been multiple problems with prior methodologies of effecting protein expression.

[0003] Introduced DNA can integrate into host cell genomic DNA, resulting in imprecise expression levels or alterations and/or damage to the host cell genomic DNA. Additionally, exogenous DNA can be inherited by daughter cells (whether or not the DNA has integrated) or by offspring. Thus use of DNA also requires multiple steps before a protein is made in a cell. First, DNA must be transported mto the nucleus where it is transcribed into RNA. The RNA transcribed from DNA must then enter the cytoplasm to be translated into a protem. Frequently DNA enters cells but is not expressed or not expressed at reasonable rates or concentrations. This can be a particular problem when DNA is introduced into cells such as primary cells or modified cell lines.

[0004] Messenger RNA (mRNA) has several advantages over DNA for gene transfer and expression, including the lack of any requirement for nuclear localization or transcription and the nearly negligible possibility of genomic integration of the delivered sequence. However, the labile nature of mRNA and its capacity to elicit innate immune responses are important limitations to its in vivo application (see R Scott Mclvor, Molecular Therapy vl9(5): 822-823 (2011)). While this approach has shown some promise in pre-clinical studies, the induction of innate immune responses, primarily mediated by toll-like receptors 7 and 8, can compromise the effectiveness of nucleic acid delivery and lead to compromised therapeutic applicability. BRIEF DESCRIPTION OF THE DRAWINGS

[0005] The foregoing and other objects, features and advantages of the invention will be apparent from the following more particular description of preferred embodiments of the invention, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the invention.

[0006] Fig. 1 depicts the mRNA sequence for G-CSF. Poly A tail of approximately 160 nucleotides is not shown in the sequence.

[0007] Fig. 2 depicts the mRNA sequence for erythropoietin. Poly A tail of approximately 160 nucleotides is not shown in the sequence.

[0008] Fig. 3 depicts the mRNA sequence for Factor IX. Poly A tail of approximately 160 nucleotides is not shown in the sequence.

[0009] Fig. 4 depicts the mRNA sequence for mCherry. Poly A tail of approximately 160 nucleotides is not shown in the sequence.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0010] The present invention relates to the use of immune regulatory oligonucleotide (IRO) compounds as antagonists of toll-like receptors (TLRs) to inhibit and/or suppress a TLR-mediated immune response induced by endogenous and/or exogenous nucleic acids such as modified messenger RNA (mmRNA) therapeutics or DNA used in gene therapy. The references cited herein reflect the level of knowledge in the field and are hereby incorporated by reference in their entirety. Any conflicts between the teachings of the cited references and this specification shall be resolved in favor of the latter.

DEFINITIONS

[0011] The term "oligonucleotide" generally refers to a polynucleoside comprising a plurality of linked nucleoside units. Such oligonucleotides can be obtained from existing nucleic acid sources, including genomic or cDNA, but are preferably produced by synthetic methods. In preferred embodiments each nucleoside unit can encompass various chemical modifications and substitutions as compared to wild-type oligonucleotides, including but not limited to modified nucleoside base and/or modified sugar unit. Examples of chemical modifications are known to the person skilled in the art and are described, for example, in Uhlmann E et al. (1990) Chem. Rev. 90:543; "Protocols for Oligonucleotides and Analogs" Synthesis and Properties & Synthesis and Analytical Techniques, S. Agrawal, Ed, Humana Press, Totowa, USA 1993; and Hunziker, J. et al. (1995) Mod. Syn. Methods 7:331 -417; and Crooke, S. et al. (1996) Ann.Rev. Pharm. Tox. 36: 107-129. The nucleoside residues can be coupled to each other by any of the numerous known internucleoside linkages. Such internucleoside linkages include, without limitation, phosphodiester, phosphorothioate, phosphorodithioate, alkylphosphonate, alkylphosphonothioate, phosphotriester, phosphoramidate, siloxane, carbonate, carboalkoxy, acetamidate, carbamate, morpholino, borano, thioether, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate, and sulfone internucleoside linkages. The term "oligonucleotide" also encompasses polynucleosides having one or more stereospecific internucleoside linkage (e.g., (Rp)- or (5 )-phosphorothioate, alkylphosphonate, or phosphotriester linkages). As used herein, the terms

"oligonucleotide" and "dinucleotide" are expressly intended to include

polynucleosides and dinucleosides having any such internucleoside linkage, whether or not the linkage comprises a phosphate group. In certain preferred embodiments, these internucleoside linkages may be phosphodiester, phosphorothioate, or phosphorodithioate linkages, or combinations thereof.

[0012] The term "2'-substituted ribonucleoside" or "2 '-substituted

arabinoside" generally includes ribonucleosides or arabinonucleosides in which the hydroxyl group at the 2' position of the pentose moiety is substituted to produce a 2'- substituted or 2'-O-substituted ribonucleoside. In certain embodiments, such substitution is with a lower hydrocarbyl group containing 1-6 saturated or unsaturated carbon atoms, with a halogen atom, or with an aryl group having 6-10 carbon atoms, wherein such hydrocarbyl, or aryl group may be unsubstituted or may be substituted, e.g., with halo, hydroxy, trifiuoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carboalkoxy, or amino groups. Examples of 2'-O-substituted

ribonucleosides or 2'-O-substituted-arabinosides include, without limitation 2 '-amino, 2'-fluoro, 2'-allyl, 2'-O-alkyl and 2'-propargyl ribonucleosides or arabinosides, 2'-O- methylribonucleosides or 2'-O-methylarabinosides and 2'-O- methoxyethoxyribonucleosides or 2' -O-methoxyethoxy arabinosides. [0013] The term " 3' ", when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 3' (downstream) from another region or position in the same polynucleotide or oligonucleotide.

[0014] The term " 5' ", when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 5' (upstream) from another region or position in the same polynucleotide or oligonucleotide.

[0015] The term "about" generally means that the exact number is not critical.

Thus, the number of nucleoside residues in the oligonucleotides is not critical, and oligonucleotides having one or two fewer nucleoside residues, or from one to several additional nucleoside residues are contemplated as equivalents of each of the embodiments described above.

[0016] The term "agonist" generally refers to a substance that binds to a receptor of a cell and induces a response. An agonist often mimics the action of a naturally occurring substance such as a ligand.

[0017] The term "antagonist" generally refers to a substance that attenuates the effects of an agonist.

[0018] The term "adjuvant" generally refers to a substance which, when added to an immunogenic agent such as vaccine or antigen, enhances or potentiates an immune response to the agent in the recipient host upon exposure to the mixture.

[0019] The term "airway inflammation" generally includes, without limitation, asthma.

[0020] The term "allergen" generally refers to an antigen or antigenic portion of a molecule, usually a protein, which elicits an allergic response upon exposure to a subject. Typically the subject is allergic to the allergen as indicated, for instance, by the wheal and flare test or any method known in the art. A molecule is said to be an allergen even if only a small subset of subjects exhibit an allergic immune response upon exposure to the molecule.

[0021] The term "allergy" generally refers to an inappropriate immune response characterized by inflammation and includes, without limitation, food allergies and respiratory allergies.

[0022] The term "antigen" generally refers to a substance that is recognized and selectively bound by an antibody or by a T cell antigen receptor, resulting in induction of an immune response. Antigens may include but are not limited to peptides, proteins, nucleosides, nucleotides, and combinations thereof. Antigens may be natural or synthetic and generally induce an immune response that is specific for that antigen.

[0023] The term "autoimmune disorder" generally refers to disorders in which

"self components undergo attack by the immune system.

[0024] The term "TLR-mediated disease" or TLR-mediated disorder" generally means any pathological condition for which activation of one or more TLRs is a contributing factor. Such conditions include but are not limited, cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, skin disorders, allergy, asthma or a disease caused by a pathogen.

[0025] The term "physiologically acceptable" generally refers to a material that does not interfere with the effectiveness of an IRO compound and that is compatible with a biological system such as a cell, cell culture, tissue, or organism. Preferably, the biological system is a living organism, such as a vertebrate.

[0026] The term "carrier" generally encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microspheres, liposomal encapsulation, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient, or diluent will depend on the route of administration for a particular application. The preparation of pharmaceutically acceptable formulations containing these materials is described in, e.g. , Remington 's Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, PA, 1990.

[0027] The term "co-administration" generally refers to the administration of at least two different substances sufficiently close in time. Co-administration refers to simultaneous administration, as well as temporally spaced order of up to several days apart, of at least two different substances in any order, either in a single dose or separate doses.

[0028] The term "complementary" generally means having the ability to hybridize to a nucleic acid. Such hybridization is ordinarily the result of hydrogen bonding between complementary strands, preferably to form Watson-Crick or Hoogsteen base pairs, although other modes of hydrogen bonding, as well as base stacking can also lead to hybridization. [0029] The term an "effective amount" or a "sufficient amount" generally refers to an amount sufficient to affect a desired biological effect, such as beneficial results. Thus, an "effective amount" or "sufficient amount" will depend upon the context in which it is being administered. In the context of administering a composition that modulates an immune response to a co-administered antigen, an effective amount of an IRO compound and antigen is an amount sufficient to achieve the desired modulation as compared to the immune response obtained when the antigen is administered alone. An effective amount may be administered in one or more administrations.

[0030] The term "in combination with" generally means in the course of treating a disease or disorder in a patient, administering an IRO compound and an agent useful for treating the disease or disorder that does not diminish the immune modulatory effect of the IRO compound. Such combination treatment may also include more than a single administration of an IRO compound and/or independently an agent. The administration of the IRO compound and/or the agent may be by the same or different routes.

[0031] The term "individual" or "patient" or "subject" or "vertebrate" generally refers to a mammal, such as a human. Mammals generally include, but are not limited to, humans, non-human primates, rats, mice, cats, dogs, horses, cattle, cows, pigs, sheep, and rabbits.

[0032] The term "nucleoside" generally refers to compounds consisting of a sugar, usually ribose or deoxyribose, and a purine or pyrimidine base.

[0033] The term "nucleotide" generally refers to a nucleoside comprising a phosphate group attached to the sugar.

[0034] As used herein, the term "pyrimidine nucleoside" refers to a nucleoside wherein the base component of the nucleoside is a pyrimidine base (e.g., cytosine (C) or thymine (T) or Uracil (U)). Similarly, the term "purine nucleoside" refers to a nucleoside wherein the base component of the nucleoside is a purine base (e.g., adenine (A) or guanine (G)).

[0035] The terms "analog" or "derivative" can be used interchangeable to generally refer to any purine and/or pyrimidine nucleotide or nucleoside that has a modified base and/or sugar. A modified base is a base that is not guanine, cytosine, adenine, thymine or uracil. A modified sugar is any sugar that is not ribose or 2'deoxyribose and can be used in the backbone for an oligonucleotide.

[0036] The term "inhibiting" or "suppressing" generally refers to a decrease in a response or qualitative difference in a response, which could otherwise arise from eliciting and/or stimulation of a response. As used herein, the expressions "inhibiting a TLR9-, TLR7- and/or TLR8-mediated immune response" or "suppressing a TLR9-, TLR7- and/or TLR8-mediated immune response" generally refers to suppressing a TLR9-mediated immune response, a TLR7-mediated immune response, a TLR8- mediated immune response, a TLR7- and TLR8-mediated immune response, a TLR9- and TLR7- mediated immune response, a TLR9- and TLR8-mediated immune response, or a TLR9-, TLR7- and TLR8-mediated immune response.

[0037] The term "non-nucleotide linker" generally refers to any linkage or moiety that can link or be linked to the oligonucleotides other than through a phosphorous-containing linkage. Preferably such linker is from about 2 angstroms to about 200 angstroms in length.

[0038] The term "nucleotide linkage" generally refers to a direct 3 '-5' linkage that directly connects the 3' and 5' hydroxy 1 groups of two nucleosides through a phosphorous-containing linkage.

[0039] The terms "oligonucleotide motif means an oligonucleotide sequence, including a dinucleotide motif. As used herein YZ is a dinucleotide motif. In some embodiments the YZ dinucleotide motif has immune stimulation activity. In some embodiments YZ is a dinucleotide motif selected from the group consisting of CpG, C*pG, C*pG* and CpG*.

[0040] An "oligonucleotide motif that would be immune stimulatory, but for one or more modifications" means an oligonucleotide motif which is immune stimulatory in a parent oligonucleotide, but not in a derivative oligonucleotide, wherein the derivative oligonucleotide is based upon the parent oligonucleotide, but has one or more modifications.

[0041] The terms CpG, C*pG, C*pG* and CpG* refer to dinucleotide motifs and comprise cytosine or a cytosine derivative and a guanine or a guanine derivative. A CpG motif, wherein C is unmethylated deoxycytidine and G is deoxyguanosine, induces an immune response through toll-like receptor 9 (TLR9). [0042] As used herein, the terms "immune response" or "innate immune response" include a cellular response to single stranded or double stranded nucleic acids, which involves the induction of cytokine expression and release, particularly the interferons, and cell death. Protein synthesis is also reduced during the innate cellular immune response.

[0043] The term "treatment" generally refers to an approach intended to obtain a beneficial or desired results, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.

[0044] In a first aspect, the invention provides methods for suppressing an immune response induced by endogenous and/or exogenous nucleic acids such as modified messenger RNA (mmRNA) therapeutics or DNA used in gene therapy.

[0045] In one embodiment, the invention provides a method for suppressing an immune response induced by a mmRNA therapeutic, said method comprising coadministering an immune regulatory compound (IRO) and the mmRNA therapeutic to an individual. In one embodiment the immune response is a toll-like receptor (TLR)- mediated immune response. In a further embodiment, the TLR-mediated immune response is a TLR7- and/or TLR8-mediated immune response.

[0046] In one embodiment, the invention provides a method for suppressing an immune response induced in response to gene therapy, said method comprising coadministering an immune regulatory compound (IRO) and the gene therapy

[therapeutic] to an individual. In one embodiment the immune response is a toll-like receptor (TLR)-mediated immune response. In a further embodiment, the TLR- mediated immune response is a TLR9-mediated immune response.

[0047] In a further aspect, the invention provides methods for potentiating the activity of a modified messenger RNA (mmRNA) therapeutics or gene therapy.

[0048] In one embodiment, the invention provides a method for potentiating the activity of a mmRNA therapeutic, said method comprising co-administering an immune regulatory compound (IRO) and the mmRNA therapeutic to an individual.

[0049] In one embodiment, the invention provides a method for potentiating the activity of gene therapy, said method comprising co-administering an immune regulatory compound (IRO) and the gene therapy to an individual. [0050] In a further aspect, the invention provides methods for therapeutically treating a patient, such methods comprising co-administering to the patient a IRO compound and a mmRNA therapeutic or gene therapy. In some embodiments the patient has a disease or disorder.

[0051] In a further aspect, the invention provides methods for preventing a disease or disorder, such methods comprising co-administering an IRO compound and a mmRNA therapeutic or gene therapy to a patient.

[0052] In some embodiments, the IRO compound and/or the mmRNA therapeutic are in a pharmaceutical formulation comprising the IRO compound and/or mmRNA therapeutic and a physiologically acceptable carrier. In some embodiments the IRO compound and the mmRNA therapeutic are in the same formulation. In some embodiments, the IRO compound and the mmRNA therapeutic are in different formulations.

[0053] In some embodiments, the IRO compound and/or the gene therapy are in a pharmaceutical formulation comprising the IRO compound and/or gene therapy and a physiologically acceptable carrier. In some embodiments the IRO compound and the gene therapy are in the same formulation. In some embodiments, the IRO compound and the gene therapy are in different formulations.

[0054] As used herein, the term "IRO" refers to an immune regulatory oligonucleotide compound that is an antagonist for one or more TLRs, wherein the compound comprises an oligonucleotide motif and at least one modification, wherein the oligonucleotide motif would be immune stimulatory (e.g., unmethylated CpG), but for the one or more modifications that suppress the activity of the oligonucleotide motif, provided that compound contains less than 4 consecutive guanosine nucleotides and preferably less than 3 consecutive guanosine nucleotides. Such modifications may be in the nucleotides flanking the oligonucleotide motif and/or within the oligonucleotide motif. These modifications result in an IRO compound that suppresses TLR-mediated immune stimulation. Such modifications can be to the bases, sugar residues and/or the phosphate backbone of the nucleotides/nucleosides flanking the oligonucleotide motif or within the oligonucleotide motif. In one embodiment, the IRO compound suppresses a TLR9-mediated immune response. In one embodiment, the IRO compound suppresses a TLR7-mediated immune response. In one embodiment, the IRO compound suppresses a TLR8-mediated immune response. In one embodiment, the IRO compound suppresses a TLR7- and TLR8- mediated immune response. In one embodiment, the IRO compound suppresses a TLR9- and TLR7- mediated immune response. In one embodiment, the IRO compound suppresses a TLR9- and TLR8-mediated immune response. In one embodiment, the IRO compound suppresses a TLR9-, TLR7- and TLR8-mediated immune response.

[0055] The general structure of the IRO compounds comprises the sequence

wherein YZ is an dinucleotide motif and Y is deoxycytidine or a cytosine nucleotide derivative, and Z is deoxy guanosine or a guanine nucleotide derivative; Ni is a nucleotide derivative that suppresses the activity of the dinucleotide motif;

at each occurrence, is independently a nucleotide or nucleotide derivative; N_m and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linker; provided that compoun

d contains less than 4 consecutive guanosine nucleotides and preferably less than 3 consecutive guanosines, and wherein m is a number from 0 to about 30. The immune stimulatory activity of the YZ is suppressed by the nucleotide derivative. In some embodiments Ni and N2 are, independently, nucleotide derivatives that suppresses the activity of the dinucleotide motif. In some embodiments, Ni, N2 and N3 are, independently, nucleotide derivatives that suppresses the activity of the dinucleotide motif. In some embodiments, the nucleotide derivative that suppresses the activity of the dinucleotide motif is selected from the group consisting of 2'- substituted-ribonucleotide, 2'-O-substituted-ribonucleotide, 2'-substituted- arabinonucleotide, and 2'-O-substituted-arabinonucleotide.

[0056] In some embodiments, the YZ dinucleotide motif comprises a nucleic acid sequence selected from CpG, C*pG, C*pG* and CpG*, wherein C is 2'- deoxycytidine, G is 2 '-deoxy guanosine, C* is 2'-deoxythymidine, l-(2'-deoxy-B-D- ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 5-Me-dC, 2'-dideoxy-5-halocytosine, 2'-dideoxy-5-nitrocytosine, arabinocytidine, 2'-deoxy-2'-substituted arabinocytidine, 2'-O-substituted arabinocytidine, 2'-deoxy-5-hydroxycytidine, 2'-deoxy-N4-alkyl- cytidine, 2'-deoxy-4-thiouridine, 2'-O-substituted ribonucleotides (including, but not limited to, 2'-O-Me-5-Me-C, 2'-O-(2-methoxyethyl)-ribonucelotides or 2'-O-Me- ribonucleotides) or other cytosine nucleotide derivative, G* is 2'-deoxy-7- deazaguanosine, 2'-deoxy-6-thioguanosine, arabinoguanosine, 2'-deoxy-2'substituted- arabinoguanosine, 2'-O-substituted-arabinoguanosine, 2'- deoxyinosine, 2'-O- substituted ribonucleotides (including, but not limited to, 2'-O-(2-methoxyethyl)- ribonucelotides; or 2'-O-Me-ribonucleotides) or other guanine nucleotide derivative, and p is an internucleoside linkage selected from the group consisting of

phosphodiester, phosphorothioate, and phosphorodithioate.

[0057] In certain embodiments of the invention, IRO compounds may comprise at least two oligonucleotides covalently linked by a nucleotide linkage, or a non-nucleotide linker, at their 5 '-, 3'- or 2'-ends or by functionalized sugar or by functionalized nucleobase via a non-nucleotide linker or a nucleotide linkage, wherein at least one of the oligonucleotides comprises the sequence 5 '-N_m - ' wherein YZ is an dinucleotide motif and Y is

deoxycytidine or a cytosine nucleotide derivative, and Z is deoxyguanosine or a guanine nucleotide derivative; Ni is a nucleotide derivative that suppresses the activity of the dinucleotide motif; N2-N3 and N^x-N³, at each occurrence, is independently a nucleotide or nucleotide derivative; N_m and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linker; provided that compound contains less than 4 consecutive guanosine nucleotides and preferably less than 3 consecutive guanosines, and wherein m is a number from 0 to about 30. The immune stimulatory activity of the YZ is suppressed by the nucleotide derivative. In some embodiments Ni and N2 are, independently, nucleotide derivatives that suppresses the activity of the dinucleotide motif. In some embodiments, N₁, N2 and N3 are, independently, nucleotide derivative that suppresses the activity of the dinucleotide motif. In some embodiments, the nucleotide derivative that suppresses the activity of the dinucleotide motif is selected from the group consisting of 2'- substituted-ribonucleotide, 2'-O-substituted-ribonucleotide, 2'-substituted- arabinonucleotide, and 2'-O-substituted-arabinonucleotide. Such IRO compounds may be linear or branched. As a non-limiting example, the linker may be attached to the 3'-hydroxyl. In such embodiments, the linker comprises a functional group, which is attached to the 3'-hydroxyl by means of a phosphate-based linkage like, for example, phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, or by non-phosphate-based linkages. Possible sites of conjugation for the

ribonucleotide are indicated in Formula I, below, wherein B represents a heterocyclic base and wherein the arrow pointing to P indicates any attachment to phosphorous.

[0058] In some embodiments, the non-nucleotide linker is a small molecule, macromolecule or biomolecule, including, without limitation, polypeptides, antibodies, lipids, antigens, allergens, and oligosaccharides. In some other embodiments, the non-nucleotidic linker is a small molecule. For purposes of the invention, a small molecule is an organic moiety having a molecular weight of less than 1,000 Da. In some embodiments, the small molecule has a molecular weight of less than 750 Da.

[0059] In some embodiments, the small molecule is an aliphatic or aromatic hydrocarbon, either of which optionally can include, either in the linear chain connecting the oligoribonucleotides or appended to it, one or more functional groups including, but not limited to, hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, or thiourea. The small molecule can be cyclic or acyclic. Examples of small molecule linkers include, but are not limited to, amino acids, carbohydrates, cyclodextrins, adamantane, cholesterol, haptens and antibiotics. However, for purposes of describing the non-nucleotidic linker, the term "small molecule" is not intended to include a nucleoside.

[0060] In some embodiments, the non-nucleotidic linker is an alkyl linker or amino linker. The alkyl linker may be branched or unbranched, cyclic or acyclic, substituted or unsubstituted, saturated or unsaturated, chiral, achiral or racemic mixture. The alkyl linkers can have from about 2 to about 18 carbon atoms. In some embodiments such alkyl linkers have from about 3 to about 9 carbon atoms. Some alkyl linkers include one or more functional groups including, but not limited to, hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, and thioether. Such alkyl linkers can include, but are not limited to, 1,2 propanediol, 1 ,2,3 propanetriol, 1 ,3 propanediol, tri ethylene glycol hexaethylene glycol, polyethylene glycollinkers (e.g. [-O-CH2-CH2-]_n (n= l -9)),methyl linkers, ethyl linkers, propyl linkers, butyl linkers, or hexyl linkers. In some embodiments, such alkyl linkers may include peptides or amino acids.

[0061] In some embodiments, the non-nucleotide linker may include, but are not limited to, those listed in Table 2.

[0062] In some embodiments, the small molecule linker is glycerol or a glycerol homolog of the formula HO-(CH2)₀-CH(OH)-(CH2)_i.-OH, wherein o and p independently are integers from 1 to about 6, from 1 to about 4, or from 1 to about 3. In some other embodiments, the small molecule linker is a derivative of 1,3-diamino- 2-hydroxypropane. Some such derivatives have the formula

HO-(CH₂)_m-C(0)NH-CH2-CH(OH)-CH2-NHC(0)-(CH₂)_m-OH, wherein m is an integer from 0 to about 10, from 0 to about 6, from 2 to about 6, or from 2 to about 4. [0063] Some non-nucleotide linkers according to the invention permit attachment of more than two oligonucleotides. For example, the small molecule linker glycerol has three hydroxyl groups to which oligonucleotides may be covalently attached. Some IROs according to the invention, therefore, comprise two or more oligonucleotides linked to a nucleotide or a non-nucleotide linker. Such IROs are referred to as being "branched."

[0064] IRO compounds may comprise at least two oligonucleotides non- covalently linked, such as by electrostatic interactions, hydrophobic interactions, π-stacking interactions, hydrogen bonding and combinations thereof. Non-limiting examples of such non-covalent linkage includes Watson-Crick base pairing,

Hoogsteen base pairing and base stacking.

Some of the ways in which two or more oligonucleotides can be linked are shown in Table 3.

[0065] In certain embodiments, pyrimidine nucleosides or nucleotides in the immune regulatory oligonucleotides used in the compositions and methods according to the invention have the structure (II):

wherein:

D is a hydrogen bond donor;

D' is selected from the group consisting of hydrogen, hydrogen bond donor, hydrogen bond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group;

A is a hydrogen bond acceptor or a hydrophilic group;

A' is selected from the group consisting of hydrogen bond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group;

X is carbon or nitrogen; and

S' is a pentose or hexose sugar ring, or a sugar analog.

[0066] In certain embodiments, the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog. [0067] In some embodiments hydrogen bond donors include, without limitation, -NH-, -NH2, -SH and -OH. Preferred hydrogen bond acceptors include, without limitation, C=0, C=S, and the ring nitrogen atoms of an aromatic heterocycle, e.g., N3 of cytosine.

[0068] In some embodiments, (II) is a pyrimidine nucleoside derivative.

Examples of pyrimidine nucleoside derivatives include, without limitation, 5- hydroxycytosine, 5-hydroxymethylcytosine, N4-alkylcytosine, or N4-ethylcytosine, araC, 5-OH-dC, N3-Me-dC, and 4-thiouracil. Chemical modified derivatives also include, but are not limited to, thymine or uracil analogues. In some embodiments, the sugar moiety S' in (II) is a sugar derivative. Suitable sugar derivatives include, but are not limited to, trehalose or trehalose derivatives, hexose or hexose derivatives, arabinose or arabinose derivatives.

[0069] In some embodiments, the purine nucleosides or nucleotides in immune regulatory oligonucleotides used in the compositions and methods according to the invention have the structure (III):

wherein:

D is a hydrogen bond donor;

D' is selected from the group consisting of hydrogen, hydrogen bond donor, and hydrophilic group;

A is a hydrogen bond acceptor or a hydrophilic group;

X is carbon or nitrogen;

each L is independently selected from the group consisting of C, O, N and S; and

S' is a pentose or hexose sugar ring, or a sugar analog. [0070] In certain embodiments, the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog.

[0071] In certain embodiments hydrogen bond donors include, without limitation, -NH-, -NH2, -SH and -OH. In certain embodiments hydrogen bond acceptors include, without limitation, C=0, C=S, -NO2 and the ring nitrogen atoms of an aromatic heterocycle, e.g., Nl of guanine.

[0072] In some embodiments, (III) is a purine nucleoside derivative.

Examples of purine nucleoside derivatives include, without limitation, guanine analogues such as 7-deaza-G, 7-deaza-dG, ara-G, 6-thio-G, Inosine, Iso-G, loxoribine, TOG(7-thio-8-oxo)-G, 8-bromo-G, 8-hydroxy-G, 5-aminoformycin B, Oxoformycin, 7-methyl-G, 9-p-chlorophenyl-8-aza-G, 9-phenyl-G, 9-hexyl-guanine, 7-deaza-9- benzyl-G, 6-Chloro-7-deazaguanine, 6-methoxy-7-deazaguanine, 8-Aza-7-deaza- G(PPG), 2-(Dimethylamino)guanosine, 7-Methyl-6-thioguanosine, 8- Benzyloxyguanosine, 9-Deazaguanosine, 1 -(B-D-ribofuranosyl)-2-oxo-7-deaza-8- methyl-purine, l-(2'-deoxy-P-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine. Chemically modified derivatives also include, but are not limited to, adenine analogues such as 9-benzyl-8-hydroxy-2-(2-methoxyethoxy)adenine, 2-Amino-N2-O- , methyladenosine, 8-Aza-7-deaza-A, 7-deaza-A, Vidarabine, 2-Aminoadenosine, Nl - Methyladenosine, 8-Azaadenosine, 5-Iodotubercidin, and Nl -Me-dG. In some embodiments, the sugar moiety S' in (III) is a sugar derivative as defined for Formula II.

[0073] In some embodiments, the immune regulatory nucleic acid comprises a nucleic acid sequence containing at least one B-L-deoxy nucleoside or 3'-deoxy nucleoside.

[0074] The sequences of specific IRO within these general structures used in the present study include, but are not limited to, those shown in Table 4. Unless otherwise noted, the nucleotides of the IRO compounds are deoxyribonucleotides and the intemucleotide linkages are phophorothioate linkages. Table 4

G, A or U = 2'-OMe; T = 3 '-OMe; Ai = 3'-OMe; Gi=7-deaza-dG; m= P-Me; A₂, T₂, C₂, and G₂ = B-L-deoxy nucleoside; Xi = abasic; X₂ = glycerol linker, X₃ = C3- linker; C3 and G3 = 3 '-deoxy -nucleoside; G₄ = araG; C₄ = araC; C5 = 5-OH-dC; C₆ = l -(2'-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine; G5 = Nl-Me-dG; C7 = N3-Me-dC; Ui=3'-OMe; U₂=dU; C* = 5-methyl-dC; C = 2'-O-Me-C; C*=2'-OMe- 5-Me-C; C8=2'-MOE-C; C9=2'-O-Propargyl-C.

[0075] In some embodiments, the oligonucleotides each have from about 6 to about 35 nucleoside residues, preferably from about 9 to about 30 nucleoside residues, more preferably from about 11 to about 23 nucleoside residues. In some

embodiments, the oligonucleotides have from about 6 to about 18.

[0076] As used herein the terms "modified messenger "RNA" or "modified messenger RNA therapeutic" (nimRNA) refers to nucleic acids, including RNA such as mRNA, which contain one or more modified nucleosides or nucleotides. The modification of the nucleic acid molecules of the present invention may ha ve useful properties including, but not limited to, increase the stability of the ramRNA therapeutic. The modified nucleic acid molecules may also exhibit enhanced efficiency of protein production, intracellular retention of nucleic acids, and viability of contacted cells as compared to unmodified nucleic acid molecules.

[0077] In some embodiments, mmRNA. therapeutics comprise a translatable region and one, two, or more than two different nucleoside modifications. Exemplary nucleic acids for use in this disclosure include ribonucleic acids (RNA), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), locked nucleic acids (LN As) or a hybrid thereof. In some embodiments, the mniRNA therapeutic comprises messenger RNA (lnRNA). mmRNA therapeutics and methods of making and using mmRNA therapeutics are described in PCX application number PCT/US2012/071 105 published as WO2013096709, PCX application number

[0078] The activation of a TLR-mediated immune response by a mmRNA therapeutic or gene therapy can be suppressed by the simultaneous, pre- or post- administration of an IRO compound. Additionally, such suppression may be maintained for an extended period of time (e.g. days) after administration.

[0079] In some embodiments, the IRO compound is administered

simultaneously with the mmRNA therapeutic or gene therapy. In some embodiments the IRO compound and the mmRNA therapeutic or gene therapy are administered simultaneously as part of the same formulation. In some embodiments the IRO compound and the mmRNA therapeutic or gene therapy are administered

simultaneously as part of different formulations. In some embodiments, the IRO compound and the mmRNA therapeutic or gene therapy are administered by the same route of administration. In some embodiments, the IRO compound and the mmRNA therapeutic or gene therapy are administered by the different routes of administration.

[0080] In some embodiments, the IRO compound is administered prior to the administration of the mmRNA therapeutic or gene therapy. In some embodiments, the IRO compound and the mmRNA therapeutic or gene therapy are administered by the same route of administration. In some embodiments, the IRO compound and the mmRNA therapeutic or gene therapy are administered by the different routes of administration.

[0081] In some embodiments, the IRO compound is administered after the administration of the mmRNA therapeutic or gene therapy. In some embodiments, the IRO compound and the mmRNA therapeutic or gene therapy are administered by the same route of administration. In some embodiments, the IRO compound and the mmRNA therapeutic or gene therapy are administered by the different routes of administration.

[0082] The co-administration of an IRO compound and a mmRNA therapeutic or gene therapy is advantageous for the prevention and/or treatment of a disease or disorder. For example, administration of the IRO simultaneously, pre and/or post administration of the TLR-agonist may allow therapeutic benefits from the mmRNA therapeutic or gene therapy while suppressing the unwanted side effect(s). Additionally, administration of an IRO could prevent an immune response to a subsequent or later challenge by a mmRNA therapeutic or gene therapy.

[0083] In any of the methods according the invention, co-administration of

IRO compound and/or the mmRNA therapeutic or gene therapy can be by any suitable route, including, without limitation, parenteral, mucosal delivery, oral, sublingual, transdermal, topical, inhalation, intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form.

[0084] Administration of the therapeutic compositions of IRO compound can be carried out using known procedures at dosages and for periods of time effective to reduce symptoms or surrogate markers of the disease. When administered systemically, the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of IRO compound from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated. Preferably, a total dosage of IRO compound ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.

[0085] In certain embodiments, compositions in accordance with the present invention may be administered at dosage levels sufficient to deliver from about 0.0001 mg/kg to about 100 mg/kg, from about 0.001 mg/kg to about 0.05 mg/kg, from about 0.005 mg/kg to about 0.05 mg/kg, from about 0.001 mg/kg to about 0.005 mg/kg, from about 0.05 mg/kg to about 0.5 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, from about 0.1 mg/kg to about 40 mg/kg, from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic, diagnostic, prophylactic, or imaging effect. The desired dosage may be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage may be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).

[0086] In some embodiments, the IRO compound may optionally be linked to one or more allergens and/or antigens (self or foreign), an immunogenic protein, such as keyhole limpet hemocyanin (KLH), cholera toxin B subunit, or any other immunogenic carrier protein. IRO can also be used in combination with other compounds (e.g. adjuvants) including, without limitation, TLR agonists (e.g. TLR2 agonists and TLR9 agonists), Freund's incomplete adjuvant, KLH, monophosphoryl lipid A (MPL), alum, and saponins, including QS-21 and imiquimod, or combinations thereof.

[0087] The methods according the invention are useful for the prophylactic or therapeutic treatment of human or animal disease. For example, the methods are useful for adult, pediatric and veterinary applications.

[0088] In any of the methods according to the invention, the IRO compound and/or the mmRNA therapeutic or gene therapy can be administered in combination with any other agent useful for treating the disease or condition that does not diminish the immune modulatory effect of the IRO compound. In any of the methods according to the invention, the agent useful for treating the disease or condition includes, but is not limited to, one or more vaccines, antigens, antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, peptides, proteins, gene therapy vectors, DNA vaccines, kinase inhibitors, adjuvants, co-stimulatory molecules such as cytokines, chemokines, protein ligands, trans-activating factors, or proteins or peptides comprising modified amino acids. For example, in the treatment of cancer, it is contemplated that the IRO compound may be administered in combination with one or more chemotherapeutic compound, targeted therapeutic agent and/or monoclonal antibody. Alternatively, the agent can include DNA vectors encoding for antigen or allergen. In these embodiments, the IRO compounds of the invention can variously act as adjuvants and/or produce direct immune modulatory effects.

[0089] The following examples are intended to further illustrate certain exemplary embodiments of the invention and are not intended to limit the scope of the invention. Example 1 Synthesis of Oligonucleotides Containing Immune regulatory Moieties.

[0090] All IRO were synthesized according to standard procedures (see e.g.

U.S. Patent Publication No. 20040097719 which is incorporated herein by reference in its entirety).

[0091] Oligonucleotides were synthesized on a 1 μΜ scale using an automated DNA synthesizer (Expedite 8909; PerSeptive Biosystems, Framingham, Mass.), following standard linear synthesis or parallel synthesis procedures.

[0092] Deoxyribonucleoside phosphoramidites were obtained from (Aldrich-

Sigma, St Louis, Mo). l',2'-dideoxyribose phosphoramidite, propyl-1- phosphoramidite, 2-deoxyuridine phosphoramidite, l,3-bis-[5-(4,4'- dimethoxytrityl)pentylamidyl]-2-propanol phosphoramidite and methyl

phosponamidite were obtained from Glen Research (Sterling, Va.). .beta.-L-2'- deoxy ribonucleoside phosphoramidite, . alpha. -2'-deoxyribonucleoside

phosphoramidite, mono-DMT-glycerol phosphoramidite and di-DMT-glycerol phosphoramidite were obtained from ChemGenes (Willmington, Mass.). (4- Aminobutyl)-l,3-propanediol phosphoramidite was obtained from Clontech (Palo Alto, Calif). Arabinocytidine phosphoramidite, arabinoguanosine, arabinothymidine and arabinouridine were obtained from Reliable Pharmaceutical (St. Louis, Mo.). Arabinoguanosine phosphoramidite, arabinothymidine phosphoramidite and arabinouridine phosphoramidite were synthesized at Idera Pharmaceuticals, Inc. (Cambridge, Mass.) (Noronha et al. (2000) Biochem, 39:7050-7062).

[0093] All nucleoside phosphoramidites were characterized by ¹P and ¾

NMR spectra. Modified nucleosides were incorporated at specific sites using normal coupling cycles. After synthesis, oligonucleotides were deprotected using concentrated ammonium hydroxide and purified by reverse phase HPLC, followed by dialysis. Purified oligonucleotides as sodium salt form were lyophilized prior to use. Purity was tested by CGE and MALDI-TOF MS.

Example 2 In Vivo Formulation Studies

[0094] Rodents (n=5) can be administered intravenously, subcutaneously or intramuscularly a single dose of a formulation comprising at least one IRO compound and a single dose of a formulation comprising at least one modified mRNA. The modified mRNA administered to the rodents can be selected from, for example, granulocyte-colony stimulating factor G-CSF (mRNA sequence shown in Figure 1; poly A tail of approximately 160 nucleotides not shown in sequence; 5' cap, Capl), erythropoietin (EPO) (mRNA sequence shown in Figure 2; polyA tail of

approximately 160 nucleotides not shown in sequence; 5' cap, Capl), Factor IX (mRNA shown in Figure 3; poly A tail of approximately 160 nucleotides not shown in sequence; 5' cap, Capl) or mCherry (mRNA sequence shown in Figure 4; polyA tail of approximately 160 nucleotides not shown in sequence; 5' cap, Capl).

[0095] The rodents can be injected with 0.1 ug/ml, 1 ug/ml or 10 ug/ml of the formulated IRO compound and 100 ug, 10 ug or 1 ug of the formulated modified mRNA and samples are collected at specified time intervals.

[0096] Serum from the rodents administered formulations containing human

G-CSF modified mRNA can be measured by specific G-CSF ELISA and serum from mice administered human factor IX modified RNA can be analyzed by specific factor IX ELISA or chromogenic assay. The liver and spleen from the mice administered with mCherry modified mRNA can be analyzed by immunohistochemistry (IHC) or fluorescence-activated cell sorting (FACS). As a control, a group of mice are not injected with any formulation and their serum and tissue can be collected analyzed by ELISA, FACS and/or IHC.

A. Time Course

[0097] The rodents can be administered formulations comprising at least one

IRO compound and at least one modified mRNA to study the time course of protein expression for the administered formulations. The rodents can be bled at specified time intervals prior to and after administration of the formulations to determine protein expression and complete blood count. Samples can also be collected from the site of administration of rodents administered subcutaneously and intramuscularly to determine the protein expression in the tissue.

B. Dose Response

[0098] The rodents can be administered formulations comprising at least one

IRO compound and at least one modified mRNA to determine dose response of each formulation. The rodents can be bled at specified time intervals prior to and after administration of the formulations to determine protein expression and complete blood count. The rodents can also be sacrificed to analyze the effect of the formulations on the internal tissue. Samples can also be collected from the site of administration of rodents administered subcutaneously and intramuscularly to determine the protein expression in the tissue.

C. Toxicity

[0099] The rodents can be administered formulations comprising at least one

IRO compound and at least one modified mRNA to study toxicity of each formulation. The rodents can be bled at specified time intervals prior to and after administration of the formulations to determine protein expression and complete blood count. The rodents can also be sacrificed to analyze the effect of the formulations on the internal tissue. Samples can also be collected from the site of administration of rodents administered subcutaneously and intramuscularly to determine the protein expression in the tissue.

[00100] While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.

Claims

CLAIMS What is claimed is:

1 . A method for suppressing an immune response induced by a mmRNA

therapeutic, said method comprising co-administering an immune regulatory compound (IRO) and the mmRNA therapeutic to an individual.

The method according to claim 1 , wherein the IRO is administered prior to the

2.

administration of the mmRNA therapeutic.

The method according to claim 1 , wherein the IRO is administered

3 .

simultaneously with the mmRNA therapeutic.

The method according to claim 1, wherein the immune response is a TLR7- 4.

and/or TLR8-mediated immune response. 5 . A method of potentiating the activity of a modified messenger RNA

(mmRNA) therapeutic, said method comprising co-administering an immune regulatory compound (IRO) and the mmRNA therapeutic to an individual. 6. The method according to claim 5, wherein the IRO is administered prior to the administration of the mmRNA therapeutic. 7. The method according to claim 5, wherein the IRO is administered

simultaneously with the mmRNA therapeutic. 8. The method according to claim 5, wherein the immune response is a TLR7- and/or TLR8-mediated immune response.